Efficient detection of 45 ppb ammonia at room temperature using Ni-doped CeO2 octahedral nanostructures

To meet the requirements in air quality monitors for the public and industrial safety, sensors are required that can selectively detect the concentration of gaseous pollutants down to the parts per million (ppm) and ppb (parts per billion) levels. Herein, we report a remarkable NH3 sensor using Ni-doped CeO2 octahedral nanostructure which efficiently detects NH3 as low as 45 ppb at room temperature. The Ni-doped CeO2 sensor exhibits the maximum response of 42 towards 225 ppm NH3, which is ten-fold higher than pure CeO2. The improved sensing performance is caused by the enhancement of oxygen vacancy, bandgap narrowing, and redox property of CeO2 caused by Ni doping. Density functional theory confirms that O vacancy with Ni at Ce site (VONiCe) augments the sensing capabilities. The Bader charge analysis predicts the amount of charge transfer (0.04 e) between the Ni-CeO2 surface and the NH3 molecule. As well, the high negative adsorption energy (≈750 meV) and lowest distance (1.40 Å) of the NH3 molecule from the sensor surface lowers the detection limit. The present work enlightens the fabrication of sensing elements through defect engineering for ultra-trace detection of NH3 to be useful further in the field of sensor applications.

Molecular editing of enabling discovery of benzodithiazinedioxide-guanidines as anticancer agents

DNA polymerase β (Polβ) is crucial for the base excision repair (BER) pathway of DNA damage repair and is an attractive target for suppressing tumorigenesis as well as chemotherapeutic intervention of cancer. In this study, a unique strategy of scaffold-hopping-based molecular editing of a bioactive agent NSC-666719 was investigated, which led to the development of new molecular motifs with Polβ inhibitory activity. NSC compound and its analogs (two series) were prepared, focusing on pharmacophore-based molecular diversity. Most compounds showed higher activities than the parent NSC-666719 and exhibited effects on apoptosis. The inhibitory activity of Polβ was evaluated in both in vitro reconstituted and in vivo intact cell systems. Compound 10e demonstrated significant Polβ interaction and inhibition characteristics, including direct, non-covalent, reversible, and comparable binding affinity. The investigated approach is useful, and the discovered novel analogs have a high potential for developing as anticancer therapeutics.

Neuronal miR-9 promotes HSV-1 epigenetic silencing and latency by repressing Oct-1 and Onecut family genes

Herpes simplex virus 1 (HSV-1) latent infection entails repression of viral lytic genes in neurons. By functional screening using luciferase-expressing HSV-1, we identify ten neuron-specific microRNAs potentially repressing HSV-1 neuronal replication. Transfection of miR-9, the most active candidate from the screen, decreases HSV-1 replication and gene expression in Neuro-2a cells. Ectopic expression of miR-9 from lentivirus or recombinant HSV-1 suppresses HSV-1 replication in male primary mouse neurons in culture and mouse trigeminal ganglia in vivo, and reactivation from latency in the primary neurons. Target prediction and validation identify transcription factors Oct-1, a known co-activator of HSV transcription, and all three Onecut family members as miR-9 targets. Knockdown of ONECUT2 decreases HSV-1 yields in Neuro-2a cells. Overexpression of each ONECUT protein increases HSV-1 replication in Neuro-2a cells, human induced pluripotent stem cell-derived neurons, and primary mouse neurons, and accelerates reactivation from latency in the mouse neurons. Mutagenesis, ChIP-seq, RNA-seq, ChIP-qPCR and ATAC-seq results suggest that ONECUT2 can nonspecifically bind to viral genes via its CUT domain, globally stimulate viral gene transcription, reduce viral heterochromatin and enhance the accessibility of viral chromatin. Thus, neuronal miR-9 promotes viral epigenetic silencing and latency by targeting multiple host transcription factors important for lytic gene activation.

Computational and in vitro screening validates the repositioning potential of Coxibs as anti-fibrotic agents

Idiopathic pulmonary fibrosis (IPF) is a life-threatening disease with a survival rate of <5 years. The TGF-β plays a significant role in the progression and severity of IPF. The TGF-β receptor type1 TGFBR1 antagonists inhibit the process of fibrosis and may have a role in the treatment of IPF. The main objective of the study was to identify promising drug candidates against IPF using In-silico and In-vitro evaluation methods. An in-silico screening was carried out of the marketed Coxibs to find their TGFBR1 inhibitory potential considering their structural resemblance with the JZO-a co-crystalized ligand of the crystal structure of the TGFBR1. The virtual screening yielded rofecoxib as a TGFBR1 ligand with a significant docking score. To further validate the outcome of molecular docking studies, MD simulation of 200 ns was carried out followed by the determination of conformational stability, binding free energy calculation using MMPBSA/MMGBSA, and Free Energy Landscape (FEL). The therapeutic efficacy of rofecoxib was compared with that of nintedanib (a therapeutic agent used in the treatment of IPF) at equimolar concentrations (5 µM). The model of TGF-β1 (1 ng/ml)-induced EMT of A549 was used to determine the effect of rofecoxib on the EMT markers like cellular morphology, cytokine expressions, fibrosis associated protein, E-cadherin, and α-smooth muscle actin. In vitro results indicated that rofecoxib significantly suppresses the TGF-β1-induced EMT of A549 cells and validates the possible preventive/protective role of rofecoxib in pulmonary fibrosis. In conclusion, rofecoxib may be considered for repositioning as an anti-fibrotic agent.Communicated by Ramaswamy H. Sarma.

Near infrared-responsive quinacrine-gold hybrid nanoparticles deregulate HSP-70/P300-mediated H3K14 acetylation in ER/PR+ breast cancer stem cells

Aim: This study aimed to determine if quinacrine-gold hybrid nanoparticles (QAuNPs) + near-infrared (NIR) deregulate HSP-70/P300 complex-mediated H3K14 acetylation in estrogen receptor/progesterone receptor (ER/PR+) breast cancer stem cells (CSCs). Materials & methods: Various cells and mouse-based systems were used as models. Results: QAuNP + NIR treatment reduced the nuclear translocation of HSP-70, affected the histone acetyltransferase activity of P300 and specifically decreased H3K14 acetylation in ER/PR+ breast CSCs. Finally, HSP-70 knockdown showed a reduction in P300 histone acetyltransferase activity, decreased H3K14 acetylation and inhibited activation of the TGF-β gene. Conclusion: This study revealed that QAuNP + NIR irradiation inhibits oncogenic activation of the TGF-β gene by decreasing H3K14 acetylation mediated through the HSP-70/P300 nuclear complex in ER/PR+ breast CSCs.

Tumor histoculture captures the dynamic interactions between tumor and immune components in response to anti-PD1 in head and neck cancer

Dynamic interactions within the tumor micro-environment drive patient response to immune checkpoint inhibitors. Existing preclinical models lack true representation of this complexity. Using a Head and Neck cancer patient derived TruTumor histoculture platform, the response spectrum of 70 patients to anti-PD1 treatment is investigated in this study. With a subset of 55 patient samples, multiple assays to characterize T-cell reinvigoration and tumor cytotoxicity are performed. Based on levels of these two response parameters, patients are stratified into five sub-cohorts, with the best responder and non-responder sub-cohorts falling at extreme ends of the spectrum. The responder sub-cohort exhibits high T-cell reinvigoration, high tumor cytotoxicity with T-cells homing into the tumor upon treatment whereas immune suppression and tumor progression pathways are pre-dominant in the non-responders. Some moderate responders benefit from combination of anti-CTLA4 with anti-PD1, which is evident from better cytotoxic T-cell: T-regulatory cell ratio and enhancement of tumor cytotoxicity. Baseline and on-treatment gene expression signatures from this study stratify responders and non-responders in unrelated clinical datasets.

Combination of Resveratrol and PARP inhibitor Olaparib efficiently deregulates homologous recombination repair pathway in breast cancer cells through inhibition of TIP60-mediated chromatin relaxation

Recently, we reported that a combination of a natural, bioactive compound Resveratrol (RES) and a PARP inhibitor Olaparib (OLA) deregulated the homologous recombination (HR) pathway, and enhanced apoptosis in BRCA1-wild-type, HR-proficient breast cancer cells. Upon DNA damage, chromatin relaxation takes place, which allows the DNA repair proteins to access the DNA lesion. But whether chromatin remodeling has any role in RES + OLA-mediated HR inhibition is not known. By using in vitro and ex vivo model systems of breast cancer, we have investigated whether RES + OLA inhibits chromatin relaxation and thereby blocks the HR pathway. It was found that RES + OLA inhibited PARP1 activity, terminated PARP1-BRCA1 interaction, and deregulated the HR pathway only in the chromatin fraction of MCF-7 cells. DR-GFP reporter plasmid-based HR assay demonstrated marked reduction in HR efficiency in I-SceI endonuclease-transfected cells treated with OLA. RES + OLA efficiently trapped PARP1 at the DNA damage site in the chromatin of MCF-7 cells. Unaltered expressions of HR proteins were found in the chromatin of PARP1-silenced MCF-7 cells, which confirmed that RES + OLA-mediated DNA damage response was PARP1-dependent. Histone Acetyltransferase (HAT) activity and histone H4 acetylation assays showed reduction in HAT activity and H4 acetylation in RES + OLA-treated chromatin fraction of cells. Western blot analysis showed that the HAT enzyme TIP60, P400 and acetylated H4 were downregulated after RES + OLA exposure. In the co-immunoprecipitation assay, it was observed that RES + OLA caused abolition of PARP1-TIP60-BRCA1 interaction, which suggested the PARP1-dependent TIP60-BRCA1 association. Unaltered expressions of PAR, BRCA1, P400, and acetylated H4 in the chromatin of TIP60-silenced MCF-7 cells further confirmed the role of TIP60 in PARP1-mediated HR activation in the chromatin. Similar results were obtained in ex vivo patient-derived primary breast cancer cells. Thus, the present study revealed that RES + OLA treatment inhibited PARP1 activity in the chromatin, and blocked TIP60-mediated chromatin relaxation, which, in turn, affected PARP1-dependent TIP60-BRCA1 association, resulting in deregulation of HR pathway in breast cancer cells.

Detection of Quinolone resistance Qnr genes and its association with Extended Spectrum β-lactamase and AmpC β-lactamase genes in Qnr Positive Enterobacteriaceae in Bangladesh

This cross-sectional study was conducted to explore quinolone resistant Enterobacteriaceae followed by searching the prevalence of three groups of quinolone resistance genes (QnrA, QnrB and QnrS) from January 2015 to December 2015 at Dhaka Medical College hospital, Bangladesh. Then genes for ESBL and AmpC β-lactamase were detected among Qnr positive strains for better understanding the role of these genes for multiple drug resistance. Total 340 urines, sputum, wound swab and blood samples were collected from DMCH. Total 270(79.41%) Enterobacteriaceae were isolated from 340 samples. Out of 270 Enterobacteriaceae, 225(83.33%) were quinolone (ciprofloxacin) resistant strains. Qnr genes were detected in 141(62.67%) of the 225 quinolone resistant Enterobacteriaceae. Total 187 Qnr genes [84(59.57%) QnrS, 70(49.64%) QnrB and 33(23.40%) QnrA] were detected from 141 quinolone resistant strains. Total 48(34.04%) ESBL producers were detected by DDS test and 47(33.33%) ESBL producers were positive by PCR among 141 Qnr positive strains. QnrA was co-existed with CTX-M-15. QnrB was co-existed with TEM, CTXM-15 and OXA-1. QnrS genes were also associated with TEM, CTX-M-15 and OXA-1. Among 52 cefoxitin resistant Qnr positive strains, 22(42.31%) AmpC β-lactamase producers were detected by Modified three-dimensional test (MTDT) and 45(86.54%) AmpC β-lactamase producers were detected by PCR. QnrA had been identified with DHA, ACC, EBC and CIT while QnrB had been identified with DHA, ACC, EBC and CIT. QnrS had also been co-existed with DHA, ACC, EBC and CIT. The results of this study provided insights into the high proportion of Qnr genes among isolated Enterobacteriaceae. Simultaneous presence of Qnr genes and genes for extended-spectrum β-lactamase or AmpC β-lactamase were observed in multidrug resistant Enterobacteriaceae.

Challenges and Future Directions in the Management of Tumor Mutational Burden-High (TMB-H) Advanced Solid Malignancies

A standardized assessment of Tumor Mutational Burden (TMB) poses challenges across diverse tumor histologies, treatment modalities, and testing platforms, requiring careful consideration to ensure consistency and reproducibility. Despite clinical trials demonstrating favorable responses to immune checkpoint inhibitors (ICIs), not all patients with elevated TMB exhibit benefits, and certain tumors with a normal TMB may respond to ICIs. Therefore, a comprehensive understanding of the intricate interplay between TMB and the tumor microenvironment, as well as genomic features, is crucial to refine its predictive value. Bioinformatics advancements hold potential to improve the precision and cost-effectiveness of TMB assessments, addressing existing challenges. Similarly, integrating TMB with other biomarkers and employing comprehensive, multiomics approaches could further enhance its predictive value. Ongoing collaborative endeavors in research, standardization, and clinical validation are pivotal in harnessing the full potential of TMB as a biomarker in the clinic settings.

Strong non-linear optical response of Sb2Se3 nanorods in a liquid suspension based on spatial self-phase modulation and their all-optical photonic device applications

The field of nonlinear optics is constantly expanding and gaining new impetus through the discovery of fresh nonlinear materials. Herein, for the first time, we have performed spatial self-phase modulation (SSPM) experiments with an emerging anisotropic Sb2Se3 layered material in a liquid suspension for an all-optical diode and all-optical switching application. The third-order broadband nonlinear optical susceptibility (χ(3)single layer ∼ 10-9 esu) and nonlinear refractive index (n2 ∼ 10-6 cm2 W-1) of Sb2Se3 have been determined using a 671 nm laser beam. This result could be unambiguously explained by the anisotropic hole mobility of Sb2Se3. The linear relationship of χ(3) and carrier mobility emphasizes the establishment of nonlocal hole coherence, the origin of the diffraction pattern. Consequently, the time evolution of diffraction rings follows the 'Wind-Chime' model. A novel photonic diode based on Sb2Se3/SnS2 has been demonstrated using the nonreciprocal propagation of light. The self-phase modulation (SPM) technique uses laser lights of different wavelengths and intensities to demonstrate the all-optical logic gates, particularly OR logic gates. The exploration of nonlinear optical phenomena in Sb2Se3 opens up a new realm for optical information processing and communication. We strongly believe that this result will help to underpin the area of optical nonlinearities among its various applications.

Artificial Visual Systems Fabricated with Ferroelectric van der Waals Heterostructure for In-Memory Computing Applications

Rapid developments in artificial neural network techniques and retina-inspired artificial visual systems are required to realize the sensing, processing, and memorization of an optical signal in a single device. Herein, a ferroelectric field-effect transistor fabricated with CuInP2S6 and α-In2Se3 van der Waals heterostructures is proposed and demonstrated for the development of an artificial visual system. The dipole polarizations are coupled and bidirectionally locked inside the ferroelectric α-In2Se3 along the in-plane and out-of-plane directions and are controlled by the gate voltages. Furthermore, light-induced polarization can change the order of polarization of the dipoles inside α-In2Se3. We demonstrate that using the combined control of these electrical and optical signals, the device may function like a retina-inspired vision system. The device can operate across a wide wavelength range (405-850 nm) and detect very low incident light (0.03 mW/cm2). Color recognition, high paired-pulse facilitation (∼170%), and short- to long-term memory transitions through quick learning are observed using this device. Additionally, this device demonstrates different complex processing abilities, including pattern recognition, light adaptation, optical logic operation, and event learning. The proposed ferroelectric heterostructure-based artificial visual system can serve as an essential bridge for fulfilling the future requirements of all-in-one sensing and memory-processing devices.

Talazoparib enhances the quinacrine-mediated apoptosis in patient-derived oral mucosa CSCs by inhibiting BER pathway through the modulation of GCN5 and P300

The presence of cancer stem cells (CSCs) in the tumor microenvironment (TME) is majorly responsible for the development and recurrence of cancer. Earlier reports suggested that upon DNA damage, poly-(ADP-ribose) polymerase-1 (PARP-1) helps in chromatin modulation and DNA repair process, thereby promoting CSC survival. But whether a combination of DNA damaging agents along with PARP inhibitors can modulate chromatin assembly, inhibit DNA repair processes, and subsequently target CSCs is not known. Hence, we have investigated the effect of nontoxic bioactive compound quinacrine (QC) and a potent PARP inhibitor Talazoparib in patient-derived oral mucosa CSCs (OM-CSCs) and in vivo xenograft mice preclinical model systems. Data showed that QC + Talazoparib inhibited the PARP-1-mediated chromatin remodelers' recruitment and deregulated HAT activity of GCN5 (general control nonderepressible-5) and P300 at DNA damage site, thereby preventing the access of repair proteins to the damaged DNA. Additionally, this combination treatment inhibited topoisomerase activity, induced topological stress, and induced apoptosis in OM-CSCs. Similar results were observed in an in vivo xenograft mice model system. Collectively, the data suggested that QC + Talazoparib treatment inhibited BER pathway, induced genomic instability and triggered apoptosis in OM-CSCs through the deregulation of PARP-1-mediated chromatin remodelers (GCN5 and P300) activity. Schematic representation of QC + Talazoparib-induced apoptosis in oral mucosa CSCs. (1) Induction of DNA damage takes place after QC treatment (2) PARP1-mediated PARylation at the site of DNA damage, which recruits multiple chromatin remodelers (3) Acetylation at the histone tails relax the structure of chromatin and recruits the BER pathway proteins at the site of DNA damage. (4) BER pathway activated at the site of DNA damage. (5) CSCs survive after successful repair of DNA damage. (6) Treatment of QC-treated CSCs with PARP inhibitor Talazoparib (7) Inhibition of PARylation results in failure of chromatin remodelers to interact with PARP1. (8) Inhibition of acetylation status leads to chromatin compaction. (9) BER pathway proteins are not recruited at the site of DNA damage, resulting in inhibition of BER pathway and accumulation of unrepaired DNA damage, leading to apoptosis and cell death.

Combining biophysical parameters with thermal and RGB indices using machine learning models for predicting yield in yellow rust affected wheat crop

Evaluating crop health and forecasting yields in the early stages are crucial for effective crop and market management during periods of biotic stress for both farmers and policymakers. Field experiments were conducted during 2017-18 and 2018-19 with objective to evaluate the effect of yellow rust on various biophysical parameters of 24 wheat cultivars, with varying levels of resistance to yellow rust and to develop machine learning (ML) models with improved accuracy for predicting yield by integrating thermal and RGB indices with crucial plant biophysical parameters. Results revealed that as the level of rust increased, so did the canopy temperature and there was a significant decrease in crop photosynthesis, transpiration, stomatal conductance, leaf area index, membrane stability index, relative leaf water content, and normalized difference vegetation index due to rust, and the reductions were directly correlated with levels of rust severity. The yield reduction in moderate resistant, low resistant and susceptible cultivars as compared to resistant cultivars, varied from 15.9-16.9%, 28.6-34.4% and 59-61.1%, respectively. The ML models were able to provide relatively accurate early yield estimates, with the accuracy increasing as the harvest approached. The yield prediction performance of the different ML models varied with the stage of the crop growth. Based on the validation output of different ML models, Cubist, PLS, and SpikeSlab models were found to be effective in predicting the wheat yield at an early stage (55-60 days after sowing) of crop growth. The KNN, Cubist, SLR, RF, SpikeSlab, XGB, GPR and PLS models were proved to be more useful in predicting the crop yield at the middle stage (70 days after sowing) of the crop, while RF, SpikeSlab, KNN, Cubist, ELNET, GPR, SLR, XGB and MARS models were found good to predict the crop yield at late stage (80 days after sowing). The study quantified the impact of different levels of rust severity on crop biophysical parameters and demonstrated the usefulness of remote sensing and biophysical parameters data integration using machine-learning models for early yield prediction under biotically stressed conditions.

Sustainable Organic Photocatalysis for Site-Selective Hydrazocoupling of Electron-Rich Arenes

An efficient photocatalytic para- and ortho-selective amination and aminative dearomatization of phenols, naphthols, and anilines with azodicarboxylates was developed using riboflavin tetraacetate (RFTA) as an organic photocatalyst. The site selectivity was controlled using tetrabutylammonium bromide (TBAB), which also acts as a phase transfer catalyst. The reaction conditions are simple and mild, giving high regioselectivity with good to excellent yields. A broad substrate scope and nice functional group tolerance with scalability and post-functionalization make this protocol both useful and regioselective.

Double-Versus Single-Bundle Anterior Cruciate Ligament Reconstructive Surgery: A Prospective Study With >1 Year Follow-Up

Background The increased prevalence of knee trauma predominantly adds to the anterior cruciate ligament (ACL) tear frequencies that require single- or double-bundle reconstructive surgeries. Few studies have demonstrated the superior results of double-bundle reconstruction compared to single-bundle approaches. This study investigated the knee function improvement capacity of both reconstruction techniques in patients with ACL tears. Methods Thirty cases with ACL tears have been enrolled and segregated equally in distinct (single-bundle versus double-bundle) batches. The diagnostic assessments were undertaken through comprehensive clinical history, knee radiographs, Lysholm scoring, the International Knee Documentation Committee (IKDC) scale, the Lachman analysis, the International Knee Documentation Committee (IKDC) scale, and the pivot shift method. Results After one year, there was a significant enhancement in the postoperative versus preoperative Lysholm scores in the single-bundle (58.5 ± 21.2 vs. 82.4 ± 26.2, p<0.001) and double-bundle (86.4 ± 22.8 vs 60.3 ± 19.2, p<0.001) groups. There was a significant improvement in the IKDC scores after a follow-up period of one year (p-value: 0.012 and p-value: 0.002, respectively) in both of the study batches. After a year of follow-up, Lysholm scores (p=0.352) and IKDC scores (p=0.574) between the study groups (82.4 ± 26.2 vs. 86.4 ± 22.8) were comparable. Conclusion The clinical outcomes remained comparable between subjects with single-bundle reconstruction versus double-bundle reconstruction subjects with ACL injuries. Findings were similar between the groups after one year and two years of surgical interventions.

Veliparib (ABT-888), a PARP inhibitor potentiates the cytotoxic activity of 5-fluorouracil by inhibiting MMR pathway through deregulation of MSH6 in colorectal cancer stem cells

OBJECTIVE

Sensitization of mismatch repair (MMR)-deficient colorectal cancer (CRC) cells by 5-Fluorouracil (5-FU) is well-documented. But not much is known about the treatment of MMR-proficient CRC cancer stem cells (CRC-CSCs). Here, we investigated whether a PARP inhibitor (ABT-888) can enhance the 5-FU-mediated apoptosis in CRC-CSCs through MMR pathway inhibition.

METHODS

The anti-cancer action of 5-FU+ABT-888 combination in CRC-CSCs has been studied by using in vitro, ex vivo, and in vivo preclinical model systems.

RESULTS

5-FU caused DNA damage in CRC-CSCs, and ABT-888 enhanced the accumulation of DNA mismatches by downregulating the MMR pathway, triggering S-phase arrest, and finally apoptosis and cell death in 5-FU-pre-treated MMR-proficient-CRC-CSCs at much lower concentrations than their individual treatments. After 5-FU treatment, PARylated-PARP1 activated MMR pathway by interacting with MSH6. But, upon ABT-888 treatment in 5-FU-pre-exposed CSCs, PARylation was inhibited, as a result of which PARP1 could not interact with MSH6, and other MMR proteins were downregulated. The role of MSH6 in PARP1-mediated MMR activation, was confirmed by silencing MSH6 gene, which resulted in MMR pathway shutdown. Similar results were obtained in ex vivo and in vivo model systems.

CONCLUSIONS

5-FU+ABT-888 combination enhanced CRC-CSCs death by increasing DNA damage accumulation and simultaneously inhibiting the MMR pathway in MMR-proficient cells. But this study does not discuss whether the combination treatment will increase the sensitivity of MMR-deficient CSCs, for which further research will be performed in the future.

Quinacrine inhibits HIF-1α/VEGF-A mediated angiogenesis by disrupting the interaction between cMET and ABCG2 in patient-derived breast cancer stem cells

BACKGROUND

Breast cancer stem cells (BCSCs) have a critical role in progression of breast cancer by inducing angiogenesis. Several therapeutic strategies have been designed for the treatment of breast cancer by specifically preventing angiogenesis. But there is a dearth of study regarding the treatment procedure which can specifically target and kill the BCSCs and cause lesser harm to healthy cells of the body. A plant-based bioactive compound Quinacrine (QC) specifically kills cancer stem cells (CSCs) without harming healthy cells and also inhibits cancer angiogenesis but the detailed mechanistic study of its anti-CSCs and anti-angiogenic activity is yet to explore.

HYPOTHESIS

Earlier report showed that both cMET and ABCG2 play an essential role in cancer angiogenesis. Both are present on the cell surface of CSCs and share an identical ATP-binding domain. Interestingly, QC a plant based and bioactive compound which was found to inhibit the function of CSCs marker cMET and ABCG2. These relevant evidence led us to hypothesize that cMET and ABCG2 may interact with each other and induce the production of angiogenic factors, resulting in activation of cancer angiogenesis and QC might disrupt the interaction between them to stop this phenomena.

METHODS

Co-immunoprecipitation assay, immunofluorescence assay, and western blotting were performed by using ex vivo patient-derived breast cancer-stem-cells (PDBCSCs) and human umbilical vein endothelial cells (HUVECs). In silico study was carried out to check the interaction between cMET and ABCG2 in presence or absence of QC. Tube formation assay using HUVECs and in ovo Chorioallantoic membrane (CAM) assay using chick fertilized eggs were performed to monitor angiogenesis. In vivo patient-derived xenograft (PDX) mice model was used to validate in silico and ex vivo results.

RESULTS

Data revealed that in a hypoxic tumor microenvironment (TME), cMET and ABCG2 interact with each other and upregulate HIF-1α/VEGF-A axis to induce breast cancer angiogenesis. In silico and ex vivo study showed that QC disrupted the interaction between cMET and ABCG2 to inhibit the angiogenic response in endothelial cells by reducing the secretion of VEGF-A from PDBCSCs within the TME. Knockdown of cMET, ABCG2 or both, significantly downregulated the expression of HIF-1α and reduced the secretion of pro-angiogenic factor VEGF-A in the TME of PDBCSCs. Additionally, when PDBCSCs were treated with QC, similar experimental results were obtained.

CONCLUSION

In silico, in ovo, ex vivo and in vivo data confirmed that QC inhibited the HIF-1α/VEGF-A mediated angiogenesis in breast cancer by disrupting the interaction between cMET and ABCG2.

Morphological and molecular characterization of Haemonchus contortus isolated from the small ruminants of south Gujarat, India

The successful design of strategic control measures against the blood-sucking gastrointestinal nematode, Haemonchus contortus in small ruminants can be facilitated by revealing its general features from morphology to the molecular level. In the south Gujarat region of India, a total of 2408 H. contortus were collected from 84 slaughtered sheep's abomasum, consisting of 347 males and 2061 females (1:6 ratio) (p<0.05). Furthermore, 726 H. contortus were collected from 61 goats, comprising 145 males and 581 females (1:4 ratio) (p<0.05). The male worms were approximately 12±0.06 mm long, while female worms were about 20±0.09 mm long. The vulvar morphotypes of the female worms were found to be 17.7% linguiform, 76.6 % knobbed/button (p<0.05), and 5.7 % smooth type, demonstrating common features of H. contortus. The nucleotide sequences of the Internal Transcribed Spacer 1 (ITS-1) of 165 bp or ITS-2 plus of 256 bp were aligned, and it was found that the genotypes of male and female specimens of either sheep or goat origin were identical, with a 100 % match. The present isolates shared >95 % and >94 % homology with published sequences of ITS-1 and ITS-2 plus of H. contortus, respectively, with more nucleotide transitions than transversions in the aligned sequences. The reconstructed phylogram of either ITS-1 or ITS-2 plus revealed two major clades, one for H. contortus and another for other nematodes, with Haemonchus placei showing its proximity with the clade of H. contortus. The study established the role of morphological and molecular features in identifying and differentiating H. contortus parasite at the local level.

Retraction Note: Weather indicators and improving air quality in association with COVID-19 pandemic in India

[This retracts the article DOI: 10.1007/s00500-021-06012-9.].

Quinacrine inhibits cMET-mediated metastasis and angiogenesis in breast cancer stem cells

A trans-membrane receptor tyrosine kinase, cMET, belonging to the MET proto-oncogene family, is responsible for cancer metastasis and angiogenesis. But not much is known about the role of cMET in growth and progression of cancer stem cells (CSCs). Earlier studies have shown that Quinacrine (QC), a bioactive agent, has anti-CSCs activity. Here, the role of QC in deregulation of cMET-mediated metastasis and angiogenesis has been systematically evaluated in vitro in highly metastatic breast CSCs (mBCSCs), ex vivo in patient-derived breast cancer stem cells (PDBCSCs) and in vivo in xenograft mice model systems. Cell proliferation, migration, invasion and representative metastasis markers were upregulated in cMET-overexpressed cells and QC exposure inhibited these processes in both mBCSCs and PDBCSCs. Interestingly, metastasis was significantly inhibited by QC in cMET-overexpressed cells but comparatively lesser significant alteration of the process was noted in cMET-silenced cells. Increase in vascularization (in in ovo CAM assay), and cell-cell tube formation (in HUVECs), and enhanced MMP9 and MMP2 enzymatic activities (in gelatin zymography) were noted after cMET overexpression but these processes got reversed after cMET knockdown or QC treatment in cMET-overexpressed cells. QC inhibited angiogenesis significantly in cMET-overexpressed cells, but lesser significant change was observed in cMET-silenced cells. Reduction in tumor volume and decreased expression of metastatic and angiogenic markers were also noted in xenograft mice after QC treatment. Furthermore, QC inhibited cMET activity by dephosphorylation of its tyrosine residues (Y1234 and Y1356) and downregulation of its downstream cascade. Thus, QC inhibited the cMET-mediated metastasis and angiogenesis in in vitro, in ovo, in vivo and ex vivo model systems. Ligand (HGF) binding leads to receptor dimerization and phosphorylation of tyrosine kinase domain of cMET. This activates the cMET signaling cascade. The representative downstream metastasis and angiogenesis-related proteins get upregulated and induce the metastasis and angiogenesis process. But after the QC treatment, cMET get dephosphorylated and inactivated. As a result, the downstream signaling proteins of cMET along with the other representative metastatic and angiogenic factors get downregulated. These lead to inhibition of cMET-mediated metastasis and angiogenesis. (Created with BioRender.com).

Abstract 4568: Evaluating response of renal cell carcinoma to tyrosine kinase inhibitor and immune checkpoint inhibitor using a human histo-culture platform

Tyrosine Kinase Inhibitors (TKIs) and Immune checkpoint inhibitors (ICIs) are used in first line treatment of clear cell renal cell carcinoma (ccRCC). Identifying patients who truly benefit from these treatments remains a challenge. Developing newer and better therapy options that fail in the clinical phase is yet another unmet need. Both these limitations could be addressed by employing testing platforms that best capture the heterogeneity and complexity of the tumor within the patient. FarcastTM TruTumor is a near native human histo-culture platform which retains the tumor and stroma along with the intra-tumoral immune compartment post culture that holds promise to improve treatment outcomes in patients. In this study, we developed a ccRCC platform using surgical excess specimens from consented patients and compared its immune profile with the head and neck squamous cell carcinoma (HNSCC) platform. ccRCC samples (n=10) were processed to generate explants and cultured for 72h and interrogated for response to treatment with Sunitinib (TKI:27.7ng/ml) or Nivolumab (anti-PD1:132µg/ml). On comparison of immune profiles between HNSCC and ccRCC at baseline, we observed a significantly lower total immune content in ccRCC. ccRCC showed comparatively higher variation in myeloid (70%CV) and lymphoid compartments (30%CV) as compared to HNSCC. Live tumor and immune cell population was found to be well preserved post-culture in ccRCC. Presence of various T cell sub-populations, monocyte and macrophage population post culture were confirmed using flowcytometry. Sunitinib treatment significantly increased caspase-3 expression (8/10 samples, p value&lt;0.01), along with decrease in tumor content in 4/10 samples (average drop 23%). Two samples which did not respond to Sunitinib treatment showed an increase in Interferon gamma (IFNg) (Log2FC ± SD, 2.7± 0.7) and Granzyme B (Log2FC ± SD, 1.05± 0.85) secretion, in response to Nivolumab treatment. Of these, in one sample we observed an increase in CD8+ Granzyme B, CD8+ Ki67 and decrease in CD4+ FoxP3 population, with concomitant decrease in Pan CK+ population by flowcytometry. In this sample, we observed a decrease in tumor content indicating anti-tumor response to Nivolumab treatment. In summary, the TruTumor platform potentially offers personalized treatment choices to patients improving their chances of recovery. In addition, this platform could provide powerful insights into the mechanisms of a wide range of therapy molecules in development to predict their efficacy better than other simplistic and non-human testing models.

Citation Format: Satish Sankaran, Kowshik Jaganathan, Gowri Shankar K, Saurabh Bhargav, Ganesh MS, Amritha Prabha, Prakash BV, Syamkumar V, Biswajit Das, Vasanth K, Manimaran A, Chandan Bhowal, Rajashekar M, Oliyarasi M, Ritu Malhotra, Govindraj K, Nandini Pal Basak. Evaluating response of renal cell carcinoma to tyrosine kinase inhibitor and immune checkpoint inhibitor using a human histo-culture platform. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4568.

Abstract 6072: Chromosomal aneuploidy, whole-genome doubling and mutational signatures in NCI PDMR models

Introduction: Structural variants (SVs) are a unique class of mutations which have certain therapeutic implications for the tumor. Certain SVs, such as chromosomal aneuploidy, whole-genome doubling (WGD), have specific therapeutic implications. The underlying cellular processes present in the tumor are reflected in mutational signatures. Here, we describe the landscape of chromosomal aneuploidy, WGD and mutational signatures in the National Cancer Institute’s Patient-Derived Models Repository (NCI PDMR) to facilitate the investigation of their roles in therapeutic responses of the preclinical models.

Method: Chromosome arm-level aneuploidy was called by scoring at the individual arm level if &gt;90% of the arm copy number (CN) was gained/lost based on whole-exome sequencing (WES) data. Aneuploidy score was defined as number of arms with aneuploidy. WGD was determined by derived allelic specific CN, purity and ploidy from tumor/normal matched samples and permutation test. Mutational signatures (COSMIC v3) including single base substitutions (SBS), doublet base substitutions (DBS), small insertions and deletions (ID) and CN signatures were derived using SigProfiler for specimens with somatic mutations and CNs.

Results: A large fraction (85%) of patient-derived xenograft (PDX) models (N=755) have at least one arm -level aneuploidy. Certain chromosomes and arms (7, 8, 17p and 18) are more frequently aneuploid, which might be biased due to the overrepresentation of gastrointestinal cancer in the cohort. Histology specific differences were observed in the frequency of arm level aneuploidies. For example, synovial sarcoma (SYNS) and endometrioid carcinoma (UEC) have much lower level of aneuploidy than non-small cell lung cancer (NSCLC) or clear cell renal carcinoma (ccRCC) models. 61% of PDX models (N=277) have WGD, in which certain histologies have more WGD [NSCLC: 81%, head and neck squamous cell carcinomas (HNSCC): 71%] than others. Samples having WGD have a higher degree of aneuploidy and chromosomal instability. WGD and aneuploidy remain stable along the passages in 78% PDX models. Intra-model heterogeneity of WGD was observed due to lineage difference. Mutational signatures (SBS6,15,20) indicating concurrent DNA polymerase epsilon (POLE) mutation and defective DNA mismatch repair were highly enriched in microsatellite instability-high models (p&lt;0.01, Fisher’s exact test). Among 30 PDX models where the patients had known platinum-based chemotherapy history, 40% of them had an identifiable platinum chemotherapy treatment signature (SBS31 or DBS5). Chromothripsis associated amplification signature (CN8) was enriched in models with WGD (p&lt;0.05).

Conclusion: We have characterized chromosomal aneuploidy, WGD and mutational signatures in NCI PDMR models. The models with SVs can be utilized in preclinical drug studies to understand their role in therapeutic response in patients.

Citation Format: Li Chen, Biswajit Das, Ting-Chia Chang, Yvonne A. Evrard, Chris A. Karlovich, Alyssa Chapman, Brandie Fullmer, Ashley Hayes, Ruth Thornton, Nikitha Nair, Shahanawaz Jiwani, Lindsay Dutko, Kelly Benauer, Gloryvee Rivera, Corinne Camalier, John Carter, Suzanne Borgel, Tiffanie Miner, Chelsea McGlynn, Justine Mills, Shannon Uzelac, Tia Shearer, Lauren Hicks, Michelle Norris, Carley Border, Sergio Alcoser, Thomas Walsh, Michael Mullendore, Michelle Eugeni, Dianne Newton, Melinda G. Hollingshead, P. Mickey Williams, James H. Doroshow. Chromosomal aneuploidy, whole-genome doubling and mutational signatures in NCI PDMR models. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6072.

Abstract 2050: Molecular subclassification of NCI PDMR breast cancer models using PAM50 gene expression signature

Background: Breast cancer is the second most common cancer in women. In 2022, it accounted for 15% of total new cancer cases and is the number four cause of death among all cancer types. To benefit from precision medicine, distinguishing molecular subtypes for prognosis and treatment in a clinical setting is essential. While intrinsic subtype classification from NGS results of patients is well established, the approach has not been comprehensively described for patient-derived xenograft (PDX) models, which have been shown to be powerful in translational research. The National Cancer Institute's Patient-Derived Models Repository (NCI PDMR; https://pdmr.cancer.gov) provides rich information in developing the method.

Materials and Methods: Normalized gene expression data of breast cancer PDX and patient specimens (originators) were extracted using tximport and DESeq2 based on RNA-seq analysis. The immunohistochemistry (IHC) was used to determine the status of ER, PR and HER2 receptor expression in these tumor specimens. The PAM50 classification was performed by the R package Genefu. For further analysis, the PAM50 centroids for all 5 subtypes were also obtained from Genefu.

Results: Using the RNA-seq data from 43 PDX models (180 PDX samples, 4~6 samples/model), we were able to predict subtypes at the model level based on the PAM50 method: There are 1 Luminal A subtypes, 5 Luminal B; 6 Her2; 30 Basal and 1 Normal, which encompasses the whole spectrum of PAM50. Thirty originators were also included and there are 8 Luminal A, 9 Luminal B, 2 Her2 and 11 Basal. With the matched 11 originators and the PDX models, 91% of their predicted subtypes are identical; 0.80 Cohen’s kappa was obtained, indicating high inter-rater agreement. We also described subsequent analysis with IHC data-based subtypes. For the 10 originators having IHC-based subtypes, 90% agreement was observed; for 24 PDX models with IHC data, 88% was observed. Of all the 180 PDX samples, 33 of the 43 PDX models (77%) have consistent predicted PAM50 molecular subtypes across different passages and lineages. Within the discordant samples, we observed cases such as a mixture of luminal B and Basal, which can be reasonably interpreted by AR positive signal from IHC. The discrepancy encourages further PDX subclassification from the Basal subtype.

Conclusions: Using our high-throughput gene expression profiles from many patients and samples from patient derived models, we have demonstrated the feasibility of applying classic PAM50 classification algorithm, which was originally developed with microarray data, to be able to recognize the expression signals from our RNA-seq data. Overall, this study should set a primer for the identification of PDX-based subtypes, starting from breast cancer.

Citation Format: Peter I. Wu, Lindsay Dutko, Shahanawaz Jiwani, Li Chen, Biswajit Das, Ting-Chia Chang, Yvonne A. Evrard, Chris A. Karlovich, Alyssa Chapman, Brandie Fullmer, Ashley Hayes, Ruth Thornton, Nikitha Nair, Kelly Benauer, Gloryvee Rivera, Thomas Forbes, John Carter, Suzanne Borgel, Tiffanie Miner, Chelsea McGlynn, Justine Mills, Shannon Uzelac, Tia Shearer, Lauren Hicks, Michelle Norris, Carley Border, Sergio Alcoser, Thomas Walsh, Michael Mullendore, Michelle Eugeni, Dianne Newton, Melinda G. Hollingshead, P. M. Williams, James H. Doroshow. Molecular subclassification of NCI PDMR breast cancer models using PAM50 gene expression signature [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2050.

Near-infrared enhances antiangiogenic potentiality of quinacrine-gold hybrid nanoparticles in breast cancer stem cells via deregulation of HSP-70/TGF-β

Aim: This study aimed to explore the antiangiogenic mechanism of quinacrine-gold hybrid nanoparticle (QAuNP) and near-infrared (NIR) radiation in patient-derived primary breast cancer stem cells. Materials & methods: Various cell-based in ovo angiogenesis and in vivo patient-derived xenograft mouse systems were used as models for the study. Results: The experimental results showed that QAuNP + NIR treatment deregulated the HSP-70/TGF-β physical interaction in primary breast cancer stem cells. Reduced TGF-β secretion in the tumor microenvironment inhibited angiogenesis activation in endothelial cells by deregulating the TGF-β-mediated PI3K/AKT/mTOR cascade. Conclusion: This study revealed that QAuNP + NIR irradiation downregulated HSP-70 expression, inhibited the HSP-70/TGF-β interaction, reduced the secretion of TGF-β in the tumor microenvironment and ultimately inhibited TGF-β-mediated angiogenesis.

Resveratrol nanoparticle attenuates metastasis and angiogenesis by deregulating inflammatory cytokines through inhibition of CAFs in oral cancer by CXCL-12/IL-6-dependent pathway

Cancer-associated fibroblasts (CAFs) are one of the highly abundant components in the tumor microenvironment (TME). They secrete several cytokines, which amplified tumor progression, invasion, stemness, metastasis, and angiogenesis. Here, we evaluate the potentiality of cytokines for the formation of cancer stem cells (CSCs) in oral cancer cells niche and investigate the anti-inflammatory and anti-carcinogenic effect of Resveratrol-nanoparticle (Res-NP). We first differentiated quiescent human fibroblasts into CAFs in vitro in response to PDGF-B and TGF-β stimulation and these CAFs were found to increase CXCL-12 and IL-6 secretion. CSCs-enriched population was created by incubating H-357 cells with CAFs and cytokine-enriched CAFs-conditioned media (CAFs-CM). Likewise, CSCs-populated environment was also generated after incubating CAFs-CM to patient-derived primary oral cancer cells. It was noted that CXCL-12 and IL-6 secreted from CAFs significantly promoted CSCs growth, proliferation, aggressiveness, metastasis, and angiogenesis. However, Res-NP reduced CSCs growth and proliferation by abrogating the secretion of CXCL-12 and IL-6. A significant decrease in the expression of metastatic and angiogenic markers, in ovo blood vascularization, intracellular NO generation, MMPs expression and tube formation was found upon Res-NP treatment. Reduction of representative CSCs and angiogenesis markers were also noted after Res-NP treatment in xenograft mice model. CXCL-12 physically interact with IL-6 and this interaction was diminished after Res-NP treatment. Moreover, the expression of CD133 and VEGF-A were down-regulated either on Res-NP or CXCL-12/IL-6-specific inhibitors treated CSCs-enriched cells. Thus, the data suggest that CSCs growth is CXCL-12 and IL-6 dependent and Res-NP obstruct carcinogenesis and metastasis by inhibiting CXCL-12 and IL-6 production in in vitro, in vivo, in ovo, and ex vivo systems.

Management of post-COVID mucormycosis at a tertiary care center in Northern India

Purpose

Our study aims to compile data on the clinical presentation, pathological and radiological findings in cases of post-COVID mucormycosis, and present the management strategy used in our center.

Methods

This is a retrospective cohort observational study based at a tertiary healthcare institution in Northern India. All COVID-positive patients presenting with clinical features of mucormycosis were included in the study. They underwent complete otorhinolaryngeal, medical, and ophthalmological examination after thorough history taking. Biochemical tests, biopsy and imaging studies were done for all the patients. The treatment strategy included a multidisciplinary team approach, that is, intravenous antifungals as well as surgical debridement of necrotic tissue via Modified Denker’s approach or open maxillectomy, and orbital exenteration, if required. Patients were followed up for six months to look for recurrence.

Results

Twenty-three patients were studied, out of which 14 were males and 9 were females. Pathological findings of 13 out of 15 patients, who underwent surgical debridement revealed mucormycosis as a causative agent, received Amphotericin. Aspergillus was found in two cases which received Voriconazole. Eleven out of 20 patients who were treated in our hospital survived. Three patients were lost to follow up. The average hospital stay of discharged patients was 14 days.

Conclusion

Post-COVID mucormycosis was reported at an alarming rate after the second COVID wave in India especially after steroid therapies in diabetic patients. Thus a timely, aggressive, team approach using Modified Denkers or open maxillectomy along with proper intravenous antifungals is the key to survival in such patients.

Weather indicators and improving air quality in association with COVID-19 pandemic in India

The COVID-19 pandemic enforced nationwide lockdown, which has restricted human activities from March 24 to May 3, 2020, resulted in an improved air quality across India. The present research investigates the connection between COVID-19 pandemic-imposed lockdown and its relation to the present air quality in India; besides, relationship between climate variables and daily new affected cases of Coronavirus and mortality in India during the this period has also been examined. The selected seven air quality pollutant parameters (PM₁₀, PM_2.5, CO, NO₂, SO₂, NH₃, and O₃) at 223 monitoring stations and temperature recorded in New Delhi were used to investigate the spatial pattern of air quality throughout the lockdown. The results showed that the air quality has improved across the country and average temperature and maximum temperature were connected to the outbreak of the COVID-19 pandemic. This outcomes indicates that there is no such relation between climatic parameters and outbreak and its associated mortality. This study will assist the policy maker, researcher, urban planner, and health expert to make suitable strategies against the spreading of COVID-19 in India and abroad.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00500-021-06012-9.

Trihexyphenidyl in young children with dystonic cerebral palsy: A single arm study

PURPOSE

The incidence of dystonic cerebral palsy causing significant morbidity is on the rise. There is a paucity of evidence for the management of dystonia in children.

METHODS

Forty-one children aged 6 months-5 years with predominantly dystonic cerebral palsy were started on a predetermined protocol of trihexyphenidyl (0.25-0.52 mg/kg) and followed up at 3, 6 and 12 weeks. Dystonia severity, motor function and developmental age at baseline and 12 weeks were compared using the Global Dystonia Scale (GDS), the Gross Motor Function Measure (GMFM), and Fine Motor/Perceptual Subscale of the Early Developmental Profile-2. Thirty-four children completed the entire 12 weeks of intervention.

RESULTS

The mean age of participants was 25±11 months. A significant decrease in median total dystonia scores on the GDS was observed post-intervention (74.5 to 59, p <  0.0001), and 64% of participants gained motor milestones. GMFM scores increased significantly from a median of 19.8% pre-intervention to 26.5% post-intervention (p <  0.0001). There was improvement in the fine motor domain as compared to the baseline (p <  0.0001). The number of children classified at Gross Motor Function Classification System levels 1 and 2 increased to 47.05% from 5.88% in the pre-intervention group.

CONCLUSION

Trihexyphenidyl significantly improved dystonia, motor function and development in children with dystonic cerebral palsy in this study. Additional studies are needed to clarify its role in larger numbers of children with this condition.

Temperature-Controlled Chemoselective Synthesis of Multisubstituted 4-Alkynyl/trans 4-Alkenyl Coumarins

A temperature-controlled facile synthesis of multisubstituted 4-alkynyl/trans 4-alkenyl coumarins with a metal salt cascade approach is reported. H₂O serves both as a nucleophile and hydrogen source. The presence of metal salt facilitates the reduction of alkyne. The present protocol bypasses the structural shortcomings of the existing Sonogashira and Heck coupling reactions. In addition, the obtained 2,3-disubstituted coumarins are readily transformed into 2,3-disubstituted dihydrocoumarins, which serve as important building blocks in organic transformations.

Experimental verification of arcsine laws in mesoscopic nonequilibrium systems

A large number of processes in the mesoscopic world occur out of equilibrium, where the time evolution of a system becomes immensely important since it is driven principally by dissipative effects. Nonequilibrium steady states (NESS) represent a crucial category in such systems, where relaxation timescales are comparable to the operational timescales. In this study, we employ a model NESS stochastic system, which is comprised of a colloidal microparticle optically trapped in a viscous fluid, externally driven by a temporally correlated noise, and show that time-integrated observables such as the entropic current, the work done on the system or the work dissipated by it, follow the three Lévy arcsine laws [A. C. Barato et al., Phys. Rev. Lett. 121, 090601 (2018)0031-900710.1103/PhysRevLett.121.090601], in the large time limit. We discover that cumulative distributions converge faster to arcsine distributions when it is near equilibrium and the rate of entropy production is small, because in that case the entropic current has weaker temporal autocorrelation. We study this phenomenon by changing the strength of the added noise as well as by perturbing our system with a flow field produced by a microbubble at close proximity to the trapped particle. We confirm our experimental findings with theoretical simulations of the systems. Our work provides an interesting insight into the NESS statistics of the meso-regime, where stochastic fluctuations play a pivotal role.

Olaparib enhances the Resveratrol-mediated apoptosis in breast cancer cells by inhibiting the homologous recombination repair pathway

Although sensitization of BRCA-mutated, homologous recombination (HR)-deficient breast cancer cells through PARP inhibitor is widely studied, not much is known about the treatment of BRCA-wild-type, HR-proficient breast cancer. Here, we aim to investigate whether a bioactive compound, Resveratrol (RES), can induce DNA double-strand breaks in HR-proficient breast cancer cells and Olaparib (OLA), a PARP inhibitor, can enhance the RES-mediated apoptosis by deregulating the HR repair pathway. The detailed mechanism of anti-cancer action of RES + OLA combination in breast cancer has been evaluated using in vitro, ex vivo, and in vivo preclinical model systems. OLA increased RES-mediated DNA damage, downregulated the HR pathway proteins, caused a late S/G2 cell cycle arrest, enhanced apoptosis and cell death in RES pre-treated breast cancer cells at much lower concentrations than their individual treatments. Direct measurement of HR pathway activity using a GFP plasmid-based assay demonstrated reduced HR efficiency in I-SceI endonuclease-transfected cells treated with OLA. Moreover, RES + OLA treatment also caused significant reduction in PARP1-mediated PARylation and efficiently trapped PARP1 at the DNA damage site. Upon RES treatment, PARylated PARP1 was found to interact with BRCA1, which then activated other HR pathway proteins. But after addition of OLA in RES pre-treated cells, PARP1 could not interact with BRCA1 due to inhibition of PARylation. This resulted in deregulation of HR pathway. To further confirm the role of BRCA1 in PARP1-mediated HR pathway activation, BRCA1 was knocked down that caused complete inhibition of HR pathway activity, and further enhanced apoptosis after RES + OLA treatment in BRCA1-silenced cells. In agreement with in vitro data, similar experimental results were obtained in ex vivo patient-derived breast cancer cells and in vivo xenograft mice. Thus, RES + OLA combination treatment enhanced breast cancer cell death by causing excessive DNA damage and also simultaneously inhibiting the HR pathway.

Establishment of decellularized extracellular matrix scaffold derived from caprine pancreas as a novel alternative template over porcine pancreatic scaffold for prospective biomedical application

In this study, the caprine pancreas has been presented as an alternative to the porcine organ for pancreatic xenotransplantation with lesser risk factors. The obtained caprine pancreas underwent a systematic cycle of detergent perfusion for decellularization. It was perfused using anionic (0.5% w/v sodium dodecyl sulfate) as well as non-ionic (0.1% v/v triton X-100, t-octyl phenoxy polyethoxy ethanol) detergents and washed intermittently with 1XPBS supplemented with 0.1% v/v antibiotic and nucleases in a gravitation-driven set-up. After 48 h, a white decellularized pancreas was obtained, and its extracellular matrix (ECM) content was examined for scaffold-like properties. The ECM content was assessed for removal of cellular content, and nuclear material was evaluated with temporal H&E staining. Quantified DNA was found to be present in a negligible amount in the resultant decellularized pancreas tissue (DPT), thus prohibiting it from triggering any immunogenicity. Collagen and fibronectin were confirmed to be preserved upon trichrome and immunohistochemical staining, respectively. SEM and AFM images reveal interconnected collagen fibril networks in the DPT, confirming that collagen was unaffected. sGAG was visualized using Prussian blue staining and quantified with DMMB assay, where DPT has effectively retained this ECM component. Uniaxial tensile analysis revealed that DPT possesses better elasticity than NPT (native pancreatic tissue). Physical parameters like tensile strength, stiffness, biodegradation, and swelling index were retained in the DPT with negligible loss. The cytocompatibility analysis of DPT has shown no cytotoxic effect for up to 72 h on normal insulin-producing cells (MIN-6) and cancerous glioblastoma (LN229) cells in vitro. The scaffold was recellularized using isolated mouse islets, which have established in vitro cell proliferation for up to 9 days. The scaffold received at the end of the decellularization cycle was found to be non-toxic to the cells, retained biological and physical properties of the native ECM, suitable for recellularization, and can be used as a safer and better alternative as a transplantable organ from a xenogeneic source.

Circulating tumor DNA sequencing provides comprehensive mutation profiling for pediatric central nervous system tumors

Molecular profiling of childhood CNS tumors is critical for diagnosis and clinical management, yet tissue access is restricted due to the sensitive tumor location. We developed a targeted deep sequencing platform to detect tumor driver mutations, copy number variations, and heterogeneity in the liquid biome. Here, we present the sensitivity, specificity, and clinical relevance of our minimally invasive platform for tumor mutation profiling in children diagnosed with CNS cancer.

Combination of talazoparib and olaparib enhanced the curcumin-mediated apoptosis in oral cancer cells by PARP-1 trapping

PURPOSE

Inhibition of Poly (ADP-ribose) Polymerases (PARP) results in the blocking of DNA repair cascades that eventually leads to apoptosis and cancer cell death. PARP inhibitors (PARPi) exhibit their actions either by inhibiting PARP-induced PARylation and/or by trapping PARP at the DNA damage site. But, the mechanism of PARPi-mediated induction of cellular toxicity via PARP-trapping is largely unknown.

METHODS

The cellular toxicity of PARPi [Talazoparib (BMN) and/or Olaparib (Ola)] was investigated in oral cancer cells and the underlying mechanism was studied by using in vitro, in silico, and in vivo preclinical model systems.

RESULTS

The experimental data suggested that induction of DNA damage is imperative for the optimal effectiveness of PARPi. Curcumin (Cur) exhibited maximum DNA damaging capacity in comparison to Resveratrol and 5-Flurouracil. Combination of BMN + Ola induced cell death in Cur pre-treated cells at much lower concentrations than their individual treatments. BMN + Ola treatment deregulated the BER cascade, potentiated PARP-trapping, caused cell cycle arrest and apoptosis in Cur pre-treated cells in a much more effective manner than their individual treatments. In silico data indicated the involvement of different amino acid residues which might play important roles in enhancing the BMN + Ola-mediated PARP-trapping. Moreover, in vivo mice xenograft data also suggested the BMN + Ola-mediated enhancement of apoptotic potentiality of Cur.

CONCLUSION

Thus, induction of DNA damage was found to be essential for optimal functioning of PARPi and BMN + Ola combination treatment enhanced the apoptotic potentiality of Cur in cancer cells by enhancing the PARP-trapping activity via modulation of BER cascade.

MIF confers survival advantage to pancreatic CAFs by suppressing interferon pathway-induced p53-dependent apoptosis

The presence of activated pancreatic stellate cells (PSCs) in the pancreatic ductal adenocarcinoma (PDAC) microenvironment plays a significant role in cancer progression. Macrophage migration inhibitory factor (MIF) is overexpressed in PDAC tissues and expressed by both cancer and stromal cells. The pathophysiological role of MIF in PDAC-associated fibroblasts or PSCs is yet to be elucidated. Here we report that the PSCs of mouse or cancer-associated fibroblast cells (CAFs) of human expresses MIF and its receptors, whose expression gets upregulated upon LPS or TNF-α stimulation. In vitro functional experiments showed that MIF significantly conferred a survival advantage to CAFs/PSCs upon growth factor deprivation. Genetic or pharmacological inhibition of MIF also corroborated these findings. Further, co-injection of mouse pancreatic cancer cells with PSCs isolated from Mif-/- or Mif+/+ mice confirmed the pro-survival effect of MIF in PSCs and also demonstrated the pro-tumorigenic role of MIF expressed by CAFs in vivo. Differential gene expression analysis and in vitro mechanistic studies indicated that MIF expressed by activated CAFs/PSCs confers a survival advantage to these cells by suppression of interferon pathway induced p53 dependent apoptosis.

Gemcitabine induces polarization of mouse peritoneal macrophages towards M1-like and confers antitumor property by inducing ROS production

In patients with pancreatic cancer (PC), the peritoneal cavity is the second-most common site of metastasis after the liver. Peritoneal macrophages (PMs) have been demonstrated to play a significant role in the peritoneal metastases of different cancers. Gemcitabine (GEM) is known to affect PC-associated immune cells, including macrophages. However, its effect on PMs and its possible clinical implication is yet to be investigated. In this study, mouse-derived PMs were treated with GEM ex vivo to analyze the polarization status. Production of GEM-induced reactive oxygen species (ROS) and reactive nitrogen species was evaluated using DCFH-DA, DAF-FM, and Griess assay. Antitumor effects of PMs on UN-KC-6141and UN-KPC-961 murine PC cells were evaluated in presence and absence of GEM in vitro. Similarly, effect of GEM on human THP-1 macrophage polarization and its tumoricidal effect was studied in vitro. Furthermore, the effect of GEM-treated PMs on peritoneal metastasis of UN-KC-6141 cells was evaluated in a syngeneic mouse model of PC. GEM upregulated M1 phenotype-associated molecular markers (Tnf-α and Inos) in vitro in PMs obtained from naïve mouse. Moreover, IL-4-induced M2-like PMs reverted to M1-like after GEM treatment. Co-culture of UN-KC-6141 and UN-KPC-961 cancer cells with PMs in the presence of GEM increased apoptosis of these cells, whereas cell death was markedly reduced after N-acetyl-L-cysteine treatment. Corroborating these findings co-culture of GEM-treated human THP-1 macrophages also induced cell death in MIAPaCa-2 cancer cells. GEM-treated PMs injected intraperitoneally along with UN-KC-6141 cells into mice extended survival period, but did not stop disease progression and mortality. Together, GEM induced M1-like polarization of PMs from naive and/or M2-polarized PMs in a ROS-dependent manner. GEM-induced M1-like PMs prompted cytotoxicity in PC cells and delayed disease progression in vivo.

MicroRNA-217 modulates pancreatic cancer progression via targeting ATAD2

AIMS

Pancreatic cancer is a fatal disease across the world with 5 years survival rate less than 10%. ATAD2, a valid cancer drug-target, is overexpressed in pancreatic malignancy with high oncogenic potential. However, the mechanism of the upregulated expression of ATAD2 in pancreatic cancer is unknown. Since microRNAs (miRNAs) could potentially control target mRNA expressions, and are involved in cancer as tumor-suppressors, oncomiR or both, we examine the possibility of miRNA-mediated regulation of ATAD2 in pancreatic cancer cells (PCCs).

MAIN METHODS

Our in-silico approach first identifies hsa-miR-217 as a candidate regulator for ATAD2 expression. For further validation, luciferase reporter assay is performed. We overexpress hsa-miRNA-217 and assess cellular viability, migration, apoptosis and cell cycle progression in three different PCCs (BxPC3, PANC1, and MiaPaCa2).

KEY FINDINGS

We find hsa-miRNA-217 has potential binding site at the 3'UTR of ATAD2. Luciferase assay confirms that ATAD2 is a direct target of hsa-miR-217. Overexpression of hsa-miR-217 drastically downregulates ATAD2 expression in PCCs, thus, corroborating binding studies. The elevated expression of hsa-miRNA-217 diminishes cell proliferation and migration as well as induces apoptosis and cell cycle arrest in PCCs. Finally, siRNA mediated ATAD2 knockdown or overexpression of hsa-miRNA-217 in PCCs showed inactivation of the AKT signaling pathway. Therefore, hsa-miR-217 abrogates pancreatic cancer progression through inactivation of the AKT signaling pathway and this might be partly due to miR-217 mediated suppression of ATAD2 expression.

SIGNIFICANCE

The application of hsa-miR-217 mimic could be a promising therapeutic strategy for the treatment of pancreatic cancer patients in near future.

Abstract 1913: Quality control workflows developed for the NCI Patient-Derived Models Repository using low pass whole genome sequencing and whole exome sequencing

Background: The National Cancer Institute's Patient-Derived Models Repository (NCI PDMR; pdmr.cancer.gov) is developing a variety of patient-derived xenograft (PDX) models for pre-clinical drug studies. All NCI PDMR models undergo quality control (QC) processes. Two unique QC challenges are: a) to assess genomic stability across PDX model passages; and b) to confirm the suitability of PDX-derived cancer associated fibroblasts (CAFs) as germline surrogates when blood is not available. Multiple bioinformatics QC assessments have been developed to measure the genomic fidelity in these PDX models using low-pass whole genome sequencing (LP-WGS) and in CAFs using whole exome sequencing (WES).

Methods: LP-WGS was performed on 502 PDX samples from 38 models of rare cancer across passages 2 through 9 and WES was performed on 92 CAFs from 32 different histologies. In the QC workflow for estimating the genomic stability of passages within models, BBSplit was used for the assessment of human/mouse DNA content. CNVkit was utilized for copy number (CN) detection. The fraction of genome changed was calculated by comparing the copy numbers of each passage sample to the original patient sample. To evaluate purity of CAFs, three QC steps were constructed: a) plot of SNP variant allele frequency (ideogram); b) variant annotation using OncoKB (www.oncokb.org); c) percentage of genomic loss of heterozygosity (LOH), based on a set of ~800,000 heterozygous SNPs from a population-level genomic database (gnomAD) based on WES data.

Results: PDX models showed genomic stability in CN profile when measured by LP-WGS. Human tumor DNA content remains stable ranging from 75-85% across different tiers of PDX passages from Donor +1 to Donor +6 and more. No models showed statistically significant evolution in CN profile, given the average 5 samples per model in each tier of passages. The QC workflow for CAFs generated five categories based on SNP ideograms, the presence/absence of oncogenic variants and LOH. Following observations were made: a) 72.5% CAFs were confirmed as matched diploid CAFs (category 1); b) 6.6% of CAFs were diploid and had &gt;= 1 germline oncogenic variant - classified as category 2. CAFs in category 1&2 were suitable as germline surrogates; c) 12% of CAFs (category 3) showed putative polyploidy on SNP ideograms with no oncogenic variants and suitable for somatic variant calling; d) 8.8% of CAFs (category 4) had polyploidy and oncogenic variants present; e) LOH high CAF (category 5) - we identified a CAF with 42% LOH, later confirmed to be a tumor cell line by immunohistochemistry (IHC). Other CAFs (n=91) showed little variance, ranging from 0.6%-1.7% LOH.

Conclusions: We developed standard QC workflows to evaluate genomic stability of PDX models during passaging and qualify CAFs as germline surrogates for pre-clinical study.

Citation Format: Ting-Chia Chang, Li Chen, Biswajit Das, Yvonne A. Evrard, Chris A. Karlovich, Tomas Vilimas, Alyssa Chapman, Nikitha Nair, Luis Romero, Anna J. Lee Fong, Amanda Peach, Brandie Fullmer, Lindsay Dutko, Kelly Benauer, Gloryvee Rivera, Erin Cantu, Shahanawaz Jiwani, Nastaran Neishaboori, Tomas Forbes, Corinne Camalier, Luke Stockwin, Michael Mullendore, Michelle A. Eugeni, Dianne Newton, Melinda G. Hollingshead, Mickey P. Williams, James H. Doroshow. Quality control workflows developed for the NCI Patient-Derived Models Repository using low pass whole genome sequencing and whole exome sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1913.

Abstract 3120: Method development for generation of PDX models from rapid autopsy samples for the NCI patient-derived models repository

NCI’s Patient-Derived Models Repository (NCI PDMR; pdmr.cancer.gov) has developed a variety of patient-derived models across most solid tumor histologies. These models are early passage, genetically characterized and associated with limited patient treatment history. As part of this effort, the NCI PDMR worked with the University of Nebraska Medical Center Rapid Autopsy Program and Johns Hopkins University Legacy Gift Rapid Autopsy Program to develop and optimize methods for collection, processing, and shipping of autopsy tumor material to maintain viability during overnight transit for use in patient-derived model development. These methods have been successfully transferred to two other participating rapid autopsy programs. To date, 412 autopsy tumor samples from 76 consented patients have been received for model development; 348 shipped overnight in media for next day implantation into NSG host mice and 64 cryopreserved prior to shipping for a comparative assessment of take-rate versus fresh tumor samples. On average 3-8 tumor samples, primary and metastatic, were collected post-mortem from the truncal region of each patient. Histologies include Pancreatic adenocarcinoma (n=43), Cholangiocarcinoma (n=6), Prostate adenocarcinoma (n=6), and 21 others with 1-2 patients/histology. The overall age range of enrolled patients was 5-88yo. The post-mortem cold ischemic time for collections ranged from 1.5 to 20 hours with a median of 3h (avg. 3.75h; outlier &gt;11h removed). Collection methods were optimized to reduce contamination and increase viability of tumor tissues for successful PDX model generation. Of 348 fresh tumor samples collected to date, 69 PDX models from 33 patients have been generated (range 1-6 models/patient) and an additional 55 samples are being monitored for growth in passage 0. The largest public single-patient PDX model sets are for melanoma (899932-113-R, n=6) and two pancreatic adenocarcinomas (521955-158-R, n=6, 217524-143-R, n=4). Important methods for reducing contaminants in autopsy tumor material include sterilization of the surface of the body prior to opening, use of sterile fields, using separate sterile instruments for each collection site, rinsing the surface of the resected tumor tissue, and use of antibiotics in the collection media. The now established SOPs are publicly available on the NCI PDMR website (pdmr.cancer.gov/sops). We recommend incorporating as many of these methods as possible within the limitations of your individual site. Of the 69 models developed to date, 48 are publicly available from the NCI PDMR while the rest are undergoing quality control process prior to public release. Models developed from autopsy material provide a research tool to investigate tumor evolution, differences between primary and metastatic lesions, and assessment of differences in therapeutic response based on differences in the tumor biology.

Citation Format: Yvonne A. Evrard, Michelle Eugeni, Michelle Ahalt-Gottholm, Carrie Bonomi, Suzanne Borgel, Thomas C. Caffrey, John Carter, Ting-Chia Chang, Li Chen, Kevin Cooper, Biswajit Das, Emily Delaney, Kelly Dougherty, Eleonora Duregon, Stephanie Ecker, Joe Geraghty, Marion Gibson, Lauren Hicks, Jenna Hull, Sharon Int Veldt, Shahanawaz Jiwani, Chris A. Karlovich, Jade Loewenstein, Candace Mallow, Chelsea McGlynn, Justine Mills, Tiffanie Miner, Jowaly Schneider, Tia Shearer, Savanna Styers, Shannon Uzelac, Paul Grandgenett, Michael Hollingsworth, Jody E. Hooper, P. Mickey Williams, Melinda Hollingshead, James H. Doroshow. Method development for generation of PDX models from rapid autopsy samples for the NCI patient-derived models repository [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3120.

Abstract 80: Genomic characterization of PDX models from rare cancer patients in the NCI Patient-Derived Models Repository

Background: The National Cancer Institute’s Patient-Derived Models Repository (NCI PDMR; https://pdmr.cancer.gov) has developed a large number of patient-derived xenograft (PDX) models from a diverse set of rare cancers. These models have been genomically characterized using whole-exome sequencing (WES) and RNAseq. The resource provides a unique opportunity to explore the genomic features of rare tumor models in NCI PDMR and to understand the oncogenic processes in pre-clinical models to identify biomarkers associated with therapeutic responses.

Methods: Genomic characterization was done in 4-6 PDX samples across multiple passages and lineages from each model. As the samples exhibited a high level of genomic stability within each model, consensus mutation and copy number variation (CNV), microsatellite instability (MSI), genomic loss of heterozygosity (LOH), homologous recombination deficiency score (scarHRD), and mutational signature data were generated from WES. Fusions were identified from RNASeq data using Star-Fusion and FusionInspector. Gene set enrichment analysis was conducted from the gene expression data obtained from RNAseq.

Results: 1) 233 PDX models have been developed and characterized from more than 45 different rare malignancies. Most frequent cancer types are different sarcomas (n=63), head & neck squamous cell carcinoma (n=61), and malignant fibrous histiocytoma (MFH) (n=11); 2) TP53 was the most frequently altered gene, mutated in 51% of models, followed by NOTCH1 (16%) and PIK3CA (11%). In terms of CNVs, ovarian epithelial cancer (OVT) showed relatively high chromosomal instability, while uterine endometrioid carcinoma (UEC) and synovial sarcoma (SYNS) had low instability; 3) MSI-H was observed in only 7 models. Esophageal adenocarcinoma (ESCA), OVT, and cervical squamous cell carcinoma (CESC) had high scarHRD and genomic LOH scores, while both scores were low in UEC and anal squamous cell carcinoma (ANSC). COSMIC v2 mutational signature 3 is significantly associated with a high scarHRD score (p-value &lt; 0.01, Wilcoxon rank-sum test); 4) Characteristic fusions were observed in certain sarcoma models: SS18-SSX1 and ASPSCR1-TFE3 fusions were observed in SYNS and alveolar soft part sarcoma (ASPS) models respectively. EWSR1-FLI1 fusion was present in 2 out of 3 Ewing sarcoma (ES) models. 5) Gene set enrichment analysis from RNASeq data showed that epithelial-mesenchymal transition score could accurately distinguish carcinoma from sarcoma models, confirming the divergent gene expression programs.

Conclusion: Comprehensive genomic characterization of NCI PDMR models generated from rare cancers solves an unmet need in the community. It will serve as a valuable resource for translational researchers interested in pre-clinical drug development and discovery.

Citation Format: Li Chen, Rini Pauly, Ting-Chia Chang, Biswajit Das, Yvonne A. Evrard, Chris A. Karlovich, Tomas Vilimas, Alyssa Chapman, Nikitha Nair, Luis Romero, Anna Lee Fong, Amanda Peach, Shahanawaz Jiwani, Nastaran Neishaboori, Lindsay Dutko, Kelly Benauer, Gloryvee Rivera, Erin Cantu, Corinne Camalier, Thomas Forbes, Michelle Gottholm-Ahalt, John Carter, Suzanne Borgel, Chelsea McGlynn, Candace Mallow, Emily Delaney, Tiffanie Miner, Michelle A. Eugeni, Dianne Newton, Melinda G. Hollingshead, P. Mickey Williams, James H. Doroshow. Genomic characterization of PDX models from rare cancer patients in the NCI Patient-Derived Models Repository [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 80.

Abstract 973: 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, 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 metastases.

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 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 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. Data processing and analysis was done using 10X Genomics’ Cell Ranger pipeline, Seurat, and cNMF.

Results: single cell RNAseq data from primary tumors, CTCs, and metastases from 9 mice were aggregated into a single dataset, and cells were classified into 17 clusters using Seurat FindNeighbors. All clusters contained 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 epithelial-like gene expression signature scores, suggesting that CTC shedding was occurring without prominent epithelial-mesenchymal transition. CTC-enriched clusters showed elevated expression of RHO pathway genes, implicating ameboid-like migration in CTC shedding in this PDX model. 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 other sites. Additionally, two of three CTC-enriched clusters had elevated expression of mitosis-associated genes, indicating that at least some subpopulations of CTCs are actively cycling. A metastasis suppressor gene KISS1 was expressed in a subset of primary tumor cells but undetectable in CTCs, suggesting that KISS1 expression loss occurs before CTC shedding.

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 exhibit enrichment of motility-associated transcripts and features of active cell cycling. Our results implicate a known metastasis suppressor gene KISS1 in CTC shedding and metastatic dissemination in this PDX model.

Citation Format: Tomas Vilimas, Brandie Fullmer, Alyssa Chapman, Rini Pauly, Ting-Chia Chang, Li Chen, Biswajit Das, Chris Karlovich, Yvonne Evrard, Melinda Hollingshead, Howard Stotler, Michelle Ahalt-Gottholm, Tara Grinnage-Pulley, Mickey Williams, James H. Doroshow. Comparative single cell transcriptome profiling of primary tumors, CTCs and metastatic sites from a bladder cancer PDX model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 973.

DIPG-47. TSO500ctDNA sequencing reveals oncogenic mutations and copy number variations in the liquid biome of children with diffuse midline glioma

BACKGROUND: Molecular profiling of childhood CNS tumors is critical for diagnosis and clinical management, yet tissue access is restricted due to sensitive neuroanatomical locations. Moreover, CNS tumors including diffuse midline glioma (DMG) exhibit mutational heterogeneity and clonal evolution, which cannot be captured by upfront diagnostic biopsy alone. To address the lack of tumor visibility, and tprovide opportunity for longitudinal sampling, we validated and optimized a commercially available deep sequencing platform for analysis of circulating tumor DNA (TSO500ctDNA^TM). METHODS: In a proof-of-concept study, we defined the sensitivity, specificity, and clinical relevance of our novel ctDNA platform via analysis of paired tissue, CSF, and blood from children with DMG (n=10). Paired samples were assessed for concordance and sequencing results were compared to digital droplet PCR (ddPCR) detection of prognostic H3K27M mutation. RESULTS: DMG associated mutations in genes including H3-3A, H3C2, TP53, and ACVR1 were detected in ctDNA, including in CSF samples with low (<5ng) starting DNA input. Of 9 H3K27M mutations identified in tumor, 8 were present in CSF and 3 in plasma/serum, for a positive percent agreement with tumor results of 89% and 33%, respectively. 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, KIT, and MDM4 gains were detected in CSF and paired tumor. Low frequency events including ACVR1, PIK3CA activating mutations 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. CONCLUSION: Targeted ctDNA deep sequencing is feasible, can inform on clinically relevant tumor mutation and CNV profiling, and provides an opportunity for longitudinal monitoring of tumor genomic evolution in the liquid biome of children with CNS tumors.

Factors Affecting School Performance in the Adolescents of USA- Youth Risk Behavior Surveillance System

Introduction

Poor academic performance has been linked to factors such as sleep, health, illicit drug use, physical fighting, social media use, cyber bullying, physical activity, homelessness, times spent in video games and television. It is difficult to get a sense of the interplay between and relative importance of different behaviours/factors on academic performance as only limited research has been aimed at quantifying these factors.

Objectives

To evaluate association of school performance and variables in five categories of the YRBSS: physical fighting, diet/lifestyle, electronic device usage, concurrent substance use, and violence/self-harm.

Methods

The CDC Youth Risk Behavior Surveillance System (YRBSS) data from 1991-2019 was used in study. Respondents were grouped by good and poor school performance and variables related to nutrition/lifestyle, electronic device use, concurrent substance use, mood/violence/self-harm were analyzed using chi-square test.

Results

A total of 41,235 student respondents.Nutrition/Lifestyle, electronic device use, concurrent substance use, mood/violence/self-harm are found to be significantly correlated with school performance.

	Poor Performance n(%)	Good Performance n(%)	Total n(%)	p-Value
Nutrition/Lifestyle
Daily breakfast	2,715(26)	11,429(38.22)	14,144(35.06)	<0.0001
Sodas ≥2/day	1,998(19.12)	2,710(9.03)	4,708(11.63)	<0.0001
Concurrent Substance Use
Alcohol use	3,544(37.55)	8,067(28.49)	11,611(30.75)	<0.0001
Cigarette smoking	1,616(15.74)	1,845(6.17)	3,461(8.61)	<0.0001
Mood/Violence/Self-Harm
Difficulty concentrating	4,188(46.34)	7,327(28.27)	11,516(32.94)	<0.0001
Felt sad or hopeless	4,373(41.06)	9,038(29.67)	13,410(32.62)	<0.0001
Considered suicide	2,567(24.14)	4,810(15.8)	7,377(17.96)	<0.0001

Conclusions

In national data, we found school performance is affected by nutrition, lifestyle, substance use, mood and exposure to surrounding violence, and self-harm. Further studies should be planned to evaluate benefits from the risk stratification to reduce this burden amongst US adolescents.

Disclosure

No significant relationships.

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Comparison of AYA versus non-AYA ovarian cancer genomic landscape in NCI-MATCH trial

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Background: NCI-MATCH, a signal-finding precision medicine trial, centrally screened tumors from ̃6000 patients age > 18 with refractory/relapsed cancer using Oncomine Comprehensive Assay (OCA) targeted gene panel. Screened cohort included a subset of patients with ovarian cancer age 18-39 yrs, overlapping adolescent and young adult (AYA) range (NCI consensus definition: 15-39 yrs). Objective of this study was to compare tumor genomic features of AYA to non-AYA ovarian cancers. Methods: Patient clinicopathologic, demographic, and tumor mutation (SNVs, Indels, CNVs by central OCA) data from NCI-MATCH were available. Analyses were restricted to mutation profiles generated by OCA version 2 (OCA v2), which assessed 143 genes and was used for most samples. Proportions of cases with mutations in each gene were compared for AYA and non-AYA groups by 2-sided Fisher’s exact tests. For each gene, association between age (continuous independent variable) and presence of mutation (binary dependent variable) was assessed using logistic regression. Benjamini-Hochberg adjusted p-values were computed; false discovery rate (FDR) was controlled at 10%. Results: Data from 455 ovarian cancers (437 epithelial, 18 stromal), including 21 AYA and 434 non-AYA cases, were included in this analysis. Among the 28 genes most frequently (in > 6 patient tumors) mutated and altered, CTNNB1 was mutated in 9.5% of AYA patients compared to 0.9% in non-AYA (unadj. p=0.027) but failed to meet 10% FDR criterion (FDR-adj. p=0.7). KRAS mutation was more frequent in AYA than non-AYA but not significantly after adjustment (FDR-adj. p=0.7). Logistic regression results showed TP53 mutation was significantly associated with older age (FDR-adj. p<0.0001), and ATM mutation was borderline associated with younger age (FDR-adj. p=0.052). No other differences, including in clinically actionable mutations ( BRCA1/2, MSH2), were observed. Table displays selected results. Conclusions: This preliminary study shows that no genes were mutated in significantly different proportion between AYA and non-AYA groups, but modeling age as a continuous variable highlighted known association of TP53 mutation with older age and a trend towards association of ATM mutation with younger age. More comprehensive tumor mutation profiling and analyses of additional tumor types may reveal further insights into rare AYA cancers. [Table: see text]

Blood-based detection of actionable alterations from NCI-MATCH patients with no tissue results

3035

Background: The National Cancer Institute Molecular Analysis for Therapy Choice (NCI-MATCH) multi-arm phase II clinical trial tested tumor tissue from 5,954 patients with advanced refractory cancer to assign treatment based on the molecular profile. Molecular profiling was successful for 93% of patients. For 267 of the patients who were not enrolled because molecular profiling was not successful, plasma cfDNA was evaluated to provide insight into the potential utility of blood-based testing in a broad spectrum of histologies when tissue is not evaluable. Methods: Cell-free DNA was extracted from plasma collected from Streck blood tubes and quantitated. Libraries were constructed using ³ 15 ng cfDNA into the Illumina TruSight Oncology 500 ctDNA RUO Assay, including unique molecular identifiers and duplex barcodes for error correction. Libraries were sequenced on the NovaSeq 6000 with S4 XP flow cells. Results: Of the 267 samples, 250 samples (94%) were evaluable, representing 72 histologies, including colorectal cancer (N = 36), lung adenocarcinoma (N = 15), pancreatic adenocarcinoma (N = 14), and invasive breast carcinoma (N = 12). Of these, 231 (92%) had ³ 1 OncoKB annotated mutation, with 208 patients (83%) having putative somatic mutations detected in genes not commonly associated with clonal hematopoiesis. The most common somatic mutations were in TP53, KRAS, APC, and PIK3CA, reported in 51%, 20%, 12%, and 12% of patients respectively. A total of 109 patients (44%) had ³ 1 actionable mutation of interest (aMOI) reported that could have been used for treatment assignment in the NCI-MATCH clinical trial. After applying histology and molecular exclusions, 75 patients (30%) had ³ 1 aMOI. The most common assignable treatment arms were Z1B/Z1BX1 (palbociclib with CCND1/2/3, N = 13), Z1F (copanlisib with PIK3CA Mutations, N = 13), S1/S1X1 (trametinib with NF1 mutation, N = 12), and Z1C/Z1CX1 (palbociclib with CDK4/CDK6 Amplification and Rb Expression by IHC, N = 10). Mutations in genes commonly associated with clonal hematopoiesis (CH) were prevalent in this population. Along with the expected high frequency of DNMT3A (21% of patients) and TET2 (11%) mutations, PPM1D mutations were the highest amongst CH genes, with 61 patients (24%) having ³ 1 PPM1D mutation, likely due to the heavily pre-treated nature of these patients. Conclusions: Variants observed in the blood are consistent with what is reported in the tissue. Using liquid biopsy when tissue is not evaluable can expand the ability of patients to obtain mutation information that can inform treatment compared to using tumor tissue only. Cell-free DNA provided valuable mutation information for these patients and could have resulted in up to an additional 75 patients being eligible for treatment selection based on their mutation profile. These results indicate that blood-based screening could be a tool for future NCI-sponsored clinical studies.

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

11509

Background: uLMS is an aggressive sarcoma subtype of smooth muscle origin. Chemotherapy provides limited benefit for advanced disease. 18-25% of uLMS harbor deleterious alterations in homologous recombination (HR) DNA repair genes. uLMS exhibits high levels of replicative stress. These findings prompted a phase 2 study of O+T in pretreated uLMS where O+T demonstrated activity: ORR 27%, mPFS 6.9 mos (Ingham M. et. al. ASCO 2021: #11506) Methods: NCI protocol #10250 is a single-arm, multicenter, phase 2 trial evaluating O+T in advanced uLMS pts with progression on ≥1 prior line. Pre-treatment (Pre) and on-treatment (On) biopsies were collected from 22 pts. In prespecified analysis, we evaluated for a relationship between clinical outcomes and HR gene alterations by whole exome sequencing (WES), SLFN11/MGMT expression by RNAseq, and RAD51 foci formation (functional assay). HRD scores were calculated from WES using scarHRD. Gene expression was evaluated using a Spearman rank-order correlation analysis to identify genes associated with PFS (p < 0.01) and overexpressed in sensitive (S: PFS > 240d) or resistant (R: PFS < 240d) pts. Gene set enrichment analysis (GSEA) was performed (q = FDR-adjusted p value). Pts with available results: WES/RNAseq (16), Pre HRD score (13), Pre RAD51 foci (12). Results: 31% (5/16) pts had a mutation (Mut) or homozygous deletion (Hd) in the HR panel: ATRX Mut (2), ATR Mut, PALB2 Hd, RAD51B Hd. Pts with PALB2 and RAD51B Hd had longest PFS on study. Recurrent alterations also occurred in TP53 (56%) and RB1 (19%). Median HRD score in Pre samples was 51 (range 36-66) and 10/13 had HRD scores ≥ 42. Pre and On SLFN11 and MGMT RNA expression were not correlated with ORR/PFS. 6/13 Pre samples were HR-deficient by the RAD51 foci assay. Of pts with PFS ≥ 200d, 4/6 were HR-deficient. In Pre samples, 81 genes were overexpressed in S pts and 73 in R pts. In On samples, 146 genes were overexpressed in S pts and 127 in R pts. In On samples, GSEA identified the epithelial-mesenchymal transition enriched in S pts (q = 3.38e-7) and cell cycle pathways (E2F targets, G2M checkpoint) in R pts (q = 7.43e-4). Only 2 genes, CXCL10 and PCDH15, were differentially expressed between paired Pre and On samples (both increased in On). Gene expression signatures for replicative stress showed borderline association with worse PFS. Conclusions: Most uLMS tumors exhibit HR defects as measured by HRD scores. A subset of pts with greater benefit from O+T were identified by WES for HR genes and the RAD51 assay. There was no correlation between SLFN11 and MGMT expression and outcomes. GSEA identified pathways differentially expressed in S and R pts in On samples. O+T induced CXCL10 which has been associated with T-cell trafficking to tumors. A randomized phase 3 trial of O+T versus investigator’s choice is planned. These results provide insight into which pts may benefit most from this novel drug combination. Clinical trial information: NCT03880019.

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.