Machine Learning Analysis of Raman Spectra To Quantify the Organic Constituents in Complex Organic-Mineral Mixtures.

Important decisions in local agricultural policy and practice often hinge on the soil's chemical composition. Raman spectroscopy offers a rapid noninvasive means to quantify the constituents of complex organic systems. But the application of Raman spectroscopy to soils presents a multifaceted challenge due to organic/mineral compositional complexity and spectral interference arising from overwhelming fluorescence. The present work compares methodologies with the capacity to help overcome common obstacles that arise in the analysis of soils. We created conditions representative of these challenges by combining varying proportions of six amino acids commonly found in soils with fluorescent bentonite clay and coarse mineral components. Referring to an extensive data set of Raman spectra, we compare the performance of the convolutional neural network (CNN) and partial least-squares regression (PLSR) multivariate models for amino acid composition. Strategies employing volume-averaged spectral sampling and data preprocessing algorithms improve the predictive power of these models. Our average test R2 for PLSR models exceeds 0.89 and approaches 0.98, depending on the complexity of the matrix, whereas CNN yields an R2 range from 0.91 to 0.97, demonstrating that classic PLSR and CNN perform comparably, except in cases where the signal-to-noise ratio of the organic component is very low, whereupon CNN models outperform. Artificially isolating two of the most prevalent obstacles in evaluating the Raman spectra of soils, we have characterized the effect of each obstacle on the performance of machine learning models in the absence of other complexities. These results highlight important considerations and modeling strategies necessary to improve the Raman analysis of organic compounds in complex mixtures in the presence of mineral spectral components and significant fluorescence.

Zinc oxide nanoparticles synthesized using Hyssopus Officinalis L. Extract Induced oxidative stress and changes the expression of key genes involved in inflammatory and antioxidant Systems.

BACKGROUND: Recent advances in the synthesis of bioactive nanoparticles resulted in the discovery and introduction of new bioactive nanoparticles to the pharmaceutical industry. In this regard, this research is aimed to synthesize the zinc oxide nanoparticles (ZnO-NPs) using Hyssopus officinalis L. extract and to evaluate the safety of nanoparticles using Balb/C mice. METHODS: Forty male mice were divided into four groups and received 0, 50, 100, and 200 mg/kg of ZnO-NPs for thirty days. At the end of the experiment, blood sugar, creatinine, aspartate aminotransferase (A.S.T.), and alanine aminotransferase (A.L.T.) were determined. Furthermore, histopathological and oxidative stress biomarker analyses in liver and kidney tissues were performed. The changes in the major inflammatory- and antioxidant-related genes were determined. RESULTS: The results showed that blood sugar and creatinine reduced significantly (P < 0.05) when 50, 100, and 200 mg/kg ZnO-NPs were supplemented to the diet. The serum ALT and AST and lipid peroxidation in the liver and kidney tissues were increased significantly (p < 0.05) when 50, 100, and 200 mg/kg ZnO-NPs were supplemented to the diet. Supplementation of ZnO-NPs suppressed the expression of antioxidant-related genes (SOD and CAT) and up-regulated the inflammatory biomarkers (iNOS and TNF- α). The concentration of 200 mg/Kg nanoparticles indicated cellular degeneration and necrosis in the liver and kidney tissues. CONCLUSIONS: Overall, it can be concluded that supplementation of ZnO-NPs synthesized using Hyssopus Officinalis L. extract in this study at 50 mg/kg or higher concentrations might be toxic to the mice.

U (VI) tolerance affects Shewanella sp. RCRI7 biological responses: growth, morphology and bioreduction ability.

Native Shewanella sp. RCRI7 is recently counted as an operative bacterium in the uranium bio-reduction. The aim of this study was to investigate the effects of uranium tolerance on the morphology and population of RCRI7, following its potential removal capacity in different time intervals. In this research, the bacterial growth and uranium removal kinetic were evaluated in aerobic TSB medium, uranium-reducing condition (URC), aerobic uranium-containing (AUC) and anaerobic uranium-free (AUF) solution, following evaluations of omcAB gene expressions. In addition, spectrophotometry analyses were performed in URC confirming the bio-reduction mechanism. It was found that the bacteria can grow efficiently in the presence of 0.5 mM uranium anaerobically, unlike AUC and AUF solutions. Since the bacterium's adsorption capacity is quickly saturated, it can be deduced that uranium reduction should be dominant as incubation times proceed up to 84 h in URC. In 92 h incubation, the adsorbed uranium containing unreduced and reduced (U (IV) monomeric), was released to the solution due to either increased pH or bacterial death. In AUC and AUF, improper conditions lead to the reduced bacterial size (coccus-shape formation) and increased bacterial aggregations; however, membrane vesicles produced by the bacteria avoid the uranium incrustation in AUC. In overall, this study implies that Shewanella sp. RCRI7 are well tolerated by uranium under anaerobic conditions and the amount of regenerated uranium increases over time in the reduced form.

Comparative Study on the Biological Effects of Sodium Citrate-Based and Apigenin-Based Synthesized Silver Nanoparticles.

The apigenin is a bioactive flavonoid mostly found in fruits and vegetables that possess various biological activities. The current study was performed to compare the biological potentials of sodium citrate-based (SC-SNPs) and apigenin-based (AP-SNPs) synthesized silver nanoparticles under the in vitro and in vivo conditions. The synthesized silver nanoparticles were physically and chemically characterized. The anticancer, pro-apoptotic, and their anti-bacterial activities were determined. Further, the mice trial was conducted to determine the possible toxic effects of the synthesized silver nanoparticles. The result of particle size analysis revealed the nanometer sizes of the SC-SNPs and AP-SNPs were about 95.5 and 93.94 nm, respectively. Both nanoparticles indicated pseudo-spherical shape, homogenous dispersion with an appropriate good degree of stability. However, the anticancer potential, pro-apoptotic effects and antibacterial activity of AP-SNPs were higher than that of SC-SNPs. Moreover, the mice trial indicated that AP-SNPs improved the liver function through modulation of liver enzymes, lipid peroxidation, and increase in the expression of antioxidant enzymes (SOD and GPx) as compared to the mice received AP-SNPs during 30 day experiment. Consequently the synthesis of silver nanoparticles using apigenin as reducing bioactive compound may result in production of silver nanoparticles with enhanced anticancer, antibacterial and antioxidant activities.

A novel mouse model of hemangiopericytoma due to loss of Tsc2.

Hemangiopericytoma (HPC) is a rare vascular tumor, which is thought to originate from pericytes. However, no direct evidence for the cell of origin has been found, and the mechanism of HPC tumorigenesis is poorly understood. Here we report that loss of the tumor suppressor gene Tsc2 in pericytes using a FoxD1 promoter driven cre allele (Foxd1tm1(GFP/cre) Amc, FoxD1GC) leads to the formation of HPC in multiple sites. Tsc2ffFoxD1GC mice had stunted growth with seizures and tail and hind limb tremor with a median survival of 110 days. They also showed recombination in brain, spinal cord, tongue, liver, intestine and skeletal muscle. Distinctive perivascular tumors consisting of cells with oval nuclei and scant cytoplasm were identified in multiple sites in all Tsc2ffFoxD1GC mice. Immunohistochemistry staining showed a high expression of phospho-S6-S240/244, a hallmark of activated mTORC1, as well as pericyte markers NG2 and vimentin in these tumors. In summary, we demonstrate that loss of Tsc2 in pericytes generates HPC, the first mouse model of HPC reported.

Evaluation of mtr cluster expression in Shewanella RCRI7 during uranium removal.

In recent years, bioremediation is considered as an efficient method to remove the pollutants from the industrial wastewater. In this study, quantitative gene expressions (Real-time RT-PCR) of mtr gene cluster (mtrA, mtrB, mtrC, mtrD, mtrE, mtrF and omcA) in five different uranium concentrations (0.1, 0.25, 0.5, 1 and 2 mM) were performed with ICP and microscopic live cell counting analysis under anaerobic condition, by Shewanella RCRI7 as a native bacterium. The results indicated that the amount of uranium removal and live-cell counting were decreased in the higher uranium concentrations (1 and 2 mM), due to the uranium toxicity, suggesting 0.5 mM as the optimum uranium concentration for Shewanella RCRI7 resistance. The expression of mtrCED and omcA genes presented increasing trend in the lower uranium concentrations (0.1, 0.25 and 0.5 mM) and a decreasing trend in 1 and 2 mM, while mtrABF, presented an inverse pattern, proving the alternative role of mtrF for mtrC and omcA, as the substantial multiheme cytochromes in Extracellular Electron Transfer (EET) pathway. These data are a proof of these gene vital roles in the EET pathway, proposing them for genetic engineering toward EET optimization, as the certain pathway in heavy metal bioremediation process.

Nuclear receptor 4A2 (NR4A2) is a druggable target for glioblastomas.

INTRODUCTION: The orphan nuclear receptor 4A2 (NR4A2) has been extensively characterized in subcellular regions of the brain and is necessary for the function of dopaminergic neurons. The NR4A2 ligand, 1,1-bis (31-indoly1)-1-(p-chlorophenyl)methane (DIM-C-pPhCl) inhibits markers of neuroinflammation and degeneration in mouse models and in this study we investigated expression and function of NR4A2 in glioblastoma (GBM). METHODS: Established and patient-derived cell lines were used as models and the expression and functions of NR4A2 were determined by western blots and NR4A2 gene silencing by antisense oligonucleotides respectively. Effects of NR4A2 knockdown and DIM-C-pPhCl on cell growth, induction of apoptosis (Annexin V Staining) and migration/invasion (Boyden chamber and spheroid invasion assay) and transactivation of NR4A2-regulated reporter genes were determined. Tumor growth was investigated in athymic nude mice bearing U87-MG cells as xenografts. RESULTS: NR4A2 knockdown and DIM-C-pPhCl inhibited GBM cell and tumor growth, induced apoptosis and inhibited migration and invasion of GBM cells. DIM-C-pPhCl and related analogs also inhibited NR4A2-regulated transactivation (luciferase activity) confirming that DIM-C-pPhCl acts as an NR4A2 antagonist and blocks NR4A2-dependent pro-oncogenic responses in GBM. CONCLUSION: We demonstrate for the first time that NR4A2 is pro-oncogenic in GBM and thus a potential druggable target for patients with tumors expressing this receptor. Moreover, our bis-indole-derived NR4A2 antagonists represent a novel class of anti-cancer agents with potential future clinical applications for treating GBM.

Natural bioactive 4-Hydroxyisophthalic acid (4-HIPA) exhibited antiproliferative potential by upregulating apoptotic markers in in vitro and in vivo cancer models.

There is tremendous scope for identifying novel anti-cancer molecules from the unexplored reserves of plant kingdom. The application of dietary supplementation or medicine derived from such sources is a promising approach towards treatment of cancer. In the present study we have evaluated the antiproliferative potential of 4-hydroxyisophthalic acid (4-HIPA), which is a novel antioxidant compound isolated from the roots of the aqueous extract of Decalepis hamiltonii. 4-HIPA was screened in vitro against human breast cancer cell lines MCF-7, MDA-MB-468 and normal human breast epithelial cell MCF-10, and demonstrated that human breast cancer cell lines, in contrast to MCF-10, are sensitive to 4-HIPA .4-HIPA showed marked reduction in cell viability and short-term proliferation assays in these cells. Results of the long-term colony formation and scratch assay further reaffirmed that 4-HIPA inhibited the growth and proliferation in breast cancer cells. We further conducted in vivo studies using murine Ehrlich Ascites Tumor (EAT) cell model. Our in vivo results established that treatment with 4-HIPA reduced the tumorigenesis by promoting apoptosis in EAT-bearing mice. The results of our molecular docking predictions further warranted our claim. This study is valuable as 4-HIPA exhibits antiproliferative potential that can be exploited in the development of anticancer drugs.

Potent inhibition of breast cancer by bis-indole-derived nuclear receptor 4A1 (NR4A1) antagonists.

BACKGROUND: Nuclear receptor 4A1 (NR4A1) is overexpressed in mammary tumors, and the methylene-substituted bis-indole derivative 1,1-bis(3'-indolyl)-1-(p-hydroxyphenyl)methane (DIM-C-pPhOH) acts as an NR4A1 antagonist (inverse agonist) and inhibits NR4A1-regulated pro-oncogenic pathways/genes in breast and other cancer cells. METHODS: Buttressed analogs of DIM-C-pPhOH were synthesized by condensation of the substituted p-hydroxybenzaldehydes with indole. Breast cancer cell growth, survival, and migration assays were carried out by cell counting, Annexin V staining, and Boyden chamber assays, respectively. Changes in RNA and protein expression were determined by RT-PCR and western blots, respectively. Analysis of RNAseq results was carried out using Ingenuity Pathway Analysis, and in vivo potencies of NR4A1 antagonists were determined in athymic nude mice bearing MDA-MB-231 cells in an orthotopic model. RESULTS: Ingenuity Pathway analysis of common genes modulated by NR4A1 knockdown or treatment with DIM-C-pPhOH showed that changes in gene expression were consistent with the observed decreased functional responses, namely inhibition of growth and migration and increased apoptosis. DIM-C-pPhOH is rapidly metabolized and the effects and potencies of buttressed analogs of DIM-C-pPhOH which contain one or two substituents ortho to the hydroxyl groups were investigated using NR4A1-regulated gene/gene products as endpoints. The buttressed analogs were more potent than DIM-C-pPhOH in both in vitro assays and as inhibitors of mammary tumor growth. Moreover, using 1,1-bis(3'-indolyl)-1-(3-chloro-4-hydroxy-5-methoxyphenyl)methane (DIM-C-pPhOh-3-Cl-5-OCH3) significant tumor growth inhibition was observed at doses as low as 2 mg/kg/d which was at least an order of magnitude more potent than DIM-C-pPhOH. CONCLUSIONS: These buttressed analogs represent a more potent set of second generation NR4A1 antagonists as inhibitors of breast cancer.

Monitoring, mapping and health risk assessment of fluoride in drinking water supplies in rural areas of Maku and Poldasht, Iran.

The aim of this study was to investigate and determine fluoride concentrations in drinking water supplies in rural areas of Maku and Poldasht in West Azerbaijan Province, the northwest of Iran. Fluorosis risk assessment and characterization was also investigated. Fluoride concentrations mapping was accomplished by using the GIS system. Totally, 356 water samples, including one sample in each season, were collected from 89 water supplies providing water for 95 and 61 rural areas of Maku and Poldasht, respectively. According to the results, in Maku and Poldasht, 25 and 30 rural areas had contaminated water sources, respectively. Average annual fluoride concentrations ranged from 3.04 to 7.31 mg/l in the contaminated villages of Maku, which is about 2-4.8 times higher than the maximum standard level of the Iranian drinking water standard, and 4.52-8.21 mg/l in the contaminated areas of Poldasht, which is about 3-5.47 times higher than the maximum standard level. The maximum fluoride level was determined 11.12 mg/l and 10.98 mg/l in one of villages of Maku and Poldasht Counties in summer, respectively. Neither in Maku nor in Poldasht, water resources showed dental cavity risk, while dental fluorosis risk and skeletal fluorosis risk were very significant in some villages of both cities. Children were at most risk of fluorosis. New alternative water supplies for the contaminated villages if possible, consumption of bottled water and application of reverse osmosis are recommended as remedial actions in the contaminated areas.

The effect of not-anaerobicization and discolored bacteria on uranium reduction by Shewanella sp. RCRI7.

Shewanella sp. RCRI7 is a native strain capable of reducing uranium in anaerobic conditions. In order to employ this bacterium for the bioremediation, the mutual effects of uranium and the bacteria are studied in two different approaches. The optimal settings for the bacterial proliferation capacity and uranium reduction without anaerobicization of the environment, as well as the related effects of bioremediation and bacterial color under uranium-reducing conditions, have been investigated in this study. Uranium reduction procedure was analyzed using XRD, spectrophotometry and ICP-AES. In addition, the uranium's effect on the population of the first-generation of the bacteria as well as the color and growth of the second-generation were investigated using neobar lam and CFU (Colony Forming Unit), respectively. Uranium toxicity reduced the population of non-anaerobicized bacteria more than the anaerobicized bacteria after one day of incubation, while the amount of uranium extracted by the bacteria was almost the same. In both situations, the bacteria were able to reduce uranium after two weeks of incubation. In addition to the cell counts, uranium toxicity disrupts the growth and development of healthy second-generation anaerobicized bacteria, as created creamy-colored colonies grow slower than red-colored colonies. Furthermore, due to malfunctioning cytochromes, unlike red bacteria, creamy-colored bacteria were unable to extract the optimum amount of uranium. This study reveals that reduced uranium can be produced in a deprived environment without anaerobicization. Creamy-colored Shewanella can remove soluble uranium, however the most effective bacteria have red cytochromes. These findings represent a big step forward in the industrialization of uranium bioremediation.

mTORC1 upregulates B7-H3/CD276 to inhibit antitumor T cells and drive tumor immune evasion.

Identifying the mechanisms underlying the regulation of immune checkpoint molecules and the therapeutic impact of targeting them in cancer is critical. Here we show that high expression of the immune checkpoint B7-H3 (CD276) and high mTORC1 activity correlate with immunosuppressive phenotypes and worse clinical outcomes in 11,060 TCGA human tumors. We find that mTORC1 upregulates B7-H3 expression via direct phosphorylation of the transcription factor YY2 by p70 S6 kinase. Inhibition of B7-H3 suppresses mTORC1-hyperactive tumor growth via an immune-mediated mechanism involving increased T-cell activity and IFN-γ responses coupled with increased tumor cell expression of MHC-II. CITE-seq reveals strikingly increased cytotoxic CD38+CD39+CD4+ T cells in B7-H3-deficient tumors. In pan-human cancers, a high cytotoxic CD38+CD39+CD4+ T-cell gene signature correlates with better clinical prognosis. These results show that mTORC1-hyperactivity, present in many human tumors including tuberous sclerosis complex (TSC) and lymphangioleiomyomatosis (LAM), drives B7-H3 expression leading to suppression of cytotoxic CD4+ T cells.

Increased glucose availability sensitizes pancreatic cancer to chemotherapy.

Pancreatic Ductal Adenocarcinoma (PDAC) is highly resistant to chemotherapy. Effective alternative therapies have yet to emerge, as chemotherapy remains the best available systemic treatment. However, the discovery of safe and available adjuncts to enhance chemotherapeutic efficacy can still improve survival outcomes. We show that a hyperglycemic state substantially enhances the efficacy of conventional single- and multi-agent chemotherapy regimens against PDAC. Molecular analyses of tumors exposed to high glucose levels reveal that the expression of GCLC (glutamate-cysteine ligase catalytic subunit), a key component of glutathione biosynthesis, is diminished, which in turn augments oxidative anti-tumor damage by chemotherapy. Inhibition of GCLC phenocopies the suppressive effect of forced hyperglycemia in mouse models of PDAC, while rescuing this pathway mitigates anti-tumor effects observed with chemotherapy and high glucose.

Preliminary report of Iranian Registry of Alzheimer's disease in Tehran province: A cross-sectional study in Iran.

Background and Aims: Alzheimer's disease (AD) is the main cause of dementia and over the 55 million people live with dementia worldwide. We aimed to establish the first database called the Iranian Alzheimer's Disease Registry to create a powerful source for future research in the country. In this report, the design and early results of the Iranian Alzheimer's Disease Registry will be described. Methods: We performed this multicenter investigation and patients' data including age, sex, educational level, disease status, Mini-Mental State Examination (MMSE), and Geriatric Depression Scale (GDS) from 2018 to 2021 were collected, registered, and analyzed by GraphPad Prism software. Results: Totally 200 AD patients were registered in our database. 107 (54%) were women and age of 147 (74%) were over 65. The mean age for men and women was 76.20 ± 8.29 and 76.40 ± 8.83 years, respectively. 132 (66%) were married and 64 (32%) were illiterate. Also, 94 (47%) were in the moderate stage of disease, and 150 (75%) lived at home together with their families. The most frequent neurological comorbidity was psychosis (n = 72, 36%), while hypertension was the most common non-neurological comorbidity (n = 104, 52%). The GDS score of women in the mild stage (5.23 ± 2.9 vs. 6.9 ± 2.6, p = 0.005) and moderate stage (5.36 ± 2.4 vs. 8.21 ± 2.06, p = <0.001) of the disease was significantly greater than men. In univariate analysis, MMSC score was remarkably associated with stroke (ß = -2.25, p = 0.03), psychosis (ß = -2.18, p = 0.009), diabetes (ß = 3.6, p = <0.001), and hypercholesteremia (ß = 1.67, p = 0.05). Also, the MMSE score showed a notable relationship with stroke (ß = -2.13, p = 0.05) and diabetes (ß = 3.26, p = <0.001) in multivariate analysis. Conclusion: Iranian Alzheimer's Disease Registry can provide epidemiological and clinical data to use for purposes such as enhancing the current AD management in clinical centers, filling the gaps in preventative care, and establishing effective monitoring and cure for the disease.

Limited nutrient availability in the tumor microenvironment renders pancreatic tumors sensitive to allosteric IDH1 inhibitors.

Nutrient-deprived conditions in the tumor microenvironment (TME) restrain cancer cell viability due to increased free radicals and reduced energy production. In pancreatic cancer cells a cytosolic metabolic enzyme, wild-type isocitrate dehydrogenase 1 (wtIDH1), enables adaptation to these conditions. Under nutrient starvation, wtIDH1 oxidizes isocitrate to generate α-ketoglutarate (αKG) for anaplerosis and NADPH to support antioxidant defense. In this study, we show that allosteric inhibitors of mutant IDH1 (mIDH1) are potent wtIDH1 inhibitors under conditions present in the TME. We demonstrate that low magnesium levels facilitate allosteric inhibition of wtIDH1, which is lethal to cancer cells when nutrients are limited. Furthermore, the Food & Drug Administration (FDA)-approved mIDH1 inhibitor ivosidenib (AG-120) dramatically inhibited tumor growth in preclinical models of pancreatic cancer, highlighting this approach as a potential therapeutic strategy against wild-type IDH1 cancers.

Tendencies towards bottled drinking water consumption: Challenges ahead of polyethylene terephthalate (PET) waste management.

Background: The main objective of this study was to investigate the logics behind tendencies towards bottled drinking water usage in spite of availability of treated tap water. The amount of waste bottle is also estimated in Iran and managing principles for resolving the issue presented. Methods: A questionnaire was used to survey the logics behind tendencies toward bottled drinking water consumption among 120 participants. In order to estimate the quantities of the PET wastes produced in the country, data about bottled water production rate as well as volume of the imported and exported drinking bottled water were collected from 1962 to 2015 and applied in the calculations. Results: Findings suggested that about 0.026 to 3.86 billion liters (about 1.04 billion literson average) of bottled water was consumed annually between 2000 and 2015. Furthermore, bottled water consumption increased from 0.41 to 48.9 L/capita-year within the same time period. In the meantime, the plastic bottle waste generation rate rose from 12.84 to 1519.38 g/capita-year. There is no efficient and suitable system for managing and recycling waste bottles in the country. The perceived unreliability of tap water quality was the main reason of bottled water consumption among 74% of the respondents. Conclusion: To reduce bottled water consumption and the associated harmful environmental and health consequences, measures such as informing people, validating public water supply quality, preventive rules enactment, and establishing extended producer responsibility (EPR) are highly recommended.

Nuclear Receptor 4A2 (NR4A2/NURR1) Regulates Autophagy and Chemoresistance in Pancreatic Ductal Adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with poor prognosis and chemotherapy with gemcitabine has limited effects and is associated with development of drug resistance. Treatment of Panc1 and MiaPaca2 pancreatic cancer cells with gemcitabine induced expression of the orphan nuclear receptor 4A2 (NURR1) and analysis of the cancer genome atlas indicated the NURR1 is overexpressed in pancreatic tumors and is a negative prognostic factor for patient survival. Results of NURR1 knockdown or treatment with the NURR1 antagonist 1,1-bis(3΄-indolyl)-1-(p-chlorophenyl)methane (C-DIM 12) demonstrated that NURR1 was pro-oncogenic in pancreatic cancer cells and regulated cancer cell and tumor growth and survival. NURR1 is induced by gemcitabine and serves as a key drug-resistance factor and is also required for gemcitabine-induced cytoprotective autophagy. NURR1 regulated genes were determined by RNA sequencing of mRNAs expressed in MiaPaCa2 cells expressing NURR1 and in CRISPR/Cas9 gene edited cells for NURR1 knockdown and KEGG enrichment analysis of the differentially expressed genes showed that autophagy was the major pathway regulated by NURR1. Moreover, NURR1 regulated expression of two major autophagic genes ATG7 and ATG12 which are also overexpressed in pancreatic tumors and like NURR1 are negative prognostic factors for patient survival. Thus, gemcitabine-induced cytoprotective autophagy is due to the NURR1 - ATG7/ATG12 axis and this can be targeted and disrupted by NURR1 antagonist C-DIM12 demonstrating the potential clinical applications for combination therapies with gemcitabine and NURR1 antagonists.

Gene Expression Signature Correlates with Outcomes in Metastatic Renal Cell Carcinoma Patients Treated with Everolimus Alone or with a Vascular Disrupting Agent.

Everolimus monotherapy use for metastatic renal cell carcinoma (mRCC) has diminished due to recent approvals of immune checkpoint and VEGF inhibitors. We hypothesized that gene expression associated with everolimus benefit may provide rationale to select appropriate patients. To address this hypothesis, tumors from a phase I/II trial that compared everolimus alone or with BNC105P, a vascular disrupting agent, were profiled using Nanostring as a discovery cohort. A phase III trial (CheckMate 025) was used for validation. Clinical benefit (CB) was defined as response or stable disease for ≥6 months. A propensity score covariate adjustment was used, and model discrimination performance was assessed using the area under the ROC curve (AUC). In a discovery cohort of 82 patients, 35 (43%) were treated with everolimus alone and 47 (57%) received everolimus + BNC105P. Median PFS (mPFS) was 4.9 (95% CI, 2.8-6.2) months. A four-gene signature (ASXL1, DUSP6, ERCC2, and HSPA6) correlated with CB with everolimus ± BNC105P [AUC, 86.9% (95% CI, 79.2-94.7)]. This was validated in 130 patients from CheckMate 025 treated with everolimus [AUC, 60.2% (95% CI, 49.7-70.7)]. Among 43 patients (52.4%) with low expression of an 18-gene signature, everolimus + BNC105P was associated with significantly longer mPFS compared with everolimus alone (10.4 vs. 6.9 months; HR, 0.49; 95% CI, 0.24-1.002; P = 0.047). These signatures warrant further validation to select patients who may benefit from everolimus alone or with a vascular disrupting agent.

MITF is a driver oncogene and potential therapeutic target in kidney angiomyolipoma tumors through transcriptional regulation of CYR61.

Tuberous sclerosis complex (TSC) is an autosomal dominant tumor suppressor syndrome, characterized by tumor development in multiple organs, including renal angiomyolipoma. Biallelic loss of TSC1 or TSC2 is a known genetic driver of angiomyolipoma development, however, whether an altered transcriptional repertoire contributes to TSC-associated tumorigenesis is unknown. RNA-seq analyses showed that MITF A isoform (MITF-A) was consistently highly expressed in angiomyolipoma, immunohistochemistry showed microphthalmia-associated transcription factor nuclear localization, and Chromatin immuno-Precipitation Sequencing analysis showed that the MITF-A transcriptional start site was highly enriched with H3K27ac marks. Using the angiomyolipoma cell line 621-101, MITF knockout (MITF.KO) and MITF-A overexpressing (MITF.OE) cell lines were generated. MITF.KO cells showed markedly reduced growth and invasion in vitro, and were unable to form xenografted tumors. In contrast, MITF.OE cells grew faster in vitro and as xenografted tumors compared to control cells. RNA-Seq analysis showed that both ID2 and Cysteine-rich angiogenic inducer 61 (CYR61) expression levels were increased in the MITF.OE cells and reduced in the MITF.KO cells, and luciferase assays showed this was due to transcriptional effects. Importantly, CYR61 overexpression rescued MITF.KO cell growth in vitro and tumor growth in vivo. These findings suggest that MITF-A is a transcriptional oncogenic driver of angiomyolipoma tumor development, acting through regulation of CYR61.

Tumors with TSC mutations are sensitive to CDK7 inhibition through NRF2 and glutathione depletion.

Tuberous sclerosis complex (TSC) is characterized by tumor development in the brain, heart, kidney, and lungs. In TSC tumors, loss of the TSC1/TSC2 protein complex leads to activation of mTORC1 with downstream effects on anabolism and cell growth. Because mTORC1 activation enhances mRNA transcription, we hypothesized that aberrant mTORC1 activation might confer TSC-null cell dependence on transcriptional regulation. We demonstrate that TSC1- or TSC2-null cells, in contrast to their wild-type counterparts, are sensitive to pharmacological inhibition of CDK7. Mechanistic studies revealed that CDK7 inhibition markedly reduces glutathione levels and increases reactive oxygen species due to reduced expression of NRF2 and glutathione biosynthesis genes. Treatment of both Tsc2+/ - mice and a TSC1-null bladder cancer xenograft model with a CDK7 inhibitor showed marked reduction in tumor volume and absence of regrowth in the xenograft model. These results suggest that CDK7 inhibition is a promising therapeutic approach for treatment of TSC-associated tumors and cancers with mutations in either TSC1 or TSC2.