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1.
Adv Sci (Weinh) ; : e2308539, 2024 May 24.
Article En | MEDLINE | ID: mdl-38790135

The orphan nuclear receptor NR2E3 (Nuclear receptor subfamily 2 group E, Member 3) is an epigenetic player that modulates chromatin accessibility to activate p53 during liver injury. Nonetheless, a precise tumor suppressive and epigenetic role of NR2E3 in hepatocellular carcinoma (HCC) development remains unclear. HCC patients expressing low NR2E3 exhibit unfavorable clinical outcomes, aligning with heightened activation of the Wnt/ß-catenin signaling pathway. The murine HCC models utilizing NR2E3 knockout mice consistently exhibits accelerated liver tumor formation accompanied by enhanced activation of Wnt/ß-catenin signaling pathway and inactivation of p53 signaling. At cellular level, the loss of NR2E3 increases the acquisition of aggressive cancer cell phenotype and tumorigenicity and upregulates key genes in the WNT/ß-catenin pathway with increased chromatin accessibility. This event is mediated through increased formation of active transcription complex involving Sp1, ß-catenin, and p300, a histone acetyltransferase, on the promoters of target genes. These findings demonstrate that the loss of NR2E3 activates Wnt/ß-catenin signaling at cellular and organism levels and this dysregulation is associated with aggressive HCC development and poor clinical outcomes. In summary, NR2E3 is a novel tumor suppressor with a significant prognostic value, maintaining epigenetic homeostasis to suppress the Wnt/ß-catenin signaling pathway that promotes HCC development.

2.
Bioorg Chem ; 143: 106966, 2024 Feb.
Article En | MEDLINE | ID: mdl-37995643

Activating mutations within FLT3 make up 30 % of all newly diagnosed acute myeloid leukemia (AML) cases, with the most common mutation being an internal tandem duplication (FLT3-ITD) in the juxtamembrane region (25 %). Currently, two generations of FLT3 kinase inhibitors have been developed, with three inhibitors clinically approved. However, treatment of FLT3-ITD mutated AML is limited due to the emergence of secondary clinical resistance, caused by multiple mechanism including on-target FLT3 secondary mutations - FLT3-ITD/D835Y and FLT3-ITD/F691L being the most common, as well as the off-target activation of alternative pathways including the BCR-ABL pathway. Through the screening of imidazo[1,2-a]pyridine derivatives, N-(3-methoxyphenyl)-6-(7-(1-methyl-1H-pyrazol-4-yl)imidazo[1,2-a]pyridin-3-yl)pyridin-2-amine (compound 1) was identified as an inhibitor of both the FLT3-ITD and BCR-ABL pathways. Compound 1 potently inhibits clinically related leukemia cell lines driven by FLT3-ITD, FLT3-ITD/D835Y, FLT3-ITD/F691L, or BCR-ABL. Studies indicate that it mediates proapoptotic effects on cells by inhibiting FLT3 and BCR-ABL pathways, and other possible targets. Compound 1 is more potent against FLT3-ITD than BCR-ABL, and it may have other possible targets; however, compound 1 is first step for further optimization for the development of a balanced FLT3-ITD/BCR-ABL dual inhibitor for the treatment of relapsed FLT3-ITD mutated AML with multiple secondary clinical resistant subtypes such as FLT3-ITD/D835Y, FLT3-ITD/F691L, and cells co-expressing FLT3-ITD and BCR-ABL.


Leukemia, Myeloid, Acute , Humans , Cell Line, Tumor , Leukemia, Myeloid, Acute/drug therapy , Leukemia, Myeloid, Acute/genetics , Protein Kinase Inhibitors/pharmacology , Protein Kinase Inhibitors/therapeutic use , Mutation , fms-Like Tyrosine Kinase 3/genetics
3.
Eur J Med Chem ; 264: 115977, 2024 Jan 15.
Article En | MEDLINE | ID: mdl-38056299

FLT3 activating mutations are detected in approximately 30 % of newly diagnosed acute myeloid leukemia (AML) cases, most commonly consisting of internal tandem duplication (ITD) mutations in the juxtamembrane region. Recently, several FLT3 inhibitors have demonstrated clinical activity and three are currently approved - midostaurin, quizartinib, and gilteritinib. Midostaurin is a first-generation FLT3 inhibitor with minimal activity as monotherapy. Midostaurin lacks selectivity and is only approved by the USFDA for use in combination with other chemotherapy agents. The second-generation inhibitors quizartinib and gilteritinib display improved specificity and selectivity, and have been approved for use as monotherapy. However, their clinical efficacies are limited in part due to the emergence of drug-resistant FLT3 secondary mutations in the tyrosine kinase domain at positions D835 and F691. Therefore, in order to overcome drug resistance and further improve outcomes, new compounds targeting FLT3-ITD with secondary mutants are urgently needed. In this study, through the structural modification of a reported compound Ling-5e, we identified compound 24 as a FLT3 inhibitor that is equally potent against FLT3-ITD and the clinically relevant mutants FLT3-ITD/D835Y, and FLT3-ITD/F691L. Its inhibitory effects were demonstrated in both cell viability assays and western blots analyses. When tested against cell lines lacking activating mutations in FLT3, no non-specific cytotoxicity effect was observed. Interestingly, molecular docking results showed that compound 24 may adopt different binding conformations with FLT3-F691L compared to FLT3, which may explain its retained activity against FLT3-ITD/F691L. In summary, compound 24 has inhibition potency on FLT3 comparable to gilteritinib, but a more balanced inhibition on FLT3 secondary mutations, especially FLT3-ITD/F691L which is gilteritinib resistant. Compound 24 may serve as a promising lead for the drug development of either primary or relapsed AML with FLT3 secondary mutations.


Leukemia, Myeloid, Acute , Protein Kinase Inhibitors , Humans , Molecular Docking Simulation , Protein Kinase Inhibitors/chemistry , Mutation , Leukemia, Myeloid, Acute/drug therapy , Leukemia, Myeloid, Acute/genetics , Leukemia, Myeloid, Acute/metabolism , Pyridines/therapeutic use , fms-Like Tyrosine Kinase 3/genetics
4.
Cancers (Basel) ; 15(23)2023 Nov 22.
Article En | MEDLINE | ID: mdl-38067237

Biomarkers play a crucial role in the diagnosis, prognosis, and therapeutics of cancer. We use biomarkers to identify, image, monitor, and target cancer. In many respects, the discovery of pertinent biomarkers that distinguish fulminant from indolent neoplasms and sensitive from refractory malignancies would be a holy grail of cancer research and therapy. We propose that a stem cell versus genetic theory of cancer may not only enable us to track and trace the biological evolution of cancer but also empower us to attenuate its clinical course and optimize the clinical outcome of patients with cancer. Hence, a biomarker that identifies cancer stem cells (CSCs) and distinguishes them from non-CSCs may serve to elucidate inter-tumoral and intra-tumoral heterogeneity, elevate the values and utility of current prognostic and predictive tests, and enhance drug versus therapy development in cancer care. From this perspective, we focus on CSC biomarkers and discuss stemness or stem-like biomarkers in the context of a unified theory and a consideration of stem cell versus genetic origin. We review their role in primary and mixed tumors, in the elaboration of tumor subtypes, and in the imaging and monitoring of minimal residual diseases. We investigate how scientific theories influence the direction of scientific research and interpretation of experimental results, and how genomics and epigenomics affect the dynamics and trajectories of biomarkers in the conduct of cancer research and in the practice of cancer care.

5.
Metabolomics ; 20(1): 6, 2023 Dec 14.
Article En | MEDLINE | ID: mdl-38095785

INTRODUCTION: Prenatal exposure to polycyclic aromatic hydrocarbons (PAHs) has been associated with adverse human health outcomes. To explore the plausible associations between maternal PAH exposure and maternal/newborn metabolomic outcomes, we conducted a cross-sectional study among 75 pregnant people from Cincinnati, Ohio. METHOD: We quantified 8 monohydroxylated PAH metabolites in maternal urine samples collected at delivery. We then used an untargeted high-resolution mass spectrometry approach to examine alterations in the maternal (n = 72) and newborn (n = 63) serum metabolome associated with PAH metabolites. Associations between individual maternal urinary PAH metabolites and maternal/newborn metabolome were assessed using linear regression adjusted for maternal and newborn factors while accounting for multiple testing with the Benjamini-Hochberg method. We then conducted functional analysis to identify potential biological pathways. RESULTS: Our results from the metabolome-wide associations (MWAS) indicated that an average of 1% newborn metabolome features and 2% maternal metabolome features were associated with maternal urinary PAH metabolites. Individual PAH metabolite concentrations in maternal urine were associated with maternal/newborn metabolome related to metabolism of vitamins, amino acids, fatty acids, lipids, carbohydrates, nucleotides, energy, xenobiotics, glycan, and organic compounds. CONCLUSION: In this cross-sectional study, we identified associations between urinary PAH concentrations during late pregnancy and metabolic features associated with several metabolic pathways among pregnant women and newborns. Further studies are needed to explore the mediating role of the metabolome in the relationship between PAHs and adverse pregnancy outcomes.


Polycyclic Aromatic Hydrocarbons , Humans , Pregnancy , Infant, Newborn , Female , Polycyclic Aromatic Hydrocarbons/urine , Cross-Sectional Studies , Metabolomics , Metabolome , Amino Acids/metabolism
6.
Int J Mol Sci ; 24(12)2023 Jun 06.
Article En | MEDLINE | ID: mdl-37372939

Endocrine-disrupting chemicals (EDCs) are chemicals, either natural or synthetic, that can interfere with the production, distribution, function, metabolism, or excretion of hormones in our body [...].


Endocrine Disruptors , Endocrine System , Humans , Hormones/pharmacology , Endocrine Disruptors/toxicity
7.
Oncotarget ; 13: 46-60, 2022.
Article En | MEDLINE | ID: mdl-35018219

G-1, a GPER1 agonist, was shown to inhibit the growth of castration-resistant mouse xenografts but not their parental androgen-dependent tumors. It is currently unknown how the androgen receptor (AR) represses GPER1 expression. Here, we found that two GPER1 mRNA variants (GPER1v2 and GPER1v4) were transcriptionally repressed, not via transcript destabilization, by the androgen-activated AR. Although no AR binding was found in all active promoters near GPER1, data from promoter assays suggested that both variants' promoters were inhibited by androgen treatment. Site-directed mutagenesis on Sp1/Sp3 binding sites revealed their role in supporting the basal expression of GPER1. Knockdown of Sp1 and Sp3 together but not separately repressed GPER1 expression whereas overexpression of both Sp1 and Sp3 together was required to alleviate AR repression of GPER1. Based on the chromatin immunoprecipitation data, Sp3 was found to bind to the promoters prior to the binding of Sp1 and RNA polymerase II. However, the binding of all three transcription factors was inhibited by DHT treatment. Concordantly, DHT treatment induced nuclear interactions between AR and Sp1 or Sp3. Taken together, these results indicate that AR represses transcription of GPER1 by binding to Sp1 and Sp3 independently to prevent their transactivation of the GPER1 promoters.


Prostatic Neoplasms , Receptors, Androgen , Androgens , Animals , Binding Sites/genetics , Humans , Male , Mice , Prostatic Neoplasms/genetics , RNA Polymerase II/metabolism , RNA, Messenger/genetics , Receptors, Androgen/genetics , Sp1 Transcription Factor/metabolism , Sp3 Transcription Factor/genetics , Sp3 Transcription Factor/metabolism
8.
J Med Chem ; 65(2): 1536-1551, 2022 01 27.
Article En | MEDLINE | ID: mdl-35081714

Mutations of the rearranged during transfection (RET) kinase are frequently reported in cancer, which make it as an attractive therapeutic target. Herein, we discovered a series of N-trisubstituted pyrimidine derivatives as potent inhibitors for both wild-type (wt) RET and RETV804M, which is a resistant mutant for several FDA-approved inhibitors. The X-ray structure of a representative inhibitor with RET revealed that the compound binds in a unique pose that bifurcates beneath the P-loop and confirmed the compound as a type I inhibitor. Through the structure-activity relationship (SAR) study, compound 20 was identified as a lead compound, showing potent inhibition of both RET and RETV804M. Additionally, compound 20 displayed potent antiproliferative activity of CCDC6-RET-driven LC-2/ad cells. Analysis of RET phosphorylation indicated that biological activity was mediated by RET inhibition. Collectively, N-trisubstituted pyrimidine derivatives could serve as scaffolds for the discovery and development of potent inhibitors of type I RET and its gatekeeper mutant for the treatment of RET-driven cancers.


Adenocarcinoma of Lung/drug therapy , Lung Neoplasms/drug therapy , Mutation , Protein Kinase Inhibitors/pharmacology , Proto-Oncogene Proteins c-ret/antagonists & inhibitors , Pyrimidines/chemistry , Adenocarcinoma of Lung/pathology , Apoptosis , Cell Proliferation , Humans , Lung Neoplasms/pathology , Protein Kinase Inhibitors/chemistry , Proto-Oncogene Proteins c-ret/genetics , Structure-Activity Relationship , Tumor Cells, Cultured , Wound Healing
9.
Nutrients ; 13(10)2021 Oct 17.
Article En | MEDLINE | ID: mdl-34684636

Gestational high butterfat (HFB) and/or endocrine disruptor exposure was previously found to disrupt spermatogenesis in adulthood. This study addresses the data gap in our knowledge regarding transgenerational transmission of the disruptive interaction between a high-fat diet and endocrine disruptor bisphenol A (BPA). F0 generation Sprague-Dawley rats were fed diets containing butterfat (10 kcal%) and high in butterfat (39 kcal%, HFB) with or without BPA (25 µg/kg body weight/day) during mating and pregnancy. Gestationally exposed F1-generation offspring from different litters were mated to produce F2 offspring, and similarly, F2-generation animals produced F3-generation offspring. One group of F3 male offspring was administered either testosterone plus estradiol-17ß (T + E2) or sham via capsule implants from postnatal days 70 to 210. Another group was naturally aged to 18 months. Combination diets of HFB + BPA in F0 dams, but not single exposure to either, disrupted spermatogenesis in F3-generation adult males in both the T + E2-implanted group and the naturally aged group. CYP19A1 localization to the acrosome and estrogen receptor beta (ERbeta) localization to the nucleus were associated with impaired spermatogenesis. Finally, expression of methyl-CpG-binding domain-3 (MBD3) was consistently decreased in the HFB and HFB + BPA exposed F1 and F3 testes, suggesting an epigenetic component to this inheritance. However, the severe atrophy within testes present in F1 males was absent in F3 males. In conclusion, the HFB + BPA group demonstrated transgenerational inheritance of the impaired spermatogenesis phenotype, but severity was reduced in the F3 generation.


Benzhydryl Compounds/toxicity , Butter , Dietary Fats/adverse effects , Infertility, Male/chemically induced , Maternal Exposure/adverse effects , Phenols/toxicity , Prenatal Exposure Delayed Effects/chemically induced , Spermatogenesis/drug effects , Animals , Diet, High-Fat/adverse effects , Disease Models, Animal , Endocrine Disruptors/toxicity , Epigenesis, Genetic , Estradiol , Female , Infertility, Male/genetics , Inheritance Patterns , Male , Maternal Nutritional Physiological Phenomena , Pregnancy , Prenatal Exposure Delayed Effects/genetics , Rats , Rats, Sprague-Dawley , Spermatogenesis/genetics , Testis/metabolism
10.
Eur J Med Chem ; 225: 113776, 2021 Dec 05.
Article En | MEDLINE | ID: mdl-34479037

FMS-like tyrosine kinase 3 (FLT3) with an internal tandem duplication (ITD) mutation has been validated as a driver lesion and a therapeutic target for acute myeloid leukemia (AML). Currently, several potent small-molecule FLT3 kinase inhibitors are being evaluated or have completed evaluation in clinical trials. However, many of these inhibitors are challenged by the secondary mutations on kinase domain, especially the point mutations at the activation loop (D835) and gatekeeper residue (F691). To overcome the resistance challenge, we identified a novel series of imidazo[1,2-a]pyridine-thiophene derivatives from a NIMA-related kinase 2 (NEK2) kinase inhibitor CMP3a, which retained inhibitory activities on FTL3-ITDD835V and FLT3-ITDF691L. Through this study, we identified the imidazo[1,2-a]pyridine-thiophene derivatives as type-I inhibitors of FLT3. Moreover, we observed compound 5o as an inhibitor displaying equal anti-proliferative activities against FLT3-ITD, FTL3-ITDD835Y and FLT3-ITDF691L driven acute myeloid leukemia (AML) cell lines. Meanwhile, the apoptotic effects of compound supported its mechanism of anti-proliferative action. These results indicate that the imidazo[1,2-a]pyridine-thiophene scaffold is promising for targeting acquired resistance caused by FLT3 secondary mutations and compound 5o is an interesting lead in this direction.


Antineoplastic Agents/pharmacology , Leukemia, Myeloid, Acute/drug therapy , NIMA-Related Kinases/antagonists & inhibitors , Protein Kinase Inhibitors/pharmacology , Pyridines/pharmacology , Thiophenes/pharmacology , fms-Like Tyrosine Kinase 3/antagonists & inhibitors , Antineoplastic Agents/chemical synthesis , Antineoplastic Agents/chemistry , Cell Line, Tumor , Cell Proliferation/drug effects , Dose-Response Relationship, Drug , Drug Discovery , Drug Screening Assays, Antitumor , Humans , Leukemia, Myeloid, Acute/metabolism , Leukemia, Myeloid, Acute/pathology , Molecular Structure , Mutation , NIMA-Related Kinases/metabolism , Protein Kinase Inhibitors/chemical synthesis , Protein Kinase Inhibitors/chemistry , Pyridines/chemical synthesis , Pyridines/chemistry , Structure-Activity Relationship , Thiophenes/chemical synthesis , Thiophenes/chemistry , fms-Like Tyrosine Kinase 3/genetics , fms-Like Tyrosine Kinase 3/metabolism
11.
Eur J Med Chem ; 225: 113763, 2021 Dec 05.
Article En | MEDLINE | ID: mdl-34419892

The tumor microenvironment contains high concentrations of TGFß, a crucial immunosuppressive cytokine. TGFß stimulates immune escape by promoting peripheral immune tolerance to avoid tumoricidal attack. Small-molecule inhibitors of TGFßR1 are a prospective method for next-generation immunotherapies. In the present study, we identified selective 4-aminoquinoline-based inhibitors of TGFßR1 through structural and rational-based design strategies. This led to the identification of compound 4i, which was found to be selective for TGFßR1 with the exception of MAP4K4 in the kinase profiling assay. The compound was then further optimized to remove MAP4K4 activity, since MAP4K4 is vital for proper T-cell function and its inhibition could exacerbate tumor immunosuppression. Optimization efforts led to compound 4s that inhibited TGFßR1 at an IC50 of 0.79 ± 0.19 nM with 2000-fold selectivity against MAP4K4. Compound 4s represents a highly selective TGFßR1 inhibitor that has potential applications in immuno-oncology.


Aminoquinolines/pharmacology , Drug Discovery , Intracellular Signaling Peptides and Proteins/antagonists & inhibitors , Protein Serine-Threonine Kinases/antagonists & inhibitors , Receptor, Transforming Growth Factor-beta Type I/antagonists & inhibitors , Aminoquinolines/chemical synthesis , Aminoquinolines/chemistry , Dose-Response Relationship, Drug , HEK293 Cells , Humans , Intracellular Signaling Peptides and Proteins/immunology , Molecular Structure , Protein Serine-Threonine Kinases/immunology , Receptor, Transforming Growth Factor-beta Type I/immunology , Structure-Activity Relationship
12.
Eur J Med Chem ; 223: 113660, 2021 Nov 05.
Article En | MEDLINE | ID: mdl-34246853

TGFß is crucial for the homeostasis of epithelial and neural tissues, wound repair, and regulating immune responses. Its dysregulation is associated with a vast number of diseases, of which modifying the tumor microenvironment is one of vital clinical interest. Despite various attempts, there is still no FDA-approved therapy to inhibit the TGFß pathway. Major mainstream approaches involve impairment of the TGFß pathway via inhibition of the TGFßRI kinase. With the purpose to identify non-receptor kinase-based inhibitors to impair TGFß signaling, an in-house chemical library was enriched, through a computational study, to eliminate TGFßRI kinase activity. Selected compounds were screened against a cell line engineered with a firefly luciferase gene under TGFß-Smad-dependent transcriptional control. Results indicated moderate potency for a molecule with phthalazine core against TGFß-Smad signaling. A series of phthalazine compounds were synthesized and evaluated for potency. The most promising compound (10p) exhibited an IC50 of 0.11 ± 0.02 µM and was confirmed to be non-cytotoxic up to 12 µM, with a selectivity index of approximately 112-fold. Simultaneously, 10p was confirmed to reduce the Smad phosphorylation using Western blot without exhibiting inhibition on the TGFßRI enzyme. This study identified a novel small-molecule scaffold that targets the TGFß pathway via a non-receptor-kinase mechanism.


Phthalazines/chemistry , Transforming Growth Factor beta/antagonists & inhibitors , Cell Survival/drug effects , Drug Evaluation, Preclinical , HEK293 Cells , Humans , Phosphorylation/drug effects , Phthalazines/metabolism , Phthalazines/pharmacology , Receptors, Transforming Growth Factor beta/metabolism , Signal Transduction/drug effects , Smad Proteins/chemistry , Smad Proteins/metabolism , Small Molecule Libraries/chemistry , Small Molecule Libraries/metabolism , Small Molecule Libraries/pharmacology , Structure-Activity Relationship , Transforming Growth Factor beta/metabolism
14.
Environ Health Perspect ; 128(12): 127005, 2020 12.
Article En | MEDLINE | ID: mdl-33296240

BACKGROUND: Bisphenol A (BPA) is known to be biologically active in experimental models even at low levels of exposure. However, its impact on endometrial cancer remains unclear. OBJECTIVES: This study aimed to investigate whether lifelong exposure to different doses of BPA induced uterine abnormalities and molecular changes in a rat model. METHODS: Sprague-Dawley rats were exposed to 5 doses of BPA [0, 25, 250, 2,500, or 25,000µg/kg body weight (BW)/d] or 2 doses of 17α-ethynylestradiol (EE2) (0.05 and 0.5µg/kg BW/d) starting from gestational day 6 up to 1 y old according to the CLARITY-BPA consortium protocol. The BW, uterus weight, and histopathology end points of the uteri were analyzed at postnatal (PND) day 21, 90, and 365. Estrous cycling status was evaluated in PND90 and PND365 rats. Transcriptomic analyses of estrus stage uteri were conducted on PND365 rats. RESULTS: Based on the analysis of the combined effects of all testing outcomes (including immunohistological, morphological, and estrous cycle data) in a semiblinded fashion, using statistical models, 25µg/kg BW/d BPA [BPA(25)], or 250µg/kg BW/d BPA [BPA(250)] exerted effects similar to that of EE2 at 0.5µg/kg BW/d in 1-y-old rats. Transcriptome analyses of estrus stage uteri revealed a set of 710 genes shared only between the BPA(25) and BPA(250) groups, with 115 of them predicted to be regulated by estradiol and 57 associated with female cancers. An interesting finding is that the expression of 476 human orthologous genes in this rat BPA signature robustly predicted the overall survival (p=1.68×10-5, hazard ratio=2.62) of endometrial cancer patients. DISCUSSION: Lifelong exposure of rats to low-dose BPA at 25 and 250µg/kg BW/d altered the estrous cycle and uterine pathology with similarity to EE2. The exposure also disrupted a unique low-dose BPA-gene signature with predictive value for survival outcomes in patients with endometrial cancer. https://doi.org/10.1289/EHP6875.


Benzhydryl Compounds/toxicity , Phenols/toxicity , Toxicity Tests , Animals , Dose-Response Relationship, Drug , Endometrial Neoplasms , Female , Rats
16.
Eur J Med Chem ; 206: 112691, 2020 Nov 15.
Article En | MEDLINE | ID: mdl-32823007

Gene fusions and point mutations of RET kinase are crucial for driving thoracic cancers, including thyroid cancer and non-small cell lung cancer. Various scaffolds based on different heterocycles have been synthesized and evaluated as RET inhibitors. In this work, we investigate pyrrolo[2,3-d]pyrimidine derivatives for inhibition of RET-wt, drug resistant mutant RET V804M and RET gene fusion driven cell lines. Several compounds were synthesized and the structure activity relationship was extensively studied to optimize the scaffold. Thieno[2,3-d]pyrimidine, a bioisostere of pyrrolo[2,3-d]pyrimidine, was also explored for the effect on RET inhibition. We identified a lead compound, 59, which shows low nanomolar potency against RET-wt and RET V804M. Further 59 shows growth inhibition of LC-2/ad cells which RET-CCDC6 driven. We also determined that 59 is a type 2 inhibitor of RET and demonstrated its ability to inhibit migration of tumor cells. Based on computational studies, we proposed a binding pose of 59 in RET pocket and have quantified the contributions of individual residues for its binding. Together, 59 is an important lead compound which needs further evaluation in biological studies.


Drug Design , Protein Kinase Inhibitors/chemistry , Protein Kinase Inhibitors/pharmacology , Proto-Oncogene Proteins c-ret/antagonists & inhibitors , Pyrimidines/chemistry , Pyrimidines/pharmacology , Pyrroles/chemistry , Antineoplastic Agents/chemical synthesis , Antineoplastic Agents/chemistry , Antineoplastic Agents/pharmacology , Cell Line, Tumor , Cell Movement/drug effects , Cell Proliferation/drug effects , Chemistry Techniques, Synthetic , Humans , Protein Kinase Inhibitors/chemical synthesis , Pyrimidines/chemical synthesis
17.
Acta Neuropathol Commun ; 8(1): 87, 2020 06 20.
Article En | MEDLINE | ID: mdl-32563269

Molecular biomarkers provide both diagnostic and prognostic results for patients with diffuse glioma, the most common primary brain tumor in adults. Here, we used a long-read nanopore-based sequencing technique to simultaneously assess IDH mutation status and MGMT methylation level in 4 human cell lines and 8 fresh human brain tumor biopsies. Currently, these biomarkers are assayed separately, and results can take days to weeks. We demonstrated the use of nanopore Cas9-targeted sequencing (nCATS) to identify IDH1 and IDH2 mutations within 36 h and compared this approach against currently used clinical methods. nCATS was also able to simultaneously provide high-resolution evaluation of MGMT methylation levels not only at the promoter region, as with currently used methods, but also at CpGs across the proximal promoter region, the entirety of exon 1, and a portion of intron 1. We compared the methylation levels of all CpGs to MGMT expression in all cell lines and tumors and observed a positive correlation between intron 1 methylation and MGMT expression. Finally, we identified single nucleotide variants in 3 target loci. This pilot study demonstrates the feasibility of using nCATS as a clinical tool for cancer precision medicine.


Brain Neoplasms/diagnosis , CRISPR-Associated Protein 9/genetics , DNA Modification Methylases/chemistry , DNA Repair Enzymes/chemistry , Glioma/diagnosis , Isocitrate Dehydrogenase/genetics , Sequence Analysis, RNA/methods , Tumor Suppressor Proteins/chemistry , Adult , Aged , Alcohol Oxidoreductases , Biomarkers, Tumor/genetics , Biopsy , Brain Neoplasms/genetics , Brain Neoplasms/pathology , Cell Line, Tumor , Female , Glioma/genetics , Glioma/pathology , Humans , Male , Methylation , Middle Aged , Pilot Projects , Young Adult
18.
PLoS One ; 15(2): e0228894, 2020.
Article En | MEDLINE | ID: mdl-32078667

Lymphangioleiomyomatosis (LAM) is a devastating lung disease caused by inactivating gene mutations in either TSC1 or TSC2 that result in hyperactivation of the mechanistic target of rapamycin complex 1 (mTORC1). As LAM occurs predominantly in women during their reproductive age and is exacerbated by pregnancy, the female hormonal environment, and in particular estrogen, is implicated in LAM pathogenesis and progression. However, detailed underlying molecular mechanisms are not well understood. In this study, utilizing human pulmonary LAM specimens and cell culture models of TSC2-deficient LAM patient-derived and rat uterine leiomyoma-derived cells, we tested the hypothesis that estrogen promotes the growth of mTORC1-hyperactive cells through pyruvate kinase M2 (PKM2). Estrogen increased the phosphorylation of PKM2 at Ser37 and induced the nuclear translocation of phospho-PKM2. The estrogen receptor antagonist Faslodex reversed these effects. Restoration of TSC2 inhibited the phosphorylation of PKM2 in an mTORC1 inhibitor-insensitive manner. Finally, accumulation of phosphorylated PKM2 was evident in pulmonary nodule from LAM patients. Together, our data suggest that female predominance of LAM might be at least in part attributed to estrogen stimulation of PKM2-mediated cellular metabolic alterations. Targeting metabolic regulators of PKM2 might have therapeutic benefits for women with LAM and other female-specific neoplasms.


Estrogens/metabolism , Pyruvate Kinase/metabolism , Tuberous Sclerosis Complex 2 Protein/genetics , Animals , Cell Line, Tumor , Estrogens/physiology , Female , Humans , Lung/pathology , Lung Neoplasms/pathology , Lymphangioleiomyomatosis/genetics , Lymphangioleiomyomatosis/physiopathology , Mechanistic Target of Rapamycin Complex 1 , Phosphorylation , Pyruvate Kinase/physiology , Rats , Signal Transduction/drug effects , Tuberous Sclerosis Complex 1 Protein/genetics , Tuberous Sclerosis Complex 1 Protein/metabolism , Tuberous Sclerosis Complex 2 Protein/metabolism , Tumor Suppressor Proteins/genetics
19.
Epigenomics ; 11(9): 987-1002, 2019 07.
Article En | MEDLINE | ID: mdl-31215230

Aim: The goal of this study was to comprehensively interrogate and map DNA methylation across 16 CpG-dense regions previously associated with oral and pharyngeal squamous cell carcinoma (OPSCC). Materials & methods: Targeted multiplex bisulfite amplicon sequencing was performed on four OPSCC cell lines and primary non-neoplastic oral epithelial cells. Real-time quantitative polymerase chain reaction (RT-qPCR) was performed for a subset of associated genes. Results: There was clear differential methylation between one or more OPSCC cell lines and control cells for the majority of CpG-dense regions. Conclusion: Targeted multiplex bisulfite amplicon sequencing allowed us to efficiently map methylation across the entire region of interest with a high degree of sensitivity and helps shed light on novel differentially methylated regions that may have value as biomarkers of OPSCC.


Biomarkers/analysis , Carcinoma, Squamous Cell/genetics , CpG Islands/genetics , Epigenomics , Mouth Neoplasms/genetics , Pharyngeal Neoplasms/genetics , Computational Biology , DNA Methylation , Sequence Analysis, DNA
20.
FASEB J ; 33(7): 8335-8348, 2019 07.
Article En | MEDLINE | ID: mdl-30991008

Damage-induced long noncoding RNA (DINO) is a long noncoding RNA that directly interacts with p53 and thereby enhances p53 stability and activity in response to various cellular stresses. Here, we demonstrate that nuclear receptor subfamily 2 group E member 3 (NR2E3) plays a crucial role in maintaining active DINO epigenetic status for its proper induction and subsequent p53 activation. In acetaminophen (APAP)- or carbon tetrachloride-induced acute liver injuries, NR2E3 knockout (KO) mice exhibited far more severe liver injuries due to impaired DINO induction and p53 activation. Mechanistically, NR2E3 loss both in vivo and in vitro induced epigenetic DINO repression accompanied by reduced DINO chromatin accessibility. Furthermore, compared with the efficient reversal by a typical antidote N-acetylcysteine (NAC) treatment of APAP-induced liver injury in wild-type mice, the liver injury of NR2E3 KO mice was not effectively reversed, indicating that an intact NR2E3-DINO-p53-signaling axis is essential for NAC-mediated recovery against APAP-induced hepatotoxicity. These findings establish that NR2E3 is a critical component in p53 activation and a novel susceptibility factor to drug- or toxicant-induced acute liver injuries.-Khanal, T., Leung, Y.-K., Jiang, W., Timchenko, N., Ho, S.-M., Kim, K. NR2E3 is a key component in p53 activation by regulating a long noncoding RNA DINO in acute liver injuries.


Chemical and Drug Induced Liver Injury/metabolism , Liver Failure, Acute/metabolism , Orphan Nuclear Receptors/metabolism , RNA, Long Noncoding/biosynthesis , Signal Transduction , Tumor Suppressor Protein p53/metabolism , Acetaminophen/adverse effects , Acetaminophen/pharmacology , Acetylcysteine/pharmacology , Animals , Chemical and Drug Induced Liver Injury/genetics , Chemical and Drug Induced Liver Injury/pathology , Epigenesis, Genetic/drug effects , Hep G2 Cells , Humans , Liver Failure, Acute/chemically induced , Liver Failure, Acute/genetics , Liver Failure, Acute/pathology , Mice , Mice, Knockout , Orphan Nuclear Receptors/genetics , RNA, Long Noncoding/genetics , Tumor Suppressor Protein p53/genetics
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