Fusion Mutants Research Articles

Understanding CYP3A4 and P-gp mediated drug-drug interactions through PBPK modeling - Case example of pralsetinib.

Pralsetinib, a potent and selective inhibitor of oncogenic RET fusion and RET mutant proteins, is a substrate of the drug metabolizing enzyme CYP3A4 and a substrate of the efflux transporter P-gp based on invitro data. Therefore, its pharmacokinetics (PKs) may be affected by co-administration of potent CYP3A4 inhibitors and inducers, P-gp inhibitors, and combined CYP3A4 and P-gp inhibitors. With the frequent overlap between CYP3A4 and P-gp substrates/inhibitors, pralsetinib is a challenging and representative example of the need to more quantitatively characterize transporter-enzyme interplay. A physiologically-based PK (PBPK) model for pralsetinib was developed to understand the victim drug-drug interaction (DDI) risk for pralsetinib. The key parameters driving the magnitude of pralsetinib DDIs, the P-gp intrinsic clearance and the fraction metabolized by CYP3A4, were determined from PBPK simulations that best captured observed DDIs from three clinical studies. Sensitivity analyses and scenario simulations were also conducted to ensure these key parameters were determined with sound mechanistic rationale based on current knowledge, including the worst-case scenarios. The verified pralsetinib PBPK model was then applied to predict the effect of other inhibitors and inducers on the PKs of pralsetinib. This work highlights the challenges in understanding DDIs when enzyme-transporter interplay occurs, and demonstrates an important strategy for differentiating enzyme/transporter contributions to enable PBPK predictions for untested scenarios and to inform labeling.

Identification of a common secondary mutation in the Neurospora crassa knockout collection conferring a cell fusion-defective phenotype.

Gene-deletion mutants represent a powerful tool to study gene function. The filamentous fungus Neurospora crassa is a well-established model organism, and features a comprehensive gene knockout strain collection. While these mutant strains have been used in numerous studies, resulting in the functional annotation of many Neurospora genes, direct confirmation of gene-phenotype relationships is often lacking, which is particularly relevant given the possibility of background mutations, sample contamination, and/or strain mislabeling. Indeed, spontaneous mutations resulting in phenotypes resembling many cell fusion mutants have long been known to occur at relatively high frequency in N. crassa, and these secondary mutations are common in the Neurospora deletion collection. The identity of these mutations, however, is largely unknown. Here, we report that the Δada-3 strain from the N. crassa knockout collection, which exhibits a cell fusion defect, harbors a secondary mutation responsible for this phenotype. Through whole-genome sequencing and genetic analyses, we found a ~30-Kb deletion in this strain affecting a known cell fusion-related gene, so/ham-1, and show that it is the absence of this gene-and not of ada-3-that underlies its cell fusion defect. We additionally found three other knockout strains harboring the same deletion, suggesting that this mutation may be common in the collection and could have impacted previous studies. Our findings provide a cautionary note and highlight the importance of proper functional validation of strains from mutant collections. We discuss our results in the context of the spread of cell fusion-defective cheater variants in N. crassa cultures. IMPORTANCE This study emphasizes the need for careful and detailed characterization of strains from mutant collections. Specifically, we found a common deletion in various strains from the Neurospora crassa gene knockout collection that results in a cell fusion-defective phenotype. This is noteworthy because this collection is known to contain background mutations-of a largely unclear nature-that produce cell fusion-defective phenotypes. Our results describe an example of such mutations, and highlight how this common genetic defect could have impacted previous studies that have used the affected strains. Furthermore, they provide a cautionary note about the use of Neurospora strains with similar phenotypes. Lastly, these findings offer additional details relevant to our understanding of the origin and spread of cell fusion-defective cheater variants in N. crassa cultures.

The triterpenoid saponin content difference is associated with the two type oxidosqualene cyclase gene copy numbers of Pulsatilla chinensis and Pulsatilla cernua.

Pulsatilla chinensis is an important medicinal herb, its dried radix is used to treat the inflammation since ancient China. Triterpenoid saponins are proved to be the main active compounds of Pulsatilla genus. The triterpenoid saponin contents vary widely in different Pulsatilla species. But no enzyme involved in the triterpenoid saponin biosynthetic pathway was identified in Pulsitilla genus. This seriously limits the explanation of the triterpene content difference of Pulsatilla species. In this article, we obtained two oxidosqualene cyclase (OSC) genes from P. chinensis and P. cernua by touchdown PCR and anchored PCR. These two OSCs converted 2,3-oxidosqualene into different triterpenoids. The OSC from P. cernua is a monofunctional enzyme for β-amyrin synthesis, while the OSC from P. chinensis is a multifunctional enzyme for lupeol and β-amyrin synthesis, and the lupeol is the main product. Then we identified the 260th amino acid residue was the key site for the product difference by gene fusion and site-directed mutant technology. When the 260th amino acid residue was tryptophan (W260) and phenylalanine (F260), the main catalysate was β-amyrin and lupeol, respectively. Then we found that the expression of these two genes was strongly correlated with the lupeol-type and β-amyrin-type triterpenoid contents in P. cernua and P. chinensis. Finally, we found the gene copy number difference of these two genotypes leaded to the triterpenoid diversity in P. cernua and P. chinensis. This study provides useful information for the molecular breeding and quality improvement of P. chinensis and a molecular marker to identify the P. chinensis decoction pieces.

In Vivo Assembly of Photosystem I‐Hydrogenase Chimera for In Vitro PhotoH2 Production

AbstractPhotosynthetic hydrogen (photoH2) production is an elegant approach to storing solar energy. The most efficient strategy is to couple the hydrogen‐producing enzyme, the hydrogenase (H2ase), directly to photosystem I (PSI), which is a light‐driven nanomachine found in photosynthetic organisms. PSI–H2ase fusions have been tested in vivo and in vitro. Both approaches have each their specific advantages and drawbacks. Here, a system to combine both approaches by assembling PSI–H2ase fusions in vivo for in vitro photoH2 production is established. For this, cyanobacterial PSI–H2ase fusion mutants are generated and characterized concerning photoH2 production in vivo. The chimeric protein is purified and embedded in a redox polymer on an electrode where it successfully produces photoH2 in vitro. The combination of in vivo and in vitro processes comes along with reciprocal benefits. The in vivo assembly ensures that the chimeric protein is fully functional and suited for the fabrication of bioelectrodes in vitro. At the same time, the photoelectrochemical in vitro characterization now permits to analyze the assemblies in detail. This will open avenues to optimize in vivo and in vitro approaches for photoH2 production in a target‐oriented manner in the future.

Structural mechanism of BRD4-NUT and p300 bipartite interaction in propagating aberrant gene transcription in chromatin in NUT carcinoma

BRD4-NUT, a driver fusion mutant in rare and highly aggressive NUT carcinoma, acts in aberrant transcription of anti-differentiation genes by recruiting histone acetyltransferase (HAT) p300 and promoting p300-driven histone hyperacetylation and nuclear condensation in chromatin. However, the molecular basis of how BRD4-NUT recruits and activates p300 remains elusive. Here, we report that BRD4-NUT contains two transactivation domains (TADs) in NUT that bind to the TAZ2 domain in p300. Our NMR structures reveal that NUT TADs adopt amphipathic helices when bound to the four-helical bundle TAZ2 domain. The NUT protein forms liquid-like droplets in-vitro that are enhanced by TAZ2 binding in 1:2 stoichiometry. The TAD/TAZ2 bipartite binding in BRD4-NUT/p300 triggers allosteric activation of p300 and acetylation-driven liquid-like condensation on chromatin that comprise histone H3 lysine 27 and 18 acetylation and transcription proteins BRD4L/S, CDK9, MED1, and RNA polymerase II. The BRD4-NUT/p300 chromatin condensation is key for activating transcription of pro-proliferation genes such as ALX1, resulting ALX1/Snail signaling and epithelial-to-mesenchymal transition. Our study provides a previously underappreciated structural mechanism illuminating BRD4-NUT’s bipartite p300 recruitment and activation in NUT carcinoma that nucleates a feed-forward loop for propagating histone hyperacetylation and chromatin condensation to sustain aberrant anti-differentiation gene transcription and perpetual tumor cell growth.

Interspecific protoplast fusion of atmospheric and room-temperature plasma mutants of Aspergillus generates an L-asparaginase hyper-producing hybrid with techno-economic benefits

The axenic culture of Aspergillus candidus (Asp-C) produced an anti-leukemic L-asparaginase while Aspergillus sydowii (Asp-S) produced the acrylamide-reduction type. Upon mutagenesis by atmospheric and room-temperature plasma (ARTP), their individual L-asparaginase activities improved 2.3-folds in each of Ile-Thr-Asp-C-180-K and Val-Asp-S-180-E stable mutants. Protoplast fusion of selected stable mutants generated fusant-09 with improved anti-leukemic activity, acrylamide reduction, higher temperature optimum and superior kinetic parameters. Submerged (SmF) and solid-state fermentation (SSF) types were compared; likewise batch, fed-batch and continuous fermentation modes; and fed-batch submerged fermentation was selected on the basis of impressive techno-economics. Fusant L-asparaginase was purified by PEG/Na+ citrate aqueous two-phase system and molecular exclusion chromatography to 69.96 and 146.21-fold, respectively, and characterized by molecular weight, specificity, activity and stability to chemical and physical agents. Michaelis–Menten kinetics, evaluated under optimum conditions gave K m, V max, K cat, and K cat/K m as 1.667 × 10−3 M, 1666.67 µmol min−1 mg−1 protein, 645.99 s−1 and 3.88 × 105 M−1 s−1 respectively. In-vitro cytotoxicity of HL-60 cell lines by fusant-09 L-asparaginase improved 3.00 and 18.71-folds from mutants Ile-Thr-Asp-C-180-K and Val-Asp-S-180-E, and from 5.73 and 32.55 from respective original strains. Free-radical scavenging and acrylamide reduction improvements were intermediate. Fusant-09 L-asparaginase is strongly recommended for sustainable economic anti-leukemic and food industry applications.

Directed evolution of the fusion enzyme for improving astaxanthin biosynthesis in Saccharomyces cerevisiae

The accumulation of the intermediate zeaxanthin and canthaxanthin in the astaxanthin biosynthesis pathway catalyzed by β-carotene hydroxylase (crtZ) and β-carotene ketolase (crtW) decreases the content of the astaxanthin. Here, we exploited directed evolution of the fusion of crtZ and crtW for improving astaxanthin biosynthesis in Saccharomyces cerevisiae. The results demonstrated that the fusion enzyme of crtZ-crtW with 2 X GGGGS peptides linker can effectively reduce the accumulation of intermediates and improves the content of astaxanthin. Compared with the control strain, the fusion enzyme of ketase and hydroxylase reduced zeaxanthin and canthaxanthin by 7 and 14 times and increased astaxanthin by 1.6 times, respectively. Moreover, 9 variant fusion mutants with improved astaxanthin production were generated through directed evolution. Combining these dominant mutants generated a variant, L95S + I206L, which increased the astaxanthin content of 3.8 times than the control strain. The AlphaFold2 assisted structural analysis indicated that these two mutations alter the interaction between the substrate and the enzymes pocket. Our research provided an efficient idea to reduce the accumulation of the intermediate products in complex biosynthesis pathway.

High accuracy of single-molecule real-time sequencing in detecting a rare α-globin fusion gene in carrier screening population.

The α-globin fusion gene between the HBA2 and HBAP1 genes becomes clinically important in thalassemia screening because this fusion gene can cause severe hemoglobin (Hb) H disease when combining with α0 -thalassemia (α0 -thal). Due to its uncommon rearrangement in the α gene cluster without dosage changes, this fusion gene is undetectable by common molecular testing approaches used for α-thal diagnosis. In this study, we used the single-molecule real-time (SMRT) sequencing technique to detect this fusion gene in 23 carriers identified by next-generation sequencing (NGS) among 16,504 screened individuals. Five primers for α and β thalassemia were utilized. According to the NGS results, the 23 carriers include 14 pure heterozygotes, eight compound heterozygotes with common α-thal alleles, and one homozygote. By using SMRT, the fusion mutant was successfully detected in all 23 carriers. Furthermore, SMRT corrected the diagnosis in two "pure" heterozygotes: one was compound heterozygote with anti-3.7 triplication, and the other was homozygote. Our results indicate that SMRT is a superior method compared to NGS in detecting the α fusion gene, attributing to its efficient, accurate, and one-step properties.

MR Imaging of Pediatric Low-Grade Gliomas: Pretherapeutic Differentiation of BRAF V600E Mutation, BRAF Fusion, and Wild-Type Tumors in Patients without Neurofibromatosis-1.

The prognosis and treatment of pediatric low-grade gliomas is influenced by their molecular subtype. MR imaging remains the mainstay for initial work-up and surgical planning. We aimed to determine the relationship between imaging patterns and molecular subtypes of pediatric low-grade gliomas. This was a retrospective bi-institutional study for patients diagnosed from 2004 to 2021 with pathologically confirmed pediatric low-grade gliomas molecularly defined as BRAF fusion, BRAF V600E mutant, or wild-type (which is neither BRAF V600E mutant nor BRAF fusion). Two neuroradiologists, blinded, independently reviewed imaging parameters from diagnostic MRIs, and discrepancies were resolved by consensus. Bivariate analysis was used followed by pair-wise comparison of the Dwass-Steel-Critchlow-Fligner method to compare the 3 molecular subtypes. Interreader agreement was assessed using κ. We included 70 patients: 30 BRAF fusion, 19 BRAF V600E mutant, and 21 wild-type. There was substantial agreement between the readers for overall imaging variables (κ = 0.75). BRAF fusion tumors compared with BRAF V600E and wild-type tumors were larger (P = .0022), and had a greater mass effect (P = .0053), increased frequency of hydrocephalus (P = .0002), and diffuse enhancement (p <.0001). BRAF V600E mutant tumors were more often hemispheric (P < .0001), appeared more infiltrative (P = .0002), and, though infrequent, were the only group demonstrating diffusion restriction (qualitatively; P = .0042) with a lower ADC ratio (quantitatively) (P = .003). BRAF fusion and BRAF V600E mutant pediatric low-grade gliomas have unique imaging features that can be used to differentiate them from each other and wild-type pediatric low-grade glioma using a standard radiology review with high interreader agreement. In the era of targeted therapy, these features can be useful for therapeutic planning before surgery.

Development of a Highly Efficient Long-Acting Cocaine Hydrolase Entity to Accelerate Cocaine Metabolism.

It is particularly challenging to develop a truly effective pharmacotherapy for cocaine use disorder (CUD) treatment. Accelerating cocaine metabolism via hydrolysis at cocaine benzoyl ester using an efficient cocaine hydrolase (CocH) is known as a promising pharmacotherapeutic approach to CUD treatment. Preclinical and clinical studies on our first CocH (CocH1), in its human serum albumin-fused form known as TV-1380, have demonstrated the promise of a general concept of CocH-based pharmacotherapy for CUD treatment. However, the biological half-life of TV-1380 (t1/2 = 8 h in rats, associated with t1/2 = 43-77 h in humans) is not long enough for practical treatment of cocaine dependence, which requires enzyme injection for no more than once weekly. Through protein fusion of a human butyrylcholinesterase mutant (denoted as CocH5) with a mutant (denoted as Fc(M6)) of Fc from human IgG1, we have designed, prepared, and tested a new fusion protein (denoted as CocH5-Fc(M6)) for its pharmacokinetic profile and in vivo catalytic activity against (-)-cocaine. CocH5-Fc(M6) represents the currently most efficient long-acting cocaine hydrolase with both the highest catalytic activity against (-)-cocaine and the longest elimination half-life (t1/2 = 229 ± 5 h) in rats. As a result, even at a single modest dose of 3 mg/kg, CocH5-Fc(M6) can significantly and effectively accelerate the metabolism of cocaine in rats for at least 60 days. In addition, ∼70 nM CocH5-Fc(M6) in plasma was able to completely block the toxicity and physiological effects induced by intraperitoneal injection of a lethal dose of cocaine (60 mg/kg).

LGG-08. MR Imaging of pediatric low-grade gliomas: Pretherapeutic differentiation ofBRAF V600E mutation,BRAF-Fused and Wild-Type tumors in patients without Neurofibromatosis-1

OBJECTIVE: The prognosis and treatment of pediatric low-grade gliomas (pLGGs) is influenced by their molecular subtype. MRI remains the mainstay for initial work-up and surgical planning. We aimed to determine the relationship between imaging patterns and molecular subtypes of pLGGs. METHODS: This is a bi-institutional retrospective study for patients diagnosed from 2004 to 2021 with pathologically confirmed pLGG, molecularly defined as BRAF fusion (KIAA1549-BRAF), BRAF V600E mutation, or wild-type (negative for both BRAF V600E mutation and BRAF fusion). Two neuroradiologists, blinded, independently reviewed imaging parameters on the initial MRI and discrepancies were solved by consensus. Bivariate analysis was used followed by pairwise comparison of Dwass, Steel, and Critchlow-Fligner methods to compare the 3 molecular subtypes. Agreement between reviewers was assessed using Kappa (k). RESULTS: 70 patients were included: 30 with BRAF fusion, 19 with BRAF V600E mutation, and 21 wild-type. There was substantial agreement between the two readers for overall imaging variables (k=0.75). BRAF fusion tumors compared to V600E and wild-type had larger size (p=0.0022), greater mass effect (p=0.0053), and increased rate of hydrocephalus (p=0.0002). BRAF fusion tumors had increased frequency of diffuse enhancement compared with BRAF V600E and wild-type (p <0.0001). BRAF V600E mutant tumors were more often located in a cerebral hemisphere (p <0.0001). Diffusion restriction (qualitatively) was uncommon but only seen in BRAF V600E (p=0.0042) with lower ADC ratio (quantitatively) (p=0.003). Additionally, BRAF V600E mutant tumors appeared more infiltrative than BRAF fusion and wild-type (p=0.0002). CONCLUSION:BRAF fusion and BRAF V600E mutant pLGG have unique imaging features that can be used to differentiate from each other and wild-type pLGG using standard radiology review with high inter-reader agreement. In the era of targeted therapy, these features can be useful for therapeutic planning prior to surgery.

Active Expression of Human Hyaluronidase PH20 and Characterization of Its Hydrolysis Pattern.

Hyaluronidases are a group of glycosidases catalyzing the degradation of hyaluronic acid (HA). Because of the advantages of effectively hydrolyzing the HA-rich matrix and low immunogenicity, human hyaluronidase PH20 (hPH20) is widely used in the medical field. Here, we realized the active expression of recombinant hPH20 by Pichia pastoris under a methanol-induced promoter PAOX1. By optimizing the composition of the C-terminal domain and fusing protein tags, we constructed a fusion mutant AP2-△491C with the extracellular hyaluronidase activity of 258.1 U·L−1 in a 3-L bioreactor, the highest expression level of recombinant hPH20 produced by microbes. Furthermore, we found recombinant hPH20 hydrolyzed the β-1,4 glycosidic bonds sequentially from the reducing end of o-HAs, with HA6 NA as the smallest substrate. The result will provide important theoretical guidance for the directed evolution of the enzyme to prepare multifunctional o-HAs with specific molecular weights.

Engineering Infrequent DNA Nicking Endonuclease by Fusion of a BamHI Cleavage-Deficient Mutant and a DNA Nicking Domain.

Strand-specific DNA nicking endonucleases (NEases) typically nick 3–7 bp sites. Our goal is to engineer infrequent NEase with a >8 bp recognition sequence. A BamHI catalytic-deficient mutant D94N/E113K was constructed, purified, and shown to bind and protect the GGATCC site from BamHI restriction. The mutant was fused to a 76-amino acid (aa) DNA nicking domain of phage Gamma HNH (gHNH) NEase. The chimeric enzyme was purified, and it was shown to nick downstream of a composite site 5′ GGATCC-N(4-6)-AC↑CGR 3′ (R, A, or G) or to nick both sides of BamHI site at the composite site 5′ CCG↓GT-N5-GGATCC-N5-AC↑CGG 3′ (the down arrow ↓ indicates the strand shown is nicked; the up arrow↑indicates the bottom strand is nicked). Due to the attenuated activity of the small nicking domain, the fusion nickase is active in the presence of Mn2+ or Ni2+, and it has low activity in Mg2+ buffer. This work provided a proof-of-concept experiment in which a chimeric NEase could be engineered utilizing the binding specificity of a Type II restriction endonucleases (REases) in fusion with a nicking domain to generate infrequent nickase, which bridges the gap between natural REases and homing endonucleases. The engineered chimeric NEase provided a framework for further optimization in molecular diagnostic applications.

Molecular locker probe enrichment of gene fusion variants from matched patient liquid biopsy specimens for magneto-bioelectrocatalytic nanosensing.

The accurate and sensitive analysis of recurrent gene fusion mutant variants in circulating tumor nucleic acids (NAs) of patient liquid biopsy samples is crucial for realizing clinical potential for cancer screening, diagnostics, and therapeutics. Gene fusion analysis is especially challenging in patient liquid biopsy samples because of trace biotarget levels in high non-target background of highly similar native and variant NA sequences. Herein, we describe accurate analysis of three prostate cancer gene fusion mutant variants in matched plasma and urine specimens from real cancer patients and healthy controls (n = 80) by (i) direct locker probe enrichment of multiple gene fusion mutant variants without tedious upstream sample processing; (ii) magneto-bioelectrocatalytic cycling readout using both NA-intercalating and freely diffusive redox probes for superior signal enhancement. For each mutant variant, an ultrabroad dynamic range (10-105 copies) was achieved with enhanced 10 copies (zmol) detection limit. With the combination of locker probe enrichment and magneto-bioelectrocatalytic cycling readout for NA mutant variant analysis, the potential of non-invasive liquid biopsies may be exploited for the benefit of cancer patients.

LysR-type transcriptional regulator FinR is required for phenazine and pyrrolnitrin biosynthesis in biocontrol Pseudomonas chlororaphis strain G05.

Phenazine-1-carboxylic acid and pyrrolnitrin, the two secondary metabolites produced by Pseudomonas chlororaphis G05, serve as biocontrol agents that mainly contribute to the growth repression of several fungal phytopathogens. Although some regulators of phenazine-1-carboxylic acid biosynthesis have been identified, the regulatory pathway involving phenazine-1-carboxylic acid synthesis is not fully understood. We isolated a white conjugant G05W03 on X-Gal-containing LB agar during our screening of novel regulator candidates using transposon mutagenesis with a fusion mutant G05Δphz::lacZ as a recipient. By cloning of DNA adjacent to the site of the transposon insertion, we revealed that a LysR-type transcriptional regulator (LTTR) gene, finR, was disrupted in the conjugant G05W03. To confirm the regulatory function of FinR, we constructed the finR-knockout mutant G05ΔfinR, G05Δphz::lacZΔfinR, and G05Δprn::lacZΔfinR, using the wild-type strain G05 and its fusion mutant derivatives as recipient strains, respectively. We found that the expressions of phz and prn operons were dramatically reduced in the finR-deleted mutant. With quantification of the production of antifungal metabolites biosynthesized by the finR-negative strain G05ΔfinR, it was shown that FinR deficiency also led to decreased yield of phenazine-1-carboxylic acid and pyrrolnitrin. In addition, the pathogen inhibition assay confirmed that the production of phenazine-1-carboxylic acid was severely reduced in the absence of FinR. Transcriptional fusions and qRT-PCR verified that FinR could positively govern the transcription of the phz and prn operons. Taken together, FinR is required for antifungal metabolite biosynthesis and crop protection against some fungal pathogens.Key points• A novel regulator FinR was identified by transposon mutagenesis.• FinR regulates antifungal metabolite production.• FinR regulates the phz and prn expression by binding to their promoter regions.

What It Takes to Transform a T Cell.

The role of fusion genes and cancer driver genes in malignant transformation has traditionally been explored using transgenic or chimeric mouse models. It has been challenging to develop models that fully resemble the characteristics and morphology of human cancers. This applies to anaplastic large-cell lymphoma (ALCL), a malignancy classified as a peripheral T-cell lymphoma. It is still unclear at which stage of T-cell development ALCL can occur, as well as the early molecular events required for malignant transformation. In this issue of Cancer Research, Pawlicki and colleagues introduced the NPM-ALK fusion gene and mutant variants into primary T cells from healthy donors. By monitoring transduced T-cell clones over time, they demonstrated that transformed T cells undergo a progressive loss of T-cell identity accompanied with upregulation of epithelial-to-mesenchymal transition program and reemergence of an immature, thymic profile. Introduction of NPM-ALK was, however, not sufficient to convert healthy T cells to malignant clones, as this process required activation of T-cell receptor signaling. The study sets the stage for modeling early genetic changes in human tumors.See related article by Pawlicki et al., p. 3241.

XBP1 increases transactivation of somatic mutants of ESR1 and loss of XBP1 reverses endocrine resistance conferred by gain-of-function Y537S ESR1 mutation

Somatic mutations of the estrogen receptor 1 gene (ESR1) is an emerging mechanism of acquired resistance to endocrine therapy in hormonal breast cancers. Hotspot point mutations in the ligand- binding domain of estrogen receptor α (ER) and genomic rearrangements producing ESR1 fusion genes are the two major types of mutations that are associated with endocrine resistance. The crosstalk between X-box binding protein 1 (XBP1), a key transcription factor of the unfolded protein response (UPR) and ER signalling creates a positive feedback loop that results in increased expression of XBP1 in ER-positive breast cancer. Here we report that XBP1 co-operated with point mutants (Y537S, D538G) and fusion mutants (ESR1-YAP1, ESR1-DAB2) of ESR1 to increase their transcriptional activity. XBP1 was required for optimal expression of estrogen-regulated genes, and up to 40% of XBP1-dependent genes were estrogen-responsive genes. Knockdown of XBP1 in genome-edited MCF7 cells expressing Y537S mutant reduced their growth, re-sensitized them to anti-estrogens and attenuated the constitutive and estrogen-stimulated expression of estrogen-regulated genes. Our study provides a rationale for overcoming endocrine resistance in breast cancers expressing ESR1 mutation by combining the XBP1 targeting agents with anti-estrogen agents.

Exploring Molecular Docking algorithm for Lung Cancer Drug Discovery – A Case Study with RET Protein

Non-small cell lung cancer (NSCLC) is one of the leading causes of cancer-related deaths across the globe.1.33% of all NSCLC cases occur due to an alteration in RET protein. Commonly occurring RET fusion partners include KIF5B, CCDC6, NCOA4, and TRIM33. Numerous multikinase inhibitors are active against rearranged RET. However, mutations in the RET-fusion protein can result in adverse effects in terms of drug resistance against NSCLC. In this context, molecular docking algorithm is certainly important to support the drug discovery pipelines. However, availability of huge number of algorithms in the literature limits the researchers to proceed further in drug discovery development. Thus, the present study focuses on finding the best docking algorithm among ArgusLab, PatchDock, AutoDock 4.0 and AutoDock Vina for drug discovery process against RET fusion cancers using Pearson’s correlation coefficient. We believe that our study will be a valuable source of information for carrying out further computational studies on RET fusion cancer, both mutant and wild type.

Abstract 3001: Drug resistant PDX models for new drug discovery

Abstract Drug resistant is one of the biggest challenge for cancer therapy. How to understand the mechanism and to overcome the drug resistant with new therapeutics represent the hot focus for oncology drug discovery. Drug resistant patient-derived xenograft (PDX) models derived from surgery samples, biopsy samples, hydrothorax or ascetic fluid provides unique tool for new therapeutics R&amp;D. We have successfully established an array of drug resistant PDX models. Representative drug resistant PDX includes: clinically AZD9291-resistant EGFR triple mutant (Ex19del, T790M, C797S) PDX model. In vivo efficacy results show that this triple mutant NSCLC PDX model was resistant to Erlotinib and AZD9291 and sensitive to the combination of Cetuximab and Brigatinib. We also established CD74-ROS1 fusion and G2032R mutant NSCLC PDX model; EML4-ALK fusion and L1196M mutant NSCLC PDX model; Olaparib resistant Ovarian cancer PDX model; Heceptin resistant gastric PDX model; Rituximab and ABT-199 resistant DLBCL PDX model, and so on. In conclusion, these precious PDX models provide insight into resistance mechanisms as well as serve as models to develop new therapeutics drug candidates that overcome the drug resistant. Citation Format: Feifei Zhang, Yuan Long, Danyi Wen. Drug resistant PDX models for new drug discovery [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3001.

Genomic analysis of biomarkers related to the prognosis of acute myeloid leukemia.

Acute myeloid leukemia (AML) is the most common childhood cancer and is a major cause of morbidity among adults with hematologic malignancies. Several novel genetic alterations, which target critical cellular pathways, including alterations in lymphoid development-regulating genes, tumor suppressors and oncogenes that contribute to leukemogenesis, have been identified. The present study aimed to identify molecular markers associated with the occurrence and poor prognosis of AML. Information on these molecular markers may facilitate prediction of clinical outcomes. Clinical data and RNA expression profiles of AML specimens from The Cancer Genome Atlas database were assessed. Mutation data were analyzed and mapped using the maftools package in R software. Kyoto Encyclopedia of Genes and Genomes, Reactome and Gene Ontology analyses were performed using the clusterProfiler package in R software. Furthermore, Kaplan-Meier survival analysis was performed using the survminer package in R software. The expression data of RNAs were subjected to univariate Cox regression analysis, which demonstrated that the mutation loads varied considerably among patients with AML. Subsequently, the expression data of mRNAs, microRNAs (miRNAs/miR) and long non-coding RNAs (lncRNAs) were subjected to univariate Cox regression analysis to determine the the 100 genes most associated with the survival of patients with AML, which revealed 48 mRNAs and 52 miRNAs. The top 1,900 mRNAs (P<0.05) were selected through enrichment analysis to determine their functional role in AML prognosis. The results demonstrated that these molecules were involved in the transforming growth factor-β, SMAD and fibroblast growth factor receptor-1 fusion mutant signaling pathways. Survival analysis indicated that patients with AML, with high MYH15, TREML2, ATP13A2, MMP7, hsa-let-7a-2-3p, hsa-miR-362-3p, hsa-miR-500a-5p, hsa-miR-500b-5p, hsa-miR-362-5p, LINC00987, LACAT143, THCAT393, THCAT531 and KHCAT230 expression levels had a shorter survival time compared with those without these factors. Conversely, a high KANSL1L expression level in patients was associated with a longer survival time. The present study determined genetic mutations, mRNAs, miRNAs, lncRNAs and signaling pathways involved in AML, in order to elucidate the underlying molecular mechanisms of the development and recurrence of this disease.