Dominant Resistance Mechanism Research Articles

Physiological resistance of Sasa argenteostriata (Regel) E.G. Camus in response to high-concentration soil Pb stress

Dwarf bamboo Sasa argenteostriata (Regel) E.G. Camus has previously been considered as potential plant for metal phytoremediation. However, the dynamic responses and correlations among physiological resistances to high-concentration Pb exposure have not been described to date. This study conducted four Pb treatments (0, 1500, 3000, and 4500 mg kg–1) to examine the physiological resistance responses at days 7, 14, and 21. The findings showed that S. argenteostriata can regulate both the enzymatic system and the nonenzymatic system to synergistically overcome Pb damage. In addition, a significant positive correlation was found between enzymes and nonenzymatic substances, which were particularly apparent with regard to the superoxide dismutase (SOD) activities with phytochelatins (PCs) levels, peroxidase (POD), and glutathione reductase (GR) activities with glutathione (GSH) levels, as well as catalase (CAT) and ascorbate peroxidase (APX) activities with soluble protein (SP) levels. Furthermore, Pb concentration was the main factor that induced the physiological responses of S. argenteostriata to Pb stress. The antioxidant enzyme system and the AsA–GSH cycle were dominant resistance mechanisms under 1500 mg kg–1 Pb. AsA–GSH cycle and plant cell chelation were dominant resistance mechanisms under 3000 mg kg–1 Pb. Antioxidant enzymes and plant cell chelation were dominant resistance mechanisms under 4500 mg kg–1 Pb. This study provides comprehensive evidence regarding how both enzymatic and nonenzymatic systems of S. argenteostriata cooperate to alleviate the high-concentration soil Pb stress. The results highlight the environmental remediation potential of this species for Pb-contaminated media.

Metagenomic analysis reveals the fate of antibiotic resistance genes in two-stage and one-stage anaerobic digestion of waste activated sludge

Waste activated sludge (WAS) from wastewater treatment plants is an important reservoir of antibiotic resistance genes (ARGs). The fate of ARGs in this process was not revealed previously. The present study applied metagenomic approach to examine the occurrence and fate of ARGs in thermophilic alkaline fermentation followed by mesophilic anaerobic digestion (TM), by comparison with mesophilic alkaline fermentation followed by mesophilic anaerobic digestion (MM) and one-stage mesophilic anaerobic digestion (M) process. The removal efficiency of two-stage anaerobic digestion (AD) to total ARGs is higher than that of one-stage AD. The hydrogen and methane production stages of two-stage AD processes have dissimilar impact on the fate of ARGs. Macrolide, lincosamide, and streptogramin (MLS) resistance genes were enriched, especially in the hydrogen production reactors of TM and MM processes. Statistical analysis of metagenomic profiles analysis suggested that bacA may be the differential ARG subtype of two-stage AD process. ARG-like sequences encoding antibiotic efflux pump, antibiotic inactivation and antibiotic target alteration mechanisms were identified as the dominant ARGs resistance mechanisms in all samples. Procrustes analysis showed that microbial community composition structured the resistome. Co-occurrence patterns between ARGs and microbial phylogeny revealed that 26 bacterial species might be potential hosts of 94 ARG subtypes.

Evolution of Gilteritinib Resistance from Residual Disease to Relapse

Evolution of Gilteritinib Resistance from Residual Disease to Relapse

Azole resistance survey on clinical Aspergillus fumigatus isolates in Spain

ObjectivesWe aimed to assess the percentage of azole resistance in Aspergillus fumigatus in Spain. MethodsThirty participating Spanish hospitals stored all morphologically identified A. fumigatus sensu lato clinical isolates—regardless their clinical significance—from 15 February to 14 May 2019. Isolates showing azole resistance according to the EUCAST 9.3.2 methodology were molecularly identified and the cyp51A gene was studied in A. fumigatus sensu stricto isolates. ResultsEight hundred and forty-seven isolates from 725 patients were collected in 29 hospitals (A. fumigatus sensu stricto (n = 828) and cryptic species (n = 19)). Isolates were mostly from the lower respiratory tract (94.0%; 797/847). Only cryptic species were amphotericin B resistant. Sixty-three (7.4%) out of the 847 isolates were resistant to ≥1 azole(s). Azole resistance was higher in cryptic species than in A. fumigatus sensu stricto (95%, 18/19 vs. 5.5%, 45/828); isavuconazole was associated to the lowest number of non-wild type isolates. The dominant mechanism of resistance was the presence of TR34-L98H substitutions (n = 24 out of 63). Out of the 725 patients, 48 (6.6%) carried either cryptic species (n = 14) or A. fumigatus sensu stricto (n = 34; 4.7%) resistant isolates. Aspergillus fumigatus sensu stricto harbouring either the TR34-L98H (n = 19) or TR46/Y121F/T289A (n = 1) mutations were detected in patients in hospitals located at 7/24 studied cities. DiscussionOf the patients, 6.6% carry azole-resistant A. fumigatus sensu lato isolates in Spain. TR34-L98H is the dominant cyp51A gene substitutions, although its presence is not widespread.

EGFR Blockade Reverts Resistance to KRASG12C Inhibition in Colorectal Cancer

Most patients with KRAS G12C-mutant non-small cell lung cancer (NSCLC) experience clinical benefit from selective KRASG12C inhibition, whereas patients with colorectal cancer bearing the same mutation rarely respond. To investigate the cause of the limited efficacy of KRASG12C inhibitors in colorectal cancer, we examined the effects of AMG510 in KRAS G12C colorectal cancer cell lines. Unlike NSCLC cell lines, KRAS G12C colorectal cancer models have high basal receptor tyrosine kinase (RTK) activation and are responsive to growth factor stimulation. In colorectal cancer lines, KRASG12C inhibition induces higher phospho-ERK rebound than in NSCLC cells. Although upstream activation of several RTKs interferes with KRASG12C blockade, we identify EGFR signaling as the dominant mechanism of colorectal cancer resistance to KRASG12C inhibitors. The combinatorial targeting of EGFR and KRASG12C is highly effective in colorectal cancer cells and patient-derived organoids and xenografts, suggesting a novel therapeutic strategy to treat patients with KRAS G12C colorectal cancer. SIGNIFICANCE: The efficacy of KRASG12C inhibitors in NSCLC and colorectal cancer is lineage-specific. RTK dependency and signaling rebound kinetics are responsible for sensitivity or resistance to KRASG12C inhibition in colorectal cancer. EGFR and KRASG12C should be concomitantly inhibited to overcome resistance to KRASG12C blockade in colorectal tumors.See related commentary by Koleilat and Kwong, p. 1094.This article is highlighted in the In This Issue feature, p. 1079.

Abstract IA17: Cellular interactions and regulatory mechanisms in head and neck cancer

Abstract Head and neck squamous cell carcinoma (HNSCC) arises through exposure to environment carcinogens or malignant transformation by human papilloma virus (HPV). Two studies will be discussed. First, we have performed transcriptional profiling of single cells from peripheral and intratumoral immune populations in HPV- and HPV+ HNSCC and healthy donors. We found a spectrum of transcriptional relationships from very similar to highly divergent between the tumor microenvironments (TME) in HPV- and HPV+ HNSCC. Our comprehensive survey of the TME in in HPV- and HPV+ HNSCC highlights the diversity of immune states and complexity of crosstalk between immune populations, and is a benchmark for analysis of the TME in human cancer. Second, many cancer patients do not develop a durable response to current standard of care immunotherapies despite substantial advances in targeting immune inhibitory receptors. A potentially important and unappreciated compounding issue, which may serve as a dominant resistance mechanism, is the inherent systemic immune dysfunction that is often associated with advanced cancer. Although this has been described for decades, primary mechanisms and drivers remain unknown. Lack of response to inhibitory receptor blockade therapy and increased disease burden has been associated with circulating, peripheral CD8+ T-cell exhaustion, which is defined by poor T-cell function linked to increased inhibitory receptor expression (PD1 or LAG3). Our recent studies have assessed if LAG3 and PD1 impact systemic T-cell function. Citation Format: Dario A.A. Vignali. Cellular interactions and regulatory mechanisms in head and neck cancer [abstract]. In: Proceedings of the AACR-AHNS Head and Neck Cancer Conference: Optimizing Survival and Quality of Life through Basic, Clinical, and Translational Research; 2019 Apr 29-30; Austin, TX. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(12_Suppl_2):Abstract nr IA17.

Dual blockade of EGFR and VEGFR pathways: Results from a pilot study evaluating apatinib plus gefitinib as a first-line treatment for advanced EGFR-mutant non-small cell lung cancer.

BackgroundDual blockade of both EGFR and VEGFR pathways in EGFR‐mutant NSCLC have shown enhanced antitumor efficacy versus EGFR‐TKIs alone. Apatinib is an orally effective VEGFR‐2 tyrosine kinase inhibitor (TKI). This pilot study aims to evaluate the tolerability, pharmacokinetic profile, and antitumor activity of apatinib plus gefitinib as a therapy for EGFR‐mutant advanced NSCLC.MethodsAdvanced non‐squamous NSCLC participants harbored with the EGFR 19 deletion or the 21 L858R point mutation were included. There were two cohorts: Cohort A: apatinib 500 mg + gefitinib 250 mg. Cohort B: apatinib 250 mg + gefitinib 250 mg. The primary endpoint was safety profile. Other endpoints consisted of PK analysis, objective response rate (ORR), and progression‐free survival (PFS). Exploratory analysis was conducted using next‐generation sequencing of plasma circulating‐tumor DNA.ResultsBetween July 2016 and April 2017, 13 of NSCLC patients were recruited. Six patients were pooled in Cohort A, while seven patients were in Cohort B. Adverse events (AEs) were tolerable (mostly grade 1–2) and the treatment‐related AEs were similar in both cohorts: rash (100% vs 71.4%), diarrhea (66.7% vs 71.4%), hypertension (66.7% vs 71.4%), proteinuria (66.7% vs 42.9%), and hand‐foot skin reaction (33.3% vs 28.6%). The area under plasma concentration‐time curve for the steady state of apatinib was 2864.73 ± 2605.54 ng mL–1 h–1 in Cohort A and 2445.09 ± 1550.89 ng mL–1 h–1 in Cohort B. Of the 11 patients evaluable for efficacy, Cohort A achieved an ORR of 80.0% and reached a median PFS of 19.2 months, while it was 83.3% and 13.4 months in Cohort B. Patients without a concomitant mutation at baseline had a prolonged PFS tendency (20.99 months v 13.21 months, P = .0624). The EGFR‐T790M mutation remained the dominant resistance mechanism.ConclusionApatinib (500 mg) plus gefitinib (250 mg) showed a tolerable safety profile and encouraging antitumor activity for advanced EGFR‐mutant NSCLC in the first‐line setting. Phase III trials of apatinib (500 mg) plus gefitinib (250 mg) are warranted.Trial registrationClinicaltrials.gov, NCT02824458, date of registration June 23, 2016.

GaSe layered nanorods formed by liquid phase exfoliation for resistive switching memory applications

The increasing interest and rapid progress in the artificial neural networks have driven extensive research in resistive switching memory based on various insulators and two-dimensional nanomaterials. Herein, we have demonstrated a kind of resistive switching memory device based on GaSe layered nanorods fabricated by liquid phase exfoliation (LPE) method with a lateral graphene/GaSe/graphene structure. The single crystalline GaSe layered nanorods mixed with a few nanoflakes were synthesized by shear and ultrasonic (bath and probe) exfoliation methods, which showed high quality and hexagonal crystalline structure. The electrical properties and the resistive switching behavior were investigated, indicating the charge trapping/detrapping effect is the dominant resistive switching mechanism. This work suggests a novel strategy to develop the resistive switching devices based on various 2D materials by using LPE method, and these 2D-nanomaterials-based memristors have the potential to be used for constructing neuromorphic computing systems.

Constructing and deconstructing the bacterial cell wall.

The history of modern medicine cannot be written apart from the history of the antibiotics. Antibiotics are cytotoxic secondary metabolites that are isolated from Nature. The antibacterial antibiotics disproportionately target bacterial protein structure that is distinct from eukaryotic protein structure, notably within the ribosome and within the pathways for bacterial cell-wall biosynthesis (for which there is not a eukaryotic counterpart). This review focuses on a pre-eminent class of antibiotics-the β-lactams, exemplified by the penicillins and cephalosporins-from the perspective of the evolving mechanisms for bacterial resistance. The mechanism of action of the β-lactams is bacterial cell-wall destruction. In the monoderm (single membrane, Gram-positive staining) pathogen Staphylococcus aureus the dominant resistance mechanism is expression of a β-lactam-unreactive transpeptidase enzyme that functions in cell-wall construction. In the diderm (dual membrane, Gram-negative staining) pathogen Pseudomonas aeruginosa a dominant resistance mechanism (among several) is expression of a hydrolytic enzyme that destroys the critical β-lactam ring of the antibiotic. The key sensing mechanism used by P. aeruginosa is monitoring the molecular difference between cell-wall construction and cell-wall deconstruction. In both bacteria, the resistance pathways are manifested only when the bacteria detect the presence of β-lactams. This review summarizes how the β-lactams are sensed and how the resistance mechanisms are manifested, with the expectation that preventing these processes will be critical to future chemotherapeutic control of multidrug resistant bacteria.

Epigenetic silencing of SALL2 confers tamoxifen resistance in breast cancer

Resistance to tamoxifen is a clinically major challenge in breast cancer treatment. Although downregulation of estrogen receptor‐alpha (ERα) is the dominant mechanism of tamoxifen resistance, the reason for ERα decrease during tamoxifen therapy remains elusive. Herein, we reported that Spalt‐like transcription factor 2 (SALL2) expression was significantly reduced during tamoxifen therapy through transcription profiling analysis of 9 paired primary pre‐tamoxifen‐treated and relapsed tamoxifen‐resistant breast cancer tissues. SALL2 transcriptionally upregulated ESR1 and PTEN through directly binding to the DNA promoters. By contrast, silencing SALL2 induced downregulation of ERα and PTEN and activated the Akt/mTOR signaling, resulting in estrogen‐independent growth and tamoxifen resistance in ERα‐positive breast cancer. Furthermore, hypermethylation of SALL2 promoter was found in tamoxifen‐resistant breast cancer. Importantly, in vivo experiments showed that DNA methyltransferase inhibitor‐mediated SALL2 restoration resensitized tamoxifen‐resistant breast cancer to tamoxifen therapy. These findings shed light on the mechanism of SALL2 in regulation of ER and represent a potential clinical signature that can be used to categorize breast cancer patients who may benefit from co‐therapy with tamoxifen and DNMT inhibitor.

Phase I Study of Apatinib in Combination with Gefitinib As First-Line Treatment in Patients with EGFR-Mutant Advanced Non-Squamous Non-Small Cell Lung Cancer

Background: Dual blockade of the EGFR and VEGFR pathways in EGFR-mutant NSCLC have shown enhanced anti-tumor efficacy versus a (v)EGFR inhibitor alone. This phase I study evaluated the safety, pharmacokinetic (PK) profile and antitumor activity of apatinib, an orally effective VEGFR-2 tyrosine kinase inhibitor (TKI), plus gefitinib as a first-line treatment for EGFR-mutant advanced NSCLC. Methods: Advanced non-squamous NSCLC patients with the EGFR 19 deletion or the 21 L858R mutation who met this study's eligibility criteria were included. There were two cohorts. Cohort A: apatinib 500mg + gefitinib 250mg. Cohort B: apatinib 250mg + gefitinib 250mg. The primary endpoint was safety profile. Other endpoints included PK analysis, objective response rate (ORR) and progression free survival (PFS). Exploratory analysis was conducted using next generation sequencing of plasma circulating-tumor DNA with samples collected at baseline, best of response and after progression disease. Findings: Between July 2016 and April 2017, 13 patients with NSCLC were enrolled in this study. Six patients were enrolled in Cohort A and seven in Cohort B. Most adverse events (AEs) were grade 1-2 and the treatment-related AEs (TRAEs) were similar in both cohorts: rash (100% v 71.4%), diarrhea (66.7% v 71.4%), hypertension (66.7% v 71.4%), proteinuria (66.7% v 42.9%), and hand-foot skin reaction (33.3% v 28.6%). The area under the plasma concentration-time curve (AUC) for the steady state of apatinib was 2864.73 ± 2605.54 ng/ml*h in Cohort A and 2445.09 ± 1550.89 ng/ml*h Cohort B. Median follow-up was 29.7 months. The ORR was 80.0% and the median PFS was 19.2 months in Cohort and it 83.3% and 13.4 months in Cohort B. Patients without a concomitant mutation at baseline had a longer PFS compared with those with a detected concomitant mutation (20.99 months v 13.21 months, P=0.0624). The EGFR-T790M mutation remained the dominant resistance mechanism. Interpretation: Apatinib (500mg) plus gefitinib (250mg) had a tolerable safety profile and promising antitumor activity for EGFR-mutant NSCLC patients in the first-line setting. Phase III trials of apatinib (500mg) plus gefitinib (250mg) are warranted. Funding: This work was supported by National Key R&D Program of China (Grant number: 2016YFC0905500, 2016YFC0905503), The Science and Technology Planning Project of Guangdong Province of China (Grant number: 2017B020227001)，Natural Science Foundation of Guangdong Province of China (Grant number: 2018A0303130243) and The 5010 Clinical Research Foundation of Sun Yat-sen University (Grant number: 2016001). Li Zhang has received research support from the Strategic Priority Research Program of the Chinese Academy of Sciences (No. XDA12020101 to J.D.). Yan Huang has received research support from Science and Technology Program of Guangzhou (201704020072). Yunpeng Yang was supported by Outstanding Young Talents Program of Sun Yat-sen University Cancer Center (16zxyc03) and Central Basic Scientific Research Fund for Colleges-Young Teacher Training Program of Sun Yat-sen University (17ykpy85). Declaration of Interest: All authors declare no competing interests. Ethical Approval: This trial has been approved by the institutional review boards (ID: 2016-FXY-023) and the independent ethics committees of Sun Yat-sen University Cancer Center (Ethic approval ID: 5010-2016-03). And other participating centers have also obtained the approval from their institutional review boards/independent ethics committees before enrollment. All patients will be required to sign the informed consent form before enrollment.

Abstract 1320: Preclinical evaluation of TQB3804, a potent EGFR C797S inhibitor

Abstract Objective: Osimertinib is the 3rd generation EGFR inhibitor, which has been approved for the treatment of NSCLC patients with EGFRT790M. More recently, a tertiary EGFRC797S mutation was reported as the dominant resistance (40~20%) mechanism to Osimertinib. The emergence of C797S mutation prevent covalent bond formation with Osimertinib, and caused the drug resistance. So, it’s an urgent demand for new EGFR inhibitors that can effectively inhibit EGFR triple mutant, d746-750/T790M/C797S & L858R/T790M/C797S. Here, we disclose our clinical candidate, TQB3804, as a novel 4th generation inhibitor that potently inhibits triple mutants. Methods: The enzyme activities of TQB3804 for EGFRd746-750/T790M/C797S, EGFRL858R/T790M/C797S, EGFRd746-750/T790M, EGFRL858R/T790M, and EGFRWT were measured with corresponding kinase assays. The anti-proliferative activity was evaluated in Ba/F3 (EGFRd746-750/T790M/C797S), NCI-H1975 (EGFRd746-750/T790M/C797S), PC9 (EGFRd746-750), and A431 (EGFRWT) cell lines, and the phosphorylation of EGFR was also evaluated in Ba/F3 (EGFRd746-750/T790M/C797S) cell line. Antitumor activity of TQB3804 was evaluated in three triple mutant cell-derived tumor xenograft (CDX) models Ba/F3 (EGFRd746-750/T790M/C797S), NCI-H1975 (EGFRd746-750/T790M/C797S), and PC9 (EGFRd746-750/T790M/C797S) and one Osimertinib resistant patient-derived xenograft (PDX) model of NSCLC (LUPF104, EGFRd746-750/T790M/C797S). Results: TQB3804 displayed potent enzymatic activities for EGFRd746-750/T790M/C797S, EGFRL858R/T790M/C797S, EGFRd746-750/T790M, and EGFRL858R/T790M with IC50 of 0.46, 0.13, 0.26, and 0.19 nM respectively, and has similar enzymatic activity for EGFRWT (IC50 = 1.07) to Osimertinib. It also showed expected anti-proliferative activity in 4 cell lines, Ba/F3 (EGFRd746-750/T790M/C797S), NCI-H1975 (EGFRd746-750/T790M/C797S), PC9 (EGFRd746-750), and A431 (EGFRWT), with IC50 of 26.8, 163, 45, and 147 nM, respectively. The phosphorylation for EGFR in Ba/F3 (EGFRd746-750/T790M/C797S) cell line was potently inhibited with IC50 =18.5 nM. TQB3804 significantly inhibited tumor growth in the triple mutant Ba/F3 (EGFRd746-750/T790M/C797S), NCI-H1975 (EGFRd746-750/T790M/C797S), and PC9 (EGFRd746-750/T790M/C797S) CDX models, as well as in the LUPF104 PDX model. Western blot analysis of the tumor samples in the Ba/F3 (EGFRd746-750/T790M/C797S) CDX model showed that TQB3804 inhibited p-EGFR, p-AKT and p-ERK indicating that the tumor growth inhibition was through inhibition of the resistant triple mutant EGFR. Conclusions: We have identified a potent orally active 4th generation EGFR inhibitor, TQB3804. It can inhibit the activity of Osimertinib resistant triple mutant EGFR, and showed strong antitumor activity in corresponding in vitro and in vivo preclinical assays. These results are considered highly promising and warrant moving the compound forward to clinical investigation. Citation Format: Xile Liu, Xiquan Zhang, Ling Yang, Xin Tian, Tiantian Dong, Charles Z Ding, Lihong Hu, Lingyu Wu, Lele Zhao, Jun Mao, Qusheng Ji, Shaoyu Yan, Zhenzhen Zhu, Yuanfeng Xia, Chichung Chan, Shuhui Chen. Preclinical evaluation of TQB3804, a potent EGFR C797S inhibitor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1320.

Prevalence and diversity of filamentous fungi in the airways of cystic fibrosis patients – A Dutch, multicentre study

BackgroundProgressive lung injury in Cystic Fibrosis (CF) patients can lead to chronic colonization with bacteria and fungi. Fungal colonization is obtained from the environment which necessitates locally performed epidemiology studies. We prospectively analyzed respiratory samples of CF patients during a 3-year period, using a uniform fungal culture protocol, focusing on filamentous fungi and azole resistance in Aspergillus fumigatus. MethodsOver a 3-year period, all respiratory specimens collected from CF patients in 5 Dutch CF centers, were analyzed. Samples were inoculated onto the fungal culture media Sabouraud dextrose agar (SDA) and Medium B+. All fungal isolates were collected and identified in one centre, using Amplified Fragment Length Polymorphism (AFLP) fingerprinting, rDNA PCR and ITS, calmodulin and β-tubulin sequencing. Azole resistance was assessed for all A. fumigatus using a qPCR assay followed by phenotypic confirmation. ResultsFilamentous fungi were recovered from 699 patients from at least one respiratory sample, corresponding with 3787 cultured fungal species. A. fumigatus was cultured most often with a mean prevalence of 31.7%, followed by Penicillium species (12.6%), non-fumigatus Aspergillus species (5.6%), Scedosporium species (4.5%) and Exophiala dermatitidis and Cladosporium species (1.1% each). In total 107 different fungal species were identified, with 39 Penicillium species and 15 Aspergillus species. Azole resistance frequency in A. fumigatus was 7.1%, with TR34/L98H being the dominant resistance mechanism. ConclusionA vast diversity of filamentous fungi was demonstrated, dominated by Aspergillus and Penicillium species. We observed a mean azole resistance prevalence of 7.1% of A. fumigatus culture positive patients.

Abstract IA22: Reprogramming the tumor microenvironment and T cells for ovarian cancer immunotherapy

Abstract Immunologic destruction of tumors is a multistep, coordinated process that can be modulated or targeted at several critical points to elicit tumor rejection. These steps in the cancer immunity cycle include: (i) generation of sufficient numbers of effector T cells with high avidity recognition of tumor antigens in vivo; (ii) trafficking and infiltration into the tumor; (iii) overcoming inhibitory networks in the tumor microenvironment; (iv) direct recognition of tumor antigens and generation of an effector antitumor response; and (v) persistence of the antitumor T cells. Although several immune-based interventions have gained regulatory approval in many solid tumors and hematologic malignancies, there are currently no approved immune therapies for ovarian cancer. A major barrier to successful deployment of cancer immunotherapy for ovarian cancer patients is the immunosuppressive tumor microenvironment. Even if large numbers of tumor-specific T cells are generated in patients by active immunization or adoptive transfer, these T cells may not persist to readily destroy tumor targets in vivo. Previous studies by our group have defined some of the dominant immune resistance mechanisms in ovarian cancer to include extrinsic suppression of CD8+ effector cells by regulatory T cells (Tregs) (1, 2); metabolic deregulation via tryptophan catabolism by the immunoregulatory enzyme indoleamine-2,3-dioxygenase (IDO) (3, 4); engagement of inhibitory receptors such as PD-1 by the ligand PD-L1/B7-H1 (5-7); development of antigen loss variants (8); myeloid-derived suppressor cells (9); and inhibitory cytokines such as TGF-β. Collectively, this redundant immunosuppressive network facilitates tumor progression by actively restraining antitumor immunity and must be overcome in order to implement efficacious immunotherapeutic strategies. This presentation will be focused on our efforts at: (i) overcoming IDO-mediated innate and adaptive immune resistance as a strategy to reprogram the ovarian tumor microenvironment and (ii) novel “next-generation” strategies for reprograming T cells for adoptive immunotherapy of ovarian cancer.

Resistance Mechanisms to Targeted Therapies in ROS1+ and ALK+ Non-small Cell Lung Cancer.

Purpose: Despite initial benefit from tyrosine kinase inhibitors (TKIs), patients with advanced non-small cell lung cancer (NSCLC) harboring ALK (ALK+) and ROS1 (ROS1+) gene fusions ultimately progress. Here, we report on the potential resistance mechanisms in a series of patients with ALK+ and ROS1+ NSCLC progressing on different types and/or lines of ROS1/ALK-targeted therapy.Experimental Design: We used a combination of next-generation sequencing (NGS), multiplex mutation assay, direct DNA sequencing, RT-PCR, and FISH to identify fusion variants/partners and copy-number gain (CNG), kinase domain mutations (KDM), and copy-number variations (CNVs) in other cancer-related genes. We performed testing on 12 ROS1+ and 43 ALK+ patients.Results: One of 12 ROS1+ (8%) and 15 of 43 (35%) ALK + patients harbored KDM. In the ROS1+ cohort, we identified KIT and β-catenin mutations and HER2-mediated bypass signaling as non-ROS1-dominant resistance mechanisms. In the ALK+ cohort, we identified a novel NRG1 gene fusion, a RET fusion, 2 EGFR, and 3 KRAS mutations, as well as mutations in IDH1, RIT1, NOTCH, and NF1 In addition, we identified CNV in multiple proto-oncogenes genes including PDGFRA, KIT, KDR, GNAS, K/HRAS, RET, NTRK1, MAP2K1, and others.Conclusions: We identified a putative TKI resistance mechanism in six of 12 (50%) ROS1 + patients and 37 of 43 (86%) ALK+ patients. Our data suggest that a focus on KDMs will miss most resistance mechanisms; broader gene testing strategies and functional validation is warranted to devise new therapeutic strategies for drug resistance. Clin Cancer Res; 24(14); 3334-47. ©2018 AACR.

Dynamics of multiple resistance mechanisms in plasma DNA during EGFR‐targeted therapies in non‐small cell lung cancer

Tumour heterogeneity leads to the development of multiple resistance mechanisms during targeted therapies. Identifying the dominant driver(s) is critical for treatment decision. We studied the relative dynamics of multiple oncogenic drivers in longitudinal plasma of 50 EGFR‐mutant non‐small‐cell lung cancer patients receiving gefitinib and hydroxychloroquine. We performed digital PCR and targeted sequencing on samples from all patients and shallow whole‐genome sequencing on samples from three patients who underwent histological transformation to small‐cell lung cancer. In 43 patients with known EGFR mutations from tumour, we identified them accurately in plasma of 41 patients (95%, 41/43). We also found additional mutations, including EGFR T790M (31/50, 62%), TP53 (23/50, 46%), PIK3CA (7/50, 14%) and PTEN (4/50, 8%). Patients with both TP53 and EGFR mutations before treatment had worse overall survival than those with only EGFR. Patients who progressed without T790M had worse PFS during TKI continuation and developed alternative alterations, including small‐cell lung cancer‐associated copy number changes and TP53 mutations, that tracked subsequent treatment responses. Longitudinal plasma analysis can help identify dominant resistance mechanisms, including non‐druggable genetic information that may guide clinical management.

Targeting EGFRL858R/T790M and EGFRL858R/T790M/C797S resistance mutations in NSCLC: Current developments in medicinal chemistry.

Both the first-generation reversible epidermal growth factor receptor (EGFR) inhibitors gefitinib and erlotinib and the second-generation covalent epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) afatinib have significantly improved the survival of non-small-cell lung cancer (NSCLC) patients with activating EGFR mutations. However, a secondary EGFRT790M mutation leads to the clinically acquired resistance to the first- and second-generation EGFR-TKIs drugs. A number of the third-generation wild-type sparing EGFR inhibitors, for example, WZ4002, CO1686, AZD9291, HM61713, EGF816, ASP8173, and PF0674775, have been developed, among which AZD9291 has been approved by US FDA for the treatment of NSCLC patients with EGFRT790M . More recently, a tertiary EGFRC797S mutation was reported as the dominant resistance mechanism to the third-generation irreversible inhibitors. It is highly desirable to develop the fourth-generation EGFR inhibitors. This review summarizes the mechanisms of acquired resistance and the latest medicinal chemistry advances on the third- and fourth-generation EGFR inhibitors, with special attention being paid to the allosteric and reversible inhibitors combating the tertiary EGFRC797S mutation.

Defining Bedaquiline Susceptibility, Resistance, Cross-Resistance and Associated Genetic Determinants: A Retrospective Cohort Study

BackgroundBedaquiline (BDQ) is a novel agent approved for use in combination treatment of multi-drug resistant tuberculosis (MDR-TB). We sought to determine BDQ epidemiological cut-off values (ECVs), define and assess interpretive criteria against putative resistance associated variants (RAVs), microbiological outcomes and cross resistance with clofazimine (CFZ). MethodsA retrospective cohort study was conducted. Minimal inhibitory concentrations (MIC) to BDQ were determined using 7H9 broth microdilution (BMD) and MGIT960. RAVs were genetically characterised using whole genome sequencing. BDQ ECVs were determined using ECOFFinder and compared with 6-month culture conversion status and CFZ MICs. FindingsA total of 391 isolates were analysed. Susceptible and intermediate categories were determined to have MICs of ≤0.125μg/ml and 0.25μg/ml using BMD and ≤1μg/ml and 2μg/ml using MGIT960 respectively. Microbiological failures occurred among BDQ exposed patients with a non-susceptible BDQ MIC, an Rv0678 mutation and ≤2 active drug classes. The Rv0678 RAVs were not the dominant mechanism of CFZ resistance and cross resistance was limited to isolates with an Rv0678 mutation. InterpretationCriteria for BDQ susceptibility are defined and will facilitate improved early detection of resistance. Cross- resistance between BDQ and CFZ is an emerging concern but in this study was primarily among those with an Rv0678 mutation.

Antibiotic resistome in a large-scale healthy human gut microbiota deciphered by metagenomic and network analyses.

The human gut microbiota is an important reservoir of antibiotic resistance genes (ARGs). A metagenomic approach and network analysis were used to establish a comprehensive antibiotic resistome catalog and to obtain co-occurrence patterns between ARGs and microbial taxa in fecal samples from 180 healthy individuals from 11 different countries. In total, 507 ARG subtypes belonging to 20 ARG types were detected with abundances ranging from 7.12 × 10-7 to 2.72 × 10-1 copy of ARG/copy of 16S-rRNA gene. Tetracycline, multidrug, macrolide-lincosamide-streptogramin, bacitracin, vancomycin, beta-lactam and aminoglycoside resistance genes were the top seven most abundant ARG types. The multidrug ABC transporter, aadE, bacA, acrB, tetM, tetW, vanR and vanS were shared by all 180 individuals, suggesting their common occurrence in the human gut. Compared to populations from the other 10 countries, the Chinese population harboured the most abundant ARGs. Moreover, LEfSe analysis suggested that the MLS resistance type and its subtype 'ermF' were representative ARGs of the Chinese population. Antibiotic inactivation, antibiotic target alteration and antibiotic efflux were the dominant resistance mechanism categories in all populations. Procrustes analysis revealed that microbial phylogeny structured the antibiotic resistome. Co-occurrence patterns obtained via network analysis implied that 12 species might be potential hosts of 58 ARG subtypes.

EGFR T790M: revealing the secrets of a gatekeeper.

Non-small-cell lung cancers that harbor activating mutations in the EGFR gene represent an important molecularly defined subset of lung cancer. Despite dramatic initial responses with first- and second-generation EGFR-directed tyrosine-kinase inhibitors (TKIs) against these cancers, the development of a dominant and frequent resistance mechanism through a threonine–methionine amino acid substitution at position 790 (T790M) of EGFR has limited the long-term efficacy of these targeted therapies. This “gatekeeper” EGFR T790M alteration remains the only validated and relevant second-site resistance mutation for EGFR, allowing for focused research to understand and overcome EGFR T790M-mediated resistance. The current review focuses on EGFR T790M by discussing mechanisms of resistance mediated by EGFR T790M, reviewing development of novel third-generation EGFR TKIs targeting EGFR T790M, and highlighting current research on overcoming resistance to third-generation EGFR T790M TKIs.