Resistant Populations Research Articles

Retrospective Analysis of Pyrotinib-Based Therapy for Metastatic Breast Cancer: Promising Efficacy in Combination with Trastuzumab.

To evaluate the efficacy and safety of a pyrotinib-based therapy for human epidermal growth factor receptor 2 (HER2)-positive metastatic breast cancer (MBC) in the real world. Clinical data of 218 patients with HER2-positive MBC who received a pyrotinib-based therapy from January 2020 to March 2023 at the First Affiliated Hospital of Zhengzhou University were retrospectively analyzed. Finally, 195 patients were included in the efficacy cohort. The median progression-free survival (PFS) in the total population is 12.4 months (95% CI, 9.8-15.0 months). More than half of the patients in the efficacy cohort received pyrotinib mono-targeted therapy (103 cases, 52.8%). Among the remaining patients, 74 (37.9%) patients chose a combined trastuzumab-targeted therapy and 17 (8.7%) chose to combine inetetamab. Median PFS in the pyrotinib group vs pyrotinib plus trastuzumab group was 10.5 months vs 20.1 months (P<0.001). The median PFS of primary trastuzumab resistance population reached to 20.1 months in pyrotinib plus trastuzumab group. Double-targets' advantage was also observed in the brain metastases subgroup (17.9 months vs 10.0 months, P=0.386). The patients who received pyrotinib plus inetetamab as second and higher-line treatment reached a median PFS of 7.9 months (95% CI, 4.0-11.8 months). Forty-one (19.8%) of 207 patients included in the safety cohort experienced grade 3 or higher diarrhea, the most common adverse event in safety analysis, and no adverse event-related deaths. The combination of pyrotinib and trastuzumab demonstrated promising efficacy in the treatment of HER2-positive metastatic breast cancer, including those who had primary resistance to trastuzumab and brain metastases. Pyrotinib plus trastuzumab is expected to be a potent option in the first-line. Additionally, the concurrent administration of pyrotinib and inetetamab could be an alternative to consider in the second and higher-line treatment for metastatic breast cancer. The adverse reactions of pyrotinib were tolerable in general.

Exploiting cooperative pathogen behaviour for enhanced antibiotic potency: A Trojan horse approach.

Antimicrobial resistance poses an escalating global threat, rendering traditional drug development approaches increasingly ineffective. Thus, novel alternatives to antibiotic-based therapies are needed. Exploiting pathogen cooperation as a strategy for combating resistant infections has been proposed but lacks experimental validation. Empirical findings demonstrate the successful invasion of cooperating populations by non-cooperating cheats, effectively reducing virulence in vitro and in vivo. The idea of harnessing cooperative behaviours for therapeutic benefit involves exploitation of the invasive capabilities of cheats to drive medically beneficial traits into infecting populations of cells. In this study, we employed Pseudomonas aeruginosa quorum sensing cheats to drive antibiotic sensitivity into both in vitro and in vivo resistant populations. We demonstrated the successful invasion of cheats, followed by increased antibiotic effectiveness against cheat-invaded populations, thereby establishing an experimental proof of principle for the potential application of the Trojan strategy in fighting resistant infections.

Efficacy of selected botanicals, phosphine and boric acid against pulse beetle, Callosobruchus chinensis under laboratory conditions

Insect pests are a threat to both growing field crops and stored grain commodities during storage. There are different stored pests which affect the mung bean (Vigna radiata) all over the world. Most important destructive pest is Pulse beetle Callosobruchus chinensis which cause lot of losses during storage of mung bean. Different pesticides are being used to control the Pulse beetle but these pesticides have harmful effect on human health, grain quality and development of insect resistant population. The replacement approaches for pest management in food items is a growing need in the food sector, which should match customer requests for pesticide reduction or eradication. In the present study impact of phosphine, boric acid and botanicals (Neem and Eucalyptus) on adult stage of pulse beetle Callosobruchus chinensis was evaluated at 65 ±5% RH, 30±1°C. The pulse beetles were exposed to phosphine, boric acid at the different concentrations like phosphine 2g, 1g, &amp; 0.5g, boric acid 0.25g, 0.12g &amp; 0.06g and botanicals leaves 2g, 5g and 10g for 24h, 48h and 72h was evaluated. Maximum mortality (98%) by phosphine at 0.25 g, boric acid (95%) at 0.25 g, neem leaves (96%) at 10g and eucalyptus (95%) at 10g after 72h was observed. This technique is a best and eco-friendly to controlling pulse beetles. This technique has no any adverse or residual effect on the quality of grains.

Understanding of G × E interactions of yield attributes in soybean MAGIC population and characterization for charcoal rot resistance

AbstractMulti‐parent advanced generation inter‐cross (MAGIC) populations have been developed and utilized in crop improvement programs in several economically important crops. In the current study, soybean (Glycine max L.) MAGIC population was evaluated at four locations to identify stable and high‐yielding MAGIC RILs (recombinant inbred lines) and to understand the genotype and environmental interaction for grain yield and attributing traits. For different traits under study, pooled analysis of variance indicated the significant genotype × environmental interactions at p &lt; 0.01. RILs such as G236, G455, G159, G493, and G488 found ideal for grain yield across the four environments. Through multi‐trait genotype‐ideotype distance index ideotype‐MAGIC RILs have been identified for each location. Significant positive correlation of grain yield with pods per plant, 100‐seed weight, plant height, number of nodes per plant, and branches per plant has been identified. Under field conditions, screening of F2:3 generation of MAGIC population revealed that only 59 progenies exhibited adult plant resistance for charcoal rot disease (caused by Macrophomina phaseolina). Although under controlled conditions parental genotypes EC 572136 and EC 572109 found to be partially resistant with least mean necrosis length, MAGIC RILs (F2:8) showed variable reaction. Thus, the study established diverse genetic resources useful for both mapping and varietal development program.

The Anopheles coluzzii range extends into Kenya: detection, insecticide resistance profiles and population genetic structure in relation to conspecific populations in West and Central Africa

BackgroundAnopheles coluzzii is a primary vector of malaria found in West and Central Africa, but its presence has hitherto never been documented in Kenya. A thorough understanding of vector bionomics is important as it enables the implementation of targeted and effective vector control interventions. Malaria vector surveillance efforts in the country have tended to focus on historically known primary vectors. The current study sought to determine the taxonomic status of samples collected from five different malaria epidemiological zones in Kenya as well as describe the population genetic structure and insecticide resistance profiles in relation to other An. coluzzii populations.MethodsMosquitoes were sampled as larvae from Busia, Kwale, Turkana, Kirinyaga and Kiambu counties, representing the range of malaria endemicities in Kenya, in 2019 and 2021 and emergent adults analysed using Whole Genome Sequencing (WGS) data processed in accordance with the Anopheles gambiae 1000 Genomes Project phase 3. Where available, historical samples from the same sites were included for WGS. Comparisons were made with An. coluzzii cohorts from West and Central Africa.ResultsThis study reports the detection of An. coluzzii for the first time in Kenya. The species was detected in Turkana County across all three time points from which samples were analyzed and its presence confirmed through taxonomic analysis. Additionally, there was a lack of strong population genetic differentiation between An. coluzzii from Kenya and those from the more northerly regions of West and Central Africa, suggesting they represent a connected extension to the known species range. Mutations associated with target-site resistance to DDT and pyrethroids and metabolic resistance to DDT were found at high frequencies up to 64%. The profile and frequencies of the variants observed were similar to An. coluzzii from West and Central Africa but the ace-1 mutation linked to organophosphate and carbamate resistance present in An. coluzzii from coastal West Africa was absent in Kenya.ConclusionsThese findings emphasize the need for the incorporation of genomics in comprehensive and routine vector surveillance to inform on the range of malaria vector species, and their insecticide resistance status to inform the choice of effective vector control approaches.

Motivation of Volunteers during Great Patriotic War (Case Study of Rostov Region)

This article explores the motivations behind citizens joining volunteer formations during the Great Patriotic War. The study relies on archival and published sources on the history of volunteer movements in the Rostov region. The research is based on a military-anthropological approach, aiming to understand the worldview of volunteers and the qualitative and quantitative parameters of volunteer movements in the Don region. The relevance of the study lies in the necessity of attracting more attention from researchers to understand what drove individuals to act during wartime. A detailed analysis of the archives at the Center for Documentation of Recent History of Rostov Region revealed characteristic models of voluntarism. The author concludes that the mechanism of agitation and propaganda intertwines with deeply personal motives of resistance against the enemy. A classification of tools influencing participants’ motives is proposed, including visual imagery, state symbolism, the work of agitators and propagandists, and oath-taking. The novelty of the research lies in the author’s exploration of the mechanism influencing public consciousness in a specific region with limited time to prepare the population for resistance against the adversary.

Survey of target site mutations linked with insecticide resistance in Italian populations of Aphis gossypii.

Aphis gossypii is a worldwide agricultural pest that causes high levels of economic losses by feeding and transmitting virus diseases. It is usually controlled by chemical insecticides, but this could lead to the selection of resistant populations. Several single nucleotide polymorphisms (SNPs) have been identified associated with insecticide resistance. Monitoring activities to detect the presence of such mutations in field populations can have an important role in insect pest management but, currently, no information on Italian strains is available. The presence of target site mutations conferring resistance to different insecticides was analysed in Italian field collected populations of A. gossypii with an allele specific approach (QSGG, Qualitative Sybr-Green Genotyping). Primers were designed to detect mutations in genes coding acetylcholinesterase (S431F), nicotinic acetylcholine receptor (R81T) and voltage-gated sodium channel (M918L and L1014F). S431F was widespread but with high variability across populations. R81T was detected for the first time in Italy but only in two populations. The L1014F mutation (kdr) was not found, while in the samples showing the M918L two different nucleotidic substitutions were detected. Mutant allele frequencies were, respectively, 0.70 (S431), 0.31 (M918) and 0.02 (R81). Further analysis on the voltage-gated sodium channel gene showed the presence of eight haplotypes and one non-synonymous mutation in the gene coding region. Multiple target-site mutations were detected within Italian populations. The combinations of genotypes observed in certain locations could affect negatively the control of this pest. Preliminary insights on the genetic structure in the Italian populations of A. gossypii were acquired. © 2024 Society of Chemical Industry.

Symbiont Diversity in Imidacloprid-Resistant and Imidacloprid-Susceptible Populations of Nilaparvata lugens (Hemiptera: Delphacidae)1

Abstract Imidacloprid, a neonicotinoid insecticide, is efficacious against hemipterans, including the brown planthopper, Nilaparvata lugens (Stål) (Hemiptera: Delphacidae). However, frequent use of this insecticide has resulted in the development of high levels of resistance among brown planthopper populations. Endosymbionts of insects have contributed to host physiology and evolution and play a role in resistance to chemical toxins. In this study, polymerase chain reaction–denaturing gradient gel electrophoresis was used to analyze the bacterial and yeast-like symbiont communities of imidacloprid-resistant and -susceptible brown planthopper populations. The Shannon-Weaver diversity index and the evenness index indicated no differences in the richness and the expression of overall species distribution of the symbiotic communities of resistant and susceptible populations. The similarity coefficients of 0.53 and 0.56 for bacterial and yeast-like symbionts, respectively, indicated the main types of differences among microorganisms in resistant and susceptible populations. Sequence comparison analysis indicated the bacterial species in the susceptible population were members of the Enterobacteriaceae and Moraxellaceae, and those in the resistant population were members of the Enterobacteriaceae, Oxalobacteriaceae, Rhodobacteriaceae, and Sphingomonadaceae. Differences also were found in the composition of yeast-like symbionts of the two populations; Cryptococcus luteolus, Pseudozyma aphidis, and Pseudozyma antarctica were detected in the susceptible population, and Cladosporium perangustum was detected in the resistant population.

Azole resistance mechanisms and population structure of the human pathogen Aspergillus fumigatus on retail plant products.

Aspergillus fumigatus is a ubiquitous saprotroph and human-pathogenic fungus that is life-threatening to the immunocompromised. Triazole-resistant A. fumigatus was found in patients without prior treatment with azoles, leading researchers to conclude that resistance had developed in agricultural environments where azoles are used against plant pathogens. Previous studies have documented azole-resistant A. fumigatus across agricultural environments, but few have looked at retail plant products. Our objectives were to determine if azole-resistant A. fumigatus is prevalent in retail plant products produced in the United States (U.S.), as well as to identify the resistance mechanism(s) and population genetic structure of these isolates. Five hundred twenty-five isolates were collected from retail plant products and screened for azole resistance. Twenty-four isolates collected from compost, soil, flower bulbs, and raw peanuts were pan-azole resistant. These isolates had the TR34/L98H, TR46/Y121F/T289A, G448S, and H147Y cyp51A alleles, all known to underly pan-azole resistance, as well as WT alleles, suggesting that non-cyp51A mechanisms contribute to pan-azole resistance in these isolates. Minimum spanning networks showed two lineages containing isolates with TR alleles or the F46Y/M172V/E427K allele, and discriminant analysis of principle components identified three primary clusters. This is consistent with previous studies detecting three clades of A. fumigatus and identifying pan-azole-resistant isolates with TR alleles in a single clade. We found pan-azole resistance in U.S. retail plant products, particularly compost and flower bulbs, which indicates a risk of exposure to these products for susceptible populations and that highly resistant isolates are likely distributed worldwide on these products.IMPORTANCEAspergillus fumigatus has recently been designated as a critical fungal pathogen by the World Health Organization. It is most deadly to people with compromised immune systems, and with the emergence of antifungal resistance to multiple azole drugs, this disease carries a nearly 100% fatality rate without treatment or if isolates are resistant to the drugs used to treat the disease. It is important to determine the relatedness and origins of resistant A. fumigatus isolates in the environment, including plant-based retail products, so that factors promoting the development and propagation of resistant isolates can be identified.

Distribution and Mechanism of Japanese Brome (Bromus japonicus) Resistance to ALS-Inhibiting Herbicides in China.

Bromus japonicus is a common monocot weed that occurs in major winter wheat fields in the Huang-Huai-Hai region of China. Pyroxsulam is a highly efficient and safe acetolactate synthase (ALS)-inhibiting herbicide that is widely used to control common weeds in wheat fields. However, B. japonicus populations in China have evolved resistance to pyroxsulam by different mutations in the ALS gene. To understand the resistance distribution, target-site resistance mechanisms, and cross-resistance patterns, 208 B. japonicus populations were collected from eight provinces. In the resistant population screening experiment, 59 populations from six provinces showed different resistance levels to pyroxsulam compared with the susceptible population, of which 17 B. japonicus populations with moderate or high levels of resistance to pyroxsulam were mainly from the Hebei (4), Shandong (4) and Shanxi (9) Provinces. Some resistant populations were selected to investigate the target site-resistance mechanism to the ALS-inhibiting herbicide pyroxsulam. Three pairs of primers were designed to amplify the ALS sequence, which was assembled into the complete ALS sequence with a length of 1932 bp. DNA sequencing of ALS revealed that four different ALS mutations (Pro-197-Ser, Pro-197-Thr, Pro-197-Phe and Asp-376-Glu) were found in 17 moderately or highly resistant populations. Subsequently, five resistant populations, QM21-41 with Pro-197-Ser, QM20-8 with Pro-197-Thr and Pro-197-Phe, and QM21-72, QM21-76 and QM21-79 with Asp-376-Glu mutations in ALS genes, were selected to characterize their cross-resistance patterns to ALS inhibitors. The QM21-41, QM20-8, QM21-72, QM21-76 and QM21-79 populations showed broad-spectrum cross-resistance to pyroxsulam, mesosulfuron-methyl and flucarbazone-sodium. This study is the first to report evolving cross-resistance to ALS-inhibiting herbicides due to Pro-197-Phe mutations in B. japonicus.

Nontarget site-based resistance to nicosulfuron and identification of candidate genes in Cucumis melo L. var. agrestis Naud. via RNA-Seq transcriptome analysis

Herbicide resistance is a worldwide concern for weed control. Cucumis melo L. var. agrestis Naud. (C. melo) is an annual trailing vine weed that is commonly controlled by nicosulfuron, acetolactate synthase (ALS)-inhibiting herbicides. However, long-term use of this herbicide has led to the emergence of resistance and several nicosulfuron resistant populations of C. melo have been found. Here we identified a resistant (R) C. melo population exhibiting 7.31-fold resistance to nicosulfuron compared with a reference sensitive (S) population. ALS gene sequencing of the target site revealed no amino acid substitution in R plants, and no difference in enzyme activity, as shown by ALS activity assays in vitro. ALS gene expression was not significantly different before and after the application of nicosulfuron. Pretreatment with the cytochrome P450 monooxygenase (P450) inhibitor malathion reduced nicosulfuron resistance in the R population. RNA-Seq transcriptome analysis was used to identify candidate genes that may confer metabolic resistance to nicosulfuron. We selected genes with annotations related to detoxification functions. A total of 20 candidate genes (7 P450 genes, 1 glutathione S-transferase (GST) gene, 2 ATP-binding cassette (ABC) transporters, and 10 glycosyltransferase (GT)) were identified; 12 of them (7 P450s, 1 GST, 2 ABC transporters, and 2 GTs) were demonstrated significantly differential expression between R and S by quantitative real-time RT-PCR (qRT–PCR). Our findings revealed that the resistance mechanism in C. melo was nontarget-site based. Our results also provide a valuable resource for studying the molecular mechanisms of weed resistance.

Mathematical models of drug-resistant tuberculosis lack bacterial heterogeneity: A systematic review.

Drug-resistant tuberculosis (DR-TB) threatens progress in the control of TB. Mathematical models are increasingly being used to guide public health decisions on managing both antimicrobial resistance (AMR) and TB. It is important to consider bacterial heterogeneity in models as it can have consequences for predictions of resistance prevalence, which may affect decision-making. We conducted a systematic review of published mathematical models to determine the modelling landscape and to explore methods for including bacterial heterogeneity. Our first objective was to identify and analyse the general characteristics of mathematical models of DR-mycobacteria, including M. tuberculosis. The second objective was to analyse methods of including bacterial heterogeneity in these models. We had different definitions of heterogeneity depending on the model level. For between-host models of mycobacterium, heterogeneity was defined as any model where bacteria of the same resistance level were further differentiated. For bacterial population models, heterogeneity was defined as having multiple distinct resistant populations. The search was conducted following PRISMA guidelines in five databases, with studies included if they were mechanistic or simulation models of DR-mycobacteria. We identified 195 studies modelling DR-mycobacteria, with most being dynamic transmission models of non-treatment intervention impact in M. tuberculosis (n = 58). Studies were set in a limited number of specific countries, and 44% of models (n = 85) included only a single level of "multidrug-resistance (MDR)". Only 23 models (8 between-host) included any bacterial heterogeneity. Most of these also captured multiple antibiotic-resistant classes (n = 17), but six models included heterogeneity in bacterial populations resistant to a single antibiotic. Heterogeneity was usually represented by different fitness values for bacteria resistant to the same antibiotic (61%, n = 14). A large and growing body of mathematical models of DR-mycobacterium is being used to explore intervention impact to support policy as well as theoretical explorations of resistance dynamics. However, the majority lack bacterial heterogeneity, suggesting that important evolutionary effects may be missed.

Assessing the impact of meropenem exposure on ceftolozane/tazobactam-resistance development in Pseudomonas aeruginosa using in vitro serial passage.

Patients infected with difficult-to-treat Pseudomonas aeruginosa are likely to receive meropenem (MEM) empirically before escalation to ceftolozane/tazobactam (C/T). We assessed whether pre-exposure to MEM affected C/T resistance development on C/T exposure. Nine clinical P. aeruginosa isolates were exposed to MEM 16 mg/L for 72 h. Then, isolates were serially passaged in the presence of C/T (concentration of 10 mg/L) for 72 h as two groups: an MEM-exposed group inoculated with MEM pre-exposed isolates and a non-MEM control group. At 24 h intervals, samples were plated on drug-free and drug-containing agar (C/T concentration 16/8 mg/L) and incubated to quantify bacterial densities (log10 cfu/mL). Growth on C/T agar indicated resistance development, and resistant population was calculated by dividing the cfu/mL on C/T plates by the cfu/mL on drug-free agar. At 72 h, resistant populations were detected in 6/9 isolates. In five isolates, MEM exposure significantly increased the prevalence of ceftolozane/tazobactam-resistance development; the percentages of resistance population were 100%, 100%, 53.5%, 31% and 3% for the MEM-exposed versus 0%, 0%, 2%, 0.35% and ≤0.0003% in the unexposed groups. One isolate had a similar resistant population at 72 h between the two groups. The remaining isolates showed no development of resistance, regardless of previous MEM exposure. MEM exposure may pre-dispose to C/T resistance development and thus limit the therapeutic utility of this β-lactam/β-lactamase inhibitor. Resistance may be a result of stress exposure or molecular-level mutations conferring cross-resistance. Further in vivo studies are needed to assess clinical implications of these findings.

Impact of Chemotherapeutic Stress Depends on The Nature of Breast Cancer Spheroid and Induce Behavioral Plasticity to Resistant Population (Adv. Biology 4/2024)

Impact of Chemotherapeutic Stress Depends on The Nature of Breast Cancer Spheroid and Induce Behavioral Plasticity to Resistant Population (Adv. Biology 4/2024)

Confirmation and characterization of the first case of acetolactate synthase (ALS)-inhibitor resistance in Japanese brome (Bromus japonicus) in the US.

Japanese brome (Bromus japonicus Thumb.) is one of the problematic annual weeds in winter wheat (Triticum aestivum L.) and is generally controlled by acetolactate synthase (ALS) inhibitors. Repeated use of the ALS inhibitor propoxycarbazone-Na resulted in the evolution of resistance to this herbicide in three B. japonicus populations, i.e., R1, R2, and R3 in Kansas (KS). However, the level of resistance and mechanism conferring resistance in these populations is unknown. The objectives of this research were to (i) evaluate the level of resistance to propoxycarbazone-Na in R1, R2, and R3 in comparison with a known susceptible population (S1), (ii) investigate the mechanism of resistance involved in conferring ALS-inhibitor resistance, and (iii) investigate the cross-resistance to other ALS inhibitors. Dose-response (0 to 16x; x = 44 g ai ha-1 of propoxycarbazone-Na) assay indicated 167, 125, and 667-fold resistance in R1, R2 and R3 populations, respectively, compared to S1 population. ALS gene sequencing confirmed the mutations resulting in amino acid substitutions, i.e., Pro-197-Thr (R3, R1)/Ser (R2, R1) bestowing resistance to these ALS inhibitors. Such amino acid substitutions also showed differential cross-resistance to sulfosulfuron, mesosulfuron-methyl, pyroxsulam, and imazamox among resistant populations. Pretreatment with malathion (a cytochrome P450 enzyme-inhibitor) followed by imazamox treatment suggested cross-resistance to this herbicide possibly via metabolism only in R3 population. Overall, these results confirm the first case of target-site based resistance to ALS inhibitors in B. japonicus in the US, highlighting the need for exploring herbicides with alternative modes of action to enhance weed control in winter wheat. © 2024 Society of Chemical Industry.

Modeling resistance to the broadly neutralizing antibody PGT121 in people living with HIV-1.

PGT121 is a broadly neutralizing antibody in clinical development for the treatment and prevention of HIV-1 infection via passive administration. PGT121 targets the HIV-1 V3-glycan and demonstrated potent antiviral activity in a phase I clinical trial. Resistance to PGT121 monotherapy rapidly occurred in the majority of participants in this trial with the sampled rebound viruses being entirely resistant to PGT121 mediated neutralization. However, two individuals experienced long-term ART-free viral suppression following antibody infusion and retained sensitivity to PGT121 upon viral rebound. Here, we develop mathematical models of the HIV-1 dynamics during this phase I clinical trial. We utilize these models to understand the dynamics leading to PGT121 resistance and to identify the mechanisms driving the observed long-term viral control. Our modeling highlights the importance of the relative fitness difference between PGT121 sensitive and resistant subpopulations prior to treatment. Specifically, by fitting our models to data, we identify the treatment-induced competitive advantage of previously existing or newly generated resistant population as a primary driver of resistance. Finally, our modeling emphasizes the high neutralization ability of PGT121 in both participants who exhibited long-term viral control.

Abstract 4310: Impact of drug combination schedules on the evolution of tumor resistance

Abstract The emergence of drug resistance during treatment is a critical limiting factor for the long-term effectiveness of anticancer therapies. The use of drug combinations limits the emergence of resistance, thereby prolonging their therapeutic utility. The effect of a drug combination is dependent both on the concentration of the individual drugs and the extent of their interaction (synergistic, additive, or antagonistic). Thus, understanding the scheduling implications for efficacy can be valuable for optimizing tumor response and time to resistance for the combination. To examine this more closely, we used a pharmacokinetic/pharmacodynamic (PK/PD) modeling approach, coupling one-compartment PK models of two hypothetical drugs based on set synchronous or asynchronous (offset) schedules with an evolutionary model of tumor clone growth. We simulated four tumor subpopulations representing binary resistance to one or both drugs, using an exponential growth model with growth penalties based on drug concentrations. We used the model to simulate the effects of pairs of antagonistic, synergistic, and additive drugs on the growth of sensitive and resistant populations in a tumor. Final tumor volume and resistant population were used to compare the efficacy of various drug schedules. As expected, the effect of a drug interaction—either synergistic or antagonistic—is greatest when dosing is synchronous, as this results in the greatest simultaneous drug concentration. The effect of a drug interaction is proportional to the sensitive population size, so the effect of drug interactions decreases over time as the sensitive population is eliminated. Intuitively, the final tumor volume decreases as the strength of a synergistic interaction increases until the sensitive population is eliminated. The resistant populations are unaffected by the strength of the interaction for both antagonistic and synergistic combinations. Resistant populations are not affected by interactions between drugs to which they are resistant, so the growth of resistant populations over time is independent of drug interactions. Crucially, for effective drugs—that is, drugs that eliminate the sensitive population—synergy and antagonism converge to additivity as the sensitive population dies out because the remaining resistant populations are not affected by drug interactions. As synergistic and additive drug combinations are equivalent in the long-term, synergy and asynchronous dosing could be used to limit toxicity without sacrificing efficacy. The evolution of resistance also explains why in vitro synergy or antagonism may not translate in vivo. Taken together, our work provides several unintuitive insights about combination drug scheduling with practical implications for therapeutic design. Citation Format: Madison Stoddard, Andrew Chen, Lin Yuan, Debra Van Egeren, Dean Bottino, Arijit Chakravarty. Impact of drug combination schedules on the evolution of tumor resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4310.

Abstract 4761: Understanding three-drug combinations: optimizing scheduling while avoiding toxicity

Abstract The promise of combination therapies in managing tumor resistance is constrained by the therapeutic window (the difference between efficacious and toxic doses). We have sought to understand the impact of dose scheduling on the emergence of resistance, using a mathematical model-based approach linking pharmacokinetics (PK) to a parsimonious evolutionary model of tumor growth incorporating the emergence of drug resistance. Here, we analyze the potential of a three-drug combination to minimize toxicity while preventing the emergence of resistance. We simulated eight tumor subpopulations representing resistance to one, two or three hypothetical drugs, using an exponential growth model with growth penalties based on drug concentrations. We used the model to simulate the effects of pairs of antagonistic, synergistic, and additive drugs on the growth of sensitive and resistant populations in a tumor. Final tumor volume and resistant population were used to compare the efficacy of various drug schedules. We assumed an overlapping neutropenia-like toxicity as the dose-limiting toxicity for the three drug combination, which we have previously shown to be proportional to the peak moving average drug concentration over 18 days. Final tumor volume and peak toxicity were used to compare the effectiveness of various dosing strategies and interaction combinations. Synchronous dosing results in the greatest drug interaction effect between any two drugs. When all interactions between the three drugs are either antagonistic or synergistic, the greatest effect is observed when all drugs are dosed simultaneously. The drugs are most toxic when all three are dosed simultaneously or nearly simultaneously. Our work shows that time sensitivity—that is, the magnitude of the changes in efficacy associated with small changes in schedule—varies with phase offset. Scheduling is most time sensitive when all drugs are dosed simultaneously or nearly simultaneously; dosing of two drugs simultaneously is less time sensitive. Three-drug combinations are an effective means of preventing complete resistance. While simultaneous dosing of two or more drugs confers the greatest efficacy, such simultaneous dosing results in greater peak toxicity because of higher simultaneous drug concentrations. A potential compromise is the simultaneous dosing of two of the three drugs, which results in an intermediate toxicity. Dosing of two drugs simultaneously is also less time sensitive, advantageous in a practical sense as it is more robust to patient dosing error. While the approach used here is based on hypothetical drug properties, it provides a framework that is readily applicable to real-world drug combinations, with the potential for practical insights to guide the framing of the Target Product Profile for three-drug combinations. Citation Format: Madison Stoddard, Lin Yuan, Debra Van Egeren, Andrew Chen, Dean Bottino, Arijit Chakravarty. Understanding three-drug combinations: optimizing scheduling while avoiding toxicity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4761.

Abstract 1998: ABCB1 promotes uveal melanoma cell resistance to FR900359 and identifies a tumor cell subpopulation with a distinct gene expression signature

Abstract Uveal melanoma (UM) is the leading form of intraocular cancer in adults and the second most common form of melanoma. Although rare, UM has a median survival rate of ~1 year after metastasis occurs. Metastatic UM is largely refractory to treatment and there are no effective pharmacological therapies, resulting in poor overall survival. In &amp;gt;90% UM cases, the oncogenic initiator proteins are constitutively active mutant GNAQ or GNA11 proteins (GNAQ/11). FR900359 (FR) is a natural compound that inhibits GNAQ/11 and has anti-proliferative effects on UM cells. To identify key oncogenic mechanisms downstream of mutant GNAQ/11, we performed a Sleeping Beauty (SB) transposon forward genetic screen to identify drivers of FR resistance. The SB screen identified ATP-binding cassette sub-family B member 1 (ABCB1) as one of the top genes upregulated by SB in FR-resistant UM cell populations. We determined that although ABCB1 does not provide immediate resistance to FR, the overexpression of ABCB1 leads to emergence of resistant colonies at a much higher rate than spontaneous resistance, validating ABCB1 as contributors to FR resistance. Unexpectedly, immunofluorescence revealed that a relatively small fraction of UM cells strongly expresses the transgenes after stable transfection. Immunoblotting confirmed that ABCB1 expression was initially modest in ABCB1-transfected populations but increased in the cells that developed resistance to FR. To examine the kinetics of FR resistance, population doubling versus time (PDVT) assays were performed in UM cells expressing ABCB1 or empty vector control treated with FR or vehicle. FR potently suppressed the proliferation of vector control cells. Drug-naïve ABCB1-transfected cells developed resistance to FR over time but accomplished fewer population doublings than vehicle-treated cells in the same time interval. Once transgenic populations emerged as resistant populations in FR, they grew similarly in drug or vehicle. Ongoing RNA-sequencing analysis from PDVT samples has identified distinct gene expression signatures associated with FR treatment and ABCB1 expression. These findings are expected to illuminate tumor cell heterogeneity amongst UM cell populations that may be related to drug resistance and metastasis. Citation Format: Sarina Dion Murray, Jesse D. Riordan, Eric R. Anderson, Michael D. Onken, Kendall J. Blumer, Adam J. Dupuy, Christopher S. Stipp. ABCB1 promotes uveal melanoma cell resistance to FR900359 and identifies a tumor cell subpopulation with a distinct gene expression signature [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1998.

Abstract 4877: Morphological detection of chemotherapy resistance in cancer cell lines using AI-based analysis

Abstract Chemoresistance can develop during the course of treatment of many cancers, which can limit the utility of standard therapeutics and lead to poor outcomes. The mechanism by which resistance arises is not well understood, and developing models to study resistance can be challenging. Resistance can spontaneously arise in cell lines, however, it is difficult to separate resistant from sensitive cells using traditional biomarkers, hampering their utility for studying mechanisms. Morphology presents another modality to examine resistance, independently of protein markers, and may solve a previously intractable problem of separating resistant from sensitive cells for further study. Here we sought to study the mechanism of chemoresistance in cell lines using multi-parameter morphology in combination with gene expression and other standard molecular approaches. We induced resistance to specific chemotherapeutic drugs in parent cancer cell lines from lung, ovarian, and melanoma cancers. IC-50s of each drug increased by ≥1 order of magnitude in the resistant cells. Whole exome sequencing and bulk RNAseq were performed to examine differentially expressed genes and pathways between the parent and resistant cell lines. Each cell line was analyzed using multi-dimensional morphology using the Deepcell platform, which extracts &amp;gt;100 morphological features from images of unlabeled single cells using artificial intelligence (AI), advanced imaging, and microfluidics. The morphology features represent both Deep Learning (DL)-derived features and human-interpretable morphometric features, such as size and shape. Unique morphotypes were observed differentiating each combination of parent and resistant cell lines, with notable changes in granularity distinguishing them. A subset of images was used to train a random forest classifier to predict the resistant state of each cell image, which performed with up to 85% accuracy on independent cell images. Strikingly, the combination of DL plus morphometric features outperformed the use of morphometric features alone, demonstrating the increased utility of combined analysis. The top gene pathways and top morphological features were examined to infer potential mechanisms underlying chemoresistance. This work demonstrates that morphology alone can be used to distinguish drug resistant vs. parent populations without the use of markers. Morphology analysis can be applied to understanding complex phenotypes, and future platform improvements will enable sorting of these resistant populations to better identify molecular pathways in both cell lines and in primary tumor samples. Citation Format: Andreja Jovic, Manisha Ray, Ryan Carelli, Kiran Saini, Tiffine Pham, Christian Corona, Stephane C. Boutet, Chassidy Johnson, Mahyar Salek, Maddison Masaeli, Matt Barnes, Cyril Y. Ramathal. Morphological detection of chemotherapy resistance in cancer cell lines using AI-based analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4877.