Understanding Of Drug Resistance Research Articles

Drug resistance in breast cancer is based on the mechanism of exocrine non-coding RNA.

Breast cancer (BC) ranks first among female malignant tumors and involves hormonal changes and genetic as well as environmental risk factors. In recent years, with the improvement of medical treatment, a variety of therapeutic approaches for breast cancer have emerged and have strengthened to accommodate molecular diversity. However, the primary way to improve the effective treatment of breast cancer patients is to overcome treatment resistance. Recent studies have provided insights into the mechanisms of resistance to exosome effects in BC. Exosomes are membrane-bound vesicles secreted by both healthy and malignant cells that facilitate intercellular communication. Specifically, exosomes released by tumor cells transport their contents to recipient cells, altering their properties and promoting oncogenic components, ultimately resulting in drug resistance. As important coordinators, non-coding RNAs (ncRNAs) are involved in this process and are aberrantly expressed in various human cancers. Exosome-derived ncRNAs, including microRNAs (miRNAs), long-noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), have emerged as crucial components in understanding drug resistance in breast cancer. This review provides insights into the mechanism of exosome-derived ncRNAs in breast cancer drug resistance, thereby suggesting new strategies for the treatment of BC.

Marine Microorganisms as Potential Source of Quorum-Sensing Inhibitory Compounds

Antibiotics are extensively utilized globally, and the rate of antibiotic resistance is increasing more rapidly than ever. Since the introduction of antibiotics, the overuse of antibiotics caused selection pressure, and almost all pathogenic bacteria have developed resistance against commonly used antibiotics, which is particularly known as antimicrobial resistance (AMR). It has proven challenging to combat and resolve the issue of microbial resistance. A growing number of microorganisms have developed different resistance mechanisms and turned into "superbugs". The identification of quorum-sensing systems has given researchers a new hope for understanding drug resistance processes. The quorum-sensing system controls a number of cellular functions, including the expression of pathogenic genes, the synthesis of toxins, and the synthesis of extracellular polysaccharides. To targeting QS systems marine bacterial samples were collected by different coastal sites of Gujarat, like Mandvi, Dwarka and Diu. A total of 52 marine isolates were obtained, out of which 16 were associated with various marine macro-organisms like sponges and algae, whereas 36 were free-living. The study has done by screening those marine isolates shown potential to inhibiting the quorum sensing molecule by co culture study against Chromobacter violaceium, followed by growth inhibition assay. The G14 and G82 isolate shows highest degradation of N-acyl homoserine lactone by AHL study. The QSI compounds were extracted using ethyl acetate extraction method. Biofilm inhibition assay with Pseudomonas aeruginosa shows potent inhibitory effect of extract. These results prove that marine microorganism have potential to inhibits quorum sensing and virulence factors regulated by Quorum Sensing phenomenon.

Establishing conditions for the generation and maintenance of estrogen receptor-positive organoid models of breast cancer

Patient-derived organoid models of estrogen receptor-positive (ER+) breast cancer would provide a much-needed tool to understand drug resistance and disease progression better. However, the establishment and long-term maintenance of ER expression, function, and response in vitro remains a significant challenge. Here, we report the development of an ER+ breast tumor organoid medium (BTOM-ER) that conserves ER expression, estrogen responsiveness, and dependence, as well as sensitivity to endocrine therapy of ER+ patient-derived xenograft organoids (PDXO). Our findings demonstrate the utility of subtype-specific culture conditions that better mimic the characteristics of the breast epithelial biology and microenvironment, providing a powerful platform for investigating therapy response and disease progression of ER+ breast cancer.

Abstract 535: Resistant PDO models: Unraveling drug resistance mechanisms for discovering new drug targets

Abstract Resistance to cancer treatment remains a significant obstacle in curing patients with cancer. Despite recent advancements in novel drug targets for cancer therapeutics, patients often develop treatment resistance even after initial disease remission, leading to tumor relapse. To investigate the mechanisms responsible for developing resistance to standard-of-care therapies, it is essential to gain insights into the stepwise progression leading to complete resistance. Recent research has revealed that cancer cells can evade the effects of chemotherapy and targeted therapy by entering a reversible and slow proliferation state known as the drug-tolerant persister (DTP) state. This DTP state allows cancer cells to survive drug therapy long enough for additional mechanisms of acquired drug resistance to develop. HUB Organoids® or patient-derived organoid (PDO) models are derived from patient tissues, making them more physiologically relevant than traditional cell lines. Thus, studying drug persistence and resistance in PDO models is more likely to reflect in vivo conditions. This study demonstrates the successful development of persistent and resistant CRC PDO models to standard-of-care therapies. All models were characterized using whole exome sequencing and RNA sequencing to confirm their persistent or resistant state and to identify possible pathways involved in developing therapy resistance, as well as potential new drug targets. In conclusion, developing persistent and resistant PDO models is crucial for understanding drug resistance mechanisms, enabling the development of more effective and personalized cancer treatments, and advancing our overall knowledge of how resistance develops in cancer patients. Citation Format: Yasmine Abouleila, Mayke Doorn, Roel Verkerk, Joris Maas, Carla Verissimo, Sylvia Boj. Resistant PDO models: Unraveling drug resistance mechanisms for discovering new drug targets [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 535.

Role and potential therapeutic value of histone methyltransferases in drug resistance mechanisms in lung cancer.

Lung cancer, ranking second globally in both incidence and high mortality among common malignant tumors, presents a significant challenge with frequent occurrences of drug resistance despite the continuous emergence of novel therapeutic agents. This exacerbates disease progression, tumor recurrence, and ultimately leads to poor prognosis. Beyond acquired resistance due to genetic mutations, mounting evidence suggests a critical role of epigenetic mechanisms in this process. Numerous studies have indicated abnormal expression of Histone Methyltransferases (HMTs) in lung cancer, with the abnormal activation of certain HMTs closely linked to drug resistance. HMTs mediate drug tolerance in lung cancer through pathways involving alterations in cellular metabolism, upregulation of cancer stem cell-related genes, promotion of epithelial-mesenchymal transition, and enhanced migratory capabilities. The use of HMT inhibitors also opens new avenues for lung cancer treatment, and targeting HMTs may contribute to reversing drug resistance. This comprehensive review delves into the pivotal roles and molecular mechanisms of HMTs in drug resistance in lung cancer, offering a fresh perspective on therapeutic strategies. By thoroughly examining treatment approaches, it provides new insights into understanding drug resistance in lung cancer, supporting personalized treatment, fostering drug development, and propelling lung cancer therapy into novel territories.

Malaria’s molecular dance: Mechanism, therapies, and emerging insights

Malaria, caused by Plasmodium parasites and transmitted through Anopheles mosquitoes, remains a formidable global health challenge. This abstract provides an overview of the intricate molecular mechanisms underlying malaria pathogenesis, explores current therapeutic approaches, and highlights emerging insights that may shape future strategies for malaria control. The intricate dance between Plasmodium parasites and their human hosts begins with the mosquito’s bite, leading to the invasion of erythrocytes by Plasmodium species. We delve into the molecular mechanisms governing parasite entry and subsequent replication within host cells, shedding light on key factors such as erythrocyte surface receptors and parasite-encoded proteins critical to invasion and survival. While malaria treatment has relied heavily on antimalarial drugs, the emergence of drug resistance necessitates ongoing exploration of novel therapeutic strategies. This abstract reviews current antimalarial drug classes, their mechanisms of action, and the challenges posed by drug resistance. We also highlight promising drug candidates and innovative approaches in the pipeline, including the use of advanced molecular techniques and immunotherapies. Emerging insights from genomics, proteomics, and transcriptomics have deepened our understanding of Plasmodium biology and host-parasite interactions. We discuss the potential of these omics approaches in identifying new drug targets, understanding drug resistance mechanisms, and developing vaccines. Additionally, we examine the role of human genetics in influencing susceptibility to malaria and response to treatment. Vector control remains a critical component of malaria prevention. We touch upon emerging strategies, such as genetically modified mosquitoes and novel insecticides, in the context of integrated vector management programs. Finally, we emphasize the importance of a multifaceted approach to malaria control, combining advances in molecular biology, drug development, vector control, and public health interventions.

Metabolic Rewiring of Mycobacterium tuberculosis upon Drug Treatment and Antibiotics Resistance.

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a significant global health challenge, further compounded by the issue of antimicrobial resistance (AMR). AMR is a result of several system-level molecular rearrangements enabling bacteria to evolve with better survival capacities: metabolic rewiring is one of them. In this review, we present a detailed analysis of the metabolic rewiring of Mtb in response to anti-TB drugs and elucidate the dynamic mechanisms of bacterial metabolism contributing to drug efficacy and resistance. We have discussed the current state of AMR, its role in the prevalence of the disease, and the limitations of current anti-TB drug regimens. Further, the concept of metabolic rewiring is defined, underscoring its relevance in understanding drug resistance and the biotransformation of drugs by Mtb. The review proceeds to discuss the metabolic adaptations of Mtb to drug treatment, and the pleiotropic effects of anti-TB drugs on Mtb metabolism. Next, the association between metabolic changes and antimycobacterial resistance, including intrinsic and acquired drug resistance, is discussed. The review concludes by summarizing the challenges of anti-TB treatment from a metabolic viewpoint, justifying the need for this discussion in the context of novel drug discovery, repositioning, and repurposing to control AMR in TB.

Interconversion of Cancer Cells and Induced Pluripotent Stem Cells.

Cancer cells, especially cancer stem cells (CSCs), share many molecular features with induced pluripotent stem cells (iPSCs) that enable the derivation of induced pluripotent cancer cells by reprogramming malignant cells. Conversely, normal iPSCs can be converted into cancer stem-like cells with the help of tumor microenvironment components and genetic manipulation. These CSC models can be utilized in oncogenic initiation and progression studies, understanding drug resistance, and developing novel therapeutic strategies. This review summarizes the role of pluripotency factors in the stemness, tumorigenicity, and therapeutic resistance of cancer cells. Different methods to obtain iPSC-derived CSC models are described with an emphasis on exposure-based approaches. Culture in cancer cell-conditioned media or cocultures with cancer cells can convert normal iPSCs into cancer stem-like cells, aiding the examination of processes of oncogenesis. We further explored the potential of reprogramming cancer cells into cancer-iPSCs for mechanistic studies and cancer dependencies. The contributions of genetic, epigenetic, and tumor microenvironment factors can be evaluated using these models. Overall, integrating iPSC technology into cancer stem cell research holds significant promise for advancing our knowledge of cancer biology and accelerating the development of innovative and tailored therapeutic interventions.

Mechanical effects modulate drug resistance in MCF-7-derived organoids: Insights into the wnt/β-catenin pathway

Addressing drug resistance poses a significant challenge in cancer treatment, as cancer cells develop diverse mechanisms to evade chemotherapy drugs, leading to treatment failure and disease relapse. Three-dimensional (3D) cell culture has emerged as a valuable model for studying drug resistance, although the underlying mechanisms remain elusive. By obtaining a better understanding of drug resistance within the 3D culture environment, we can develop more effective strategies to overcome it and improve the success of cancer treatments. Notably, the physical structure undergoes notable changes in 3D culture, with mechanical effects believed to play a pivotal role in drug resistance. Hence, our study aimed to explore the influence of mechanical effects on drug resistance by analyzing data related to "drug resistance" and "mechanobiology". Through this analysis, we identified β-catenin and JNK1 as potential factors, which were further examined in MCF-7 cells cultivated under both 2D and 3D culture conditions. Our findings demonstrate that β-catenin is activated through canonical and non-canonical pathways and associated with the drug resistance, particularly in organoids obtained under 3D culture.

Distribution characteristics of the Legionella CRISPR-Cas system and its regulatory mechanism underpinning phenotypic function.

Legionella is a common intracellular parasitic bacterium that infects humans via the respiratory tract, causing Legionnaires' disease, with fever and pneumonia as the main symptoms. The emergence of highly virulent and azithromycin-resistant Legionella pneumophila is a major challenge in clinical anti-infective therapy. The CRISPR-Cas acquired immune system provides immune defense against foreign nucleic acids and regulates strain biological functions. However, the distribution of the CRISPR-Cas system in Legionella and how it regulates gene expression in L. pneumophila remain unclear. Herein, we assessed 915 Legionella whole-genome sequences to determine the distribution characteristics of the CRISPR-Cas system and constructed gene deletion mutants to explore the regulation of the system based on growth ability in vitro, antibiotic sensitivity, and intracellular proliferation of L. pneumophila. The CRISPR-Cas system in Legionella was predominantly Type II-B and was mainly concentrated in the genome of L. pneumophila ST1 strains. The Type II-B CRISPR-Cas system showed no effect on the strain's growth ability in vitro but significantly reduced resistance to azithromycin and decreased proliferation ability due to regulation of the lpeAB efflux pump and the Dot/Icm type IV secretion system. Thus, the Type II-B CRISPR-Cas system plays a crucial role in regulating the virulence of L. pneumophila. This expands our understanding of drug resistance and pathogenicity in Legionella, provides a scientific basis for the prevention of Legionnaires' disease outbreaks and the rational use of clinical drugs, and facilitates effective treatment of Legionnaires' disease.

Deciphering the Pathways to PARP Sensitivity in Pancreatic Cancer.

A recent article analyzed paired cell-free DNA among patients with platinum-sensitive BRCA- or PALB2-mutated pancreatic cancer who received maintenance olaparib. Reversion mutations were linked with worse outcomes. These types of paired correlative studies are needed to improve our understanding of drug resistance and guide future clinical trials. See related article by Brown et al., p. 5207.

Drug resistance mechanism and reversal strategy in lung cancer immunotherapy.

Among all malignant tumors, lung cancer has the highest mortality and morbidity rates. The non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC) are the most common histological subtypes. Although there are a number of internationally recognized lung cancer therapy regimens, their therapeutic effects remain inadequate. The outlook for individuals with lung carcinoma has ameliorated partly thanks to the intensive study of the tumor microenvironment and immune checkpoint inhibitors. Numerous cancers have been effectively treated with immunotherapy, which has had positive therapeutic results. Global clinical trials have validated that PD-1/PD-L1 inhibitors are effective and safe for treating lung cancer either independently or in combination, and they are gradually being recommended as systemic treatment medications by numerous guidelines. However, the immunotherapy resistance restricts the immunotherapy efficacy due to the formation of tumor immunosuppressive microenvironment and tumor mutations, and immunotherapy is only effective for a small percentage of lung cancer patients. To summarize, while tumor immunotherapy is benefiting an increasing number of lung cancer patients, most of them still develop natural or acquired resistance during immunotherapy. Consequently, a crucial and urgent topic is understanding and tackling drug resistance triggered by immunotherapy in lung cancer treatment. This review will outline the presently recognized mechanisms of immunotherapy resistance and reversal strategies in lung cancer.

Unlocking the Molecular Secrets of Antifolate Drug Resistance: A Multi-Omics Investigation of the NCI-60 Cell Line Panel.

Drug resistance continues to be a significant problem in cancer therapy, leading to relapse and associated mortality. Although substantial progress has been made in understanding drug resistance, significant knowledge gaps remain concerning the molecular underpinnings that drive drug resistance and which processes are unique to certain drug classes. The NCI-60 cell line panel program has evaluated the activity of numerous anticancer agents against many common cancer cell line models and represents a highly valuable resource to study intrinsic drug resistance. Furthermore, great efforts have been undertaken to collect high-quality omics datasets to characterize these cell lines. The current study takes these two sources of data-drug response and omics profiles-and uses a multi-omics investigation to uncover molecular networks that differentiate cancer cells that are sensitive or resistant to antifolates, which is a commonly used class of anticancer drugs. Results from a combination of univariate and multivariate analyses showed numerous metabolic processes that differentiate sensitive and resistant cells, including differences in glycolysis and gluconeogenesis, arginine and proline metabolism, beta-alanine metabolism, purine metabolism, and pyrimidine metabolism. Further analysis using multivariate and integrated pathway analysis indicated purine metabolism as the major metabolic process separating cancer cells sensitive or resistant to antifolates. Additional pathways differentiating sensitive and resistant cells included autophagy-related processes (e.g., phagosome, lysosome, autophagy, mitophagy) and adhesion/cytoskeleton-related pathways (e.g., focal adhesion, regulation of actin cytoskeleton, tight junction). Volcano plot analysis and the receiver operating characteristic (ROC) curves of top selected variables differentiating Q1 and Q4 revealed the importance of genes involved in the regulation of the cytoskeleton and extracellular matrix (ECM). These results provide novel insights toward mechanisms of intrinsic antifolate resistance as it relates to interactions between nucleotide metabolism, autophagy, and the cytoskeleton. These processes should be evaluated in future studies to potentially derive novel therapeutic strategies and personalized treatment approaches to improve antifolate response.

Theoretical insights into the binding interaction of Nirmatrelvir with SARS-CoV-2 Mpro mutants (C145A and C145S): MD simulations and binding free-energy calculation to understand drug resistance

Mpro, the main protease and a crucial enzyme in SARS-CoV-2 is the most fascinating molecular target for pharmacological treatment and is also liable for viral protein maturation. For antiviral therapy, no drugs have been approved clinically to date. Targeting the Mpro with a compound having inhibitory properties against it can hinder viral replication. The therapeutic potential of the antiviral compound Nirmatrelvir (NMV) against SARS-CoV-2 Mpro was investigated using a systematic approach of molecular docking, MD simulations, and binding free energy calculation based on the MM-GBSA method. NMV, a covalent inhibitor with a recently revealed chemical structure, is a promising oral antiviral clinical candidate with significant in vitro anti-SARS-CoV-2 action in third-phase clinical trials. To explore the therapeutic ability and possible drug resistance, the Mpro system was studied for WT and two of its primary mutants (C145A & C145S). The protein-ligand (Mpro/NMV) complexes were further examined through long MD simulations to check the possible drug resistance in the mutants. To understand the binding affinity, the MM-GBSA method was applied to the Mpro/NMV complexes. Moreover, PCA analysis confirms the detachment of the linker region from the major domains in C145S and C145A mutants allowing for conformational alterations in the active-site region. Based on the predicted biological activities and binding affinities of NMV to WT and mutant (C145A & C145S) Mpro, it can be stipulated that NMV may have conventional potency to act as an anti-viral agent against WT Mpro, while the catalytic-dyad mutations may show substantial mutation-induced drug resistance. Communicated by Ramaswamy H. Sarma

Single-cell sequencing in primary intraocular tumors: understanding heterogeneity, the microenvironment, and drug resistance.

Retinoblastoma (RB) and uveal melanoma (UM) are the most common primary intraocular tumors in children and adults, respectively. Despite continued increases in the likelihood of salvaging the eyeball due to advancements in local tumor control, prognosis remains poor once metastasis has occurred. Traditional sequencing technology obtains averaged information from pooled clusters of diverse cells. In contrast, single-cell sequencing (SCS) allows for investigations of tumor biology at the resolution of the individual cell, providing insights into tumor heterogeneity, microenvironmental properties, and cellular genomic mutations. SCS is a powerful tool that can help identify new biomarkers for diagnosis and targeted therapy, which may in turn greatly improve tumor management. In this review, we focus on the application of SCS for evaluating heterogeneity, microenvironmental characteristics, and drug resistance in patients with RB and UM.

MP04-12 PHARMACOLOGICAL INHIBITION OF THE MOLECULAR CHAPERONE HSP70 OVERCOMES BELZUTIFAN RESISTANCE IN CCRCC

You have accessJournal of UrologyCME1 Apr 2023MP04-12 PHARMACOLOGICAL INHIBITION OF THE MOLECULAR CHAPERONE HSP70 OVERCOMES BELZUTIFAN RESISTANCE IN CCRCC Michael Basin, Sarah Backe, Michael Bratslavsky, Mark Woodford, Dimitra Bourboulia, Mehdi Mollapour, and Gennady Bratslavsky Michael BasinMichael Basin More articles by this author , Sarah BackeSarah Backe More articles by this author , Michael BratslavskyMichael Bratslavsky More articles by this author , Mark WoodfordMark Woodford More articles by this author , Dimitra BourbouliaDimitra Bourboulia More articles by this author , Mehdi MollapourMehdi Mollapour More articles by this author , and Gennady BratslavskyGennady Bratslavsky More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000003215.12AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Patients with von-Hippel Lindau (VHL) mutations are predisposed to developing clear cell renal cell carcinoma (ccRCC) through constitutive activation of transcription factor hypoxia-inducible factor 2a (HIF2a). The HIF2a antagonist Belzutifan has recently been FDA approved for treatment VHL disease associated tumors. Results of the recent clinical trial (MK-4682) revealed that a certain proportion of VHL patients progress on therapy. Our objective here was to decipher the molecular mechanisms of Belzutifan mediated downregulation of HIF2a and therefore provide better understanding of drug resistance. The molecular chaperone Hsp70 promotes the stability of hundreds of client proteins, thereby protecting them from degradation. Since HIF2a interacts with Hsp70, we hypothesized that Hsp70 maintains HIF2a stability in ccRCC and is a potential alternative therapeutic target in cases of Belzutifan resistance. METHODS: Cell line models of VHL-null ccRCC (786-0, A498, 769-P) were treated with 2 mM Belzutifan. HIF2a expression levels were evaluated by immunoblotting. Wild-type (WT) or Belzutifan resistant (S304M, G323E) HIF2a were transiently expressed in 786-O cells prior to treatment with Belzutifan or an Hsp70 inhibitor (JG-98). HIF2a degradation was examined by immunoblot. RESULTS: Here, we show that HIF2a is an Hsp70 client in VHL null ccRCC cell line 786-O. Further, we demonstrated a time dependent decrease in HIF2a expression with Belzutifan (2 mM) as early as 2 hours after treatment in three VHL null ccRCC cell lines 786-0, A498, and 769-P cells. Pretreatment of ccRCC cells with the proteasome inhibitor bortezomib blocked Belzutifan mediated downregulation of HIF2a, indicating Belzutifan leads to proteasomal degradation of HIF2a through a VHL independent pathway. Utilizing previously characterized Belzutifan resistant HIF2a-S304M and -G323E mutants we demonstrated that treating ccRCC cells with Hsp70 inhibitor JG-98 leads to mutant-HIF2a degradation, therefore overcoming Belzutifan resistance. CONCLUSIONS: The FDA-approved HIF2a inhibitor Belzutifan causes proteasomal degradation of WT-HIF2a, but not of resistant mutants. Our data indicates that HIF2a stability is reliant on the molecular chaperone Hsp70. Further, treatment with an Hsp70 inhibitor could potentially be used in the clinic to overcome resistance to Belzutifan in patients with VHL disease and ccRCC. Source of Funding: None © 2023 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 209Issue Supplement 4April 2023Page: e37 Advertisement Copyright & Permissions© 2023 by American Urological Association Education and Research, Inc.MetricsAuthor Information Michael Basin More articles by this author Sarah Backe More articles by this author Michael Bratslavsky More articles by this author Mark Woodford More articles by this author Dimitra Bourboulia More articles by this author Mehdi Mollapour More articles by this author Gennady Bratslavsky More articles by this author Expand All Advertisement PDF downloadLoading ...

Treatment failure shortcomings, possible causes and upcoming phyto-optimism in oral cancer

Oral cancer is a dangerous health problem and the sixth foremost cancer globally. Current oral cancer treatments include surgery, chemoradiation therapy, targeted therapy, and immunotherapy. Despite recent progress, resistance to classical chemotherapeutic drugs, radiation therapy, targeted chemo-drug/monoclonal antibodies, and even the resistance to Immuno-Checkpoint Inhibitors remain hurdles for OSCC treatment and cause disease relapses. Many therapeutic agents induce drug resistance (DR), which varies among oral cancer patients. The DR can be intrinsic or acquired; knowing the DR mechanisms is essential. The constantly evolving OSCC cells with effective energy management, though, get adapted to drug pressure but respond to many plant-based extracts and purified phytochemicals. Though DR appears to be a never-ending process, improvising plant-based phytochemical/s with different cocktail formulations, nano-based modifications, or modern technology has tremendous potential. A better understanding of DR and chemoprevention can show the path to future personalized therapy approaches.

Inferring density-dependent population dynamics mechanisms through rate disambiguation for logistic birth-death processes.

Density dependence is important in the ecology and evolution of microbial and cancer cells. Typically, we can only measure net growth rates, but the underlying density-dependent mechanisms that give rise to the observed dynamics can manifest in birth processes, death processes, or both. Therefore, we utilize the mean and variance of cell number fluctuations to separately identify birth and death rates from time series that follow stochastic birth-death processes with logistic growth. Our nonparametric method provides a novel perspective on stochastic parameter identifiability, which we validate by analyzing the accuracy in terms of the discretization bin size. We apply our method to the scenario where a homogeneous cell population goes through three stages: (1) grows naturally to its carrying capacity, (2) is treated with a drug that reduces its carrying capacity, and (3) overcomes the drug effect to restore its original carrying capacity. In each stage, we disambiguate whether the dynamics occur through the birth process, death process, or some combination of the two, which contributes to understanding drug resistance mechanisms. In the case of limited sample sizes, we provide an alternative method based on maximum likelihood and solve a constrained nonlinear optimization problem to identify the most likely density dependence parameter for a given cell number time series. Our methods can be applied to other biological systems at different scales to disambiguate density-dependent mechanisms underlying the same net growth rate.

Understanding Drug Resistance of Wild-Type and L38HL Insertion Mutant of HIV-1 C Protease to Saquinavir.

Acquired immunodeficiency syndrome (AIDS) is one of the most challenging infectious diseases to treat on a global scale. Understanding the mechanisms underlying the development of drug resistance is necessary for novel therapeutics. HIV subtype C is known to harbor mutations at critical positions of HIV aspartic protease compared to HIV subtype B, which affects the binding affinity. Recently, a novel double-insertion mutation at codon 38 (L38HL) was characterized in HIV subtype C protease, whose effects on the interaction with protease inhibitors are hitherto unknown. In this study, the potential of L38HL double-insertion in HIV subtype C protease to induce a drug resistance phenotype towards the protease inhibitor, Saquinavir (SQV), was probed using various computational techniques, such as molecular dynamics simulations, binding free energy calculations, local conformational changes and principal component analysis. The results indicate that the L38HL mutation exhibits an increase in flexibility at the hinge and flap regions with a decrease in the binding affinity of SQV in comparison with wild-type HIV protease C. Further, we observed a wide opening at the binding site in the L38HL variant due to an alteration in flap dynamics, leading to a decrease in interactions with the binding site of the mutant protease. It is supported by an altered direction of motion of flap residues in the L38HL variant compared with the wild-type. These results provide deep insights into understanding the potential drug resistance phenotype in infected individuals.

Bioinformatics toolbox for exploring target mutation-induced drug resistance.

Drug resistance is increasingly among the main issues affecting human health and threatening agriculture and food security. In particular, developing approaches to overcome target mutation-induced drug resistance has long been an essential part of biological research. During the past decade, many bioinformatics tools have been developed to explore this type of drug resistance, and they have become popular for elucidating drug resistance mechanisms in a low cost, fast and effective way. However, these resources are scattered and underutilized, and their strengths and limitations have not been systematically analyzed and compared. Here, we systematically surveyed 59 freely available bioinformatics tools for exploring target mutation-induced drug resistance. We analyzed and summarized these resources based on their functionality, data volume, data source, operating principle, performance, etc. And we concisely discussed the strengths, limitations and application examples of these tools. Specifically, we tested some predictive tools and offered some thoughts from the clinician's perspective. Hopefully, this work will provide a useful toolbox for researchers working in the biomedical, pesticide, bioinformatics and pharmaceutical engineering fields, and a good platform for non-specialists to quickly understand drug resistance prediction.