Molecular Mechanisms Of Drug Resistance Research Articles

Combating antimicrobial resistance in malaria, HIV and tuberculosis.

Antimicrobial resistance poses a significant threat to the sustainability of effective treatments against the three most prevalent infectious diseases: malaria, human immunodeficiency virus (HIV) infection and tuberculosis. Therefore, there is an urgent need to develop novel drugs and treatment protocols capable of reducing the emergence of resistance and combating it when it does occur. In this Review, we present an overview of the status and underlying molecular mechanisms of drug resistance in these three diseases. We also discuss current strategies to address resistance during the research and development of next-generation therapies. These strategies vary depending on the infectious agent and the array of resistance mechanisms involved. Furthermore, we explore the potential for cross-fertilization of knowledge and technology among these diseases to create innovative approaches for minimizing drug resistance and advancing the discovery and development of new anti-infective treatments. In conclusion, we advocate for the implementation of well-defined strategies to effectively mitigate and manage resistance in all interventions against infectious diseases.

How do Mutations of Mycobacterium Genes Cause Drug Resistance in Tuberculosis?

A steady increase in the prevalence of drug-resistant tuberculosis (DR-TB) has already been reported in Pakistan. In addition, DR-TB is gradually changing from one-drug resistance to multi-drug resistance, which is a serious challenge for tuberculosis treatment. This review provides an overview of the anti-tuberculosis drugs and focuses on the molecular mechanisms of drug resistance in Mycobacterium tuberculosis, with the hope that it will contribute to the study of drug resistance in response to the emergence of multidrug-resistant tuberculosis.

The molecular mechanisms of drug resistance of glioblastoma: differentiation and apoptosis

Glioblastomas (GBM) are among the most malignant and frequent human tumors, characterized by rapid growth, metastasis, resistance to therapy and formation of relapses. The appearance of multidrug resistances (MDR) in GBM cells are often combined with inhibition of cell death and differentiation pathways and prevents an increase in the effectiveness of therapy in this group of patients. The review examines the relationship of molecular mechanisms of MDR with differentiation and apoptosis of GBM with an emphasis on identifying new targets among proteins, microRNAs, suppressor genes, and oncogenes.

The role of circRNAs in regulation of drug resistance in ovarian cancer.

Ovarian cancer is one of the female reproductive system tumors. Chemotherapy is used for advanced ovarian cancer patients; however, drug resistance is a pivotal cause of chemotherapeutic failure. Hence, it is critical to explore the molecular mechanisms of drug resistance of ovarian cancer cells and to ameliorate chemoresistance. Noncoding RNAs (ncRNAs) have been identified to critically participate in drug sensitivity in a variety of human cancers, including ovarian cancer. Among ncRNAs, circRNAs sponge miRNAs and prevent miRNAs from regulation of their target mRNAs. CircRNAs can interact with DNA or proteins to modulate gene expression. In this review, we briefly describe the biological functions of circRNAs in the development and progression of ovarian cancer. Moreover, we discuss the underneath regulatory molecular mechanisms of circRNAs on governing drug resistance in ovarian cancer. Furthermore, we mention the novel strategies to overcome drug resistance via targeting circRNAs in ovarian cancer. Due to that circRNAs play a key role in modulation of drug resistance in ovarian cancer, targeting circRNAs could be a novel approach for attenuation of chemoresistance in ovarian cancer.

The molecular mechanisms of drug resistance of glioblastoma. Part 3. Differentiation and apoptosis of glioblastoma cells

Glioblastomas are one of the most malignant and frequent human tumors, characterized by rapid growth, metastasis, resistance to therapy and the formation of relapses. The formation of multidrug resistance mechanisms in glioblastomas cells is often combined with inhibition of cell death and differentiation pathways and prevents an increase in the effectiveness of therapy in this group of patients. The review examines the relationship of molecular mechanisms of multidrug resistance with differentiation and apoptosis of glioblastomas with an emphasis on identifying new targets among proteins, microRNAs, suppressor genes, and oncogenes.

Translational mRNA Profiling Analysis of Pseudopalisading Cells in Bevacizumab Resistance of GBM

AbstractGlioblastoma (GBM) is a malignant brain tumor with a poor prognosis that easily recurs. The antiangiogenic agent bevacizumab is used to treat recurrent GBM. However, GBM treated with bevacizumab easily rebounds due to evasive mechanisms that induce resistance to treatment, such as hypoxia‐inducible factor (HIF) associated pathways. The transcription factor HIFs are oxygen‐dependent and are degraded via the ubiquitin‐dependent proteasomal pathway. Therefore, it is necessary to study bevacizumab resistance with HIF‐associated pathways through translational mRNA profiling. This work applies a hypoxia response element (HRE) promoter to the ribosome affinity purification (TRAP) system for hypoxia‐specific translational mRNA profiling analysis. Here, this work analyzes the translatome of pseudopalisading cells in the brain samples of orthotopic mouse models using hypoxia‐responsive 5× HRE‐TRAP system to investigate the molecular mechanism of drug resistance on pseudopalisading cells around the necrotic area induced by bevacizumab resistance. The translatomic analysis result shows that pseudopalisading cells exhibit notable enrichment of gene sets associated with neurodegenerative diseases, such as Alzheimer's disease. The outcomes of this study enhance clinical relevance, meaning that the translatomic analysis result of pseudopalisading cells during bevacizumab treatment‐induced resistance provides new insight into a promising approach for developing targeted therapeutics.

Molecular mechanisms of immunotherapy resistance in triple-negative breast cancer.

The emergence of immunotherapy has profoundly changed the treatment model for triple-negative breast cancer (TNBC). But the heterogeneity of this disease resulted in significant differences in immunotherapy efficacy, and only some patients are able to benefit from this therapeutic modality. With the recent explosion in studies on the mechanism of cancer immunotherapy drug resistance, this article will focus on the processes of the immune response; summarize the immune evasion mechanisms in TNBC into three categories: loss of tumor-specific antigen, antigen presentation deficiency, and failure to initiate an immune response; together with the aberrant activation of a series of immune-critical signaling pathways, we will discuss how these activities jointly shape the immunosuppressive landscape within the tumor microenvironment. This review will attempt to elucidate the molecular mechanism of drug resistance in TNBC, identify potential targets that may assist in reversing drug resistance, and lay a foundation for research on identifying biomarkers for predicting immune efficacy and selection of breast cancer populations that may benefit from immunotherapy.

Forward genetic analysis of monensin and diclazuril resistance in Eimeria tenella

Worldwide distributed coccidiosis is caused by infection of both Eimeria species and Cystoisospora in the host intestine and causes huge economic losses to the livestock industry, especially the poultry industry. The control of such diseases relies mainly on chemoprophylaxis with anticoccidials, which has led to a very common drug resistance in this field. However, the genetic mechanisms underlying resistance to many anticoccidial drugs remain unknown. In this study, strains of E. tenella resistant to 250 mg/kg monensin were generated and characterized. Forward genetic approaches based on pooled genome sequencing, including experimental evolution and linkage group selection, were used to locate candidate targets responsible for resistance to monensin and diclazuril in E. tenella. A total of 16 nonsynonymous mutants in protein-coding genes were identified in monensin-resistant strains, and two genomic regions with strong selection signals were also detected in diclazuril-resistant strains. Our study reveals the genetic characterization of the experimental evolution and linkage group selection in Eimeria species, and also provides important information that contributes to the understanding of the molecular mechanism of drug resistance in coccidia.

Molecular mechanisms of drug resistance in breast cancer and potential strategies for overcoming resistance

Breast cancer is the most common cause of death from cancer in the world, and drug resistance is one of the most significant barriers to successful therapy for the disease. It is critical to have a solid understanding of the molecular processes driving treatment resistance in breast cancer to design targeted therapies with the potential to overcome this resistance. These complex and multifaceted mechanisms include the activation of signaling pathways that promote cell survival and proliferation, the upregulation of drug efflux pumps, the emergence of cancer stem cells, and genetic and epigenetic changes. This literature review provides an overview of these mechanisms. It discusses potential strategies for overcoming drug resistance in breast cancer, including targeted therapies that specifically target the pathways and mechanisms involved in drug resistance. The review also highlights the need for further research to identify effective strategies for overcoming drug resistance and improving treatment outcomes in breast cancer patients.

Tp53 haploinsufficiency is involved in hotspot mutations and cytoskeletal remodeling in gefitinib-induced drug-resistant EGFRL858R-lung cancer mice

Tumor heterogeneity is the major factor for inducing drug resistance. p53 is the major defender to maintain genomic stability, which is a high proportion mutated in most of the cancer types. In this study, we established in vivo animal models of gefitinib-induced drug-resistant lung cancer containing EGFRL858R and EGFRL858R*Tp53+/− mice to explore the molecular mechanisms of drug resistance by studying the genomic integrity and global gene expression. The cellular morphology of the lung tumors between gefitinib-induced drug-resistant mice and drug-sensitive mice were very different. In addition, in drug-resistant mice, the expression of many cytoskeleton-related genes were changed, accompanied by decreased amounts of actin filaments and increased amounts of microtubule, indicating that significant cytoskeletal remodeling is induced in gefitinib-induced drug-resistant EGFRL858R and EGFRL858R*Tp53+/− lung cancer mice. The gene expression profiles and involved pathways were different in gefitinib-sensitive, gefitinib-resistant and Tp53+/−-mice. Increases in drug resistance and nuclear size (N/C ratio) were found in EGFRL858R*Tp53+/− drug-resistant mice. Mutational hotspot regions for drug resistance via Tp53+/+- and Tp53+/−-mediated pathways are located on chromosome 1 and chromosome 11, respectively, and are related to prognosis of lung cancer cohorts. This study not only builds up a gefitinib-induced drug-resistant EGFRL858R lung cancer animal model, but also provides a novel mutation profile in a Tp53+/+- or Tp53+/−-mediated manner and induced cytoskeleton remodeling during drug resistance, which could contribute to the prevention of drug resistance during cancer therapy.

Abstract P5-02-47: Quantitative proteomic analysis of plasma exosomes from patients with advanced hormone receptor-positive/HER2-negative breast cancer receiving palbociclib and tamoxifen

Abstract Background: A CDK4/6 inhibitor (CDK4/6i) in combination with endocrine therapy (ET) is standard first-line therapy for advanced, hormone receptor (HR)-positive, HER2-negative breast cancer (BC). However, not all patients respond and responders eventually develop drug resistance and disease progression. Exosomes are small extracellular vesicles that are secreted by both normal and tumor cells as a mechanism for intercellular communication. The protein cargo of exosomes reflects biological processes activated in cancer cells and may serve as predictive biomarkers to select patients most likely to benefit from treatment and to identify mechanisms of resistance. Methods: Whole blood was collected in Streck tubes at baseline and at time points during treatment from patients with advanced, HR+/HER2- BC enrolled in a single arm, phase 2 trial of first line therapy with palbociclib plus tamoxifen that was conducted by The Big Ten Cancer Research Consortium (NCT02668666). Plasma was separated and stored at -80C within 48 hours of collection. Different exosome protein isolation methods were evaluated and optimized to maximize protein recovery. Exosome and plasma proteins were extracted, purified, and digested with trypsin. Tryptic peptides were isotopically labeled with Tandem Mass Tag (TMT) 10plex for protein expression level quantitation. Triplicate samples from each patient were analyzed by LC-MS/MS with QExactive HF Orbitrap mass spectrometer. An unsupervised clustering method was used to classify patients based on exosomal proteomic profiles. Results: We developed a sensitive and efficient exosome extraction method to obtain exosome protein from minimal volumes of patient plasma. The optimized exosome isolation method quantitatively identified 800 proteins from a 100 µl plasma sample. Significant enrichment of exosome-specific markers was observed when comparing patient samples with healthy donor samples. A network model was developed to differentiate responders/stable disease patients from non-responders using exosome proteomics data generated from pretreatment plasma samples. Preliminary data from the first 22 patients analyzed (responders, n= 6; stable disease, n=12, and non-responder, n=4) identified a network of 45 proteins that predicted response/stable disease vs progressive disease with high specificity (95%) and sensitivity (89%). We also noted significant differences in the exosome proteomic profiles of patients with de novo vs. recurrent metastatic disease. A network of 22 proteins differentiated de novo vs recurrent metastatic disease with > 85% sensitivity and 78% specificity, providing molecular evidence differentiating the two disease states. This finding is relevant in light of the higher response rate and improved PFS in patients with de novo metastatic disease in this trial, and confirms that this approach may provide molecular insight into mechanisms of primary resistance to CDK4/6i. Results for the entire trial cohort of 46 patients will be presented, along with analysis of serial samples collected at various time points during treatment. Conclusion: This proof-of-concept study demonstrates that an ultrasensitive exosome proteomics platform combined with deep learning methods is ideally suited for developing predictive protein biomarkers and for exploring molecular mechanisms of drug resistance. If results are confirmed, this novel approach holds great promise for identifying protein biomarkers that could be used to select patients unlikely to respond to ET and CDK4/6i in order to spare them ineffective treatment and for selecting participants for clinical trials of novel agents. Additionally, exosome proteomics data generated from serially collected specimens can be used to identify mechanisms of resistance that emerge during therapy. This approach can be widely applied to other treatment regimens and disease sites. This study was funded by Pfizer. Citation Format: Ziwei Zhang, Xiuyuan Ma, Julia Ekiert, Gayatry Mohapatra, Louis Coleman, Cristina I. Truica, Anne Blaes, Jatin Rana, Tandra Pavankumar, Lauren Green, Menggang Yu, Deborah Toppmeyer, Ruth O’Regan, Kari B. Wisinski, Oana C. Danciu, Kent Hoskins, Yu Gao. Quantitative proteomic analysis of plasma exosomes from patients with advanced hormone receptor-positive/HER2-negative breast cancer receiving palbociclib and tamoxifen [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-02-47.

Establishment of A Novel Paclitaxel-Resistant Triple-Negative Breast Cancer Cell Line

Objective: Triple-negative breast cancer (TNBC) is one of the most aggressive subtypes of breast cancer, and is associated with poor prognosis. Paclitaxel, a microtubule-binding agent, and chemotherapeutic agent, has been widely used in the management of TNBC. However, acquired chemoresistance is one of the main obstacles leading to ineffective TNBC treatment. Therefore, this study aimed to establish and characterize paclitaxel-resistant triple-negative breast cancer cell lines for investigating the molecular mechanisms of drug resistance. Material and Methods: Hs578T cancer cell lines were used to develop paclitaxel-resistant (Hs578T-PR) cells, via repeated exposure to increasing concentrations of paclitaxel in a stepwise manner. Drug response and growth curves were then measured by Sulforhodamine B assay. Changes in cell morphology were examined by microscopy. Furthermore, expression of mRNA, related to molecular mechanisms in drug-resistant cells, was identified by using real-time polymerase chain reaction (qPCR). Results: The Hs578T-PR cell lines were successfully established in just 4 months. They were highly resistant to paclitaxel, with their IC50 and resistance index at 72.8±3.08 nM and 7.4-folds, respectively, compared to the parental cells. For identifying molecular mechanisms underlining paclitaxel resistance, using the RT-qPCR analysis, it was found that Hs578T-PR cells exhibited kinesin family member 3C overexpression. Furthermore, the pro-apoptotic protein BAX was down-regulated; whereas the anti-apoptotic Bcl-2 was up-regulated in Hs578T-PR cells. Conclusion: Novel, highly paclitaxel-resistant (Hs578T-PR) cell lines established in this study could represent a useful model for identifying the molecular mechanisms of chemoresistance, and for evaluating the efficacy of novel anti-cancer drugs to overcome chemoresistance in TNBC.­­

In Silico Study of the Acquired Resistance Caused by the Secondary Mutations of KRAS G12C Protein Using Long Time Molecular Dynamics Simulation and Markov State Model Analysis.

Kirsten rat sarcoma viral oncogene homolog (KRAS) is a small GTPase protein which plays an important role in the treatment of KRAS mutant cancers. The FDA-approved AMG510 and MRTX849 (phase III clinical trials) are two potent KRASG12C-selective inhibitors that target KRAS G12C. However, the drug resistance caused by the second-site mutation in KRAS has emerged, and the mechanisms of drug resistance at atom level are still unclear. To clarify the mechanisms of drug resistance, we conducted long time molecular dynamics simulations (75 μs in total) to study the structural and energetic features of KRAS G12C and its four drug resistant variants to inhibitors. The combined binding free energy calculation and protein-ligand interaction fingerprint revealed that these second-site mutations indeed caused KRAS to produce different degrees of resistance to AMG510 and MRTX849. Furthermore, Markov State Models and 2D-free energy landscapes analysis revealed the difference in conformational changes of mutated KRAS bound with and without inhibitors. Furthermore, the comparative analysis of these systems showed that there were differences in their allosteric signal pathways. These findings provide the molecular mechanism of drug resistance, which helps to guide novel KRAS G12C inhibitor design to overcome drug resistance.

Analysis of molecular mechanisms of drug resistance of Mycobacterium tuberculosis in patients with pulmonary tuberculosis and its pharmacoeconomics

Purpose: To investigate the molecular mechanisms of drug resistance of Mycobacterium tuberculosis in patients with pulmonary tuberculosis and its pharmacoeconomics. 
 Methods: Data pertaining to patients with primary tuberculosis treated in the First Affiliated Hospital of Zhaoqing Medical College, Zhaoqing, China from January 2020 to June 2021 were retrospectively analyzed. Sputum specimens were collected from all eligible patients, and 151 uncontaminated specimens with good bacteriophage activity were screened. 
 Results: A total of 107 Mycobacterium tuberculosis strains were isolated from the 151 specimens, 31 of which strains were resistant to varying degrees to rifampicin, isoniazid, streptomycin, and ethambutol with an overall resistance of 28.97 %. There were 16 strains with rpoB mutation, 22 strains with katG mutation, and 8 strains with inhA mutation. The difference in the sputum negative rate, lesion absorption rate, and tuberculosis cavity closure rate, and total medical cost between the two group were not statistically significant (p > 0.05). The incidence of adverse reactions in the FDC group was significantly lower than that in the blister pack group (p < 0.05). 
 Conclusion: The total resistance of Mycobacterium tuberculosis in primary tuberculosis patients remains at a high level, and the development of resistance is associated with mutations in rpoB, katG, and inhA genes. FDC regimen provides more pharmacoeconomic and therapeutic benefits than blister pack regimen.

Exosome-Mediated Transfer of miR-3613-5p Enhances Doxorubicin Resistance by Suppression of PTEN Expression in Breast Cancer Cells.

Breast cancer is the most common malignancy among women worldwide, and patients easily develop resistance to the first-line drug doxorubicin. To elucidate the molecular mechanism of drug resistance in breast cancer is imperative. Exosomes mediate the crosstalk between neighboring cells and intercellular communication. Incorporation of miRNAs into exosomes prevents the degradation and facilitates the intercellular communication, which has been indicated in regulation of drug resistance. qRT-PCR revealed that miR-3613-5p is upregulated in drug-resistant breast cancer, and miR-3613-5p exists in exosomes. It is predicted that miR-3613-5p can bind to the tumor suppressor gene PTEN. In this study, our results showed that miR-3613-5p was upregulated in drug-resistant tissue and in exosomes of breast cancer cells resistant to doxorubicin. CCK8, crystal violet staining, and flow cytometry analysis demonstrated that exosome mediated miR-3613-5p transfer and enhanced the resistance to doxorubicin of breast cancer cells. Western blotting showed that miR-3613-5p could target PTEN and regulate the expression of PTEN. Exosome-mediated transfer of miR-3613-5p enhanced the resistance to doxorubicin by inhibition of PTEN in breast cancer cells.

CURRENT APPROACHES TO CONTROL OF ISONIAZID-RESISTANT TUBERCULOSIS

Isoniazid (H; INH) is an important first-line drug for the treatment of active tuberculosis (TB) and latent TB infection because of its potent early bactericidal activity against Мycobacterium tuberculosis. Currently, TB resistant to INH, alone or in combination with other drugs, is the most common type of drug-resistant TB. Epidemiology of INH-resistant TB, the molecular mechanisms of drug resistance, current methods for diagnosis and therapeutic regimens of this TB form are presented. Studies in the last years have shown that resistance to INH reduces the probability of treatment success and increases the risk of acquiring resistance to other impor­tant first-line drugs. Based on the most recent meta-analyses, the last WHO recommendations for treatment of INH-resistant TB are to include rifampicin (RIF), ethambutol, pyrazinamide and levofloxacin for 6 months, and not to add streptomycin or other injectable agents to the drug regimen. The guideline emphasizes the importance of excluding resistance to RIF before starting the regimen for INH-resistant TB because of the risk for development of multidrug-resistant TB during the treatment course. The WHO recommendations are based on observational studies, not randomized controlled trials, and are thus conditional and based on low certainty in the estimates of effect. There­fore, further work is needed to optimize the treatment and control of INH-resistant TB.

Molecular mechanisms of drug resistance of glial tumor of brain. Part 2: Proliferation, angiogenesis, metastasis and recurrency

The main reason for the low efficiency of glioblastoma therapy is its resistance to therapeutic procedures. The development of multidrug resistance occurs as a result of the selection of tumor clones during therapy. The resistant cell clones to radiotherapy and chemotherapy can proliferate, leading to tumor growth, in which its own vascular network is formed (angiogenesis), which promotes cell migration, invasion and the appearance of metastases and recurrent glioblastoma. The review examines the relationship at the molecular level of multidrug resistance with proliferation, angiogenesis, migration, metastasis, and the formation of glioblastoma relapses, with an emphasis on identifying new targets among proteins, microRNAs, signal transduction kinases, transcription factors, tumor-supressor genes and oncogenes.

Cryo-EM structures of wild-type and E138K/M184I mutant HIV-1 RT/DNA complexed with inhibitors doravirine and rilpivirine

Structures trapping a variety of functional and conformational states of HIV-1 reverse transcriptase (RT) have been determined by X-ray crystallography. These structures have played important roles in explaining the mechanisms of catalysis, inhibition, and drug resistance and in driving drug design. However, structures of several desired complexes of RT could not be obtained even after many crystallization or crystal soaking experiments. The ternary complexes of doravirine and rilpivirine with RT/DNA are such examples. Structural study of HIV-1 RT by single-particle cryo-electron microscopy (cryo-EM) has been challenging due to the enzyme's relatively smaller size and higher flexibility. We optimized a protocol for rapid structure determination of RT complexes by cryo-EM and determined six structures of wild-type and E138K/M184I mutant RT/DNA in complexes with the nonnucleoside inhibitors rilpivirine, doravirine, and nevirapine. RT/DNA/rilpivirine and RT/DNA/doravirine complexes have structural differences between them and differ from the typical conformation of nonnucleoside RT inhibitor (NNRTI)-bound RT/double-stranded DNA (dsDNA), RT/RNA-DNA, and RT/dsRNA complexes; the primer grip in RT/DNA/doravirine and the YMDD motif in RT/DNA/rilpivirine have large shifts. The DNA primer 3'-end in the doravirine-bound structure is positioned at the active site, but the complex is in a nonproductive state. In the mutant RT/DNA/rilpivirine structure, I184 is stacked with the DNA such that their relative positioning can influence rilpivirine in the pocket. Simultaneously, E138K mutation opens the NNRTI-binding pocket entrance, potentially contributing to a faster rate of rilpivirine dissociation by E138K/M184I mutant RT, as reported by an earlier kinetic study. These structural differences have implications for understanding molecular mechanisms of drug resistance and for drug design.

Resistance and tolerance of Mycobacterium tuberculosis to antimicrobial agents-How M. tuberculosis can escape antibiotics.

Tuberculosis (TB) poses a serious threat to public health worldwide since it was discovered. Until now, TB has been one of the top 10 causes of death from a single infectious disease globally. The treatment of active TB cases majorly relies on various anti-tuberculosis drugs. However, under the selection pressure by drugs, the continuous evolution of Mycobacterium tuberculosis (Mtb) facilitates the emergence of drug-resistant strains, further resulting in the accumulation of tubercle bacilli with multiple drug resistance, especially deadly multidrug-resistant TB and extensively drug-resistant TB. Researches on the mechanism of drug action and drug resistance of Mtb provide a new scheme for clinical management of TB patients, and prevention of drug resistance. In this review, we summarized the molecular mechanisms of drug resistance of existing anti-TB drugs to better understand the evolution of drug resistance of Mtb, which will provide more effective strategies against drug-resistant TB, and accelerate the achievement of the EndTB Strategy by 2035. This article is categorized under: Infectious Diseases > Molecular and Cellular Physiology.

Analysis of the lncRNA–miRNA–mRNA Network Reveals a Potential Regulatory Mechanism of EGFR-TKI Resistance in NSCLC

Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) are widely used for patients with EGFR-mutated lung cancer. Despite its initial therapeutic efficacy, most patients eventually develop drug resistance, which leads to a poor prognosis in lung cancer patients. Previous investigations have proved that non-coding RNAs including long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs) contribute to drug resistance by various biological functions, whereas how they regulate EGFR-TKI resistance remains unclear. In this study, we examined gene expression using the microarray technology on gefitinib-resistant NSCLC cells to obtain differentially expressed (DE) lncRNAs and mRNAs. A total of 45 DE-lncRNAs associated with overall survival and 1799 target DE-mRNAs were employed to construct a core lncRNA–miRNA–mRNA network to illustrate underlying molecular mechanisms of how EGFR-TKI resistance occurs in NSCLC. We found that target DE-mRNAs were mainly enriched in pathways involved in EGFR-TKI resistance, especially the target DE-mRNAs regulated by LINC01128 were significantly enriched in the PI3K/Akt signaling pathway, where the synergy of these target DE-mRNAs may play a key role in EGFR-TKI resistance. In addition, downregulated LINC01128, acting as a specific miRNA sponge, decreases PTEN via sponging miR-25-3p. Furthermore, signaling reactions caused by the downregulation of PTEN would activate the PI3K/Akt signaling pathway, which may lead to EGFR-TKI resistance. In addition, a survival analysis indicated the low expression of LINC01128, and PTEN is closely related to poor prognosis in lung adenocarcinoma (LUAD). Therefore, the LINC01128/miR-25-3p/PTEN axis may promote EGFR-TKI resistance via the PI3K/Akt signaling pathway, which provides new insights into the underlying molecular mechanisms of drug resistance to EGFR-TKIs in NSCLC. In addition, our study sheds light on developing novel therapeutic approaches to overcome EGFR-TKI resistance in NSCLC.