Development Of Therapeutic Resistance Research Articles

Emerging advances in defining the molecular and therapeutic landscape of small-cell lung cancer.

Small-cell lung cancer (SCLC) has traditionally been considered a recalcitrant cancer with a dismal prognosis, with only modest advances in therapeutic strategies over the past several decades. Comprehensive genomic assessments of SCLC have revealed that most of these tumours harbour deletions of the tumour-suppressor genes TP53 and RB1 but, in contrast to non-small-cell lung cancer, have failed to identify targetable alterations. The expression status of four transcription factors with key roles in SCLC pathogenesis defines distinct molecular subtypes of the disease, potentially enabling specific therapeutic approaches. Overexpression and amplification of MYC paralogues also affect the biology and therapeutic vulnerabilities of SCLC. Several other attractive targets have emerged in the past few years, including inhibitors of DNA-damage-response pathways, epigenetic modifiers, antibody-drug conjugates and chimeric antigen receptor T cells. However, the rapid development of therapeutic resistance and lack of biomarkers for effective selection of patients with SCLC are ongoing challenges. Emerging single-cell RNA sequencing data are providing insights into the plasticity and intratumoural and intertumoural heterogeneity of SCLC that might be associated with therapeutic resistance. In this Review, we provide a comprehensive overview of the latest advances in genomic and transcriptomic characterization of SCLC with a particular focus on opportunities for translation into new therapeutic approaches to improve patient outcomes.

RICTOR/mTORC2 downregulation in BRAFV600E melanoma cells promotes resistance to BRAF/MEK inhibition.

The main drawback of BRAF/MEK inhibitors (BRAF/MEKi)-based targeted therapy in the management of BRAF-mutated cutaneous metastatic melanoma (MM) is the development of therapeutic resistance. We aimed to assess in this context the role of mTORC2, a signaling complex defined by the presence of the essential RICTOR subunit, regarded as an oncogenic driver in several tumor types, including MM. After analyzing The Cancer Genome Atlas MM patients' database to explore both overall survival and molecular signatures as a function of intra-tumor RICTOR levels, we investigated the effects of RICTOR downregulation in BRAFV600E MM cell lines on their response to BRAF/MEKi. We performed proteomic screening to identify proteins modulated by changes in RICTOR expression, and Seahorse analysis to evaluate the effects of RICTOR depletion on mitochondrial respiration. The combination of BRAFi with drugs targeting proteins and processes emerged in the proteomic screening was carried out on RICTOR-deficient cells in vitro and in a xenograft setting in vivo. Low RICTOR levels in BRAF-mutated MM correlate with a worse clinical outcome. Gene Set Enrichment Analysis of low-RICTOR tumors display gene signatures suggestive of activation of the mitochondrial Electron Transport Chain (ETC) energy production. RICTOR-deficient BRAFV600E cells are intrinsically tolerant to BRAF/MEKi and anticipate the onset of resistance to BRAFi upon prolonged drug exposure. Moreover, in drug-naïve cells we observed a decline in RICTOR expression shortly after BRAFi exposure. In RICTOR-depleted cells, both mitochondrial respiration and expression of nicotinamide phosphoribosyltransferase (NAMPT) are enhanced, and their pharmacological inhibition restores sensitivity to BRAFi. Our work unveils an unforeseen tumor-suppressing role for mTORC2 in the early adaptation phase of BRAFV600E melanoma cells to targeted therapy and identifies the NAMPT-ETC axis as a potential therapeutic vulnerability of low RICTOR tumors. Importantly, our findings indicate that the evaluation of intra-tumor RICTOR levels has a prognostic value in metastatic melanoma and may help to guide therapeutic strategies in a personalized manner.

Bone marrow stromal cells induce chromatin remodeling in multiple myeloma cells leading to transcriptional changes.

The natural history of multiple myeloma is characterized by its localization to the bone marrow and its interaction with bone marrow stromal cells. The bone marrow stromal cells provide growth and survival signals, thereby promoting the development of drug resistance. Here, we show that the interaction between bone marrow stromal cells and myeloma cells (using human cell lines) induces chromatin remodeling of cis-regulatory elements and is associated with changes in the expression of genes involved in the cell migration and cytokine signaling. The expression of genes involved in these stromal interactions are observed in extramedullary disease in patients with myeloma and provides the rationale for survival of myeloma cells outside of the bone marrow microenvironment. Expression of these stromal interaction genes is also observed in a subset of patients with newly diagnosed myeloma and are akin to the transcriptional program of extramedullary disease. The presence of such adverse stromal interactions in newly diagnosed myeloma is associated with accelerated disease dissemination, predicts the early development of therapeutic resistance, and is of independent prognostic significance. These stromal cell induced transcriptomic and epigenomic changes both predict long-term outcomes and identify therapeutic targets in the tumor microenvironment for the development of novel therapeutic approaches.

Abstract 307: Generation and characterization of a glioblastoma stem cell model with acquired resistance to LSD1 inhibition

Abstract Epigenetic modifications play an important role in the initiation of various cancer types, including glioblastoma (GBM), and in the development of therapeutic resistance. Patients with GBM, a common malignant brain tumor, have an average survival of 12-15 months after first-line therapy. Lysine-specific demethylase 1 (LSD1) is a histone demethylase that is overexpressed in glioblastoma stem cells (GSCs) and functions to promote proliferation, inhibit differentiation, and enhance motility. Previous work from our group has investigated LSD1 as a therapeutic target in glioblastoma and identified genes that may predict resistance to pharmacological LSD1 inhibitors using RNA-seq. Five upregulated genes, HKDC1, RAB3IL1, RAB39B, FTH1, and FAM213A, were associated with LSD1 inhibitor (LSD1i) resistance and were validated in brain tissue of a GBM model treated with GSK-LSD1 after succumbing to tumor burden. In order to determine whether selection pressure from LSD1 inhibitor treatment caused upregulation of these genes, we created a model of acquired resistance in GSC lines in vitro. Isogenic resistant lines were generated by treating MDA-GSC17 cells with increasing concentrations of LSD1i or diluent (DMSO), as tolerated starting at 50 uM (which was five fold below the IC50 for these lines). In parallel, MDA-GSC17 controls were exposed to DMSO. The resistant line was created over 4 weeks and monitored by cell number and viability to reach 90%. To assess the change in gene expression, we conducted quantitative PCR for the five genes in the parental and resistant MDA-GSC17 line and saw upregulation in 3 of the 5 genes. Two genes, HKDC1 and RAB3IL1, were unable to be assessed due to low basal expression. However, 3 genes were upregulated which are RAB39B, FTH1, and FAM213A. RAB39B is a Ras-analog in brain (RAB) small GTPase and a member of the RAS oncogene family, involved in vesicular trafficking. High expression of ferritin heavy chain 1 (FTH1) is correlated with high-grade gliomas and poor prognosis in glioblastoma. Lastly, the redox regulatory protein, FAM213A, can activate antioxidant proteins and elevated expression is associated with worse outcomes for AML patients. This suggests that modulating the RAS signaling pathways and specific redox pathways may overcome LSD1 resistance. Understanding the changes in gene expression as the cells acquire resistance to LSD1 inhibitors will help us understand the mechanism of resistance to LSD1 inhibitors in glioblastoma and to design new treatment strategies. Citation Format: Kareena H. Patel, Lea Stitzlein, Deokhwa Nam, Frederick Lang, Joy Gumin, Joya Chandra. Generation and characterization of a glioblastoma stem cell model with acquired resistance to LSD1 inhibition [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 307.

Abstract 2271: Conservation and faithful representation of circular extrachromosomal DNA in orthotopic patient-derived medulloblastoma xenografts

Abstract Background: Extrachromosomal DNA (ecDNA) is a driver of tumor heterogeneity and is associated with poor survival in many different adult and childhood cancer types. Patient-derived xenograft (PDX) models facilitate preclinical drug testing in an in vivo environment that enables analysis of tumor growth and survival and molecular tumor profiling. These models, combined with single-cell profiling, can be used to study intratumoral heterogeneity under therapeutic pressure and the emergence of drug resistance. Here we investigate the abundance and conservation of ecDNA in PDX models with the aim of assessing the faithful representation of ecDNA compared to the tumors from which they are derived. Methods: Whole-genome sequencing (WGS) was applied to 27 medulloblastoma (MB) PDX models and their tumors of origin using Amplicon Architect, a tool used to reconstruct focally amplified regions of DNA to provide insights into the landscape of cancer genomes. The frequency of ecDNA in these models was also compared to that of ecDNA in the MB patient population. Optical genome mapping enabled accurate and reliable ecDNA sequence reconstructions. Multiome single-cell RNA and ATAC-sequencing of a PDX tumor enabled analysis of ecDNA conservation and intratumoral heterogeneity compared to similar data previously obtained from the primary tumor. Results: Comparative analyses revealed that ecDNA is largely conserved in PDX models, emphasizing their relevance as faithful models of the primary tumors. In addition, we find that ecDNA is significantly more frequent in MB PDX models (16 out of 27 analyzed patient-derived tumors) as compared to their frequency in the overall patient population (~18% of all medulloblastoma tumors contain ecDNA), suggesting ecDNA as a driver for successful establishment of MB PDX models. Single-cell analysis revealed that ecDNA is omnipresent in almost all PDX tumor cells, while its presence was limited to only ~9% of tumor cells in the primary tumor. Conclusion: Analysis of ecDNA in medulloblastoma primary tumors and in PDX models revealed that ecDNA is preserved in PDX models. This is an important characteristic that renders patient-derived mouse xenografts as faithful models of their primary tumors. These results emphasize the relevance of PDX models for preclinical in vivo studies aimed at analyzing the role of ecDNA under therapeutic pressure and for analyzing clonal selection along with molecular evolution of ecDNA during the development of therapeutic resistance. Citation Format: Rishaan Kenkre, Owen Chapman, Jens Luebeck, Vineet Bafna, Robert Wechsler-Reya, Jill Mesirov, Lukas Chavez. Conservation and faithful representation of circular extrachromosomal DNA in orthotopic patient-derived medulloblastoma xenografts [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 2271.

Abstract 4102: Treatment with androgen receptor targeting vaccines provides an overall survival benefit in AR-V7 expressing tumor models

Abstract Background: Androgen receptor (AR) signaling inhibition is part of the mechanism behind many effective prostate cancer therapies, including androgen deprivation and next generation anti-androgens. However in castration resistant prostate cancer up to 50% of treatment resistance has been linked to AR amplification or expression of the constitutively active RNA splice variant, AR-V7. Although the use of immune checkpoint blockade has failed to demonstrate clinical success, immunotherapeutic interventions remain attractive as prostate cancer’s relatively slow progression provides time for anti-tumor immune responses to develop. Cancer specific vaccines have the potential to enable and enhance tumor specific immune responses by stimulating and directing T cell immunity to important oncologic targets. We hypothesized that a cancer vaccine designed to induce a T cell response against cells expressing high levels of AR would result in an anti-tumor effect and potentially prevent or delay the development of therapeutic resistance. Methods: Adenoviral vaccines against AR (Ad-AR) or AR splice variant 7 (Ad-AR-V7) were used to evaluate the potential of AR targeting vaccination in mouse models. We evaluated AR and AR variant specific adaptive responses produced by our vaccines with naïve and tumor-bearing mice by ex vivo peptide restimulation. We challenged vaccinated mice with multiple syngeneic subcutaneous tumor models that we engineered to express AR-V7, including a PTEN-/- p53-/- prostate tumor cell line. Finally we tested our vaccines in a therapeutic regimen, vaccinating mice after implanting our subcutaneous AR-V7 expressing models. Results: Across multiple strains of mice, AR or AR-V7 targeting adenoviral vaccination induced robust adaptive immune responses against the N-terminal domain of AR. Vaccination with either Ad-AR or Ad-AR-V7 resulted in significant anti-tumor responses, providing a significant overall survival benefit and complete tumor rejection by the majority of mice vaccinated against AR or AR-V7. Similarly tumor bearing mice treated with Ad-AR or Ad-AR-V7 vaccination displayed tumor growth inhibition or complete tumor regression resulting in an overall survival benefit. Additionally, we found that vaccine responses were unaffected by the use of the approved antiandrogen drug enzalutamide, suggesting that vaccinations could be deployed in tandem with standard-of-care therapies. Conclusions: Vaccination against AR and AR splice variants can induce AR specific adaptive immune responses capable of inhibiting the growth of AR-V7 expressing tumor models, illustrating the potential of AR and its splice variants as immunologic targets in prostate cancer. Citation Format: Robert D. Marek, Junping Wei, Tao Wang, Xiao-Yi Yang, Gangjun Lei, Zachary C. Hartman. Treatment with androgen receptor targeting vaccines provides an overall survival benefit in AR-V7 expressing tumor models [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 4102.

Harnessing the potential of long non-coding RNAs in breast cancer: from etiology to treatment resistance and clinical applications.

Breast cancer (BC) is the most common malignancy among women and a leading cause of cancer-related deaths of females worldwide. It is a complex and molecularly heterogeneous disease, with various subtypes that require different treatment strategies. Despite advances in high-resolution single-cell and multinomial technologies, distant metastasis and therapeutic resistance remain major challenges for BC treatment. Long non-coding RNAs (lncRNAs) are non-coding RNAs with more than 200 nucleotides in length. They act as competing endogenous RNAs (ceRNAs) to regulate post-transcriptional gene stability and modulate protein-protein, protein-DNA, and protein-RNA interactions to regulate various biological processes. Emerging evidence suggests that lncRNAs play essential roles in human cancers, including BC. In this review, we focus on the roles and mechanisms of lncRNAs in BC progression, metastasis, and treatment resistance, and discuss their potential value as therapeutic targets. Specifically, we summarize how lncRNAs are involved in the initiation and progression of BC, as well as their roles in metastasis and the development of therapeutic resistance. We also recapitulate the potential of lncRNAs as diagnostic biomarkers and discuss their potential use in personalized medicine. Finally, we provide lncRNA-based strategies to promote the prognosis of breast cancer patients in clinical settings, including the development of novel lncRNA-targeted therapies.

Abstract A090: An inflammatory adipose microenvironment promotes ovarian cancer tumor growth and cisplatin resistance

Abstract Epithelial ovarian cancer (EOC) commonly targets the omentum, an adipocyte rich organ of the peritoneum. Omental adipocytes have been shown to promote EOC development and chemoresistance via transfer of free fatty acids (FFAs) and the induction of bi-directional metabolic changes. Furthermore, obesity and adiposity are risk factors for EOC incidence and prognosis. The metastatic peritoneal tumor microenvironment (TME) is highly inflamed, while obesity is often characterized by chronic inflammation of adipose tissue and hyperlipidemia. Given that inflammation of adipocytes is associated with increased release of FFAs, we hypothesized that acute inflammation in the ovarian metastatic TME exacerbates pro-tumorigenic effects of cancer-associated adipocytes. Using a three-dimensional transwell co-culture model, we explore the impact of inflamed adipocytes on EOC activity. Adipocytes generated from human adipose-derived stem cells were inflamed with 100ng/ml TNFα and cultured alongside tumor spheroids generated from EOC cell lines. Cytokine abundance in serum samples from ovarian cancer patients undergoing cisplatin treatment were also analyzed. We found that inflammation of adipocytes increased cellular lipolysis and release of FFAs, as well as inducing de-differentiation and loss of lipid droplets. Upon co-culture with inflamed adipocytes, EOC cells displayed increased proliferation in 2D monolayer and 3D spheroid cultures. Transfer of FFAs from adipocytes to cancer cells was visualized and quantified using a fluorescent fatty acid analog via confocal microscopy and flow cytometry. Co-culture induced expression of fatty acid chaperone protein FABP4 in EOC cell lines, while blocking fatty acid metabolism in cancer cells reversed pro-tumor effects of adipocytes. To understand signaling mechanisms generating bi-directional phenotypic changes, cytokine content of secretome of co-cultures was assessed by Luminex. IL-6 and IL-8 were highly abundant in co-cultures, and increased expression was confirmed by qPCR. Treatment of EOC cell lines with recombinant IL-6 and IL-8 induced increased uptake of FFAs and blocking of IL-6 and IL-8 signaling reversed pro-cancer effects of adipocytes. Serum samples from patients undergoing cisplatin therapy were analyzed and IL-6 and IL-8 levels were found to be associated with resistance to therapy. To further investigate the impact of inflamed adipocyte signaling on therapeutic resistance, co-culture were treated with cisplatin and tumor spheroids were found to be highly resistant in the presence of inflamed adipocytes. STAT3 activity is known to be upregulated by both IL-6 and IL-8 and we found that STAT3 expression was increased in co-cultures. Knockdown of STAT3 in EOC reversed the chemoprotective effects of inflamed adipocytes. These data suggest an important role for inflammation of adipose tissue in the development of therapeutic resistance in EOC and highlight a potential mechanism linking clinically observed associations between obesity and ovarian cancer risk. Citation Format: Michael E. Williams, David Howard, Deyarina Gonzalez, Francesca Taraballi. An inflammatory adipose microenvironment promotes ovarian cancer tumor growth and cisplatin resistance [abstract]. In: Proceedings of the AACR Special Conference on Ovarian Cancer; 2023 Oct 5-7; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_2):Abstract nr A090.

Cathepsin B-Responsive Programmed Brain Targeted Delivery System for Chemo-Immunotherapy Combination Therapy of Glioblastoma.

Tumor-associated macrophages (TAMs) are closely related to the progression of glioblastoma multiform (GBM) and its development of therapeutic resistance to conventional chemotherapy. TAM-targeted therapy combined with conventional chemotherapy has emerged as a promising strategy to combat GBM. However, the presence of the blood-brain barrier (BBB) severely limits the therapeutic efficacy. Meanwhile, the lack of ability to distinguish different targeted cells also poses a challenge for precise therapy. Herein, we propose a cathepsin B (CTSB)-responsive programmed brain-targeted delivery system (D&R-HM-MCA) for simultaneous TAM-targeted and GBM-targeted delivery. D&R-HM-MCA could cross the BBB via low density lipoprotein receptor-associated protein 1 (LRP1)-mediated transcytosis. Upon reaching the GBM site, the outer angiopep-2 modification could be detached from D&R-HM-MCA via cleavage of the CTSB-responsive peptide, which could circumvent abluminal LRP1-mediated efflux. The exposed p-aminophenyl-α-d-mannopyranoside (MAN) modification could further recognize glucose transporter-1 (GLUT1) on GBM and macrophage mannose receptor (MMR) on TAMs. D&R-HM-MCA could achieve chemotherapeutic killing of GBM and simultaneously induce TAM polarization from anti-inflammatory M2 phenotype to pro-inflammatory M1 phenotype, thus resensitizing the chemotherapeutic response and improving anti-GBM immune response. This CTSB-responsive brain-targeted delivery system not only can improve brain delivery efficiency, but also can enable the combination of chemo-immunotherapy against GBM. The effectiveness of this strategy may provide thinking for designing more functional brain-targeted delivery systems and more effective therapeutic regimens.

Epigenetic reprogramming of T cells: unlocking new avenues for cancer immunotherapy.

T cells, a key component of cancer immunotherapy, undergo a variety of histone modifications and DNA methylation changes since their bone marrow progenitor stages before developing into CD8+ and CD4+ T cells. These T cell types can be categorized into distinct subtypes based on their functionality and properties, such as cytotoxic T cells (Tc), helper T cells (Th), and regulatory T cells (Treg) as subtypes for CD8+ and CD4+ T cells. Among these, the CD4+ CD25+ Tregs potentially contribute to cancer development and progression by lowering T effector (Teff) cell activity under the influence of the tumor microenvironment(TME). This contributes to the development of therapeutic resistance in patients with cancer. Subsequently, these individuals become resistant to monoclonal antibody therapy as well as clinically established immunotherapies. In this review, we delineate the different epigenetic mechanisms in cancer immune response and its involvement in therapeutic resistance. Furthermore, the possibility of epi-immunotherapeutic methods based on histone deacetylase inhibitors and histone methyltransferase inhibitors are under investigation. In this review we highlight EZH2 as the principal driver of cancer cell immunoediting and an immune escape regulator. We have addressed in detail how understanding T cell epigenetic regulation might bring unique inventive strategies to overcome drug resistance and increase the efficacy of cancer immunotherapy.

Abstract A065: Lineage tracing oncogenic isoforms of HER2 in a mouse model of pancreatic cancer

Abstract Among the numerous clinical challenges of pancreatic ductal adenocarcinoma (PDAC) is the eventual development of therapeutic resistance. Although previous studies report that only about 3% of PDAC cases are HER2 gene amplified, as many as 82% of PDAC tumors may have HER2 overexpressed. Anti-HER2 therapy with trastuzumab has yielded tremendous therapeutic success in breast cancer and multiple gastrointestinal malignancies, however minimal benefit is found in PDAC. Experimental mouse models have demonstrated initiation and acceleration of pancreatic tumorigenesis through overexpression of activated mutant HER2, yet the role of HER2 alone as a driver of PDAC and treatment resistance is still unknown. Multiple HER2 isoforms exist that are generated either via alternative splicing and loss of exon 16 (d16 HER2) or through N-terminal truncations (p95 HER2). These isoforms are implicated in differential responses to anti-HER2 therapy in the breast. Previously we described a HER2+ cancer rainbow mouse model in which human wild-type HER2 (WT HER2), d16 HER2, and p95 HER2 were expressed in the same mouse and lineage traced through co-expression of fluorescent protein reporters. Studies in the mammary gland revealed that each isoform drives distinct tumor phenotypes. Herein, we hypothesize that these isoforms drive HER2 positive PDAC. HER2 Crainbow mice were crossed with mice expressing PDX1-Cre recombinase to initiate recombination and expression of each fluorescently labelled HER2 isoform during pancreas development. PDX1-Cre/HER2 Crainbow (PHBOW) mice were followed for up to one year and sacrificed to lineage trace each isoform and register HER2 lineages with histopathology. Within our pilot cohort, early-stage pre-malignant pancreatic intraepithelial neoplasia (PanIN-1) was observed in 75% of PDAC HER2bow mice as early as five weeks. By one year, 50% demonstrated high grade PanIN (i.e. PanIN-3) and features of early invasion. Although WT HER2 was expressed abundantly throughout the pancreas, lineage tracing revealed WT HER2 was not found in pre-malignant lesions. Conversely, the pre-malignant PanIN lesions and early invasive histopathologic features traced to d16 HER2 expressing cells, while p95 HER2 traced with areas of acinar-to-ductal metaplasia, lesions known to be early initiators of pancreatic dysplasia. Our data show how the oncogenic HER2 isoforms, and not WT HER2, are able to drive PanIN lesions and, at lower frequency, invasive PDAC after one year. Future work seeks to complete HER2 Crainbow lineage tracing in PHBOW mice, test HER2 targeted therapy in PHBOW mice, and quantify HER2 isoforms in HER2+ human PDAC cases. Citation Format: Elishama N. Kanu, Joelle Sills, Rebecca Shelley, Joshua D. Ginzel, Joseph Fernandes, Ashley A. Fletcher, Peter J. Allen, Daniel P. Nussbaum, Joshua C. Snyder. Lineage tracing oncogenic isoforms of HER2 in a mouse model of pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A065.

Single-cell genomics analysis reveals complex genetic interactions in an in vivo model of acquired BRAF inhibitor resistance.

The evolution of therapeutic resistance is a major obstacle to the success of targeted oncology drugs. While both inter- and intratumoral heterogeneity limit our ability to detect resistant subpopulations that pre-exist or emerge during treatment, our ability to analyze tumors with single-cell resolution is limited. Here, we utilized a cell-based transposon mutagenesis method to identify mechanisms of BRAF inhibitor resistance in a model of cutaneous melanoma. This screen identified overexpression of NEDD4L and VGLL3 as significant drivers of BRAF inhibitor resistance in vivo. In addition, we describe a novel single-cell genomics profiling method to genotype thousands of individual cells within tumors driven by transposon mutagenesis. This approach revealed a surprising genetic diversity among xenograft tumors and identified recurrent co-occurring mutations that emerge within distinct tumor subclones. Taken together, these observations reveal an unappreciated genetic complexity that drives BRAF inhibitor resistance.

Interpreting the effect of mutations to protein binding sites from large-scale genomic screens

Predicting the functionality of missense mutations is extremely difficult. Large-scale genomic screens are commonly performed to identify mutational correlates or drivers of disease and treatment resistance, but interpretation of how these mutations impact protein function is limited. One such consequence of mutations to a protein is to impact its ability to bind and interact with partners or small molecules such as ATP, thereby modulating its function. Multiple methods exist for predicting the impact of a single mutation on protein–protein binding energy, but it is difficult in the context of a genomic screen to understand if these mutations with large impacts on binding are more common than statistically expected. We present a methodology for taking mutational data from large-scale genomic screens and generating functional and statistical insights into their role in the binding of proteins both with each other and their small molecule ligands. This allows a quantitative and statistical analysis to determine whether mutations impacting protein binding or ligand interactions are occurring more or less frequently than expected by chance. We achieve this by calculating the potential impact of any possible mutation and comparing an expected distribution to the observed mutations. This method is applied to examples demonstrating its ability to interpret mutations involved in protein–protein binding, protein-DNA interactions, and the evolution of therapeutic resistance.

M6A demethylase ALKBH5 regulates FOXO1 mRNA stability and chemoresistance in triple-negative breast cancer

Resistance to chemotherapy is the main reason for treatment failure and poor prognosis in patients with triple-negative breast cancer (TNBC). Although the association of RNA N6-methyladenosine (m6A) modifications with therapy resistance is noticed, its role in the development of therapeutic resistance in TNBC is not well documented. This study aimed to investigate the potential mechanisms underlying reactive oxygen species (ROS) regulation in doxorubicin (DOX)-resistant TNBC. Here, we found that DOX-resistant TNBC cells displayed low ROS levels because of increased expression of superoxide dismutase (SOD2), thus maintaining cancer stem cells (CSCs) characteristics and DOX resistance. FOXO1 is a master regulator that reduces cellular ROS in DOX-resistant TNBC cells, and knockdown of FOXO1 significantly increased ROS levels by inhibiting SOD2 expression. Moreover, the m6A demethylase ALKBH5 promoted m6A demethylation of FOXO1 mRNA and increased FOXO1 mRNA stability in DOX-resistant TNBC cells. The analysis of clinical samples revealed that the increased expression levels of ALKBH5, FOXO1, and SOD2 were significantly positively correlated with chemoresistance and poor prognosis in patients with TNBC. To our knowledge, this is the first study to highlight that ALKBH5-mediated FOXO1 mRNA demethylation contributes to CSCs characteristics and DOX resistance in TNBC cells. Furthermore, pharmacological targeting of FOXO1 profoundly restored the response of DOX-resistant TNBC cells, both in vitro and in vivo. In conclusion, we demonstrated a critical function of ALKBH5-mediated m6A demethylation of FOXO1 mRNA in restoring redox balance, which in turn promoting CSCs characteristics and DOX resistance in TNBC, and suggested that targeting the ALKBH5/FOXO1 axis has therapeutic potential for patients with TNBC refractory to chemotherapy.

DDDR-28. DNA DAMAGE SENSING KINASES ATR AND ATM-DEPENDENT PHOSPHORYLATION OF RRM2 PROMOTES PROTEIN STABILIZATION AND CHEMO-ADAPTATION

Abstract Glioblastoma (GBM) is a highly heterogeneous, primary malignant brain tumor in adults that shows limited response to standard-of-care therapies, such as chemotherapy and radiation. This is due, in part, to the development of therapeutic resistance. To characterize the adaptive mechanisms GBM cells use to evade the standard chemotherapy, temozolomide (TMZ), single-cell RNA sequencing analysis was conducted on an in vivo patient-derived xenograft (PDX) model of GBM, before, during, and following TMZ-based therapy. Our data revealed 149 genes to be uniquely expressed in the during-TMZ condition (p< 0.0001), including the rate-limiting regulatory enzyme of dNTP metabolism, ribonucleotide reductase (RNR) enzyme. Network analysis of pathways enriched during therapy revealed an interaction between the (RNR) enzyme, RRM2, and DNA damage response genes in the ATM and ATR kinase-signaling pathways. RRM2-dependent deoxynucleotide (dNTP) production is required for DNA repair and cell survival following TMZ treatment. Therefore, we investigated whether ATR and ATM kinases directly interact with RRM2 to promote its stability. TMZ treatment triggered the activation of DNA damage response machinery and protein kinases, ATM, ATR, CHK1, and CHK2, which physically interacted with RRM2 across multiple GBM PDX cell lines. Co-IP and immunoblot analyses along with cycloheximide chase analysis showed increased phosphorylation of the threonine residue on RRM2 during therapy, preventing its degradation. As such, we hypothesize that early DNA damage sensing by ATM and ATR kinases, and their subsequent phosphorylation of RRM2, promotes the maintenance of purine nucleotide pools needed for DNA repair and development of chemo-resistance. This novel and targetable TMZ response axis presents a promising clinical opportunity for GBM therapy, using FDA-approved inhibitors of these targets to block the purine metabolic adaptations that drive resistance and sensitize GBM cells to TMZ therapy.

The role of exosomes in therapeutic resistance of hepatocellular carcinoma

Hepatocellular carcinoma (HCC) stands as one of the most prevalent malignant tumors globally. Despite considerable advancements in HCC therapies, therapeutic resistance remains a significant challenge that compromises patient prognosis. Increasing evidence indicates that exosomes, which are secreted by cells in the tumor microenvironment (TME), are pivotal players in the development of therapeutic resistance in HCC. These nano-sized vesicles mediate intercellular communication in TME through the transfer of bioactive molecules such as nucleic acids, lipids, and proteins. A comprehensive understanding of the role of exosomes in therapeutic resistance could provide promising strategies for both the diagnosis and treatment of HCC. This review mainly summarizes the involvement of exosomal cargos and elucidates their underlying mechanisms in resistance to therapeutic treatments for HCC, and further discusses the potential clinical applications of exosomes as diagnostic biomarkers and therapeutic targets to overcome drug resistance in HCC.

Defining new biomarkers for overcoming therapeutical resistance in cervical cancer using lncRNA.

Despite improvements in cervical cancer diagnosis and treatment, the prognosis for cervical cancer patients remains dismal due to the development of drug resistance, metastasis, and invasion resulting leading to treatment failure. Long non-coding RNAs (lncRNAs), a class of RNA transcripts have been reported in mediating carcinogenesis as well as drug, and radio-resistance in tumor cells. These lncRNAs regulate various cancer hallmarks and contribute to the development of therapeutic resistance. They regulates multiple signalling pathways, recruits polycomb group, function as miRNA sponge and scaffolds. Additionally, lncRNAs can act as oncogenes or tumor suppressors in cervical cancer. This comprehensive review outlines the biogenesis of lncRNA and its role in cancer development. It delves into the mechanisms through which various lncRNAs mediate chemoresistance and radioresistance in cervical cancer. By shedding into the light of mechanism, this review will also aids researchers in understanding lncRNAs as biomarkers and latest advancements in clinically targeting them with the help of Artificial Intelligence for overcoming chemoresistance and radioresistance, thereby improving cervical cancer treatment.

Neferine Targets the Oncogenic Characteristics of Androgen-Dependent Prostate Cancer Cells via Inducing Reactive Oxygen Species.

Castration resistance poses a significant challenge in the management of advanced prostate cancer (PCa), with androgen deprivation therapy (ADT) or chemotherapy being the primary treatment options. However, these approaches often lead to significant side effects and the development of therapeutic resistance. Therefore, it is crucial to explore novel treatment options that can efficiently target PCa, improve patient survival, and enhance their quality of life. Neferine (Nef), a bioactive compound derived from plants, has emerged as a promising candidate for cancer treatment due to its ability to induce apoptosis, autophagy, and cell cycle arrest. In this study, we investigated the potential anticancer effects of Nef in androgen receptor (AR)-positive LNCaP and VCaP cells, representative models of androgen-dependent PCa. Our findings demonstrate that Nef effectively inhibits cell growth, proliferation, and the tumorigenic potential of androgen-dependent PCa cells. Furthermore, Nef treatment resulted in the excessive production of reactive oxygen species (ROS), leading to the activation of key markers of autophagy and apoptosis. These results suggest that Nef has the potential to target the oncogenic characteristics of androgen-dependent PCa cells by exploiting the potency of ROS and inducing autophagy and apoptosis in AR-positive PCa cells. These findings shed light on the therapeutic potential of Nef as a novel treatment option with reduced side effects for androgen-dependent prostate cancer. Further investigations are warranted to assess its efficacy and safety in preclinical and clinical settings.

Engineered Extracellular Vesicle-Delivered CRISPR/Cas9 for Radiotherapy Sensitization of Glioblastoma.

Radiotherapy is a mainstay of glioblastoma (GBM) treatment; however, the development of therapeutic resistance has hampered the efficacy of radiotherapy, suggesting that additional treatment strategies are needed. Here, an in vivo loss-of-function genome-wide CRISPR screen was carried out in orthotopic tumors in mice subjected to radiation treatment to identify synthetic lethal genes associated with radiotherapy. Using functional screening and transcriptome analyses, glutathione synthetase (GSS) was found to be a potential regulator of radioresistance through ferroptosis. High GSS levels were closely related to poor prognosis and relapse in patients with glioma. Mechanistic studies demonstrated that GSS was associated with the suppression of radiotherapy-induced ferroptosis in glioma cells. The depletion of GSS resulted in the disruption of glutathione (GSH) synthesis, thereby causing the inactivation of GPX4 and iron accumulation, thus enhancing the induction of ferroptosis upon radiotherapy treatment. Moreover, to overcome the obstacles to broad therapeutic translation of CRISPR editing, we report a previously unidentified genome editing delivery system, in which Cas9 protein/sgRNA complex was loaded into Angiopep-2 (Ang) and the trans-activator of the transcription (TAT) peptide dual-modified extracellular vesicle (EV), which not only targeted the blood-brain barrier (BBB) and GBM but also permeated the BBB and penetrated the tumor. Our encapsulating EVs showed encouraging signs of GBM tissue targeting, which resulted in high GSS gene editing efficiency in GBM (up to 67.2%) with negligible off-target gene editing. These results demonstrate that a combination of unbiased genetic screens, and CRISPR-Cas9-based gene therapy is feasible for identifying potential synthetic lethal genes and, by extension, therapeutic targets.

Mutant PIK3CA as a negative predictive biomarker for treatment with a highly selective PIM1 inhibitor in human colon cancer

ABSTRACT Significant improvement in targeted therapy for colorectal cancer (CRC) has occurred over the past few decades since the approval of the EGFR inhibitor cetuximab. However, cetuximab is used only for patients possessing the wild-type oncogene KRAS, NRAS, and BRAF, and even most of these eventually acquire therapeutic resistance, via activation of parallel oncogenic pathways such as RAS-MAPK or PI3K/Akt/mTOR. The two aforementioned pathways also contribute to the development of therapeutic resistance in CRC patients, due to compensatory and feedback mechanisms. Therefore, combination drug therapies (versus monotherapy) targeting these multiple pathways may be necessary for further efficacy against CRC. In this study, we identified PIK3CA mutant (PIK3CA MT) as a determinant of resistance to SMI-4a, a highly selective PIM1 kinase inhibitor, in CRC cell lines. In CRC cell lines, SMI-4a showed its effect only in PIK3CA wild type (PIK3CA WT) cell lines, while PIK3CA MT cells did not respond to SMI-4a in cell death assays. In vivo xenograft and PDX experiments confirmed that PIK3CA MT is responsible for the resistance to SMI-4a. Inhibition of PIK3CA MT by PI3K inhibitors restored SMI-4a sensitivity in PIK3CA MT CRC cell lines. Taken together, these results demonstrate that sensitivity to SMI-4a is determined by the PIK3CA genotype and that co-targeting of PI3K and PIM1 in PIK3CA MT CRC patients could be a promising and novel therapeutic approach for refractory CRC patients.