Biology subjects

Olivas, V.

Publications and source records attributed to Olivas, V..

10 recordsLinked to original sources

bioRxiv2025

Actionable biological programs to enhance EGFR-targeted therapy response unveiled by single-cell lineage tracing in clinically relevant lung cancer models

Developing high-resolution approaches to capture both tumor architectural clonality and transcriptional state(s) in individual cells within heterogeneous tumor cell populations could shed light on the evolution of pre-existing and newly emergent tumor subclones and their phenotypes, elucidating their trajectories in response to selective pressures such as drug treatment. Reports to date have focused primarily on analyzing the drug-induced evolution of lung cancer cells in in vitro preclinical models with limited complexity and a relative lack of characterization of actionable biological programs to induce durable responses. Here, we challenged this paradigm and employed a lineage tracing single-cell RNAseq method to track the evolution of primary non-small cell lung cancer (NSCLC) patient-derived organoids (PDOs) and tumor xenografts in response to the standard-of-care EGFR inhibitor osimertinib, with a focus on understanding drug persistence and resistance. Our single-cell lineage tracing-RNAseq system revealed the presence of a discrete set of lineages with distinct transcriptional phenotypes over the course of the treatment. We identified two lineage populations that became predominant during drug treatment and resisted therapy in the PDOs and tumor xenografts. These lineages were present before treatment and harbored Hedgehog pathway and FOXD1 transcriptional programs, respectively. These specific transcriptomic lineages were otherwise undetectable by lower-resolution profiling. Functional studies confirmed the protective role that the baseline expression of the Hedgehog pathway and FOXD1 programs in the lineage tumor cell sub-populations exerts upon targeted therapy. The potential clinical relevance of these regulatory programs was validated by cross-analysis of single-cell transcriptomic data obtained from human NSCLC specimens. Overall, our approach identified pre-existing seeds of resistance before therapy and convergent, adaptive mechanisms supporting tumor residual disease and resistant states. This study highlights the utility of high-resolution tracing of tumor clonal heterogeneity with matched single-cell profiling to reveal occult cell states and molecular mechanisms of therapy resistance and develop counteracting strategies.

cancer biology↗

bioRxiv2024

CDK4 and CDK6 upregulation promotes DNA replication stress, genomic instability and resistance to EGFR targeted therapy in lung cancer

Epidermal growth factor receptor (EGFR) mutant lung adenocarcinomas (LUAD) harbor a complex landscape of genetic co-alterations and potential oncogenic interactions. Among them are recurrent amplifications of the cell cycle regulatory genes CDK4 and CDK6, which have been clinically implicated in resistance to EGFR tyrosine kinase inhibitors (TKIs). However, the mechanisms by which CDK4/6 upregulation promotes therapy resistance remain poorly defined. Here, we demonstrate that CDK4 or CDK6 overexpression limits EGFR inhibitor-induced proliferative arrest, promoting continued cell cycle progression. This is accompanied by elevated replication stress, increased TPX2 expression, DNA damage leading to ATM activation, and ultimately genomic instability. Integrative transcriptomic and copy number analyses of EGFR-mutant LUAD tumors from both patients and preclinical models revealed that CDK4 or CDK6 amplification is associated with the upregulation of genes linked to tumor progression, including AGR2, ASNS, and STEAP1. CDK4 amplification was also highly correlated with gene expression changes associated with epithelial-to-mesenchymal transition (EMT) in a single-cell RNA sequencing dataset from patient biopsies. In preclinical models, co-treatment with CDK4/6 and EGFR inhibitors restored proliferative arrest, induced tumor cell apoptosis, and reduced replication stress, DNA damage, and genomic instability. Our findings uncover a mechanistic basis for EGFR inhibitor resistance of CDK4 and CDK6 amplified EGFR-mutant LUAD. They also provide a rationale for the biomarker-driven clinical development of combination EGFR and CDK4/6-targeted therapies for the treatment of a subset of EGFR-mutant LUAD patients.

cancer biology↗

bioRxiv2021

3-Phosphoinositide-dependent kinase 1 drives acquired resistance to osimertinib

Osimertinib sensitive and resistant NSCLC NCI-H1975 clones were used to model osimertinib acquired resistance in humanized mice and delineate potential resistance mechanisms. No new EGFR mutations or loss of the EGFR T790M mutation were found in resistant clones. Resistant tumors in humanized mice were initially partially responsive to osimertinib, then aggressive tumor regrowth occurred accompanied by an immunosuppressive tumor microenvironment. 3-phosphoinositide-dependent kinase 1 (PDK1) was identified as a potential driver of osimertinib acquired resistance, and its selective inhibition by BX795 and CRISPR gene knock out, sensitized resistant clones and a patient derived xenograft (PDX) with acquired resistance to osimertinib. PDK1 knock-out dysregulated PI3K/Akt/mTOR signaling, promoted cell cycle arrest at the G1 phase, and inhibited nuclear translocation of yes-associated protein (YAP). Higher expression of PDK1 was found in patients with progressive disease following osimertinib treatment. PDK1 is a central upstream regulator of two critical drug resistance pathways: PI3K/AKT/mTOR and YAP.

cancer biology↗

bioRxiv2021

A focal adhesion kinase-YAP signaling axis drives drug tolerant persister cells and residual disease in lung cancer

Targeted therapy is effective in many tumor types including lung cancer, the leading cause of cancer mortality. Paradigm defining examples are targeted therapies directed against non-small cell lung cancer (NSCLC) subtypes with oncogenic alterations in EGFR, ALK and KRAS. The success of targeted therapy is limited by drug-tolerant tumor cells which withstand and adapt to treatment and comprise the residual disease state that is typical during treatment with clinical targeted therapies. Here, we integrate studies in patient-derived and immunocompetent lung cancer models and clinical specimens obtained from patients on targeted therapy to uncover a focal adhesion kinase (FAK)-YAP signaling axis that promotes residual disease during oncogenic EGFR-, ALK-, and KRAS-targeted therapies. FAK-YAP signaling inhibition combined with the primary targeted therapy suppressed residual drug-tolerant cells and enhanced tumor responses. This study unveils a FAK-YAP signaling module that promotes residual disease in lung cancer and mechanism-based therapeutic strategies to improve tumor response.

cancer biology↗

bioRxiv2020

Deficiency of the splicing factor RBM10 limits EGFR inhibitor response in EGFR mutant lung cancer

Molecularly targeted cancer therapy has improved outcomes for cancer patients with targetable oncoproteins, such as mutant epidermal growth factor receptor (EGFR) in lung cancer. Yet, long-term patient survival remains limited because treatment responses are typically incomplete. One potential explanation for the lack of complete and durable responses is that oncogene-driven cancers with activating mutations in the EGFR often harbor additional co-occurring genetic alterations. This hypothesis remains untested for most genetic alterations that co-occur with mutant EGFR. Here, we report the functional impact of inactivating genetic alteration of the mRNA splicing factor RBM10 that co-occur with mutant EGFR. RBM10 deficiency decreased EGFR inhibitor efficacy in patient-derived EGFR mutant tumor models. RBM10 modulated mRNA alternative splicing of the mitochondrial apoptotic regulator Bcl-x to regulate tumor cell apoptosis during treatment. Genetic inactivation of RBM10 diminished EGFR inhibitor-mediated apoptosis by decreasing the ratio of Bcl-xS-(pro-apoptotic)-to-Bcl-xL(anti-apoptotic) Bcl-x isoforms. RBM10 deficiency was a biomarker of poor response to EGFR inhibitor treatment in clinical samples. Co-inhibition of Bcl-xL and mutant EGFR overcame resistance induced by RBM10 deficiency. This study sheds light on the role of co-occurring genetic alterations, and on the impact of splicing factor deficiency in the modulation of sensitivity to targeted kinase inhibitor cancer therapy.

cancer biology↗

bioRxiv2020

A tyrosine kinase protein interaction map reveals targetable EGFR network oncogenesis in lung cancer

SUMMARYSignaling networks balance the activities of many physically interacting proteins and perturbations to this network influence downstream signaling, potentially leading to oncogenic states. Using affinity purification-mass spectrometry we defined this network for all 90 human tyrosine kinases revealing 1,463 mostly novel interactions between these key cancer proteins and diverse molecular complexes. Modulation of interactor levels altered growth phenotypes associated with corresponding tyrosine kinase partners suggesting that tumors may alter the stoichiometries of interactors to maximize oncogenic signaling. We show that the levels of EGFR interactors delineates this form of network oncogenesis in 19% of EGFR wild-type lung cancer patients which were mostly otherwise oncogene negative, predicting sensitivity to EGFR inhibitors in vitro and in vivo. EGFR network oncogenesis occurs through mechanistically distinct network alleles often in cooperation with weak oncogenes in the MAPK pathway. Network oncogenesis may be a common and targetable convergent mechanism of oncogenic pathway activation in cancer.HIGHLIGHTSA human tyrosine kinome protein interaction map reveals novel physical and functional associations.Dependence on oncogenic tyrosine kinases is modulated through perturbation of their interactors.EGFR network oncogenesis in up to 19% of EGFR wild-type lung cancers is targetable.EGFR network oncogenesis cooperates with weak oncogenes in the MAPK pathway.Competing Interest StatementS.L.W. is an employee of Pfizer. D.C., I.S., E.M., are employees of Champions oncology. S.B. has received funding from Clovis Oncology, Pfizer, Revolution Medicines and Ideaya Biosciences.View Full Text

cancer biology↗

bioRxiv2018

The CIC-DUX4 fusion oncoprotein drives metastasis and tumor growth via distinct downstream regulatory programs and therapeutic targets in sarcoma

Transcription factor fusion genes create oncoproteins that drive oncogenesis, and represent challenging therapeutic targets. Understanding the molecular targets by which such fusion oncoproteins promote malignancy offers an approach to develop rational treatment strategies to improve clinical outcomes. CIC-DUX4 is a transcription factor fusion that defines certain undifferentiated round cell sarcomas with high metastatic propensity and poor clinical outcomes. The molecular targets regulated by the CIC-DUX4 oncoprotein that promote this aggressive malignancy remain largely unknown. We show that increased expression of ETV4 and CCNE1 occurs via neo-morphic, direct effects of CIC-DUX4 and drives tumor metastasis and survival, respectively. We demonstrate a molecular dependence on the CCNE-CDK2 cell cycle complex that renders CIC-DUX4 tumors sensitive to inhibition of the CCNE-CDK2 complex, highlighting a therapeutic strategy for CIC-DUX4 tumors. Our findings highlight a paradigm of functional diversification of transcriptional repertoires controlled by a genetically-aberrant transcriptional regulator, with therapeutic implications.

cancer biology↗

bioRxiv2018

Synthetic essentiality of metabolic regulator PDHK1 in PTEN-deficient cells and cancers

PTEN is a tumor suppressor that is often inactivated in cancer and possesses both lipid and protein phosphatase activities. We report the metabolic regulator PDHK1 (pyruvate dehydrogenase kinase1) is a synthetic-essential gene in PTEN-deficient cancer and normal cells. The predominant mechanism of PDHK1 regulation and dependency is the PTEN protein phosphatase dephosphorylates NF{kappa};B activating protein (NKAP) and limits NF{kappa}B activation to suppress expression of PDHK1, a NF{kappa}B target gene. Loss of the PTEN protein phosphatase upregulates PDHK1 to drive aerobic glycolysis and induce PDHK1 cellular dependence. PTEN-deficient human tumors harbor increased PDHK1, which is a biomarker of decreased patient survival, establishing clinical relevance. This study uncovers a PTEN-regulated signaling pathway and reveals PDHK1 as a potential target in PTEN-deficient cancers.\n\nSIGNIFICANCEThe tumor suppressor PTEN is widely inactivated in cancers and tumor syndromes. PTEN antagonizes PI3K/AKT signaling via its lipid phosphatase activity. The modest success of PI3K/AKT inhibition in PTEN-deficient cancer patients provides rationale for identifying other vulnerabilities in PTEN-deficient cancers to improve clinical outcomes. We show that PTEN-deficient cells are uniquely sensitive to PDHK1 inhibition. PTEN and PDHK1 co-suppression reduced colony formation and induced cell death in vitro and tumor regression in vivo. PDHK1 levels were high in PTEN-deficient patient tumors and associated with inferior patient survival, establishing clinical relevance. Our study identifies a PTEN-regulated signaling pathway linking the PTEN protein phosphatase to the metabolic regulator PDHK1 and provides a mechanistic basis for PDHK1 targeting in PTEN-deficient cancers.

cancer biology↗

bioRxiv2017

Evolution and clinical impact of genetic epistasis within EGFR-mutant lung cancers

Introductory paragraph Introductory paragraph Main text Methods Author Contributions Author Information References The current understanding of tumorigenesis is largely centered on a monogenic driver oncogene model. This paradigm is incompatible with the prevailing clinical experience in most solid malignancies: monotherapy with a drug directed against an individual oncogenic driver typically results in incomplete clinical responses and eventual tumor progression1-7. By profiling the somatic genetic alterations present in over 2,000 cases of lung cancer, the leading cause of cancer mortality worldwide8,9, we show that combinations of functional genetic alterations, i.e. genetic collectives dominate the landscape of ...

cancer biology↗

bioRxiv2016

Novel computational method for predicting polytherapy switching strategies to overcome tumor heterogeneity and evolution

1The success of targeted cancer therapy is limited by drug resistance that can result from tumor genetic heterogeneity. The current approach to address resistance typically involves initiating a new treatment after clinical/radiographic disease progression, ultimately resulting in futility in most patients. Towards a potential alternative solution, we developed a novel computational framework that uses human cancer profiling data to systematically identify dynamic, pre-emptive, and sometimes non-intuitive treatment strategies that can better control tumors in real-time. By studying lung adenocarcinoma clinical specimens and preclinical models, our computational analyses revealed that the best anti-cancer strategies addressed existing resistant subpopulations as they emerged dynamically during treatment. In some cases, the best computed treatment strategy used unconventional therapy switching while the bulk tumor was responding, a prediction we confirmed in vitro. The new framework presented here could guide the principled implementation of dynamic molecular monitoring and treatment strategies to improve cancer control.

cancer biology↗