Genetic Amplifications Research Articles

Tumor-associated genetic amplifications impact extracellular vesicle miRNA cargo and their recruitment of nerves in head and neck cancer.

Cancer neuroscience is an emerging field of cancer biology focused on defining the interactions and relationships between the nervous system, developing malignancies, and their environments. Our previous work demonstrates that small extracellular vesicles (sEVs) released by head and neck squamous cell carcinomas (HNSCCs) recruit loco-regional nerves to the tumor. sEVs contain a diverse collection of biological cargo, including microRNAs (miRNAs). Here, we asked whether two genes commonly amplified in HNSCC, CCND1, and PIK3CA, impact the sEV miRNA cargo and, subsequently, sEV-mediated tumor innervation. To test this, we individually overexpressed these genes in a syngeneic murine HNSCC cell line, purified their sEVs, and tested their neurite outgrowth activity on dorsal root ganglia (DRG) neurons invitro. sEVs purified from Ccnd1-overexpressing cells significantly increased neurite outgrowth of DRG compared to sEVs from parental or Pik3ca over-expressing cells. When implanted into C57BL/6 mice, Ccnd1 over-expressing tumor cells promoted significantly more tumor innervation invivo. qPCR analysis of sEVs shows that increased expression of Ccnd1 altered the packaging of miRNAs (miR-15-5p, miR-17-5p, and miR-21-5p), many of which target transcripts important in regulating axonogenesis. These data indicate that genetic amplifications harbored by malignancies impose changes in sEV miRNA cargo, which can influence tumorc innervation.

Pancancer Analysis of NSUN2 with a Focus on Prognostic and Immunological Roles in Endometrial Cancer.

The significance of NSUN2 in carcinogenesis is gradually being recognized, yet a comprehensive analysis across pan-cancer remains a pivotal void in existing research. In our investigation, we capitalized on the UCSC Xena platform to evaluate NSUN2 expression levels and their prognostic implications across a range of cancer types. Furthermore, we employed the cBioPortal database to delve into the genomic variations of NSUN2 within human cancers. Our study encompassed the use of molecular docking, genomic tumor profiling, and an assessment of the gene's responsiveness to pharmacological treatments. Additionally, we utilized algorithmic techniques to measure the relationship between NSUN2 expression and key clinical biomarkers, such as microsatellite instability (MSI), tumor mutational burden (TMB), and immune cell infiltration. Our results have established a notable association between NSUN2 and endometrial cancer (UCEC), thereby confirming its clinical significance through an analysis of tumoral expression patterns, mutational spectra, methylation profiles, and drug sensitivity. Gene Set Enrichment Analysis (GSEA) and Gene Set Variation Analysis (GSVA) were crucial tools in elucidating the biological roles of NSUN2 in endometrial cancer. Consistently, elevated NSUN2 expression was associated with unfavorable clinical outcomes and was primarily observed in the context of genetic amplifications. Across 22 distinct tumor types, our analysis revealed a notable correlation between NSUN2 expression and various metrics related to immune cell infiltration, tumor stroma, and immune scores. Notably, higher levels of NSUN2 expression have been linked to a reduced response to certain chemotherapeutic agents, including PHA-793887. In UCEC, a positive correlation between NSUN2 methylation and gene expression hints at a potential epigenetic regulatory mechanism underlying cancer progression. Our study highlights the potential of NSUN2 as a key oncogene and its promising role as a therapeutic target as well as a prognostic biomarker for endometrial cancer. This underscores its potential importance in predicting responses to immunotherapy.

Abstract B019: Tumor-derived PTHrP molds an immunosuppressive microenvironment

Abstract Purpose[JP1] : Molecular phenotyping of PDAC [PJ2] has revealed an aggressive squamous/basal/quasi-mesenchymal[JP3] subtype, clinically presenting as highly metastatic and harboring genetic amplifications of KRAS. Our previous work indicated that a squamous identity gene, Parathyroid Hormone Like Hormone (PTHLH; encoding for the PTHrP protein), is frequently co-amplified with KRAS and skews PDAC towards a squamous identity. Further, PTHrP is secreted by tumor cells and promotes tumor growth and metastasis through autocrine signaling. However, pathological analysis of PTHrP-null tumors indicated that the tumor microenvironment (TME) was re-organized upon loss of PTHrP. Thus, we hypothesized that PTHrP is a tumor-derived factor that shapes the TME through its systemic secretion and mobilization of immunosuppressive myeloid cells. Methods: In vivo experiments used KrasG12D; p53R172H; Pdx1-Cre; YFP (KPCY) and KPCY-PthlhloxP/WT (KPCY-Pthlhhet) for spontaneous tumor formation in immune competent mice. Orthotopic implantation experiments used Pthlh overexpressing KPCY tumor cells (herein KPCY-PthlhOE) or empty vector control cells (KPCY-PthlhEV). Tumor immunophenotyping was done using flow cytometry. Cytokine expression was performed using qPCR and ELISA. Results: In vivo investigation of tumors from KPCY-Pthlhhet mice revealed less MDSC and greater CD8+ T cell infiltration than KPCY controls, demonstrating the necessity of PTHrP for immunosuppression[PJ4]. Orthotopic implantation of KPCY-PthlhOE cell lines reduced overall TME immune cell recruitment, while simultaneously increasing the proportion of polymorphonuclear myeloid-derived suppressor cells (PMN-MDSC) infiltration. A concomitant decrease in the frequency of T cells in the KPCY-PthlhOE tumors was also observed, showing the sufficiency of PTHrP to organize an immunosuppressive TME[PJ5]. Additionally, a reduction of PD-1+ and CD44high CD8+ T cells revealed they were less activated. Interestingly, recombinant human PTHrP was sufficient to induce MDSC mobilization in vivo.[JP6] To interrogate the mechanism of MDSC trafficking into the TME, cytokine production by was analyzed in vitro. KPCY-PthlhOE exhibited a pronounced increase and decrease of Cxcl1 and Cxcl10 expression, respectively, relative to the KPCY-EV control. Conclusions: The work herein describes a new mechanism for the mobilization and infiltration of immune suppressive MDSC in the tumor microenvironment, initiated by PTHrP. The PTHrP-dependent immunosuppressive TME excludes and inhibits effector immune cells, such as CD8+ T cells. This phenomenon has been described in squamous-like PDAC but may also apply to other squamous adenocarcinomas. [PJ7] Further elucidation of the mechanism by which PTHrP is the genesis of the immune suppressive TME may spur the development of novel treatments for these more clinically severe cancer subtypes. Citation Format: Calvin P. Johnson, Boyang Ma, Jason Pitarresi. Tumor-derived PTHrP molds an immunosuppressive microenvironment [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 B019.

Systemic treatment of advanced and metastatic urothelial cancer: The landscape in Australia.

The 5-year survival rate of metastatic urothelial carcinoma (mUC) is estimated to be as low as 5%. Currently, systemic platinum-based chemotherapy followed by avelumab maintenance therapy is the only first-line treatment for mUC that has an overall survival benefit. Cisplatin-based chemotherapy (usually in combination with gemcitabine) is the preferred treatment but carboplatin is substituted where contraindications to cisplatin exist. Treatment with immune checkpoint inhibitors, antibody-drug conjugates, and kinase inhibitors has not yet demonstrated superiority to chemotherapy as first-line therapy and remains investigational in this setting. A recent media release indicates that chemotherapy plus nivolumab gives an OS advantage as first-line treatment but results of this study have not yet been made public. Pembrolizumab remains an option in those having primary progression on first-line chemotherapy or within 12 months of neoadjuvant chemotherapy. The antibody-drug conjugate, enfortumab vedotin has TGA approval for patients whose cancer has progressed following chemotherapy and immunotherapy and has just received a positive Pharmaceutical Benefits Scheme recommendation. The use of molecular screens for somatic genetic mutations, gene amplifications, and protein expression is expanding as drugs that target such abnormalities show promise. However, despite these advances, a substantial proportion of patients with mUC have significant barriers to receiving any treatment, including advancing age, frailty, and comorbidities, and less toxic, effective therapies are needed.

Targeting Transcription Factors in Cancer: From "Undruggable" to "Druggable".

Deregulation of transcription factors is critical to hallmarks of cancer. Genetic mutations, gene fusions, amplifications or deletions, epigenetic alternations, and aberrant post-transcriptional modification of transcription factors are involved in the regulation of various stages of carcinogenesis, including cancer initiation, progression, and metastasis. Thus, targeting the dysfunctional transcription factors may lead to new cancer therapeutic strategies. However, transcription factors are conventionally considered as "undruggable." Here, we summarize the recent progresses in understanding the regulation of transcription factors in cancers and strategies to target transcription factors and co-factors for preclinical and clinical drug development, particularly focusing on c-Myc, YAP/TAZ, and β-catenin due to their significance and interplays in cancer.

Tumor evolution-targeted nanomedicine<sup>EVT</sup>

<p indent="0mm">With the recent development of nanotechnology, the integration of nanotechnology with cancer therapy significantly improves the patients’ treatment outcomes. Nanomedicines have drawn great attention due to their increased drug solubility, prolonged blood circulation, increased accumulation and retention in the tumors, thereby ultimately resulting in improved therapeutic effects and biosafety. Notably, tumor biology study has indicated that tumor is constant in dynamic evolution under the internal survival pressure as well as external treatment pressure during therapeutic interventions, including radiotherapy, chemotherapy, molecular targeted therapy, and immunotherapy. These pressures further induced genetic mutations or amplifications of specific genes, resulting in tumor proliferation, drug resistance, and metastasis. Therefore, the therapeutic drugs and regimens should be tuned according to the tumor evolution characteristics. Unfortunately, current design of nanomedicines fails to take into consideration of tumor evolution. Herein, we propose a unique concept of tumor evolution-targeted nanomedicine (nanomedicine^EVT) by fully understanding the tumor evolution process related to proliferation, drug resistance, and metastasis under natural selection or therapeutic pressures. On this basis, nanomedicine^EVT could be designed, which therefore would actively, tactically, and timely attack the tumors. In this way, tumors are expected to become chronic diseases by combination of nanomedicine^EVT and other therapeutic regimens in clinic.

Cancer Therapy Guided by Mutation Tests: Current Status and Perspectives.

The administration of many cancer drugs is tailored to genetic tests. Some genomic events, e.g., alterations of EGFR or BRAF oncogenes, result in the conformational change of the corresponding proteins and call for the use of mutation-specific compounds. Other genetic perturbations, e.g., HER2 amplifications, ALK translocations or MET exon 14 skipping mutations, cause overproduction of the entire protein or its kinase domain. There are multilocus assays that provide integrative characteristics of the tumor genome, such as the analysis of tumor mutation burden or deficiency of DNA repair. Treatment planning for non-small cell lung cancer requires testing for EGFR, ALK, ROS1, BRAF, MET, RET and KRAS gene alterations. Colorectal cancer patients need to undergo KRAS, NRAS, BRAF, HER2 and microsatellite instability analysis. The genomic examination of breast cancer includes testing for HER2 amplification and PIK3CA activation. Melanomas are currently subjected to BRAF and, in some instances, KIT genetic analysis. Predictive DNA assays have also been developed for thyroid cancers, cholangiocarcinomas and urinary bladder tumors. There is an increasing utilization of agnostic testing which involves the analysis of all potentially actionable genes across all tumor types. The invention of genomically tailored treatment has resulted in a spectacular improvement in disease outcomes for a significant portion of cancer patients.

EMBR-20. ELONGATION CONTROL OF MRNA TRANSLATION DRIVES GROUP 3 MEDULLOBLASTOMA

Medulloblastoma (MB) is the most common pediatric intracranial tumor and leading cause of childhood related cancer deaths. Group 3 affiliation and genetic amplifications of the MYC oncogene are predictors of adverse outcome in MB, underscoring a dire need for novel and more effective therapeutic approaches. The let-7 family of small non-coding RNAs (miRNAs) is known to inhibit tumor progression and regulate metabolism by targeting and degrading several cellular mRNAs, including MYC. Indeed, let-7 miRNAs are frequently repressed in several cancer types, including in MYC-driven MB. We previously reported that the mRNA translation elongation regulator eukaryotic Elongation Factor-2 Kinase (eEF2K) is a pivotal mediator of cancer cell adaptation to nutrient deprivation. In the current work, we identified a potential binding site for let-7 miRNAs on the eEF2K 3’ untranslated region (UTR). In addition, eEF2K mRNA and let-7 miRNA expressions negatively correlate in MB, suggesting a potential regulation of the former by the latter. Let-7 miRNAs transfection decreases eEF2K mRNA and protein levels (by ~40–50%). Down-regulation of luciferase activity by let-7 miRNAs is impaired upon mutation of the let-7 binding site on the eEF2K 3’UTR. Inhibition of eEF2K significantly reduces survival of MYC-amplified MB cell lines under nutrient deprivation, altering their mRNA translation rates. Knockout of eEF2K increases survival of MYC-amplified MB xenografts when mice are kept under calorie restricted diets. We conclude that let-7 miRNAs degrade the eEF2K mRNA by binding to its 3’UTR, indicating that let-7 repression in MYC-driven MB is partially responsible for increased eEF2K levels. Moreover, the let-7-eEF2K axis constitutes a critical mechanism for MYC-driven MB adaptation to acute metabolic stress, representing a promising therapeutic target. Future therapeutic studies will aim to combine eEF2K inhibition with caloric restriction mimetic drugs, as eEF2K activity appears critical under metabolic stress conditions.

Store-Operated Calcium Entry: Shaping the Transcriptional and Epigenetic Landscape in Pancreatic Cancer.

Pancreatic ductal adenocarcinoma (PDAC) displays a particularly poor prognosis and low survival rate, mainly due to late diagnosis and high incidence of chemotherapy resistance. Genomic aberrations, together with changes in the epigenomic profile, elicit a shift in cellular signaling response and a transcriptional reprograming in pancreatic tumors. This endows them with malignant attributes that enable them to not only overcome chemotherapeutic challenges, but to also attain diverse oncogenic properties. In fact, certain genetic amplifications elicit a rewiring of calcium signaling, which can confer ER stress resistance to tumors while also aberrantly activating known drivers of oncogenic programs such as NFAT. While calcium is a well-known second messenger, the transcriptional programs driven by aberrant calcium signaling remain largely undescribed in pancreatic cancer. In this review, we focus on calcium-dependent signaling and its role in epigenetic programs and transcriptional regulation. We also briefly discuss genetic aberration events, exemplifying how genetic alterations can rewire cellular signaling cascades, including calcium-dependent ones.

Association of high-risk neuroblastoma classification based on expression profiles with differentiation and metabolism.

Neuroblastoma, the most common extracranial solid malignancy among children, originates from undifferentiated neural crest cells (NCC). Despite recent intensified treatment, high-risk patients still have a high mortality rate. To explore a new therapeutic strategy, we performed an integrated genomic and transcriptomic analysis of 30 high-risk neuroblastoma cases. Based on the expression profiling of RNA sequencing, neuroblastoma was classified into Mesenchymal (MES; n = 5) and Noradrenergic (ADRN; n = 25) clusters, as previously reported in the super-enhancer landscape. The expression patterns in MES-cluster cases were similar to normal adrenal glands, with enrichment in secretion-related pathways, suggesting chromaffin cell-like features built from NCC-derived Schwann cell precursors (SCPs). In contrast, neuron-related pathways were enriched in the ADRN-cluster, indicating sympathoblast features reported to originate from NCC but not via SCPs. Thus, MES- and ADRN-clusters were assumed to be corresponding to differentiation pathways through SCP and sympathoblast, respectively. ADRN-cluster cases were further classified into MYCN- and ATRX-clusters, characterized by genetic alterations, MYCN amplifications and ATRX alterations, respectively. MYCN-cluster cases showed high expression of ALDH18A1, encoding P5CS related to proline production. As reported in other cancers, this might cause reprogramming of proline metabolism leading to tumor specific proline vulnerability candidate for a target therapy of metabolic pathway. In ATRX-cluster, SLC18A2 (VMAT2), an enzyme known to prevent cell toxicity due to the oxidation of dopamine, was highly expressed and VMAT2 inhibitor (GZ-793A) represented significant attenuation of cell growth in NB-69 cell line (high SLC18A2 expression, no MYCN amplification) but not in IMR-32 cell line (MYCN amplification). In addition, the correlation of VMAT2 expression with metaiodobenzylguanidine (MIBG) avidity suggested a combination of VMAT2 inhibitor and MIBG radiation for a novel potential therapeutic strategy in ATRX-cluster cases. Thus, targeting the characteristics of unique neuroblastomas may prospectively improve prognosis.

Fibroblast growth factor receptor (FGFR) inhibitors: A review of a novel therapeutic class

Comprehensive genomic profiling has an emerging role in cancer therapeutics. As treatment options remain needed for advanced cancers, patients are relying increasingly more on tumor genomic alterations as possible targets for cancer treatment. Frequent tumor fibroblast growth factor receptor (FGFR) alterations are seen in many cancers, and include genetic amplifications, mutations, rearrangements and fusions. FGFR inhibitors target these receptor alterations and show promise as a drug class. Currently 2 medications are currently FDA approved: erdafitinib and pemigatinib. Through the FDA accelerated approval process, erdafitinib is indicated to treat metastatic urothelial carcinoma with FGFR2 and FGFR3 alterations, whereas pemigatinib is indicated to treat unresectable cholangiocarcinoma with FGFR2 alterations. Despite growing knowledge about such advanced cancers, treatment is usually palliative. With multiple FGFR inhibitors in the pipeline, further FDA approvals are possible, and it is likely their role in therapy will extend to other cancer types. This review outlines erdafitinib, pemigatinib, their role in cancer, as well as outlining the possible future use of other FGFR inhibitors in urothelial carcinoma, cholangiocarcinoma, and other malignancies.

Single-cell lineage analysis reveals genetic and epigenetic interplay in glioblastoma drug resistance

BackgroundTumors can evolve and adapt to therapeutic pressure by acquiring genetic and epigenetic alterations that may be transient or stable. A precise understanding of how such events contribute to intratumoral heterogeneity, dynamic subpopulations, and overall tumor fitness will require experimental approaches to prospectively label, track, and characterize resistant or otherwise adaptive populations at the single-cell level. In glioblastoma, poor efficacy of receptor tyrosine kinase (RTK) therapies has been alternatively ascribed to genetic heterogeneity or to epigenetic transitions that circumvent signaling blockade.ResultsWe combine cell lineage barcoding and single-cell transcriptomics to trace the emergence of drug resistance in stem-like glioblastoma cells treated with RTK inhibitors. Whereas a broad variety of barcoded lineages adopt a Notch-dependent persister phenotype that sustains them through early drug exposure, rare subclones acquire genetic changes that enable their rapid outgrowth over time. Single-cell analyses reveal that these genetic subclones gain copy number amplifications of the insulin receptor substrate-1 and substrate-2 (IRS1 or IRS2) loci, which activate insulin and AKT signaling programs. Persister-like cells and genomic amplifications of IRS2 and other loci are evident in primary glioblastomas and may underlie the inefficacy of targeted therapies in this disease.ConclusionsA method for combined lineage tracing and scRNA-seq reveals the interplay between complementary genetic and epigenetic mechanisms of resistance in a heterogeneous glioblastoma tumor model.

Abstract B27: A link between small noncoding RNAs and mRNA translation elongation: The let7-eEF2K axis in pediatric tumor adaptation to nutrient deprivation

Abstract Background: Medulloblastoma (MB) and neuroblastoma (NB) are the most common pediatric solid cancers and the leading cause of childhood cancer-related deaths. Genetic amplifications of the MYC and MYCN oncogenes are the strongest independent predictor of adverse outcomes in MB and NB, underscoring a dire need to improve therapeutic approaches. Tumors continually weather stress from acute microenvironmental changes, including limited nutrient availability. The let-7 family of small noncoding RNAs (miRNAs) inhibits tumor progression and regulates metabolism by selectively targeting and degrading mRNAs, including MYC and MYCN. Indeed, let-7 miRNAs are frequently repressed in several cancers, including in MYC-driven MB and NB. We previously reported that the mRNA translation elongation regulator eukaryotic eEF2K is a pivotal mediator of cancer cell adaptation to nutrient deprivation. Our preliminary data indicate that the eEF2K 3´ untranslated region (UTR) harbors a potential binding site for let-7 miRNAs. In addition, eEF2K mRNA and let-7 miRNA expressions negatively correlate in MB and NB. We therefore hypothesized that let-7 downregulation induces eEF2K expression, thereby supporting MYC-driven MB and NB adaptation to nutrient deprivation and tumor progression. Methods: Effects of eEF2K pharmacologic and genetic inhibition on MB and NB cell death were evaluated in vitro by flow cytometry, while cellular mRNA translation rates were studied by polysome fractionation and Click chemistry. The ability of let-7 to degrade eEF2K mRNA was assessed by let-7 miRNAs transfection into MB cells, followed by RT-PCR and Western blotting for eEF2K. Binding of let-7 to the eEF2K 3´UTR was validated by luciferase reporter assay. Finally, NB xenograft mouse models confirmed in vitro observations. Results: Inhibition of eEF2K significantly reduces survival of MYC/MYCN-amplified NB and MB cell lines under nutrient deprivation, altering their mRNA translation rates. Let-7 miRNAs transfection decreases eEF2K mRNA and protein levels by 40-50%. Downregulation of luciferase activity by let-7 miRNAs is impaired upon mutation of the let-7 binding site on the eEF2K 3´UTR. eEF2K knockdown decreases growth twofold in MYCN-amplified NB xenografts in mice under calorie-restriction diets. Conclusions: Let-7 miRNAs degrade the eEF2K mRNA by binding to its 3´UTR, indicating that let-7 repression in MYC-driven NB and MB is partially responsible for increased eEF2K levels. Moreover, the let-7-eEF2K axis constitutes a critical mechanism for MYC-driven MB and NB adaptation to acute metabolic stress, representing a promising therapeutic target. Future therapeutic studies will aim to combine eEF2K inhibition with caloric restriction mimetic drugs, as eEF2K activity appears critical under metabolic stress conditions. Citation Format: Alberto Delaidelli, Gian Luca Negri, Xue Qi Wang, Simran Sidhu, Brian Cho, Gabriel Leprivier, Volker Hovestadt, Stefan Pfister, Michael Taylor, Marcel Kool, Poul Sorensen. A link between small noncoding RNAs and mRNA translation elongation: The let7-eEF2K axis in pediatric tumor adaptation to nutrient deprivation [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr B27.

A Complicated Neighborhood: Insights into the Hodgkin Lymphoma Microenvironment

Classical Hodgkin Lymphoma (cHL) is a heterogenous and complex biological entity. Whereas early studies focussed on characterization of the Reed-Sternberg (RS) cell, there is now increasing recognition of the importance of the tumor microenvironment (TME). This critical but only partially understood component of cHL biology is likely to impact pathogenesis, chemo-sensitivity and long-term outcome. Here, the non-malignant infiltrate is variably comprised of macrophages, regulatory T cells, and stroma, with the relative composition varying by histological sub-type. Notably, relative to other B cell lymphomas, cHL expresses high levels of immune checkpoint receptors such as PD-1 and LAG3, and immune checkpoint ligands such as PD-L1, PD-L2, the latter of which are frequently the subject of genetic amplifications. Hence the bi-directional relationship between the microenvironment and the malignant cell is now a valid target. Breakthroughs in our understanding of the TME in cHL have contributed to its status as the 'poster-child' for how checkpoint blockade can de-activate tumor-tolerance to induce meaningful clinical benefit. A further layer of complexity within the TME is the potential aetiological relationship between cHL and the Epstein-Barr virus, a ubiquitous virus found to reside within the RS cells in 40% of cases, particularly in those cases that have mixed cellularity. Unlike benign EBV-infected B cells, within RS cells the virus is in a highly aberrant latency state with expression of the viral oncoprotein LMP1, a virus that is known to induce immunosuppression and drive PD-L1 expression through the NFkB and the JAK-STAT pathways. But numerous unanswered mechanistic questions remain, not least in the light of the frequent genetically driven deficiencies in antigen presentation present in RS cells, particularly in cases of nodular sclerosing disease. This has reignited debate about the relative roles of adaptive and innate immunity in this disease. Remaining questions that need to be addressed include the evolution of the interaction between the TME and the malignant compartment during the course of cHL, the role of other immune checkpoints and their impact on combinatorial immune based strategies, and the contribution to immune-evasion played by stromal cells. Further understanding will assist the rational development of new immune-based strategies, and potentially one day a chemo-free regimen that is as clinically efficacious but less toxic than current chemotherapies. Disclosures Gandhi: Bristol Myers Squibb: Membership on an entity's Board of Directors or advisory committees, Research Funding; Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding; Gilead: Honoraria, Research Funding; Roche: Honoraria, Other: Travel Support; Janssen: Membership on an entity's Board of Directors or advisory committees, Research Funding; Merck: Membership on an entity's Board of Directors or advisory committees; Amgen: Honoraria.

Characterization of iPSCs derived from low grade gliomas revealed early regional chromosomal amplifications during gliomagenesis.

IDH1 mutation has been identified as an early genetic event driving low grade gliomas (LGGs) and it has been proven to exerts a powerful epigenetic effect. Cells containing IDH1 mutation are refractory to epigenetical reprogramming to iPSC induced by expression of Yamanaka transcription factors, a feature that we employed to study early genetic amplifications or deletions in gliomagenesis. We made iPSC clones from freshly surgically resected IDH1 mutant LGGs by forced expression of Yamanaka transcription factors. We sequenced the IDH locus and analyzed the genetic composition of multiple iPSC clones by array-based comparative genomic hybridization (aCGH). We hypothesize that the primary cell pool isolated from LGG tumor contains a heterogeneous population consisting tumor cells at various stages of tumor progression including cells with early genetic lesions if any prior to acquisition of IDH1 mutation. Because cells containing IDH1 mutation are refractory to reprogramming, we predict that iPSC clones should originate only from LGG cells without IDH1 mutation, i.e. cells prior to acquisition of IDH1 mutation. As expected, we found that none of the iPSC clones contains IDH1 mutation. Further analysis by aCGH of the iPSC clones reveals that they contain regional chromosomal amplifications which are also present in the primary LGG cells. These results indicate that there exists a subpopulation of cells harboring gene amplification but without IDH1 mutation in the LGG primary cell pool. Further analysis of TCGA LGG database demonstrates that these regional chromosomal amplifications are also present in some cases of low grade gliomas indicating they are reoccurring lesions in glioma albeit at a low frequency. Taken together, these data suggest that regional chromosomal alterations may exist prior to the acquisition of IDH mutations in at least some cases of LGGs.

Algorithm for the treatment of advanced or metastatic squamous non-small-cell lung cancer: an evidence-based overview.

The treatment of squamous non-small-cell lung cancer (nsclc) is evolving. In the past, the backbone of treatment was chemotherapy, with very few other options available. Fortunately, that situation is changing, especially with a better understanding of tumour biology. Various strategies have been tried to improve patient outcomes. The most notable advance must be immunotherapy, which has revolutionized the treatment paradigm for lung cancer in patients without a driver mutation. Immunotherapy is now the treatment of choice in patients who have progressed after chemotherapy and is replacing chemotherapy as upfront therapy in a selected population. Other strategies have also been tried, such as the addition of targeted therapy to chemotherapy. Targeted agents include ramucirumab, an inhibitor of vascular endothelial growth factor receptor 2, and necitumumab, a monoclonal antibody against epithelial growth factor receptor. Recently, advances in molecular profiling have also been applied to tumours of squamous histology, in which multiple genetic alterations, including mutations and amplifications, have been described. Research is actively seeking targetable mutations and testing various therapies in the hopes of further improving prognosis for patients with squamous nsclc. Here, we review the various advances in the treatment of squamous nsclc and present a proposed treatment algorithm based on current evidence.

Mir-34a-5p Mediates Cross-Talk between M2 Muscarinic Receptors and Notch-1/EGFR Pathways in U87MG Glioblastoma Cells: Implication in Cell Proliferation.

Glioblastoma (GBM) is the most aggressive human brain tumor. The high growth potential and decreased susceptibility to apoptosis of the glioma cells is mainly dependent on genetic amplifications or mutations of oncogenic or pro-apoptotic genes, respectively. We have previously shown that the activation of the M2 acetylcholine muscarinic receptors inhibited cell proliferation and induced apoptosis in two GBM cell lines and cancer stem cells. The aim of this study was to delve into the molecular mechanisms underlying the M2-mediated cell proliferation arrest. Exploiting U87MG and U251MG cell lines as model systems, we evaluated the ability of M2 receptors to interfere with Notch-1 and EGFR pathways, whose activation promotes GBM proliferation. We demonstrated that the activation of M2 receptors, by agonist treatment, counteracted Notch and EGFR signaling, through different regulatory cascades depending, at least in part, on p53 status. Only in U87MG cells, which mimic p53-wild type GBMs, did M2 activation trigger a molecular circuitry involving p53, Notch-1, and the tumor suppressor mir-34a-5p. This regulatory module negatively controls Notch-1, which affects cell proliferation mainly through the Notch-1/EGFR axis. Our data highlighted, for the first time, a molecular circuitry that is deregulated in the p53 wild type GBM, based on the cross-talk between M2 receptor and the Notch-1/EGFR pathways, mediated by mir-34a-5p.

Multicopy plasmids allow bacteria to escape from fitness trade-offs during evolutionary innovation.

Understanding the mechanisms governing innovation is a central element of evolutionary theory. Novel traits usually arise through mutations in existing genes, but trade-offs between new and ancestral protein functions are pervasive and constrain the evolution of innovation. Classical models posit that evolutionary innovation circumvents the constraints imposed by trade-offs through genetic amplifications, which provide functional redundancy. Bacterial multicopy plasmids provide a paradigmatic example of genetic amplification, yet their role in evolutionary innovation remains largely unexplored. Here, we reconstructed the evolution of a new trait encoded in a multicopy plasmid using TEM-1 β-lactamase as a model system. Through a combination of theory and experimentation, we show that multicopy plasmids promote the coexistence of ancestral and novel traits for dozens of generations, allowing bacteria to escape the evolutionary constraints imposed by trade-offs. Our results suggest that multicopy plasmids are excellent platforms for evolutionary innovation, contributing to explain their extreme abundance in bacteria.

Stromal-derived IGF2 promotes colon cancer progression via paracrine and autocrine mechanisms.

The insulin-like growth factor (IGF)2/IGF1 receptor (IGF1R) signaling axis has an important role in intestinal carcinogenesis and overexpression of IGF2 is an accepted risk factor for colorectal cancer (CRC) development. Genetic amplifications and loss of imprinting contribute to the upregulation of IGF2, but insufficiently explain the extent of IGF2 expression in a subset of patients. Here, we show that IGF2 was specifically induced in the tumor stroma of CRC and identified cancer-associated fibroblasts (CAFs) as the major source. Further, we provide functional evidence that stromal IGF2, via the paracrine IGF1R/insulin receptor axis, activated pro-survival AKT signaling in CRC cell lines. In addition to its effects on malignant cells, autocrine IGF2/IGF1R signaling in CAFs induced myofibroblast differentiation in terms of alpha-smooth muscle actin expression and contractility in floating collagen gels. This was further augmented in concert with transforming growth factor-β (TGFβ) signaling suggesting a cooperative mechanism. However, we demonstrated that IGF2 neither induced TGFβ/smooth muscle actin/mothers against decapentaplegic (SMAD) signaling nor synergized with TGFβ to hyperactivate this pathway in two dimensional and three dimensional cultures. IGF2-mediated physical matrix remodeling by CAFs, but not changes in extracellular matrix-modifying proteases or other secreted factors acting in a paracrine manner on/in cancer cells, facilitated subsequent tumor cell invasion in organotypic co-cultures. Consistently, colon cancer cells co-inoculated with CAFs expressing endogenous IGF2 in mouse xenograft models exhibited elevated invasiveness and dissemination capacity, as well as increased local tumor regrowth after primary tumor resection compared with conditions with IGF2-deficient CAFs. In line, expression of IGF2 correlated with elevated relapse rates and poor survival in CRC patients. In agreement with our results, high-level coexpression of IGF2 and TGFβ was predicting adverse outcome with higher accuracy than increased expression of the individual genes alone. Taken together, we demonstrate that stroma-induced IGF2 promotes colon cancer progression in a paracrine and autocrine manner and propose IGF2 as potential target for tumor stroma cotargeting strategies.

Abstract CT101: NCI-molecular analysis for therapy choice (NCI-MATCH) clinical trial: interim analysis

Abstract The NCI MATCH is an efficacy signal-finding trial to identify molecular alterations that can be matched to targeted treatments in tumor biopsies from patients (pts) with refractory solid tumors or lymphomas.br /&amp;gt;METHODS: An Ion Torrent Oncomine panel sequencing assay and a binary PTEN immunohistochemistry assay were employed. NCI-MATCH opened in August 2015. A protocol-directed pause in screening for interim analysis occurred in November 2015 with goals to assess tumor biopsy feasibility and quality, performance of the CLIA-accredited laboratories, any unanticipated concerns with the study, the match rate for the first activated 10 arms and for planned arms, the spectrum of molecular abnormalities identified, histologic tumor types and demographics. RESULTS: Between 8-12-15 and 11-11-15, 795 pts enrolled for screening and 739 biopsies were submitted. Biopsies were submitted from community (2/3) and academic (1/3) sites. Sequencing was completed on 645 of these specimens (87%). Median turn around time was 27 days but increased from 14 days in the first month to 36 days in the last month, correlating with marked increase in weekly accrual. The highest toxicity (Grade 3) possibly related to biopsy was &amp;lt; 1%. The most frequent tumor types sequenced were colorectal (13%), breast (13%), ovarian (11%), non-small cell lung (7.4%), endometrial (7%), pancreatic (5%), head/neck (5%) esophageal/gastric (4%), cholangiocarcinoma and neuroendocrine (3% each), and small cell lung, prostate, bladder, and unknown primary (&amp;lt;3% each). Fifty-six patients (9%) had actionable mutations of interest (aMOIs); of these, 33 pts (5.1%, 95%CI 3.5, 7.1%) met molecular eligibility for assignment to one of 10 treatment arms. The most common genetic mutations, amplifications or translocations were: PercentMutation/amplification/translocation52TP5319KRAS12PIK3CA10APC, CDH14-5CDKN2A3-4CCND13BRAF, PTEN, ESR1, CTNNB1, ERBB2, CCNE12.5EGFR, FBXW7,FGFR 1/2/3, MDM22KIT, BRCA 1/2, IDH 1/2, NF1, RB1 CONCLUSIONS: Accrual was brisk and biopsies were feasible and safe with adequate tumor yield and results. The match rate was lower than predicted for the first 10 treatment arms. Accrual of less common tumor histologic types exceeded expectations. Results from the interim analysis will inform the types of treatment and predicted match rate for additional MATCH arms. NCI-MATCH will re-open with increased capacity and additional treatment arms with a match rate goal of at least 20%. Citation Format: Barbara A. Conley, Robert Gray, Alice Chen, Peter O’Dwyer, Carlos Arteaga, Brent Coffey, David Patton, Shuli Li, Lisa M. McShane, Larry Rubinstein, Robert Comis, Jeffrey Abrams, Paul M. Williams, Chih-Jian Lih, Stanley Hamilton, Edith Mitchell, James Zwiebel, Keith Flaherty, NCI MATCH team. NCI-molecular analysis for therapy choice (NCI-MATCH) clinical trial: interim analysis. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr CT101.