tbuckley/cabot-search huggingface dataset:
Association of FGFR1 with ERα Maintains Ligand-Independent ER Transcription and Mediates Resistance to Estrogen Deprivation in ER+ Breast Cancer
Authors: Luigi Formisano, Kimberly M. Stauffer, Christian D. Young, Neil E. Bhola, Angel L. Guerrero-Zotano, Valerie M. Jansen, Mónica M. Estrada, Katherine E. Hutchinson, Jennifer M. Giltnane, Luis J. Schwarz, Yao Lu, Justin M. Balko, Olivier Deas, Stefano Cairo, Jean-Gabriel Judde, Ingrid A. Mayer, Melinda Sanders, Teresa C. Dugger, Roberto Bianco, Thomas Stricker, Carlos L. Arteaga
Journal: Clinical Cancer Research (2017)

Purpose:FGFR1 amplification occurs in approximately 15% of estrogen receptor-positive (ER+) human breast cancers. We investigated mechanisms by which FGFR1 amplification confers antiestrogen resistance to ER+ breast cancer.Experimental Design: ER+ tumors from patients treated with letrozole before surgery were subjected to Ki67 IHC, FGFR1 FISH, and RNA sequencing (RNA-seq). ER+/FGFR1-amplified breast cancer cells, and patient-derived xenografts (PDX) were treated with FGFR1 siRNA or the FGFR tyrosine kinase inhibitor lucitanib. Endpoints were cell/xenograft growth, FGFR1/ERα association by coimmunoprecipitation and proximity ligation, ER genomic activity by ChIP sequencing, and gene expression by RT-PCR.Results: ER+/FGFR1-amplified tumors in patients treated with letrozole maintained cell proliferation (Ki67). Estrogen deprivation increased total and nuclear FGFR1 and FGF ligands expression in ER+/FGFR1-amplified primary tumors and breast cancer cells. In estrogen-free conditions, FGFR1 associated with ERα in tumor cell nuclei and regulated the transcription of ER-dependent genes. This association was inhibited by a kinase-dead FGFR1 mutant and by treatment with lucitanib. ChIP-seq analysis of estrogen-deprived ER+/FGFR1-amplified cells showed binding of FGFR1 and ERα to DNA. Treatment with fulvestrant and/or lucitanib reduced FGFR1 and ERα binding to DNA. RNA-seq data from FGFR1-amplified patients' tumors treated with letrozole showed enrichment of estrogen response and E2F target genes. Finally, growth of ER+/FGFR1-amplified cells and PDXs was more potently inhibited by fulvestrant and lucitanib combined than each drug alone.Conclusions: These data suggest the ERα pathway remains active in estrogen-deprived ER+/FGFR1-amplified breast cancers. Therefore, these tumors are endocrine resistant and should be candidates for treatment with combinations of ER and FGFR antagonists. Clin Cancer Res; 23(20); 6138-50. ©2017 AACR.
Abstract 3581: GATK ACNV: allelic copy-number variation discovery from SNPs and coverage data
Authors: Aaron Chevalier, Lee Lichtenstein, Andrey Smirnov, Samuel K. Lee, Mehrtash Babidi, David I. Benjamin, Valentin Ruano-Rubio
Journal: Cancer Research (2017)

Abstract The presence of somatic copy-number alterations in tumor genomes can be used to predict both patient sensitivity to treatments as well as outcomes. The inclusion of allelic data improves statistical power to detect copy-number events and allows for discovery of copy-neutral events. We present GATK ACNV, an allelic copy-number variation method built on the Genome Analysis Toolkit. ACNV is a tool for detecting somatic copy-number activity from whole exome and whole genome sequencing data by segmenting the genome into regions of constant copy number and estimating copy ratio and minor-allele fraction in those regions. ACNV uses a novel probabilistic model to account for reference bias (optionally using a panel of normals), which improves the estimation of minor-allele fraction. We combine this with the coverage model from GATK CNV by segmenting with a unified hidden Markov model, improving the statistical power to detect copy-number variation. We validate ACNV using a purity series of the cell line HCC1143 and cancer samples from The Cancer Genome Atlas. Our results show that ACNV is able to discover regions of somatic copy-number activity accurately and with high resolution in both whole exome and whole genome sequencing data. Citation Format: Aaron Chevalier, Lee Lichtenstein, Andrey Smirnov, Samuel K. Lee, Mehrtash Babidi, David I. Benjamin, Valentin Ruano-Rubio. GATK ACNV: allelic copy-number variation discovery from SNPs and coverage data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3581. doi:10.1158/1538-7445.AM2017-3581
Abstract 3162: HRAS G12V predicts for innate resistance to PI3Kα inhibition in head and neck squamous cell cancer
Authors: Kara M. Ruicci, Ren Sun, Morgan Black, Nicole Pinto, John Yoo, Kevin Fung, Danielle Macneil, Lauire Aillies, Joseph S. Mymryk, Paul C. Boutros, John W. Barrett, Anthony C. Nichols
Journal: Cancer Research (2017)

Abstract Introduction: Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide, with an incidence of ~600 000 new cases per year and a 50% mortality rate for advanced disease. The mutational landscape of HNSCC has been recently elucidated, introducing the possibility for targeted therapeutic approaches. PIK3CA—which encodes the α-catalytic subunit of PI3K (PI3Kα)—is the most frequently altered actionable target in HNSCC, however it is not presently clear which patients benefit most from PI3Kα-inhibition. BYL719 is a leading PI3Kα inhibitor in clinical development for HNSCC. We previously examined the responses of a large panel of genetically-characterized HNSCC cell lines to BYL719 and identified activating HRAS G12V mutations as strong predictors for BYL719 resistance. Here we examine if this mutation is able to individually modulate BYL719 response through overexpression and knockdown studies. Methods: To determine if HRAS G12V was able to modulate BYL719 sensitivity, we knocked down HRAS in HRAS G12V and HRAS wild-type (WT) cell lines using RNA interference, and then treated cells over 10-point dose ranges with BYL719. Sensitivity was determined by calculating IC50 (half-maximal inhibitory concentration) values at 72 hours using PrestoBlue®. Constructs expressing wildtype (WT) HRAS or HRAS G12V were transfected into BYL719-sensitive cells for overexpression studies and cells were selected using G418 Sulfate for 1 month. Proliferation and BYL719 sensitivity (IC50 values) were measured as described. Immunoblotting was used to examine activity of the PI3K-AKT axis with and without BYL719 (1μM) for 24 hours. Results &amp; Conclusions: HRAS knockdown sensitized HRAS G12V lines to BYL719 (lower IC50), but did not affect the response of WT HRAS cells. WT HRAS and HRAS G12V overexpression significantly increased cellular proliferation and promoted BYL719 resistance. In HRAS G12V cell lines, we observed high levels of active phosphorylated AKT (S473/T308), even in the presence of BYL719. Collectively these findings highlight the predictive role of HRAS G12V for innate BYL719 resistance and contribute to our understanding of which patients may respond best on BYL719 therapy. Citation Format: Kara M. Ruicci, Ren Sun, Morgan Black, Nicole Pinto, John Yoo, Kevin Fung, Danielle Macneil, Lauire Aillies, Joseph S. Mymryk, Paul C. Boutros, John W. Barrett, Anthony C. Nichols. HRAS G12V predicts for innate resistance to PI3Kα inhibition in head and neck squamous cell cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3162. doi:10.1158/1538-7445.AM2017-3162
Abstract 1507: Fatty acid oxidation mediated autophagy regulation in triple negative breast cancer
Authors: Kwang Hwa Jung, Jun Hyoung Park, Tirupataiah Sirupangi, Sajna Vithayathil, Lee-Jun Wong, Benny A. Kaipparettu
Journal: Cancer Research (2017)

Abstract Compared to hormone regulated/responsive (ER+) breast cancer (BC), triple negative BC (TNBC) patients have a worse overall survival, a significantly shorter disease-free survival, and a shorter post-recurrence survival. Using transmitochondrial cybrid (cybrid) (compares different mitochondria under a common defined nuclear background)-based discovery and validation in cell lines, patient derived xenografts (PDXs) and BC clinical tissues/data, we recently published that fatty acid oxidation (FAO) is a major energy pathway in TNBC. We also showed that FAO is a major regulator of Src activation by autophosphorylation at Src Y419 in metastatic TNBC. Our data suggest that inhibition of FAO induce cell growth inhibition. Short-term treatment of FAO inhibitors induces both cell cycle arrest and apoptosis. We observed cell cycle arrest in G1-S phase in FAO inhibitor treated TNBC cells. Apoptotic markers like cleaved Caspase-3 and cleaved PARP induced in FAO inhibited cells. Short-term treatment of FAO inhibitor also showed induction of AKT pathway. Further analysis on the role of FAO in TNBC suggests that FAO is a critical player in autophagy signaling in TNBC. Long-term treatment with FAO inhibitors or knockdown of FAO rate-limiting proteins carnitine palmitoyltransferase I (CPT1) induce autophagic cell death with beclin-1 and LC3-II induction in TNBC. However, no such phenomenon observed in estrogen receptor positive (ER+) breast cancer cell lines. Treatment with autophagy inhibitor 3-methyladenine (3-MA) abolished the FAO-induced cell growth inhibition and reduced beclin-1 and LC3-II induction. Ongoing studies using knock-down and over expression approaches focus on the role of specific pathways that are responsible for mitochondrial energy reprogramming regulated autophagy signaling in metastatic TNBC. Citation Format: Kwang Hwa Jung, Jun Hyoung Park, Tirupataiah Sirupangi, Sajna Vithayathil, Lee-Jun Wong, Benny A. Kaipparettu. Fatty acid oxidation mediated autophagy regulation in triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1507. doi:10.1158/1538-7445.AM2017-1507
Abstract 1168: Efficacy of the IRAK4 inhibitor CA-4948 in patient-derived xenograft models of diffuse large B cell lymphoma
Authors: Robert N. Booher, Maria Elena Samson, Guang-Xin Xu, Hongsheng Cheng, David P. Tuck
Journal: Cancer Research (2017)

Abstract IRAK4 kinase activity is required for toll-like receptor (TLR) and interleukin-1 receptor (IL-1R) signaling in a variety of myeloid and lymphoid cell types. Recruitment of IRAK4 to these receptors and its subsequent activation is facilitated by the MYD88 adaptor protein, which is mutated in ~22% of DLBCL cases. The MYD88 L265P activating mutation is found in ~30% of the activated B-cell (ABC) and ~6% of germinal center B-cell (GCB) subtypes of DLBCL and leads to constitutive activation of NF-κB signaling that is associated with worse prognosis. Thus, the development of small molecule inhibitors targeting IRAK4 is an attractive anticancer strategy for MYD88 mutation-containing cancers such as DLBCL. We are developing an IRAK4 inhibitor, CA-4948, as a therapeutic agent for hematological cancers with dysregulated TLR/MYD88/IRAK4 signaling. CA-4948 (previously AU-4948) is a selective and potent IRAK4 kinase inhibitor with in vivo activity in a TLR4-induced cytokine release model. CA-4948 exhibits favorable DMPK properties, oral bioavailability, and is well tolerated in mice. Furthermore, CA-4948 was previously shown to exhibit dose-dependent efficacy in ABC-DLBCL MYD88-L265P xenograft tumor models using cell lines OCI-LY3 and OCI-LY10. Here, we report the efficacy results from testing CA-4948 in a panel of well characterized, patient-derived DLBCL tumor xenograft (PDX) mouse models. CA-4948 exhibited the greatest efficacy in four of the five ABC-DLBCL PDX models tested as compared to GBC-DLBCL and ABC/GCB DLBCL PDX models. Furthermore, CA-4948 was efficacious in ABC-DLBCL PDX tumors containing activating mutations in both TLR/IL-1R and BCR signaling pathways (MYD88 and CD79B double mutants). Interestingly, the one ABC-DLBCL PDX model that failed to respond to CA-4948 treatment contained a MYD88 L265P mutation as well as a BCL6 translocation. While this particular PDX model was resistant to CA-4948, and showed a weak anti-tumor response to single-agent ibrutinib, the combination treatment of ibrutinib and CA-4948 exhibited a synergistic tumor growth inhibition effect. In summary, CA-4948 exhibited anti-tumor activity in ABC-type DLCBL PDX tumor models including those containing combinations of activating mutations in the TLR/IL-1R and BCR signaling pathways. These results underscore the therapeutic potential of IRAK4 kinase inhibition by CA-4948, as a single-agent or in combination with BCR inhibitors, for the treatment of DLBCL. Citation Format: Robert N. Booher, Maria Elena Samson, Guang-Xin Xu, Hongsheng Cheng, David P. Tuck. Efficacy of the IRAK4 inhibitor CA-4948 in patient-derived xenograft models of diffuse large B cell lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1168. doi:10.1158/1538-7445.AM2017-1168
Multifaceted Role of BTLA in the Control of CD8+ T-cell Fate after Antigen Encounter
Authors: Krit Ritthipichai, Cara L. Haymaker, Melisa Martinez, Andrew Aschenbrenner, Xiaohui Yi, Minying Zhang, Charuta Kale, Luis M. Vence, Jason Roszik, Yared Hailemichael, Willem W. Overwijk, Navin Varadarajan, Roza Nurieva, Laszlo G. Radvanyi, Patrick Hwu, Chantale Bernatchez
Journal: Clinical Cancer Research (2017)

Purpose: Adoptive T-cell therapy using autologous tumor-infiltrating lymphocytes (TIL) has shown an overall clinical response rate 40%-50% in metastatic melanoma patients. BTLA (B-and-T lymphocyte associated) expression on transferred CD8+ TILs was associated with better clinical outcome. The suppressive function of the ITIM and ITSM motifs of BTLA is well described. Here, we sought to determine the functional characteristics of the CD8+BTLA+TIL subset and define the contribution of the Grb2 motif of BTLA in T-cell costimulation.Experimental Design: We determined the functional role and downstream signal of BTLA in both human CD8+ TILs and mouse CD8+ T cells. Functional assays were used including single-cell analysis, reverse-phase protein array (RPPA), antigen-specific vaccination models with adoptively transferred TCR-transgenic T cells as well as patient-derived xenograft (PDX) model using immunodeficient NOD-scid IL2Rgammanull (NSG) tumor-bearing mice treated with autologous TILs.Results: CD8+BTLA- TILs could not control tumor growth in vivo as well as their BTLA+ counterpart and antigen-specific CD8+BTLA- T cells had impaired recall response to a vaccine. However, CD8+BTLA+ TILs displayed improved survival following the killing of a tumor target and heightened "serial killing" capacity. Using mutants of BTLA signaling motifs, we uncovered a costimulatory function mediated by Grb2 through enhancing the secretion of IL-2 and the activation of Src after TCR stimulation.Conclusions: Our data portrays BTLA as a molecule with the singular ability to provide both costimulatory and coinhibitory signals to activated CD8+ T cells, resulting in extended survival, improved tumor control, and the development of a functional recall response. Clin Cancer Res; 23(20); 6151-64. ©2017 AACR.
Abstract 5081: Disruption of DNA methyltransferase (DNMT) 1 confers resistance to DNMT inhibitors in human colorectal cancer cells
Authors: Angelo B. Laranjeira, Dat Nguyen, Erich Huang, James H. Doroshow, Sherry X. Yang
Journal: Cancer Research (2017)

Abstract DNA methyltransferase (DNMT) 1 is responsible for the maintenance and propagation of DNA methylation pattern, and plays an important role in cell survival and proliferation. Thus, targeting DNMT represents a promising approach for cancer treatment. However, the role of DNMT1 in treatment efficacy with DNMT inhibitors remains controversial. The aim of this study was to investigate potential alterations of DNMT inhibitor-induced cytotoxicity and cellular survival after disruption/knockout of DNMT1 in cancer cells. The human colorectal cancer cell line HCT116 and its isogenic DNMT1 knockout pair were treated with increasing concentrations of 4’-thio-5-aza-2’-deoxycytidine (aza-TdCyd), a novel DNMT inhibitor, and 5-aza-2’-deoxycytidine (aza-dCyd). Cytotoxic effects and cell survival were evaluated by MTT and clonogenic assays. Apoptosis was measured by annexin-V/propidium iodide test, and expression of DNMT1, DNMT3A and DNMT3B was detected by western blot. After 96h of drug exposure, IC50s of aza-TdCyd and aza-dCyd were 0.031µM and 0.28 µM, respectively, in HCT116 cells. In contrast, DNMT1 knockout cells were remarkably resistant to both drugs with IC50s all higher than 10 µM. The treatments resulted in a significant increase in apoptosis in the parental line versus its knockout counterpart. As for the cell survival, IC50s were ~0.12 µM for aza-TdCyd and ~4.62 µM for aza-dCyd in HCT116 cells, compared to ~43.77 µM and ~62.09 µM in DNMT1 knockout cells. As such, disruption of DNMT1 caused over 300-fold and 10-fold increase in resistance to aza-TdCyd and aza-dCyd. Moreover, we observed a G2/M arrest produced by aza-TdCyd versus aza-dCyd in the parental cells, and no apparent alteration in cell cycle phase distribution in DNMT1 knockout cells. Notably, aza-TdCyd was more potent than aza-dCyd in depleting DNMT3A and/or DNMT1 in both cell lines after 48h of treatment. Our findings demonstrate that disruption of DNMT1 leads to a significantly increased resistance to aza-TdCyd and aza-dCyd, suggesting that DNMT1 is critical to the antitumor activity of DNMT inhibitors. Aza-TdCyd is much more potent than aza-dCyd for both inhibition of DNMTs and growth of cancer cells. Citation Format: Angelo B. Laranjeira, Dat Nguyen, Erich Huang, James H. Doroshow, Sherry X. Yang. Disruption of DNA methyltransferase (DNMT) 1 confers resistance to DNMT inhibitors in human colorectal cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5081. doi:10.1158/1538-7445.AM2017-5081
Abstract 3414: Novel MGMT variant association in Mexican patients with astrocytoma
Authors: Liliana Gomez-Flores-Ramos, Talia Wegman-Ostrosky
Journal: Cancer Research (2017)

Abstract Introduction: Astrocytomas are the most common and lethal brain tumors with a median survival of 15 months. Different biomarkers have arisen to classify and treat this type of tumors; one of these markers is MGMT. The methylation status of this gene is a prognostic and predictive factor. The MGMT (O-6-Methylguanine-DNA Methyltransferase) is involved in the cellular response to the effects of O6-methylguanine (O6-MeG) in DNA. Repairs alkylated guanine in DNA by transferring the alkyl group at the O-6 position to a cysteine residue in the enzyme. The dysregulation of this methylation is critical in the development of certain cancers. Objective: To identify germinal MGMT gene variations in patients with astrocytoma. Material and methods: 55 randomly selected Mexican patients diagnosed with astrocytoma between 2008-2014 were consented to perform the molecular analysis of the whole gene and 5´UTR and 3´UTR regions of MGMT at Ion Torrent platform. Each amplified region had a depth of minimum 1500x. Ion Reporter software was used to analyze the genetic variants and using Integrative Genomic Viewer we confirmed that each variant had a Phred higher than 25. Genotypic frequencies were compared with HapMapMex and Mexican ancestry population from the 1000 Genomes project. Results. In lymphocytes DNA, eight genetic variants were found, and two of them were statistically significant risk factors: rs7896488 alternative allele A with a frequency of 15% in patients with astrocytoma, and only 4% of the control group (OR=5.53, IC 1.96-15.59 p = 0.0007) and rs2308326 ancestral allele C, where 93% of the patients were carriers of allele C in contrast with 73% of controls (OR=5.39, IC 2.29-12.69 p = 0.000019). These variants are non-coding single nucleotide polymorphisms, rs7896488 is a 3' UTR genetic variant, while rs2308326 is an intronic variant. Conclusion: Our study found two new risk SNV for Astrocytoma in a Mexican population. Citation Format: Liliana Gomez-Flores-Ramos, Talia Wegman-Ostrosky. Novel MGMT variant association in Mexican patients with astrocytoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3414. doi:10.1158/1538-7445.AM2017-3414
Comment on “Using geospatial mapping to design HIV elimination strategies for sub-Saharan Africa”
Authors: Christopher Fontaine, Mary Mahy, José-Antonio Izazola, Peter D. Ghys
Journal: Science Translational Medicine (2017)

A recent study showed how geospatial mapping can be used to improve Lesotho's HIV treatment program to achieve the 90-90-90 targets set by the United Nations but incorrectly describes "treatment as prevention" as the UN's strategy for a successful national AIDS response.
Abstract 1145: Overcoming chemoresistance and blocking metastasis in breast cancer by targeting HuR
Authors: Xiaoqing Wu, Rebecca Marquez, Shuang Han, Lan Lan, Dan A. Dixon, Jeffrey Aubé, Danny R. Welch, Liang Xu
Journal: Cancer Research (2017)

Abstract Patients with metastatic breast cancer have a dismal 5-year survival rate of only 24%. Chemoresistance is another contributor to the high mortality of advanced breast cancer. The RNA-binding protein, Hu antigen R (HuR), is overexpressed at all stages of breast cancer development. Cytoplasmic HuR accumulation correlates with high-grade malignancy, poor distant disease-free survival and serves as a prognostic factor for poor clinical outcome in breast cancer. HuR promotes tumorigenesis by promoting mRNA stability and translation of proteins implicated in proliferation, survival, angiogenesis, invasion, and metastasis. HuR also modulates sensitivity of breast cancer cells to chemotherapy. Taken together, HuR is an emerging target for breast cancer therapy, especially metastatic breast cancer. Using shRNA and CRISPR technologies to modulate HuR expression in breast cancer cells, we found that cells with HuR KD/KO were less invasive and more sensitive to chemotherapy. In an effort to discover small molecules that disrupt the HuR-mRNA interaction and block HuR functions in breast cancer progression, metastasis and chemoresistance, high throughput screening (HTS) was carried out in several chemical libraries (~23,000 compounds) using fluorescence polarization (FP) assay, which identified several initial hits with sub-micromolar inhibitory constants (Ki). Those potential inhbitors were then validated by ALPHA assay (Amplified Luminescent Proximity Homogeneous Assay), confirmed by Surface Plasmon Resonance (SPR). In cell-based assays, top hit KH-3 and its optimized analogs, specifically shortened HuR target mRNA half-lifes and decreased the level of the encoded proteins. Moreover, those compounds inhibited invasion and restored chemosensitivity. qPCR arrays focusing on specific pathways revealed that HuR inhibitors potently upregulated metastatic suppressors and downregulated genes frequently overexpressed in lung metastases. In animal studies, KH-3 not only exhibited potent antitumor efficacy in orthotopic xenografts of breast cancer, but also efficiently blocked experimental metastasis. In conclusion, we identified potent and specific small molecule inhibitors of HuR-mRNA interaction for potential anti-metastatic therapy for breast cancer with HuR overexpression. Citation Format: Xiaoqing Wu, Rebecca Marquez, Shuang Han, Lan Lan, Dan A. Dixon, Jeffrey Aubé, Danny R. Welch, Liang Xu. Overcoming chemoresistance and blocking metastasis in breast cancer by targeting HuR [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1145. doi:10.1158/1538-7445.AM2017-1145