bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 65: A novel tool for functional characterization of mutations and their response to targeted therapy
Authors: Barbash Zohar , Haham DIkla , Fillipov-Levy Natalie , Cohen Limor , Birnbaum Lea , Rotkopf Shay , Kifer Ilona , Tarcic Gabi 
Published: June 2022

Abstract
Genomic profiling of tumors has uncovered staggering amounts of novel alterations, termed variants of uncertain significance (VUS), even in well-studied oncogenes. Strikingly, as the number of sequenced samples increases so does the number of VUS. While the study of alterations identified as VUS has shown that some are inconsequential, it has also been shown that many can cause protein activation and are involved in oncogenicity and resistance to therapy or might serve as novel drug targets. We developed a high-throughput cell-based assay that allows functional annotation of VUS and their sensitivity to different inhibitors. The system quantifies signaling pathway activation using fluorescent imaging coupled with image analysis of cells expressing the mutated protein together with a fluorescently labeled signaling pathway reporter. We show that this method accurately identifies known driver mutations in 10 different oncogenes, including receptor tyrosine kinases and signaling proteins, spanning the four major signaling pathways involved in cancer. We then deployed this system to characterize over 100 different VUS in these genes. We also show that the method correctly recapitulates differential sensitivity of cKIT and EGFR mutations to different inhibitors. Finally, we highlight the importance of concurrent mutations in KRAS which abrogate the response to EGFR inhibitors. Altogether, this system provides significant information both for development of new targeted agents as well as tailoring of optimal treatment for patients.
Citation Format: Zohar Barbash, DIkla Haham, Natalie Fillipov-Levy, Limor Cohen, Lea Birnbaum, Shay Rotkopf, Ilona Kifer, Gabi Tarcic. A novel tool for functional characterization of mutations and their response to targeted therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 65.
Abstract 657: Impact of therapy induced APOBEC3A mutagenesis on tumor evolution in non small cell lung cancer
Authors: Isozaki Hideko , Abbasi Ammal , Nikpour Naveed , Stanzione Marcello , Sakhtemani Ramin , Monroe Susanna L. , Shaw Alice T. , Lin Jessica J. , Sequist Lecia V. , Piotrowska Zofia , Buisson Rémi , Lawrence Michael S. , Hata Aaron N. 
Published: June 2022

Abstract
Acquired drug resistance to even the most effective anti cancer targeted therapies remains an unsolved clinical problem. Although many drivers of acquired drug resistance have been identified, the underlying molecular mechanisms shaping tumor evolution during treatment are incompletely understood. We have seen that lung cancer targeted therapies commonly used in the clinic induce the expression of cytidine deaminase APOBEC3A (A3A), leading to sustained mutagenesis in drug tolerant cancer cells persisting during therapy. Preventing therapy induced A3A mutagenesis by gene deletion delayed the emergence of drug resistance. Here, we show that therapy induced A3A mutagenesis contributes to tumor evolution in NSCLC. Whole genome sequencing revealed that resistant clones that evolved from persistent drug tolerant cells (late clones) harbored more A3A mutations compared to the parental cell population than pre existing resistant clones (early clones). In a subset of NSCLC patients who received targeted therapies, we observed A3A mutations accompanied clonal evolution during treatment. Comparison of APOBEC mutation fractions in short vs long term responders suggests that short responders with acquired resistance mechanisms that evolved from pre existing resistant clones have less accumulation of APOBEC mutations. Collectively, these findings insist that an increase in mutagenic processes drives tumor evolution during targeted therapy treatment and leads to acquired resistance. Thus, suppressing expression or enzymatic activity of A3A may represent a potential therapeutic strategy to halt the evolution of resistant clones and prevent acquired resistance to lung cancer targeted therapy.
Citation Format: Hideko Isozaki, Ammal Abbasi, Naveed Nikpour, Marcello Stanzione, Ramin Sakhtemani, Susanna L. Monroe, Alice T. Shaw, Jessica J. Lin, Lecia V. Sequist, Zofia Piotrowska, Rémi Buisson, Michael S. Lawrence, Aaron N. Hata. Impact of therapy induced APOBEC3A mutagenesis on tumor evolution in non small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 657.
Abstract 661: Androgen deprivation therapy allows for effective anti-TIGIT immunotherapy in murine model of castration resistant prostate cancer
Authors: Polesso Fanny , Guan Xiangnan , Xia Zheng , Moran Amy E. 
Published: June 2022

Abstract
Prostate cancer is the second leading cause of cancer associated mortality in men, and for reasons that remain unclear, immunotherapy treatments have largely failed in patients with advanced prostate cancer. Standard of care therapy for these patients relies on androgen deprivation therapies (ADT) to block testosterone production combined with small molecules that inhibit androgen synthesis and/or the function of the androgen receptor (AR). Importantly, androgens are reported to be immunosuppressive; therefore, we postulated that androgen axis blockade might promote response to immunotherapy. In the recent years, the co-inhibitory receptor TIGIT has emerged as a promising immunotherapy target, and we observed that TIGIT is highly expressed on tumor infiltrating T cells and NK cells in metastatic castration resistant prostate cancer (CRPC) patients treated with the AR antagonist enzalutamide. Likewise, in a mouse model of CRPC, we show that tumor infiltrating T cells express TIGIT and that treatment with enzalutamide increases its expression. In this model, neither treatment with anti-TIGIT alone nor with chemical castration and enzalutamide affects tumor growth. Remarkably, the combination of anti-TIGIT with chemical castration and enzalutamide leads to delayed tumor growth and long-term cures in about 60% of the animals. Taken together, our data suggest that androgen receptor blockade sensitizes immune cells in the tumor to respond to anti-TIGIT immunotherapy.
Citation Format: Fanny Polesso, Xiangnan Guan, Zheng Xia, Amy E. Moran. Androgen deprivation therapy allows for effective anti-TIGIT immunotherapy in murine model of castration resistant prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 661.
Abstract 671: Cryo-electronmicroscopy of PI3K reveals additional regulatory features
Authors: Hart Jonathan R. , Yang Su , Liu Xiao , Xu Yingna , Zou Xinyu , Zhang Huibing , Zhou Qingtong , Xia Tian , Zhang Yan , Yang Dehua , Wang Ming-Wei , Vogt Peter K. 
Published: June 2022

Abstract
Many solid tumors have alterations in phosphoinositide 3-kinase (PI3K) signaling. These can occur through mutation of the p110alpha and p85alpha proteins of PI3Kalpha itself as well as through alterations to upstream receptor tyrosine kinases (RTKs) and phosphatases of PIP3, including PTEN. As a whole, PI3K signaling is one of the most frequently altered in cancer. These mutations lead to activation of the PI3K complex and to constitutive downstream signaling. This signaling allows cells to enter a pro-growth and pro-survival state which is beneficial to the cancer cells.
The structure of PI3K has been extensively studied by crystallography and NMR. Here, we present our work on the full-length complex of p110alpha with p85alpha using cryo-EM. When compared with the previous structural studies, cryo-EM shows a similar structure and major structural features are unchanged. However, our cryo-EM studies revealed several additional structural features of the PI3K complex.
Cryo-EM showed that SH3, BH and cSH2 domains of p85alpha can bind to p110alpha. When inhibited with Alpelisib, these domains form a stable cover of the active site of the kinase. These domains interact with the helical and kinase domains of p110alpha and the iSH2 domain of p85alpha. The position of these domains restricts access to the kinase active site and may contribute to the inhibition of PI3K activity by Alpelisib.
When the PI3K complex binds to phosphorylated RTKs, the nSH2 binds to phosphotyrosine and relieves inhibitory interactions with the helical domain of p110alpha. Using cryo-EM, we have studied this activation by incubating the full-length PI3K complex with synthetic phosphopeptides. 2D cryo-EM class averages showed a dramatic rearrangement of the PI3K complex. In addition to the expected displacement of the nSH2 domain, the ABD and iSH2 domains undergo structural changes.
Acknowledgments: This work was supported by the National Cancer Institute of the National Institutes of Health under awards R35 CA197582 (PKV) and R50 CA243899 (JRH).
Citation Format: Jonathan R. Hart, Su Yang, Xiao Liu, Yingna Xu, Xinyu Zou, Huibing Zhang, Qingtong Zhou, Tian Xia, Yan Zhang, Dehua Yang, Ming-Wei Wang, Peter K. Vogt. Cryo-electronmicroscopy of PI3K reveals additional regulatory features [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 671.
Abstract 679: Inhibition of Notch signaling causes progenitor-to-hepatocyte differentiation and regressions in a subset of hepatocellular carcinoma by controlling C/EBPα expression and HNF4α activity
Authors: Seidel Kerstin , Piskol Robert , Nguyen Thi Thu Thao , Cottonham Charisa , Merchant Mark , Siebel Christian 
Published: June 2022

Abstract
​​Notch signaling regulates cell fate decisions during development and maintenance of many organs. During hepatogenesis, an active NOTCH2 signal is required for specification of the cholangiocyte lineage, while hepatoblasts remaining in a Notch-off state contribute to the default hepatocyte lineage. Notch pathway activation has been reported in liver tumors, although Notch-related liver cancer mutations are rare. We identified a subset of hepatocellular carcinoma that is exceptionally sensitive to the inhibition of a JAG1-NOTCH2 signal in a mouse preclinical trial using 47 liver cancer PDX models.
Transcriptional profiling revealed that the sensitive models resemble a progenitor-like state. Highly selective therapeutic antibodies targeting either the JAG1 ligand or the NOTCH2 receptor triggered hepatocyte differentiation programs and tumor regressions.Single cell analyses revealed heterogeneous transcriptional states at baseline, some of which were profoundly perturbed upon Notch inhibition. Topic modeling combined with inference of transcription factor activities suggested the involvement of HNF4α and C/EBPα in treatment induced changes. Through its target HES1, Notch signaling directly represses C/EBPα expression. Notch inhibition derepresses C/EBPα which then binds chromatin in cooperation with HNF4α. We found that this cooperative binding results in expression of genes associated with mature hepatocyte activity, which was incompatible with tumor maintenance.
Importantly, we identify hallmarks to aid the identification of this relatively rare tumor type. We suggest that inducing cell states towards differentiated, less aggressive states, especially using targeted single-agent therapeutics, holds great promise for the treatment of certain tumors in the liver and, by extension, possibly in other progenitor-like cancers.
Citation Format: Kerstin Seidel, Robert Piskol, Thi Thu Thao Nguyen, Charisa Cottonham, Mark Merchant, Christian Siebel. Inhibition of Notch signaling causes progenitor-to-hepatocyte differentiation and regressions in a subset of hepatocellular carcinoma by controlling C/EBPα expression and HNF4α activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 679.
Abstract 691: Antineoplastic effect of marina crystal minerals (MCM) against the growth of murine mammary adenocarcinoma cells in vivo
Authors: El-Din Nariman K. Badr , El-Dein Mai Alaa , Ghoneum Mamdooh 
Published: June 2022

Abstract
Purpose: Marina crystal minerals (MCM) is a crystallized mixture of minerals and trace elements from sea water. Earlier in vitro studies have shown that MCM possesses apoptotic and immune modulatory effects in human breast cancer cells MDA-MB-231. The current study aimed to evaluate the anticancer effect of MCM in vivo against the growth of murine mammary adenocarcinoma cells and to explore the mechanisms underlying its effect.
Materials and Methods: Mice were inoculated intramuscularly with Ehrlich ascites carcinoma (EAC) cells, a breast adenocarcinoma of mouse origin. The tumors grew and became palpable within 9 days post-inoculation. Tumor-bearing mice were injected with MCM intraperitoneally (IP) or intratumorally (IT) at a dose of 40 mg/kg BW for 6 days/week. Different parameters were evaluated, including tumor growth, cell cycle progression, cell cycle regulatory proteins, apoptosis, apoptotic regulatory markers, mitochondrial membrane potential (MMP), natural killer (NK) cell activity, and histopathological effects.
Results: Treatment with MCM caused a reduction in tumor volume by 49.4% for IP and 59.5% for IT injection. MCM induced apoptosis in cancer cells, as indicated by the appearance of a sub-G1 peak and confirmed by Annexin V/PI assay and histopathological examination. This was mediated by increased Bax expression, caspase-3 activation, decreased Bcl-2 expression, and MMP disruption. Furthermore, MCM treatment induced G1 cell cycle arrest which was mediated through significantly increased expression of p53, p21, and p27 and decreased expression of Cyclin D1 and PCNA in cancer cells. Finally, MCM treatment markedly enhanced NK cell cytotoxicity.
Conclusion: MCM possesses chemopreventive potential to reduce tumor growth by suppressing cell proliferation, inducing apoptosis in EAC cells via a mitochondrial dependent pathway, and activating the immune system. Our results suggest that MCM may have clinical implications for the treatment of breast adenocarcinoma in humans. MCM was provided by the Foundation for Basic Research Institute of Oncology, Japan.
Citation Format: Nariman K. Badr El-Din, Mai Alaa El-Dein, Mamdooh Ghoneum. Antineoplastic effect of marina crystal minerals (MCM) against the growth of murine mammary adenocarcinoma cells in vivo [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 691.
Abstract 712: Cytokine and TGF-β levels are associated with changes in cervicovaginal microbiota in a cohort of Caribbean women
Authors: Rodríguez Eduardo Lemuel Tosado , Dominicci-Maura Anelisse , Mendez Loyda , Dorta Stephanie , Romaguera Josefina , Godoy-Vitorino Filipa 
Published: June 2022

Abstract
Recent studies suggest that the cervical microbiome can strongly influence inflammation and pre-cancerous lesion progression. However, research focused on understanding the role of microbial communities in the progression of pre-cancerous lesions to cancer in Latino women is scarce. We aimed to investigate the relationship between the cervicovaginal microbiome and inflammation while considering cervical neoplasia and HPV infection in Puerto Rican women. We collected cervical swabs and lavages from 142 participants coming to colposcopy clinics in San Juan, Puerto Rico. Genomic DNA was extracted from swabs, and 16S rDNA V4 region genes were amplified and sequenced by Illumina MiSeq. Inflammatory (IL-1β, TNFa, IFNg, IL-6), anti-inflammatory (IL-4, IL-10, TGFβ1), and trafficking (IL-8, MIP1a, MCP1, IP10) cytokines were measured from cervical lavages, using Luminex MAGPIX technology. Cytokines were related to microbes via an inflammation scoring index based on the quartile and tercile distribution of the cytokine’s concentration. IL-10 (p value= 0.0455) was significantly different when evaluating HPV risk, while IL1-β (p value= 0.0005) and INF-γ (p value= 0.0258) were significant when evaluating cervical disease. We found significant differences in diversity and composition of the microbiota among HPV risk, cervical disease, pro-inflammatory, anti-inflammatory, and trafficking cytokine abundances. The increasing concentration of IL1-β, IL-10, and INF-γ, associated with a decrease in Lactobacillus communities. While contrarily, bacteria associated with dysbiosis such as Gardnerella, Prevotella, Atopobium increased. This study also revealed that the most dominant community state types (CST) among Puerto Rican women regardless of lesion or HPV status, are CST3 and 4 featuring high diversity and anaerobic bacteria typical of vaginosis in Caucasians. These CSTs are especially abundant with ~ 90% dominance in participants with high grade disease (HGSIL) and high-risk HPV. Our study evidence that the cervical microbiota of Puerto Ricans is characteristically diverse and that the joint host-microbe interaction analyses via cytokine signaling and microbiota in pre-cancerous lesions has great translational potential.
Citation Format: Eduardo Lemuel Tosado Rodríguez, Anelisse Dominicci-Maura, Loyda Mendez, Stephanie Dorta, Josefina Romaguera, Filipa Godoy-Vitorino. Cytokine and TGF-β levels are associated with changes in cervicovaginal microbiota in a cohort of Caribbean women [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 712.
Abstract 765: Hybridized-capture sequencing methods bias analysis of antigen presentation genes
Authors: Medina Egmidio , Campbell Katie , Ribas Antoni 
Published: June 2022

Abstract
Introduction: Tumor-immune dynamics are often interrogated using hybridized capture-based sequencing approaches which require the use of baits that target the protein-coding regions of the genome. However, the genes encoding the antigen presentation machinery, including human leukocyte antigen (HLA) proteins, are very polymorphic, resulting in thousands of unique genotypes across patient cohorts. Here, using whole exome sequencing (WES) and hybridized capture-based RNA sequencing (RNAseq) from melanoma patients, we show that these genes are not uniformly assessed by common sequencing methods, and require careful analysis for accurate detection of copy number and somatic alterations.
Methods: WES and RNAseq data was analyzed from 760 melanoma tumor biopsies, with WES derived from patient-matched normal blood samples. Coverage metrics for 26 antigen presentation genes, including classical and non-classical HLA genes, were evaluated, and the difference in coverage was calculated for heterozygous alleles. Each individual was assessed for heterozygous single nucleotide polymorphisms (SNPs) within each allele, and with respect to the haplotype of the human reference genome.
Results: Focusing on the 26 genes assessed, HLA-A, HLA-B, HLA-C, and HLA-DRB1 were the most diverse across our patient cohort; there was an average of 134 unique pairs of HLA alleles in these genes. We compared the SNP profiles of allele combinations to the haplotype of the human reference genome, and observed four patterns: heterozygous alleles are similar to each other and the reference haplotype, heterozygous alleles are different from each other and different to the reference, alleles are very similar to each other and greatly differ from the reference, or one allele is more similar to the reference haplotype. The fourth pattern showed the greatest bias in sequencing, where the allele more similar to the human reference genome had a median 4-fold increase in coverage in normal WES data.
Conclusions: Capture-based sequencing shows selection bias, as exome probes have been designed based upon the reported human reference genome, but results in selection bias in hybridized capture sequencing approaches. Alleles that have higher polymorphic differences with respect to the reference are not equally captured, resulting in nonuniform sequencing of heterozygous alleles.
Citation Format: Egmidio Medina, Katie Campbell, Antoni Ribas. Hybridized-capture sequencing methods bias analysis of antigen presentation genes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 765.
Abstract 772: Single cell whole genome sequencing to assess tumor heterogeneity in endometrial cancer
Authors: Villarreal Enrique Velazquez , Gibbs Lee D. , Mahinbakht Dana , Da Silva Diane M. , Roman Lynda D. , Craig David W. , Carpten John D. 
Published: June 2022

Abstract
Introduction: Endometrial cancer (EC) is the most common gynecological malignancy among women in developed countries. In the United States, it is estimated that 66,570 new cases and 12,940 deaths will occur in 2021. EC is more common in white women, but black women have a worse prognosis with higher mortality rates. Molecular characteristics in tumor tissue have been reported for potential clinical utility. Integrated genomic characterization efforts have shown common molecular alterations occurring in oncogenic pathways from bulk molecular profiling of EC tumors. However, little is known about the tumor heterogeneity in endometrial cancer. Thus, using high resolution single cell technologies, we assessed tumor heterogeneity in endometrial cancers. Our preliminary study includes endometrial tumors from five (3 African Americans, 1 Hispanic/Latino, 1 Caucasian) cases. We utilize bulk whole exome sequencing and single cell whole genome sequencing copy number variation to study tumor heterogeneity. Frozen tumor sections were used to collect and sequence single nuclei utilizing the 10x ChromiumTM single cell copy number variation (scCNV). Illumina NovasEQ600 was used to sequence the single cell libraries.
Results: 1,546 cells were sequenced across five tumors. Each tumor was visually inspected through hierarchical clustering from the scCNV data. Beyond describing the heterogeneity through chromosome or chromosome arm level gains and losses in samples that included single and mixed histology tumors, we assessed clonal populations suggesting apparently different clonal evolution within samples. Mutations in cancer related genes such as TP53, PTEN and PIK3CA among others suggested a clonal tumor cell stratification. The single cell whole genome data was compared to bulk exome sequencing data to determine the power of scCNV to detect clonal populations of tumor cells.
Conclusions: Using varied histologies in five EC tumors, we performed DNA-CNV analysis using single cell sequencing. This level of resolution enhanced our analysis to provide clear evidence of heterogeneity in all tumors that were assessed in our study. We plan to further expand our sample size to study the degree of heterogeneity in endometrial cancer.
Citation Format: Enrique Velazquez Villarreal, Lee D. Gibbs, Dana Mahinbakht, Diane M. Da Silva, Lynda D. Roman, David W. Craig, John D. Carpten. Single cell whole genome sequencing to assess tumor heterogeneity in endometrial cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 772.