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1.
Cell ; 184(8): 2239-2254.e39, 2021 04 15.
Article in English | MEDLINE | ID: mdl-33831375

ABSTRACT

Intra-tumor heterogeneity (ITH) is a mechanism of therapeutic resistance and therefore an important clinical challenge. However, the extent, origin, and drivers of ITH across cancer types are poorly understood. To address this, we extensively characterize ITH across whole-genome sequences of 2,658 cancer samples spanning 38 cancer types. Nearly all informative samples (95.1%) contain evidence of distinct subclonal expansions with frequent branching relationships between subclones. We observe positive selection of subclonal driver mutations across most cancer types and identify cancer type-specific subclonal patterns of driver gene mutations, fusions, structural variants, and copy number alterations as well as dynamic changes in mutational processes between subclonal expansions. Our results underline the importance of ITH and its drivers in tumor evolution and provide a pan-cancer resource of comprehensively annotated subclonal events from whole-genome sequencing data.


Subject(s)
Genetic Heterogeneity , Neoplasms/genetics , DNA Copy Number Variations , DNA, Neoplasm/chemistry , DNA, Neoplasm/metabolism , Databases, Genetic , Drug Resistance, Neoplasm/genetics , Humans , Neoplasms/pathology , Polymorphism, Single Nucleotide , Whole Genome Sequencing
2.
Am J Hum Genet ; 110(8): 1249-1265, 2023 08 03.
Article in English | MEDLINE | ID: mdl-37506692

ABSTRACT

The Healthy Oregon Project (HOP) is a statewide effort that aims to build a large research repository and influence the health of Oregonians through providing no-cost genetic screening to participants for a next-generation sequencing 32-gene panel comprising genes related to inherited cancers and familial hypercholesterolemia. This type of unbiased population screening can detect at-risk individuals who may otherwise be missed by conventional medical approaches. However, challenges exist for this type of high-throughput testing in an academic setting, including developing a low-cost high-efficiency test and scaling up the clinical laboratory for processing large numbers of samples. Modifications to our academic clinical laboratory including efficient test design, robotics, and a streamlined analysis approach increased our ability to test more than 1,000 samples per month for HOP using only one dedicated HOP laboratory technologist. Additionally, enrollment using a HIPAA-compliant smartphone app and sample collection using mouthwash increased efficiency and reduced cost. Here, we present our experience three years into HOP and discuss the lessons learned, including our successes, challenges, opportunities, and future directions, as well as the genetic screening results for the first 13,670 participants tested. Overall, we have identified 730 pathogenic/likely pathogenic variants in 710 participants in 24 of the 32 genes on the panel. The carrier rate for pathogenic/likely pathogenic variants in the inherited cancer genes on the panel for an unselected population was 5.0% and for familial hypercholesterolemia was 0.3%. Our laboratory experience described here may provide a useful model for population screening projects in other states.


Subject(s)
Hyperlipoproteinemia Type II , Neoplasms , Humans , Oregon/epidemiology , Early Detection of Cancer , Genetic Testing , Hyperlipoproteinemia Type II/diagnosis , Hyperlipoproteinemia Type II/epidemiology , Hyperlipoproteinemia Type II/genetics , Neoplasms/diagnosis , Neoplasms/epidemiology , Neoplasms/genetics
3.
Nature ; 578(7793): 122-128, 2020 02.
Article in English | MEDLINE | ID: mdl-32025013

ABSTRACT

Cancer develops through a process of somatic evolution1,2. Sequencing data from a single biopsy represent a snapshot of this process that can reveal the timing of specific genomic aberrations and the changing influence of mutational processes3. Here, by whole-genome sequencing analysis of 2,658 cancers as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA)4, we reconstruct the life history and evolution of mutational processes and driver mutation sequences of 38 types of cancer. Early oncogenesis is characterized by mutations in a constrained set of driver genes, and specific copy number gains, such as trisomy 7 in glioblastoma and isochromosome 17q in medulloblastoma. The mutational spectrum changes significantly throughout tumour evolution in 40% of samples. A nearly fourfold diversification of driver genes and increased genomic instability are features of later stages. Copy number alterations often occur in mitotic crises, and lead to simultaneous gains of chromosomal segments. Timing analyses suggest that driver mutations often precede diagnosis by many years, if not decades. Together, these results determine the evolutionary trajectories of cancer, and highlight opportunities for early cancer detection.


Subject(s)
Evolution, Molecular , Genome, Human/genetics , Neoplasms/genetics , DNA Repair/genetics , Gene Dosage , Genes, Tumor Suppressor , Genetic Variation , Humans , Mutagenesis, Insertional/genetics
5.
N Engl J Med ; 374(2): 135-45, 2016 Jan 14.
Article in English | MEDLINE | ID: mdl-26536169

ABSTRACT

BACKGROUND: Papillary renal-cell carcinoma, which accounts for 15 to 20% of renal-cell carcinomas, is a heterogeneous disease that consists of various types of renal cancer, including tumors with indolent, multifocal presentation and solitary tumors with an aggressive, highly lethal phenotype. Little is known about the genetic basis of sporadic papillary renal-cell carcinoma, and no effective forms of therapy for advanced disease exist. METHODS: We performed comprehensive molecular characterization of 161 primary papillary renal-cell carcinomas, using whole-exome sequencing, copy-number analysis, messenger RNA and microRNA sequencing, DNA-methylation analysis, and proteomic analysis. RESULTS: Type 1 and type 2 papillary renal-cell carcinomas were shown to be different types of renal cancer characterized by specific genetic alterations, with type 2 further classified into three individual subgroups on the basis of molecular differences associated with patient survival. Type 1 tumors were associated with MET alterations, whereas type 2 tumors were characterized by CDKN2A silencing, SETD2 mutations, TFE3 fusions, and increased expression of the NRF2-antioxidant response element (ARE) pathway. A CpG island methylator phenotype (CIMP) was observed in a distinct subgroup of type 2 papillary renal-cell carcinomas that was characterized by poor survival and mutation of the gene encoding fumarate hydratase (FH). CONCLUSIONS: Type 1 and type 2 papillary renal-cell carcinomas were shown to be clinically and biologically distinct. Alterations in the MET pathway were associated with type 1, and activation of the NRF2-ARE pathway was associated with type 2; CDKN2A loss and CIMP in type 2 conveyed a poor prognosis. Furthermore, type 2 papillary renal-cell carcinoma consisted of at least three subtypes based on molecular and phenotypic features. (Funded by the National Institutes of Health.).


Subject(s)
Carcinoma, Papillary/metabolism , Kidney Neoplasms/metabolism , Mutation , NF-E2-Related Factor 2/metabolism , Proto-Oncogene Proteins c-met/metabolism , Carcinoma, Papillary/genetics , CpG Islands/physiology , DNA Methylation , Humans , Kidney Neoplasms/genetics , MicroRNAs/chemistry , NF-E2-Related Factor 2/genetics , Phenotype , Proto-Oncogene Proteins c-met/chemistry , Proto-Oncogene Proteins c-met/genetics , RNA, Messenger/chemistry , RNA, Neoplasm/chemistry , Sequence Analysis, RNA , Signal Transduction/physiology
6.
Proc Natl Acad Sci U S A ; 113(43): E6600-E6609, 2016 10 25.
Article in English | MEDLINE | ID: mdl-27791031

ABSTRACT

Forkhead box protein A1 (FOXA1) is a pioneer factor of estrogen receptor α (ER)-chromatin binding and function, yet its aberration in endocrine-resistant (Endo-R) breast cancer is unknown. Here, we report preclinical evidence for a role of FOXA1 in Endo-R breast cancer as well as evidence for its clinical significance. FOXA1 is gene-amplified and/or overexpressed in Endo-R derivatives of several breast cancer cell line models. Induced FOXA1 triggers oncogenic gene signatures and proteomic profiles highly associated with endocrine resistance. Integrated omics data reveal IL8 as one of the most perturbed genes regulated by FOXA1 and ER transcriptional reprogramming in Endo-R cells. IL-8 knockdown inhibits tamoxifen-resistant cell growth and invasion and partially attenuates the effect of overexpressed FOXA1. Our study highlights a role of FOXA1 via IL-8 signaling as a potential therapeutic target in FOXA1-overexpressing ER-positive tumors.


Subject(s)
Breast Neoplasms/genetics , Estrogen Receptor alpha/genetics , Gene Expression Regulation, Neoplastic , Hepatocyte Nuclear Factor 3-alpha/genetics , Interleukin-8/genetics , Transcriptome , Antineoplastic Agents, Hormonal/therapeutic use , Breast Neoplasms/diagnosis , Breast Neoplasms/drug therapy , Breast Neoplasms/mortality , Cell Line, Tumor , Drug Resistance, Neoplasm/genetics , Estrogen Receptor alpha/metabolism , Female , Hepatocyte Nuclear Factor 3-alpha/metabolism , Humans , Interleukin-8/antagonists & inhibitors , Interleukin-8/metabolism , Prognosis , RNA, Small Interfering/genetics , RNA, Small Interfering/metabolism , Signal Transduction , Survival Analysis , Tamoxifen/therapeutic use
7.
Biochem Biophys Res Commun ; 482(4): 1271-1277, 2017 Jan 22.
Article in English | MEDLINE | ID: mdl-27939881

ABSTRACT

ASPP2 is a tumor suppressor that works, at least in part, through enhancing p53-dependent apoptosis. We now describe a new ASPP2 isoform, ΔN-ASPP2, generated from an internal transcription start site that encodes an N-terminally truncated protein missing a predicted 254 amino acids. ΔN-ASPP2 suppresses p53 target gene transactivation, promoter occupancy, and endogenous p53 target gene expression in response to DNA damage. Moreover, ΔN-ASPP2 promotes progression through the cell cycle, as well as resistance to genotoxic stress-induced growth inhibition and apoptosis. Additionally, we found that ΔN-ASPP2 expression is increased in human breast tumors as compared to adjacent normal breast tissue; in contrast, ASPP2 is suppressed in the majority of these breast tumors. Together, our results provide insight into how this new ASPP2 isoform may play a role in regulating the ASPP2-p53 axis.


Subject(s)
Apoptosis Regulatory Proteins/chemistry , Tumor Suppressor Protein p53/metabolism , Tumor Suppressor Proteins/chemistry , Animals , Apoptosis , Apoptosis Regulatory Proteins/metabolism , Breast Neoplasms/metabolism , Cell Line, Tumor , Cell Proliferation , Cell Survival , Cloning, Molecular , DNA Damage , Female , Humans , Mice , Protein Domains , Transcriptional Activation , Tumor Suppressor Protein p53/genetics
8.
Breast Cancer Res ; 16(5): 430, 2014 Sep 11.
Article in English | MEDLINE | ID: mdl-25212826

ABSTRACT

INTRODUCTION: Activation of the phosphatidylinositol 3-kinase (PI3K) pathway in estrogen receptor α (ER)-positive breast cancer is associated with reduced ER expression and activity, luminal B subtype, and poor outcome. Phosphatase and tensin homolog (PTEN), a negative regulator of this pathway, is typically lost in ER-negative breast cancer. We set out to clarify the role of reduced PTEN levels in endocrine resistance, and to explore the combination of newly developed PI3K downstream kinase inhibitors to overcome this resistance. METHODS: Altered cellular signaling, gene expression, and endocrine sensitivity were determined in inducible PTEN-knockdown ER-positive/human epidermal growth factor receptor 2 (HER2)-negative breast cancer cell and/or xenograft models. Single or two-agent combinations of kinase inhibitors were examined to improve endocrine therapy. RESULTS: Moderate PTEN reduction was sufficient to enhance PI3K signaling, generate a gene signature associated with the luminal B subtype of breast cancer, and cause endocrine resistance in vitro and in vivo. The mammalian target of rapamycin (mTOR), protein kinase B (AKT), or mitogen-activated protein kinase kinase (MEK) inhibitors, alone or in combination, improved endocrine therapy, but the efficacy varied by PTEN levels, type of endocrine therapy, and the specific inhibitor(s). A single-agent AKT inhibitor combined with fulvestrant conferred superior efficacy in overcoming resistance, inducing apoptosis and tumor regression. CONCLUSIONS: Moderate reduction in PTEN, without complete loss, can activate the PI3K pathway to cause endocrine resistance in ER-positive breast cancer, which can be overcome by combining endocrine therapy with inhibitors of the PI3K pathway. Our data suggests that the ER degrader fulvestrant, to block both ligand-dependent and -independent ER signaling, combined with an AKT inhibitor is an effective strategy to test in patients.


Subject(s)
Antineoplastic Agents, Hormonal/pharmacology , Breast Neoplasms/drug therapy , PTEN Phosphohydrolase/metabolism , Sirolimus/pharmacology , Animals , Breast Neoplasms/metabolism , Doxycycline/pharmacology , Drug Resistance, Neoplasm , Estradiol/analogs & derivatives , Estradiol/pharmacology , Female , Fulvestrant , Gene Expression , Gene Knockdown Techniques , Humans , MCF-7 Cells , Mice, Nude , Mitogen-Activated Protein Kinases/antagonists & inhibitors , Mitogen-Activated Protein Kinases/metabolism , Molecular Targeted Therapy , Neoplasms, Hormone-Dependent/drug therapy , Neoplasms, Hormone-Dependent/metabolism , Phosphatidylinositol 3-Kinases/metabolism , Protein Kinase Inhibitors/pharmacology , Proto-Oncogene Proteins c-akt/antagonists & inhibitors , Proto-Oncogene Proteins c-akt/metabolism , Receptors, Estrogen/metabolism , Signal Transduction , TOR Serine-Threonine Kinases/antagonists & inhibitors , TOR Serine-Threonine Kinases/metabolism , Tamoxifen/pharmacology , Xenograft Model Antitumor Assays
9.
J Clin Transl Sci ; 8(1): e32, 2024.
Article in English | MEDLINE | ID: mdl-38384895

ABSTRACT

Background: Cancer health research relies on large-scale cohorts to derive generalizable results for different populations. While traditional epidemiological cohorts often use costly random sampling or self-motivated, preselected groups, a shift toward health system-based cohorts has emerged. However, such cohorts depend on participants remaining within a single system. Recent consumer engagement models using smartphone-based communication, driving projects, and social media have begun to upend these paradigms. Methods: We initiated the Healthy Oregon Project (HOP) to support basic and clinical cancer research. HOP study employs a novel, cost-effective remote recruitment approach to effectively establish a large-scale cohort for population-based studies. The recruitment leverages the unique email account, the HOP website, and social media platforms to direct smartphone users to the study app, which facilitates saliva sample collection and survey administration. Monthly newsletters further facilitate engagement and outreach to broader communities. Results: By the end of 2022, the HOP has enrolled approximately 35,000 participants aged 18-100 years (median = 44.2 years), comprising more than 1% of the Oregon adult population. Among those who have app access, ∼87% provided consent to genetic screening. The HOP monthly email newsletters have an average open rate of 38%. Efforts continue to be made to improve survey response rates. Conclusion: This study underscores the efficacy of remote recruitment approaches in establishing large-scale cohorts for population-based cancer studies. The implementation of the study facilitates the collection of extensive survey and biological data into a repository that can be broadly shared and supports collaborative clinical and translational research.

10.
Mol Cancer ; 12: 32, 2013 Apr 26.
Article in English | MEDLINE | ID: mdl-23621864

ABSTRACT

BACKGROUND: Treatment of advanced stage ovarian cancer continues to be challenging due to acquired drug resistance and lack of early stage biomarkers. Genes identified to be aberrantly expressed at the 3q26.2 locus (i.e. SnoN/SkiL) have been implicated in ovarian cancer pathophysiology. We have previously shown that SnoN expression is increased in advanced stage ovarian cancers and alters cellular response to arsenic trioxide (As2O3). FINDINGS: We now demonstrate increased DNA copy number levels (TCGA data) of phospholipid scramblase 1 (PLSCR1, located at 3q23) whose transcript expression in ovarian cell lines is highly correlated with SnoN mRNA. Interestingly, SnoN can modulate PLSCR1 mRNA levels in the absence/presence of interferon (IFN-2α). Both IFN-2α and As2O3 treatment can modulate PLSCR1 mRNA levels in ovarian carcinoma cells. However, SnoN siRNA does not lead to altered PLSCR1 protein implicating other events needed to modulate its protein levels. In addition, we report that PLSCR1 can modulate aspects of the As2O3 cellular response. CONCLUSIONS: Our findings warrant further investigation into the role of PLSCR1 in ovarian cancer development and chemoresistance.


Subject(s)
Gene Expression Regulation, Neoplastic , Intracellular Signaling Peptides and Proteins/genetics , Ovarian Neoplasms/genetics , Phospholipid Transfer Proteins/genetics , Proto-Oncogene Proteins/genetics , Arsenic Trioxide , Arsenicals/pharmacology , Cell Death/drug effects , Cell Death/genetics , Cell Line, Tumor , Chromosomes, Human, Pair 3 , Female , Gene Dosage , Gene Knockdown Techniques , Humans , Interferon-alpha/metabolism , Intracellular Signaling Peptides and Proteins/metabolism , Ovarian Neoplasms/metabolism , Oxides/pharmacology , Proto-Oncogene Proteins/metabolism , RNA Interference , RNA, Messenger/genetics
11.
NPJ Precis Oncol ; 6(1): 28, 2022 Apr 25.
Article in English | MEDLINE | ID: mdl-35468987

ABSTRACT

Cell-free RNA (cfRNA) in plasma reflects phenotypic alterations of both localized sites of cancer and the systemic host response. Here we report that cfRNA sequencing enables the discovery of messenger RNA (mRNA) biomarkers in plasma with the tissue of origin-specific to cancer types and precancerous conditions in both solid and hematologic malignancies. To explore the diagnostic potential of total cfRNA from blood, we sequenced plasma samples of eight hepatocellular carcinoma (HCC) and ten multiple myeloma (MM) patients, 12 patients of their respective precancerous conditions, and 20 non-cancer (NC) donors. We identified distinct gene sets and built classification models using Random Forest and linear discriminant analysis algorithms that could distinguish cancer patients from premalignant conditions and NC individuals with high accuracy. Plasma cfRNA biomarkers of HCC are liver-specific genes and biomarkers of MM are highly expressed in the bone marrow compared to other tissues and are related to cell cycle processes. The cfRNA level of these biomarkers displayed a gradual transition from noncancerous states through precancerous conditions and cancer. Sequencing data were cross-validated by quantitative reverse transcription PCR and cfRNA biomarkers were validated in an independent sample set (20 HCC, 9 MM, and 10 NC) with AUC greater than 0.86. cfRNA results observed in precancerous conditions require further validation. This work demonstrates a proof of principle for using mRNA transcripts in plasma with a small panel of genes to distinguish between cancers, noncancerous states, and precancerous conditions.

12.
Alzheimer Dis Assoc Disord ; 25(3): 276-82, 2011.
Article in English | MEDLINE | ID: mdl-21297427

ABSTRACT

Brain development in the early stages of life has been suggested to be one of the factors that may influence an individual's risk of Alzheimer disease (AD) later in life. Four microcephaly genes, which regulate brain development in utero and have been suggested to play a role in the evolution of the human brain, were selected as candidate genes that may modulate the risk of AD. We examined the association between single nucleotide polymorphisms tagging common sequence variations in these genes and risk of AD in two case-control samples. We found that the G allele of rs2442607 in microcephalin 1 was associated with an increased risk of AD (under an additive genetic model, P=0.01; odds ratio=3.41; confidence interval, 1.77-6.57). However, this association was not replicated using another case-control sample research participants from the Alzheimer Disease Neuroimaging Initiative. We conclude that the common variations we measured in the 4 microcephaly genes do not affect the risk of AD or that their effect size is small.


Subject(s)
Alzheimer Disease/genetics , Genetic Predisposition to Disease/genetics , Intracellular Signaling Peptides and Proteins/genetics , Microtubule-Associated Proteins/genetics , Nerve Tissue Proteins/genetics , Age of Onset , Aged, 80 and over , Cell Cycle Proteins , Cytoskeletal Proteins , Female , Humans , Male , Polymorphism, Single Nucleotide
13.
Cancer Cell ; 35(4): 588-602.e10, 2019 04 15.
Article in English | MEDLINE | ID: mdl-30930117

ABSTRACT

The roles of tumor-associated macrophages (TAMs) and circulating monocytes in human cancer are poorly understood. Here, we show that monocyte subpopulation distribution and transcriptomes are significantly altered by the presence of endometrial and breast cancer. Furthermore, TAMs from endometrial and breast cancers are transcriptionally distinct from monocytes and their respective tissue-resident macrophages. We identified a breast TAM signature that is highly enriched in aggressive breast cancer subtypes and associated with shorter disease-specific survival. We also identified an auto-regulatory loop between TAMs and cancer cells driven by tumor necrosis factor alpha involving SIGLEC1 and CCL8, which is self-reinforcing through the production of CSF1. Together these data provide direct evidence that monocyte and macrophage transcriptional landscapes are perturbed by cancer, reflecting patient outcomes.


Subject(s)
Biomarkers, Tumor/metabolism , Breast Neoplasms/metabolism , Cellular Reprogramming , Macrophages/metabolism , Monocytes/metabolism , Paracrine Communication , Transcription, Genetic , Antineoplastic Agents/pharmacology , Biomarkers, Tumor/genetics , Breast Neoplasms/drug therapy , Breast Neoplasms/genetics , Breast Neoplasms/pathology , Chemokine CCL8/genetics , Chemokine CCL8/metabolism , Endometrial Neoplasms/genetics , Endometrial Neoplasms/metabolism , Endometrial Neoplasms/pathology , Female , Gene Expression Regulation, Neoplastic , Humans , Induced Pluripotent Stem Cells/metabolism , Macrophage Colony-Stimulating Factor/genetics , Macrophages/pathology , Molecular Targeted Therapy , Monocytes/pathology , Sialic Acid Binding Ig-like Lectin 1/genetics , Sialic Acid Binding Ig-like Lectin 1/metabolism , Signal Transduction , THP-1 Cells , Tumor Microenvironment
14.
Radiat Res ; 190(1): 88-97, 2018 07.
Article in English | MEDLINE | ID: mdl-29749794

ABSTRACT

Chromosome rearrangements are large-scale structural variants that are recognized drivers of oncogenic events in cancers of all types. Cytogenetics allows for their rapid, genome-wide detection, but does not provide gene-level resolution. Massively parallel sequencing (MPS) promises DNA sequence-level characterization of the specific breakpoints involved, but is strongly influenced by bioinformatics filters that affect detection efficiency. We sought to characterize the breakpoint junctions of chromosomal translocations and inversions in the clonal derivatives of human cells exposed to ionizing radiation. Here, we describe the first successful use of DNA paired-end analysis to locate and sequence across the breakpoint junctions of a radiation-induced reciprocal translocation. The analyses employed, with varying degrees of success, several well-known bioinformatics algorithms, a task made difficult by the involvement of repetitive DNA sequences. As for underlying mechanisms, the results of Sanger sequencing suggested that the translocation in question was likely formed via microhomology-mediated non-homologous end joining (mmNHEJ). To our knowledge, this represents the first use of MPS to characterize the breakpoint junctions of a radiation-induced chromosomal translocation in human cells. Curiously, these same approaches were unsuccessful when applied to the analysis of inversions previously identified by directional genomic hybridization (dGH). We conclude that molecular cytogenetics continues to provide critical guidance for structural variant discovery, validation and in "tuning" analysis filters to enable robust breakpoint identification at the base pair level.


Subject(s)
Cytogenetic Analysis , High-Throughput Nucleotide Sequencing , Translocation, Genetic/radiation effects , Cell Line , Fibroblasts/metabolism , Fibroblasts/radiation effects , Humans
15.
J Proteomics ; 176: 13-23, 2018 03 30.
Article in English | MEDLINE | ID: mdl-29331515

ABSTRACT

To build a catalog of peptides presented by breast cancer cells, we undertook systematic MHC class I immunoprecipitation followed by elution of MHC class I-loaded peptides in breast cancer cells. We determined the sequence of 3196 MHC class I ligands representing 1921 proteins from a panel of 20 breast cancer cell lines. After removing duplicate peptides, i.e., the same peptide eluted from more than one cell line, the total number of unique peptides was 2740. Of the unique peptides eluted, more than 1750 had been previously identified, and of these, sixteen have been shown to be immunogenic. Importantly, half of these immunogenic peptides were shared between different breast cancer cell lines. MHC class I binding probability was used to plot the distribution of the eluted peptides in accordance with the binding score for each breast cancer cell line. We also determined that the tested breast cancer cells presented 89 mutation-containing peptides and peptides derived from aberrantly translated genes, 7 of which were shared between four or two different cell lines. Overall, the high throughput identification of MHC class I-loaded peptides is an effective strategy for systematic characterization of cancer peptides, and could be employed for design of multi-peptide anticancer vaccines. SIGNIFICANCE: By employing proteomic analyses of eluted peptides from breast cancer cells, the current study has built an initial HLA-I-typed antigen collection for breast cancer research. It was also determined that immunogenic epitopes can be identified using established cell lines and that shared immunogenic peptides can be found in different cancer types such as breast cancer and leukemia. Importantly, out of 3196 eluted peptides that included duplicate peptides in different cells 89 peptides either contained mutation in their sequence or were derived from aberrant translation suggesting that mutation-containing epitopes are on the order of 2-3% in breast cancer cells. Finally, our results suggest that interfering with MHC class I function is one of the mechanisms of how tumor cells escape immune system attack.


Subject(s)
Breast Neoplasms/immunology , Histocompatibility Antigens Class I/analysis , Amino Acid Sequence , Antigen Presentation , Antigens, Neoplasm , Breast Neoplasms/pathology , Cell Line, Tumor , Epitopes/genetics , HLA Antigens , High-Throughput Screening Assays , Humans , Ligands , Mutation , Proteomics/methods
16.
Cancer Cell ; 33(2): 244-258.e10, 2018 02 12.
Article in English | MEDLINE | ID: mdl-29438696

ABSTRACT

Thymic epithelial tumors (TETs) are one of the rarest adult malignancies. Among TETs, thymoma is the most predominant, characterized by a unique association with autoimmune diseases, followed by thymic carcinoma, which is less common but more clinically aggressive. Using multi-platform omics analyses on 117 TETs, we define four subtypes of these tumors defined by genomic hallmarks and an association with survival and World Health Organization histological subtype. We further demonstrate a marked prevalence of a thymoma-specific mutated oncogene, GTF2I, and explore its biological effects on multi-platform analysis. We further observe enrichment of mutations in HRAS, NRAS, and TP53. Last, we identify a molecular link between thymoma and the autoimmune disease myasthenia gravis, characterized by tumoral overexpression of muscle autoantigens, and increased aneuploidy.


Subject(s)
Mutation/genetics , Neoplasms, Glandular and Epithelial/genetics , Thymoma/genetics , Thymus Neoplasms/genetics , Transcription Factors, TFII/genetics , Adolescent , Adult , Aged , Aged, 80 and over , Female , Genomics , Humans , Male , Middle Aged , Young Adult
17.
Cell Rep ; 23(1): 194-212.e6, 2018 04 03.
Article in English | MEDLINE | ID: mdl-29617660

ABSTRACT

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smoking and/or human papillomavirus (HPV). SCCs harbor 3q, 5p, and other recurrent chromosomal copy-number alterations (CNAs), DNA mutations, and/or aberrant methylation of genes and microRNAs, which are correlated with the expression of multi-gene programs linked to squamous cell stemness, epithelial-to-mesenchymal differentiation, growth, genomic integrity, oxidative damage, death, and inflammation. Low-CNA SCCs tended to be HPV(+) and display hypermethylation with repression of TET1 demethylase and FANCF, previously linked to predisposition to SCC, or harbor mutations affecting CASP8, RAS-MAPK pathways, chromatin modifiers, and immunoregulatory molecules. We uncovered hypomethylation of the alternative promoter that drives expression of the ΔNp63 oncogene and embedded miR944. Co-expression of immune checkpoint, T-regulatory, and Myeloid suppressor cells signatures may explain reduced efficacy of immune therapy. These findings support possibilities for molecular classification and therapeutic approaches.


Subject(s)
Carcinoma, Squamous Cell/classification , Gene Expression Regulation, Neoplastic , Metabolic Networks and Pathways , Carcinoma, Squamous Cell/genetics , Carcinoma, Squamous Cell/immunology , Carcinoma, Squamous Cell/metabolism , Cell Line, Tumor , DNA Methylation , Epithelial-Mesenchymal Transition , Genomics/methods , Humans , Polymorphism, Genetic
18.
Cancer Res ; 73(14): 4510-20, 2013 Jul 15.
Article in English | MEDLINE | ID: mdl-23704208

ABSTRACT

The emergence of anti-estrogen resistance in breast cancer is an important clinical phenomenon affecting long-term survival in this disease. Identifying factors that convey cell survival in this setting may guide improvements in treatment. Estrogen (E2) can induce apoptosis in breast cancer cells that have been selected for survival after E2 deprivation for long periods (MCF-7:5C cells), but the mechanisms underlying E2-induced stress in this setting have not been elucidated. Here, we report that the c-Src kinase functions as a key adapter protein for the estrogen receptor (ER, ESR1) in its activation of stress responses induced by E2 in MCF-7:5C cells. E2 elevated phosphorylation of c-Src, which was blocked by 4-hydroxytamoxifen (4-OHT), suggesting that E2 activated c-Src through the ER. We found that E2 activated the sensors of the unfolded protein response (UPR), IRE1α (ERN1) and PERK kinase (EIF2AK3), the latter of which phosphorylates eukaryotic translation initiation factor-2α (eIF2α). E2 also dramatically increased reactive oxygen species production and upregulated expression of heme oxygenase HO-1 (HMOX1), an indicator of oxidative stress, along with the central energy sensor kinase AMPK (PRKAA2). Pharmacologic or RNA interference-mediated inhibition of c-Src abolished the phosphorylation of eIF2α and AMPK, blocked E2-induced ROS production, and inhibited E2-induced apoptosis. Together, our results establish that c-Src kinase mediates stresses generated by E2 in long-term E2-deprived cells that trigger apoptosis. This work offers a mechanistic rationale for a new approach in the treatment of endocrine-resistant breast cancer.


Subject(s)
Apoptosis/physiology , Breast Neoplasms/metabolism , Estrogens/deficiency , Estrogens/metabolism , Oxidative Stress/physiology , src-Family Kinases/metabolism , AMP-Activated Protein Kinases/metabolism , Breast Neoplasms/enzymology , Breast Neoplasms/pathology , CSK Tyrosine-Protein Kinase , Cell Line, Tumor , Endoplasmic Reticulum/metabolism , Endoribonucleases/metabolism , Eukaryotic Initiation Factor-2/metabolism , Female , Heme Oxygenase-1/metabolism , Humans , MCF-7 Cells , Phosphorylation , Protein Serine-Threonine Kinases/metabolism , Reactive Oxygen Species/metabolism , Receptors, Estrogen/metabolism , Unfolded Protein Response/physiology , eIF-2 Kinase/metabolism
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