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  • 1
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 369, No. 6509 ( 2020-09-11)
    Abstract: Many complex human phenotypes exhibit sex-differentiated characteristics. However, the molecular mechanisms underlying these differences remain largely unknown. We generated a catalog of sex differences in gene expression and in the genetic regulation of gene expression across 44 human tissue sources surveyed by the Genotype-Tissue Expression project (GTEx, v8 release). We demonstrate that sex influences gene expression levels and cellular composition of tissue samples across the human body. A total of 37% of all genes exhibit sex-biased expression in at least one tissue. We identify cis expression quantitative trait loci (eQTLs) with sex-differentiated effects and characterize their cellular origin. By integrating sex-biased eQTLs with genome-wide association study data, we identify 58 gene-trait associations that are driven by genetic regulation of gene expression in a single sex. These findings provide an extensive characterization of sex differences in the human transcriptome and its genetic regulation.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2020
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  • 2
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 369, No. 6509 ( 2020-09-11)
    Abstract: Telomere shortening is a hallmark of aging. Telomere length (TL) in blood cells has been studied extensively as a biomarker of human aging and disease; however, little is known regarding variability in TL in nonblood, disease-relevant tissue types. Here, we characterize variability in TLs from 6391 tissue samples, representing 〉 20 tissue types and 952 individuals from the Genotype-Tissue Expression (GTEx) project. We describe differences across tissue types, positive correlation among tissue types, and associations with age and ancestry. We show that genetic variation affects TL in multiple tissue types and that TL may mediate the effect of age on gene expression. Our results provide the foundational knowledge regarding TL in healthy tissues that is needed to interpret epidemiological studies of TL and human health.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2020
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  • 3
    In: Journal of Nuclear Medicine, Society of Nuclear Medicine, Vol. 59, No. 3 ( 2018-03), p. 486-493
    Type of Medium: Online Resource
    ISSN: 0161-5505 , 2159-662X
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    Language: English
    Publisher: Society of Nuclear Medicine
    Publication Date: 2018
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  • 4
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 82, No. 12_Supplement ( 2022-06-15), p. 3403-3403
    Abstract: Background: Detection of MRD after curative intent treatment may identify patients at high risk for recurrence. Most ctDNA-based MRD assays require a priori knowledge of genomic alterations from tumor tissue to achieve acceptable sensitivity and specificity. However, tissue availability may be limited in some patients with breast cancer, particularly following neoadjuvant therapy. Here we report results of a pilot study evaluating a plasma-only multiomic ctDNA MRD assay and its association with breast cancer recurrence. Methods: 47 plasma samples from 38 patients with early-stage breast cancer were collected through the BRandO BiO Registry at 12- or 36-months post-diagnosis and/or at the time of clinical recurrence. BRandO BiO is a multi-center regional registry with longitudinal biobanking from patients with newly diagnosed breast cancer at 20 affiliated network hospitals in Germany. The presence of ctDNA was evaluated using the Guardant Reveal multi-cancer assay, a next generation sequencing panel covering ~500 genes and ~4Mb of epigenomic regions that undergo differential methylation in multiple solid tumor types. The presence/absence of ctDNA is determined by a custom bioinformatics classifier that identifies tumor-derived somatic variants and methylation profiles specific to individual cancer types without the need for tumor tissue or peripheral blood mononuclear cell analysis. Samples were analyzed blinded to recurrence status.Results: 20 patients were confirmed to have clinical recurrence (7 local, 13 distant). ctDNA was detected at or prior to distant recurrence in 11/13 (85%) patients and in 1/7 (14%) patients with local recurrence. Five patients with distant recurrence had a sample available that was collected prior to distant recurrence; ctDNA was detected in 4/5 with a 3.8-18.6 month lead time. Among 15 ctDNA+ samples, 5 were positive for both methylation and somatic variant calls, 1 by somatic variants only, and 9 by methylation only. Somatic mutations were identified in AKT, RB1, KRAS, PIK3CA, ERBB2, MAP3K1, GATA3, and ESR1. The ESR1 mutation occurred in a patient with endocrine therapy resistance, confirming the ability of the assay to identify acquired treatment resistance mutations. ctDNA was not detected in samples from the 14 patients who had no confirmed clinical recurrence (100% specificity). Conclusions: This is the first study to demonstrate the feasibility of MRD detection in breast cancer using a plasma-only multiomic ctDNA-based approach. The Guardant Reveal assay demonstrated high sensitivity and specificity to detect distant breast cancer recurrence. Larger studies in this population are ongoing to further validate the clinical performance of the assay and demonstrate its applications in the management of early-stage breast cancer. Citation Format: Wolfgang Janni, Jens Huober, Tatjana Braun, Volkmar Müller, Angelina Fink, Amelie de Gregorio, Brigitte Rack, Thomas W. Friedl, Lisa Wiesmüller, Klaus Pantel, Thereasa Rich, Princy Parsana, Elena Zotenko, Shile Zhang, Sophia Huesmann. Multiomic, plasma-only circulating tumor DNA (ctDNA) assay identifies breast cancer patients with minimal residual disease (MRD) and predicts distant recurrence [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 3403.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2022
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  • 5
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2015
    In:  Cancer Research Vol. 75, No. 22_Supplement_2 ( 2015-11-15), p. B2-24-B2-24
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 75, No. 22_Supplement_2 ( 2015-11-15), p. B2-24-B2-24
    Abstract: Aberrant activation of Epithelial to Mesenchymal Transition (EMT) and its reverse MET is a hallmark of cancer metastasis. Also, the carcinoma cells can undergo partial transitions to attain a hybrid epithelial/mesenchymal (E/M) phenotype, which can allow them to migrate collectively and form clusters of Circulating Tumor Cells (CTCs). These clusters can be up to 50 times more metastatic compared to cells that undergo complete EMT or individually migrating CTCs. Here, using experimental data and bioinformatics, we devised a dedicated model to study the role of transcription factor OVOL in regulating these bidirectional epithelial-hybrid-mesenchymal transitions. The new model incorporates the coupling between OVOL and miR-200/ZEB - the three-way EMT/MET decision-making switch that allows for three phenotypes (E, M and E/M). We found that OVOL operates as a brake holder of complete EMT and as an expander of the hybrid E/M phenotype (it extends the range of physiological parameters for which the cells can attain the hybrid E/M phenotype). Inhibition of OVOL, for example by Wg signaling, removes that brake and supports a complete EMT. Conversely, overexpression of OVOL, for example by BMP7/Smad4, leads to the reverse of EMT, i.e. MET. In addition, OVOL elevates the phenotypic plasticity of cells by turning both EMT and MET into a two-step process (E to E/M to M, and M to E/M to E). We show that depending on the context-specific coupling manner of OVOL with miR-200/ZEB, OVOL can shepherd cellular plasticity in multiple ways - by driving MET, by restricting EMT, and by expanding the existence of the hybrid E/M phenotype. In particular, we explain how the differences between the observed effects of OVOL in breast and prostate cancer are associated with the results of different miR-200/ZEB/OVOL couplings. Our computational framework can be tailored to include other signals such as p53, TGF-beta, inflammation and hypoxia that affect the cellular plasticity during metastasis, thus providing a platform to design novel anti-metastasis therapies. Citation Format: Dongya Jia, Mohit Kumar Jolly, Marcelo Boareto, Princy Parsana, Steven Mooney, Kenneth J. Pienta, Herbert Levine, Eshel Ben-Jacob. OVOL: A brake on EMT, driver of MET and expander of the hybrid E/M phenotype. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B2-24.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2015
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  • 6
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 73, No. 8_Supplement ( 2013-04-15), p. 4619-4619
    Abstract: Epigenetic alterations driving carcinogenesis and cancer progression can be specifically targeted by the demethylating agent azacitidine (Aza) and the histone deacetylase inhibitor entinostat. While this treatment combination has been effective in a limited number of patients (pts) with treatment-refractory non-small cell lung cancer (NSCLC), we observed clinical benefit in 5 of 5 patients who received immunotherapy with PD-1/PD-L1 pathway blockade immediately following epigenetic therapy. Three of 5 pts developed partial tumor regressions (RECIST criteria, duration 10+ to 20+ mo.) and 2 pts had stable disease ≥6 mo. This compares to the objective response + SD rates of NSCLC to monotherapy with anti-PD-1 (18% + 5%) or anti-PD-L1 (10% + 12%). To understand how epigenetic therapy may synergize with blockade of the immunosuppressive PD-1 pathway, we used genome wide methylation and expression profiling on 8 NSCLC cell lines treated with low dose Aza. We discovered complex immunomodulatory effects of Aza with up-regulation of diverse immune related pathways including Jun/Jnk, NFKB, viral defense, type I interferon signaling, the inflammasome, antigen processing and presentation and immune evasion including up-regulation of PD-L1 expression. Multiple cancer-testes antigens were also up-regulated, thereby conferring de novo antigenicity. Supporting the idea that Aza acts specifically through inhibition and degradation of DNA methyltransferase proteins, colon cancer cells genetically haplo-insufficient for DNMT1 and devoid of DNMT3b mirror the immunomodulatory effects of Aza. Upstream events potentially controlling these pathways were defined, and prominent among them was up-regulation of the transcription factor, interferon regulatory factor 7 (IRF7), a DNA hypermethylated gene. These data were used to query hundreds of primary NSCLC samples from the Cancer Genome Atlas project (TCGA). A low basal expression signature of interferon pathway related genes was significantly associated with low IRF7 expression and promoter methylation in squamous tumors. Another hypermethylated transcription factor, PITX1, which inhibits a subset of type I interferon signaling genes, tracked with non-squamous cancers. Together, these findings support a model in which epigenetic modulation activates innate and adaptive immune responses within the tumor microenvironment together with induction of counter-regulatory immune checkpoint ligands which can be therapeutically blocked with antibodies. Based on these findings, a clinical trial testing the efficacy of DNMT and HDAC inhibition combined with PD-1 pathway blockade is under development. This work will form the basis for an immune-classification of NSCLC, as well as biomarker discovery for a novel therapeutic paradigm combining epigenetic and immunotherapy with potentially synergistic activity against the world's most deadly malignancy. Supported by Stand Up to Cancer. Citation Format: John Wrangle, Wei Wang, Alexander Koch, Hariharan Easwaran, Helai Mohammad, Princy Parsana, Frank Vendetti, Kristen Rodgers, Xiaoyu Pan, Kirsten Harbom, Cynthia Zahnow, Janis Taube, Julie Brahmer, Peter Jones, Suzanne Topalian, Charles Rudin, Malcolm Brock, Drew Pardoll, Stephen Baylin. Epigenetic therapy and sensitization of lung cancer to immunotherapy. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4619. doi:10.1158/1538-7445.AM2013-4619
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2013
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  • 7
    In: Cell, Elsevier BV, Vol. 183, No. 1 ( 2020-10), p. 269-283.e19
    Type of Medium: Online Resource
    ISSN: 0092-8674
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    Language: English
    Publisher: Elsevier BV
    Publication Date: 2020
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  • 8
    In: Genome Research, Cold Spring Harbor Laboratory, Vol. 26, No. 6 ( 2016-06), p. 768-777
    Abstract: The X Chromosome, with its unique mode of inheritance, contributes to differences between the sexes at a molecular level, including sex-specific gene expression and sex-specific impact of genetic variation. Improving our understanding of these differences offers to elucidate the molecular mechanisms underlying sex-specific traits and diseases. However, to date, most studies have either ignored the X Chromosome or had insufficient power to test for the sex-specific impact of genetic variation. By analyzing whole blood transcriptomes of 922 individuals, we have conducted the first large-scale, genome-wide analysis of the impact of both sex and genetic variation on patterns of gene expression, including comparison between the X Chromosome and autosomes. We identified a depletion of expression quantitative trait loci (eQTL) on the X Chromosome, especially among genes under high selective constraint. In contrast, we discovered an enrichment of sex-specific regulatory variants on the X Chromosome. To resolve the molecular mechanisms underlying such effects, we generated chromatin accessibility data through ATAC-sequencing to connect sex-specific chromatin accessibility to sex-specific patterns of expression and regulatory variation. As sex-specific regulatory variants discovered in our study can inform sex differences in heritable disease prevalence, we integrated our data with genome-wide association study data for multiple immune traits identifying several traits with significant sex biases in genetic susceptibilities. Together, our study provides genome-wide insight into how genetic variation, the X Chromosome, and sex shape human gene regulation and disease.
    Type of Medium: Online Resource
    ISSN: 1088-9051 , 1549-5469
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    Language: English
    Publisher: Cold Spring Harbor Laboratory
    Publication Date: 2016
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  • 9
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 369, No. 6509 ( 2020-09-11)
    Abstract: Rare genetic variants are abundant across the human genome, and identifying their function and phenotypic impact is a major challenge. Measuring aberrant gene expression has aided in identifying functional, large-effect rare variants (RVs). Here, we expanded detection of genetically driven transcriptome abnormalities by analyzing gene expression, allele-specific expression, and alternative splicing from multitissue RNA-sequencing data, and demonstrate that each signal informs unique classes of RVs. We developed Watershed, a probabilistic model that integrates multiple genomic and transcriptomic signals to predict variant function, validated these predictions in additional cohorts and through experimental assays, and used them to assess RVs in the UK Biobank, the Million Veterans Program, and the Jackson Heart Study. Our results link thousands of RVs to diverse molecular effects and provide evidence to associate RVs affecting the transcriptome with human traits.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2020
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  • 10
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2019
    In:  Genome Biology Vol. 20, No. 1 ( 2019-12)
    In: Genome Biology, Springer Science and Business Media LLC, Vol. 20, No. 1 ( 2019-12)
    Type of Medium: Online Resource
    ISSN: 1474-760X
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2019
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