Immune Characteriza/on of Basal- like Bladder Cancer
|
|
|
- Cecily Porter
- 6 years ago
- Views:
Transcription
1 Immune Characteriza/on of - like Bladder Cancer William Y. Kim, M.D. Departments of Medicine and Gene2cs Lineberger Comprehensive Cancer Center University of North Carolina Chapel Hill, NC
2 5 year survival rates Stage 5 year survival* 0 98% I 88% II 63% III 46% IV 15% * American Cancer Society Wong-You Cheong J J et al. Radiographics 2006;26:
3 Are there intrinsic subtypes of high-grade bladder cancer?
4 Can we define subtypes of bladder cancer focusing exclusively on high grade tumors? Normal urothelium FGFR3 RAS PTEN RB1 Recurrence LG papillary Progression PTEN RB1 HG muscle-invasive -like
5 Consensus Clustering identifies 2 subtypes of high grade UC MSKCC (n=58) Meta-dataset (n=262) TCGA (n=131) Meta K1 Meta K K1 K2 K1 K2 MSKCC TCGA Damrauer et al., PNAS, 2014
6 Significance Analysis of Microarrays (SAM) determines differences in gene expression Meta-dataset (n=262) K1 vs- K2, FDR = 0 SAM K1 KRT5 KRT6A CD44 K2 PPARG GATA3 KRT20 UPK2
7 Normal urothelium is characterized by different differentiation states HMWK LMWK Umbrella cells Uroplakin KRT 20 (Castillo-Martin 2010) -like cells KRT 14 KRT 5
8 Development of the BASE47 (Bladder cancer Analysis of Subtype by gene Expression)
9 BASE47 can accurately classify basal and luminal bladder cancers Centroid Centroid BASE47 Prediction Training CCP Meta BASE Predictor Generation by PAM Validation MSKCC CCP p< BASE Consensus Clustering of Meta Dataset Validation CCP TCGA p< BASE p< Damrauer et al., PNAS, 2014
10 bladder cancer has a relatively poor prognosis MSKCC TCGA Overall Survival Overall Specific Survival in Choi Overall Survival Probability Log Rank p= Months Overall Survival Log Rank p= Days Overall Survival Probability Months Log Rank p= Damrauer et al., PNAS, 2014 Choi et al., Cancer Cell, 2014 TCGA, Nature, 2014
11 Intrinsic subtypes of bladder cancer reflect breast cancer biology
12 Breast cancer related genes are coregulated with urothelial specific genes K1 K2 CYP2J2 DHRS2 FXYD3 CROT GPX2 MECOM MAOA RAPGEFL 1 S100P MGST2 ICA1 CNGA1 MCCC1 IFNA14 ATP8B1 ACSF2 CYP4F12 TJP3 CYP4B1 ELF3 FOXA1 HMGCS2 FAM174B BCAS1 CYB5A GPD1L GATA3 EPN3 ERBB3 EVPL BCAT2 ADIRF CAPN5 PPFIBP2 UPK1A PLCE1 UPK2 TRAK1 SCNN1B SCNN1G TMPRSS2 TLE2 TBX2 TMEM97 ZBTB7C TOP2B RAB15 NR2F6 TM7SF2 PIK3C2B PLEKHG6 SUOX SNCG RAB11A VIPR1 VGLL1 SH3GLB2 ZNF443 TBX3 SLC9A2 SPINK1 SLC29A3 PSCA PPARG Text Color Breast Cancer Related Urothelial Related Breast Bladder Breast Damrauer et al., PNAS, 2014
13 bladder cancer is enriched for signatures related to basal breast cancer PAM50 Calls LumA LumB Her2 Normal Bladder Subtypes Breast Signatures Cluster PMID: GATA3 PMID: GATA3 PMID: Estrogen Reg. PMID: Cluster PMID: Breast Signatures Mature Down PMID: Progenitor PMID: Metaplastic PMID: MaSC PMID: Pathway Signatures Myc Targets PMID: Oncogenic E2F3 PMID: Her2 Amplicon PMID: Damrauer et al., PNAS, 2014
14 Breast and Bladder subtypes Damrauer et al., PNAS, 2014
15 Intrinsic subtypes defined by MDACC and TCGA
16 Intrinsic subtypes defined by MDACC Choi et al., Cancer Cell, 2014
17 Intrinsic subtypes defined by TCGA TCGA, Nature, 2014
18 Subtype summary McConkey, Eur Urol, 2014
19 Proposed model for intrinsic bladder subtypes Recurrence FGFR3 RAS LG papillary Normal urothelium BC BC PTEN RB1 TP53 BC PTEN RB1 TP53 HG non-papillary UC urothelial cells increased TICs Squamous differentiation RB pathway alterations Female gender HG papillary UC Umbrella urothelial cells Papillary features FGFR3 alterations Damrauer et al., PNAS, 2014
20 Intrinsic bladder cancer subtypes express different markers of immune infiltration
21 Gene expression pathways in basal-bladder Ingenuity Pathway Analysis (IPA) migration of cells cell movement homing homing of cells chemotaxis cell movement tumor cell lnes chemotaxis of cells leukocyte migration cell movement of blood cells migration of tumor cell lines adhesion of immune cells homing of leukocytes adhesion of blood cells chemotaxis of leukocytes development of blood cells development of leukocytes homing of blood cells inflammatory response organization of cytoplasm chemotaxis of phagocytes z - activation score
22 Gene expression pathways in basal-bladder Gene Set Enrichment Analysis (GSEA) Functional*Annotation*Clusters*Enriched*in** Cluster(Rank( Representative(Pathway( Enrichment(Score( PValue( FDR( 1( IPR007110:ImmunoglobulinClike( 16.04( 1.76EC13( 3.10EC10( 2( GO: ~leukocyte(activation( 13.74( 2.44EC14( 4.62EC11( 3( GO: ~chemotaxis( 13.05( 4.15EC16( 8.44EC13( 4( GO: ~cell(migration( 9.93( 3.62EC12( 6.84EC09( 5( GO: ~regulation(of(cell(motion( 8.98( 3.42EC10( 6.47EC07( 6( GO: ~regulation(of(apoptosis( 8.86( 1.04EC09( 1.96EC06( 7( GO: ~regulation(of(T(cell(activation( 8.80( 1.35EC08( 2.56EC05( 8( GO: ~glycosaminoglycan(binding( 8.64( 8.88EC10( 1.47EC06( 9( GO: ~vasculature(development( 8.04( 1.90EC09( 3.59EC06( 10( GO: ~chemokine(activity( 7.97( 1.22EC08( 2.03EC05( 11( hsa05332:graftcversuschost(disease( 7.81( 4.78EC10( 5.91EC07( 12( GO: ~negative(regulation(of(apoptosis( 7.38( 2.46EC08( 4.66EC05( 13( GO: ~positive(regulation(of(cell(motion( 6.99( 7.35EC08( 1.39EC04( 14( GO: ~immune(system(development( 6.53( 6.95EC07( ( 15( hydroxylysine( 6.50( 5.37EC08( 8.16EC05(
23 Immune signatures are enriched in basal bladder A TCGA Bladder RNA seq B_Cell signature Mac_CSF1 T_Cell_cluster T test p value: 1.89e T test p value: 1.44e T test p value: 5.82e 06 B MAC_CSF1 CD68_CLUSTER enrichment score: 0.71 p-value = 0.04 enrichment score: 0.92 p-value = 0.0
24 Immunecheckpoint genes are enriched in basal bladder cancer CTLA4 FOXP3 IDO1 Log2 Median Centered Expression p = 2.63e p = 1.28e p = 4.28e 14 PD1 PDL1 IL10 Log2 Median Centered Expression p = 2.74e p = 8.3e p = 8.42e 08
25 PD-L1 highly expressed in basal bladder cancer Log2 Median Centered Expression PD L1 Expression By Tumor Type Her2 LumA LumB COAD GBM KIRC LAML LUAD LUSC OV READ UCEC Bladder Breast
26 Row Z Score A subset of basal bladder tumors have clonal expansion of B cells B
27 Conclusions Intrinsic subtypes of HG bladder cancer exist and have similari2es to breast cancer. - like and luminal subtypes are associated with specific molecular altera2ons and clinico- pathologic characteris2cs. bladder tumors have increased immune infiltrates and a subset of tumors may have clonal expansion of B cells.
28 Acknowledgements Kim Lab Jeff Damrauer Sara Wobker Ryoichi Saito David Chism Bhavani Krishnan Bing Zhou Sean Bailey Janet Leung HyoJin Lee Harper Wilson Jonathan Serody Ben Vincent Chuck Perou Ka2e Hoadley Joel Parker Chris Fan Gopa Iyer FUNDING SOURCES NIH/NCI Department of Defense Damon Runyon Founda2on University Cancer Research Fund (UCRF) AACR Kure It
Genetically Engineered Murine Models of RCC William Y. Kim, M.D.
Genetically Engineered Murine Models of RCC William Y. Kim, M.D. Co-director, Mouse Phase 1 Unit (MP1U) Departments of Medicine, Genetics, and Urology Lineberger Comprehensive Cancer Center University
Genomic Analyses across Six Cancer Types Identify Basal-like Breast Cancer as a Unique Molecular Entity
Genomic Analyses across Six Cancer Types Identify Basal-like Breast Cancer as a Unique Molecular Entity Aleix Prat, Barbara Adamo, Cheng Fan, Vicente Peg, Maria Vidal, Patricia Galván, Ana Vivancos, Paolo
Supplementary Figure 1: LUMP Leukocytes unmethylabon to infer tumor purity
Supplementary Figure 1: LUMP Leukocytes unmethylabon to infer tumor purity A Consistently unmethylated sites (30%) in 21 cancer types 174,696
The Cancer Genome Atlas Pan-cancer analysis Katherine A. Hoadley
The Cancer Genome Atlas Pan-cancer analysis Katherine A. Hoadley Department of Genetics Lineberger Comprehensive Cancer Center The University of North Carolina at Chapel Hill What is TCGA? The Cancer Genome
Exploring TCGA Pan-Cancer Data at the UCSC Cancer Genomics Browser
Exploring TCGA Pan-Cancer Data at the UCSC Cancer Genomics Browser Melissa S. Cline 1*, Brian Craft 1, Teresa Swatloski 1, Mary Goldman 1, Singer Ma 1, David Haussler 1, Jingchun Zhu 1 1 Center for Biomolecular
Update on bladder neoplasia: 2016 WHO classification and recent developments within the pathologic, molecular & clinical domains of the disease
Update on bladder neoplasia: 2016 WHO classification and recent developments within the pathologic, molecular & clinical domains of the disease Biology of urothelial tumorigenesis: insights from genetically
Supplementary Figure 1. Copy Number Alterations TP53 Mutation Type. C-class TP53 WT. TP53 mut. Nature Genetics: doi: /ng.
Supplementary Figure a Copy Number Alterations in M-class b TP53 Mutation Type Recurrent Copy Number Alterations 8 6 4 2 TP53 WT TP53 mut TP53-mutated samples (%) 7 6 5 4 3 2 Missense Truncating M-class
ncounter Assay Automated Process Immobilize and align reporter for image collecting and barcode counting ncounter Prep Station
ncounter Assay ncounter Prep Station Automated Process Hybridize Reporter to RNA Remove excess reporters Bind reporter to surface Immobilize and align reporter Image surface Count codes Immobilize and
Molecular Classification of Triple-Negative Breast Cancer (TNBC) Aleix Prat, MD
Molecular Classification of Triple-Negative Breast Cancer (TNBC) Emerging genomic and clinical data Aleix Prat, MD Postdoctoral Research Associate at Perou Lab Lineberger Comprehensive Cancer Center University
Transcriptional Profiles from Paired Normal Samples Offer Complementary Information on Cancer Patient Survival -- Evidence from TCGA Pan-Cancer Data
Transcriptional Profiles from Paired Normal Samples Offer Complementary Information on Cancer Patient Survival -- Evidence from TCGA Pan-Cancer Data Supplementary Materials Xiu Huang, David Stern, and
ncounter Assay Automated Process Capture & Reporter Probes Bind reporter to surface Remove excess reporters Hybridize CodeSet to RNA
ncounter Assay Automated Process Hybridize CodeSet to RNA Remove excess reporters Bind reporter to surface Immobilize and align reporter Image surface Count codes mrna Capture & Reporter Probes slides
Disclosure. Astellas. Research funding. Advisory board (to institute) Roche/Genentech Astra Zeneca/Medimmune Astellas
Disclosure Activity Company Research funding Advisory board (to institute) Astellas Roche/Genentech Astra Zeneca/Medimmune Astellas Immunotherapy for urothelial cell carcinoma A NEW HOPE Michiel van der
Genomic landscape of breast cancer
Genomic landscape of breast cancer Aleix Prat MD PhD Head of the Translational Genomics Group Attending Physician at the Breast Cancer Unit VHIO, Barcelona, Spain Major research advance for breast cancer
Breast cancer classification: beyond the intrinsic molecular subtypes
Breast cancer classification: beyond the intrinsic molecular subtypes Britta Weigelt, PhD Signal Transduction Laboratory CRUK London Research Institute Summary Breast cancer heterogeneity Molecular classification
RNA preparation from extracted paraffin cores:
Supplementary methods, Nielsen et al., A comparison of PAM50 intrinsic subtyping with immunohistochemistry and clinical prognostic factors in tamoxifen-treated estrogen receptor positive breast cancer.
Machine-Learning on Prediction of Inherited Genomic Susceptibility for 20 Major Cancers
Machine-Learning on Prediction of Inherited Genomic Susceptibility for 20 Major Cancers Sung-Hou Kim University of California Berkeley, CA Global Bio Conference 2017 MFDS, Seoul, Korea June 28, 2017 Cancer
Clasificación Molecular del Cáncer de Próstata. JM Piulats
Clasificación Molecular del Cáncer de Próstata JM Piulats Introduction The Gleason score is the major method for prostate cancer tissue grading and the most important prognostic factor in this disease.
Heterogeneidad tumoral. Federico Rojo
Heterogeneidad tumoral Federico Rojo Outline of the presentation Definition and evidences Intertumor heterogeneity Spatial and temporal intratumor heterogeneity Clinical implications of tumor heterogeneity.
Comparison of Triple Negative Breast Cancer between Asian and Western Data Sets
2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops Comparison of Triple Negative Breast Cancer between Asian and Western Data Sets Lee H. Chen Bioinformatics and Biostatistics
Endogenous retroviral signatures predict immunotherapy response in clear cell renal cell carcinoma
Endogenous retroviral signatures predict immunotherapy response in clear cell renal cell carcinoma Christof C. Smith,, Sara R. Selitsky, Benjamin G. Vincent J Clin Invest. 2018. https://doi.org/10.1172/jci121476.
Non Muscle Invasive Bladder Cancer (NMIBC) Experts Discuss Treatment Options. Part II: The Future Treatment of NMIBC
Non Muscle Invasive Bladder Cancer (NMIBC) Experts Discuss Treatment Options Wednesday, June 14, 2017 Part II: The Future Treatment of NMIBC Presented by Dr. Arlene Siefer-Radtke is an Associate Professor
TCGA. The Cancer Genome Atlas
TCGA The Cancer Genome Atlas TCGA: History and Goal History: Started in 2005 by the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI) with $110 Million to catalogue
Biomarkers in Imunotherapy: RNA Signatures as predictive biomarker
Biomarkers in Imunotherapy: RNA Signatures as predictive biomarker Joan Carles, MD PhD Director GU, CNS and Sarcoma Program Department of Medical Oncology Vall d'hebron University Hospital Outline Introduction
Identification of Tissue Independent Cancer Driver Genes
Identification of Tissue Independent Cancer Driver Genes Alexandros Manolakos, Idoia Ochoa, Kartik Venkat Supervisor: Olivier Gevaert Abstract Identification of genomic patterns in tumors is an important
10/15/2012. Biologic Subtypes of TNBC. Topics. Topics. Histopathology Molecular pathology Clinical relevance
Biologic Subtypes of TNBC Andrea L. Richardson M.D. Ph.D. Brigham and Women s Hospital Dana-Farber Cancer Institute Harvard Medical School Boston, MA Topics Histopathology Molecular pathology Clinical
Development and verification of the PAM50-based Prosigna breast cancer gene signature assay
Washington University School of Medicine Digital Commons@Becker Open Access Publications 2015 Development and verification of the PAM50-based Prosigna breast cancer gene signature assay Jacqueline Snider
How Many Diseases in Carcinoma in situ?
How Many Diseases in Carcinoma in situ? Eva Compérat La Pitié Salpêtrière Assistance Publique Université Pierre et Marie Curie, Paris VI Carcinogenesis of Bladder Cancer (BC) BC is a panurothelial disease
Bum-Sup Jang and In Ah Kim. ¹Department of Radiation Oncology, Seoul National University Graduate School of Medicine 2
A Radiosensitivity Gene Signature and PD-L1 Predict Clinical Outcome of Patients with Invasive Breast Carcinoma in The Cancer Genome Atlas (TCGA) Dataset Bum-Sup Jang and In Ah Kim ¹Department of Radiation
Computer Science, Biology, and Biomedical Informatics (CoSBBI) Outline. Molecular Biology of Cancer AND. Goals/Expectations. David Boone 7/1/2015
Goals/Expectations Computer Science, Biology, and Biomedical (CoSBBI) We want to excite you about the world of computer science, biology, and biomedical informatics. Experience what it is like to be a
Nature Genetics: doi: /ng Supplementary Figure 1. SEER data for male and female cancer incidence from
Supplementary Figure 1 SEER data for male and female cancer incidence from 1975 2013. (a,b) Incidence rates of oral cavity and pharynx cancer (a) and leukemia (b) are plotted, grouped by males (blue),
Genomic tests to personalize therapy of metastatic breast cancers. Fabrice ANDRE Gustave Roussy Villejuif, France
Genomic tests to personalize therapy of metastatic breast cancers Fabrice ANDRE Gustave Roussy Villejuif, France Future application of genomics: Understand the biology at the individual scale Patients
Nature Genetics: doi: /ng Supplementary Figure 1. Workflow of CDR3 sequence assembly from RNA-seq data.
Supplementary Figure 1 Workflow of CDR3 sequence assembly from RNA-seq data. Paired-end short-read RNA-seq data were mapped to human reference genome hg19, and unmapped reads in the TCR regions were extracted
RNA SEQUENCING AND DATA ANALYSIS
RNA SEQUENCING AND DATA ANALYSIS Download slides and package http://odin.mdacc.tmc.edu/~rverhaak/package.zip http://odin.mdacc.tmc.edu/~rverhaak/rna-seqlecture.zip Overview Introduction into the topic
The 16th KJC Bioinformatics Symposium Integrative analysis identifies potential DNA methylation biomarkers for pan-cancer diagnosis and prognosis
The 16th KJC Bioinformatics Symposium Integrative analysis identifies potential DNA methylation biomarkers for pan-cancer diagnosis and prognosis Tieliu Shi tlshi@bio.ecnu.edu.cn The Center for bioinformatics
Package AIMS. June 29, 2018
Type Package Package AIMS June 29, 2018 Title AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype Version 1.12.0 Date 2014-06-25 Description This package contains the AIMS implementation.
Transcriptomic classification of genetically engineered mouse models of breast cancer identifies human subtype counterparts
Pfefferle et al. Genome Biology 2013, 14:R125 RESEARCH Transcriptomic classification of genetically engineered mouse models of breast cancer identifies human subtype counterparts Open Access Adam D Pfefferle
Molecular subtypes of urothelial carcinoma are defined by specific gene regulatory systems
Eriksson et al. BMC Medical Genomics (2015) 8:25 DOI 10.1186/s12920-015-0101-5 RESEARCH ARTICLE Open Access Molecular subtypes of urothelial carcinoma are defined by specific gene regulatory systems Pontus
User s Manual Version 1.0
User s Manual Version 1.0 #639 Longmian Avenue, Jiangning District, Nanjing,211198,P.R.China. http://tcoa.cpu.edu.cn/ Contact us at xiaosheng.wang@cpu.edu.cn for technical issue and questions Catalogue
THE SEARCH FOR BIOMARKERS IN BLADDER CANCER
THE SEARCH FOR BIOMARKERS IN BLADDER CANCER CDDP and IO WORLD ALEJO RODRÍGUEZ-VIDA MD PhD Consultant Medical Oncologist Associate Professor Hospital del Mar, Barcelona November 23 rd 2018 DISCLOSURE OF
Expanded View Figures
Molecular Systems iology Tumor CNs reflect metabolic selection Nicholas Graham et al Expanded View Figures Human primary tumors CN CN characterization by unsupervised PC Human Signature Human Signature
Supplementary Materials for
advances.sciencemag.org/cgi/content/full/2/9/e1600220/dc1 Supplementary Materials for Portraying breast cancers with long noncoding RNAs Olivier Van Grembergen, Martin Bizet, Eric J. de Bony, Emilie Calonne,
Molecular Heterogeneity of Triple Negative Breast Cancer
Molecular Heterogeneity of Triple Negative Breast Cancer Katherine A. Hoadley Department of Genetics Lineberger Comprehensive Cancer Center The University of North Carolina at Chapel Hill Estimated Cancer
Alternate Gene Signatures, or Not
Charles M. Perou, Ph.D. Departments of Genetics and Pathology Lineberger Comprehensive Cancer Center University of North Carolina Chapel Hill, North Carolina, USA Alternate Gene Signatures, or Not Charles
Kinome Profiling: The Potential in ER-Negative Patients. Charles M. Perou, Ph.D. Departments of Genetics and Pathology
Kinome Profiling: The Potential in ER-Negative Patients Charles M. Perou, Ph.D. Departments of Genetics and Pathology Lineberger Comprehensive Cancer Center University of North Carolina Chapel Hill, North
Perspectivas moleculares en la disección del cáncer de mama esporádico y hereditario
Perspectivas moleculares en la disección del cáncer de mama esporádico y hereditario Aleix Prat, MD PhD Medical Oncology, Hospital Clínic Barcelona, Spain mrna microrna Protein DNA Copy Number DNA Methylation
Supplemental Figure legends
Supplemental Figure legends Supplemental Figure S1 Frequently mutated genes. Frequently mutated genes (mutated in at least four patients) with information about mutation frequency, RNA-expression and copy-number.
RNA SEQUENCING AND DATA ANALYSIS
RNA SEQUENCING AND DATA ANALYSIS Length of mrna transcripts in the human genome 5,000 5,000 4,000 3,000 2,000 4,000 1,000 0 0 200 400 600 800 3,000 2,000 1,000 0 0 2,000 4,000 6,000 8,000 10,000 Length
Characterization of cell lines derived from breast cancers and normal mammary tissues for the study of the intrinsic molecular subtypes
Breast Cancer Res Treat (2013) 142:237 255 DOI 10.1007/s10549-013-2743-3 PRECLINICAL STUDY Characterization of cell lines derived from breast cancers and normal mammary tissues for the study of the intrinsic
EARLY ONLINE RELEASE
EARLY ONLINE RELEASE Note: This article was posted on the Archives Web site as an Early Online Release. Early Online Release articles have been peer reviewed, copyedited, and reviewed by the authors. Additional
Expression and methylation patterns partition luminal-a breast tumors into distinct prognostic subgroups
Netanely et al. Breast Cancer Research (2016) 18:74 DOI 10.1186/s13058-016-0724-2 RESEARCH ARTICLE Open Access Expression and methylation patterns partition luminal-a breast tumors into distinct prognostic
Plasma-Seq conducted with blood from male individuals without cancer.
Supplementary Figures Supplementary Figure 1 Plasma-Seq conducted with blood from male individuals without cancer. Copy number patterns established from plasma samples of male individuals without cancer
New breast cancer classification: traditional pathology and molecular subtypes. Dr. PN Mainwaring Centre for Personalised NanoMedicine
New breast cancer classification: traditional pathology and molecular subtypes Dr. PN Mainwaring Centre for Personalised NanoMedicine AIBN@UQ Outline Traditional Pathology Haematoxylin & Eosin Descriptors;
Classification of Breast Cancer Subtypes by combining Gene Expression and DNA Methylation Data
Journal of Integrative Bioinformatics, 11(2):236, 214 Classification of Breast Cancer Subtypes by combining Expression and DNA Data Markus List 1,2,3,*, Anne-Christin Hauschild 4, Qihua Tan 3,5, Torben
HepaRG LX2. HepaRG HepaRG LX2 LX2
C Supporting Figure 1. Experimental design of s between and cells. (A) -hepatocytes were isolated from a 30 days of -progenitors. Differentiation into mature hepatocytes was achieved following a 2-weeks
Genetic alterations of histone lysine methyltransferases and their significance in breast cancer
Genetic alterations of histone lysine methyltransferases and their significance in breast cancer Supplementary Materials and Methods Phylogenetic tree of the HMT superfamily The phylogeny outlined in the
Supplementary Figures
Supplementary Figures Supplementary Figure 1. Pan-cancer analysis of global and local DNA methylation variation a) Variations in global DNA methylation are shown as measured by averaging the genome-wide
Supplementary Data for:
Supplementary Data for: Tumour sampling method can significantly influence gene expression profiles derived from neoadjuvant window studies Dominic A. Pearce 1, Laura M. Arthur 1, Arran K. Turnbull 1,
Exploring New Strategies in Bladder Cancer
Exploring New Strategies in Bladder Cancer Daniel P. Petrylak, MD Professor of Medicine and Urology Director, Genitourinary Translational Working Group Co-Director, Signal Transduction Program Smilow Cancer
SUPPLEMENTARY INFORMATION
doi:10.1038/nature10866 a b 1 2 3 4 5 6 7 Match No Match 1 2 3 4 5 6 7 Turcan et al. Supplementary Fig.1 Concepts mapping H3K27 targets in EF CBX8 targets in EF H3K27 targets in ES SUZ12 targets in ES
Breast Cancer: ASCO Poster Review
Breast Cancer: ASCO Poster Review Carmen Criscitiello, MD, PhD Istituto Europeo di Oncologia Milano HER2+ SUBTYPE Research questions in early HER2+ BC De-escalation of toxicity without compromising efficacy
Novel treatments for SCC Andrés Felipe Cardona, MD MS PhD.
Novel treatments for SCC Andrés Felipe Cardona, MD MS PhD. Clinical and Transla,onal Oncology Group Ins,tute of Oncology, Fundación Santa fe de Bogotá Clinical Epidemiology Cochrane Colombian Branch /
Relevancia práctica de la clasificación de subtipos intrínsecos en cáncer de mama Miguel Martín Instituto de Investigación Sanitaria Gregorio Marañón
Relevancia práctica de la clasificación de subtipos intrínsecos en cáncer de mama Miguel Martín Instituto de Investigación Sanitaria Gregorio Marañón Universidad Complutense Madrid The new technologies
Reviewing Immunotherapy for Bladder Carcinoma In Situ
Reviewing Immunotherapy for Bladder Carcinoma In Situ Samir Bidnur Dept of Urologic Sciences, Grand Rounds March 1 st, 2017 Checkpoint Inhibition and Bladder Cancer, an evolving story with immunotherapy
Microarray Analysis and Liver Diseases
Microarray Analysis and Liver Diseases Snorri S. Thorgeirsson M.D., Ph.D. Laboratory of Experimental Carcinogenesis Center for Cancer Research, NCI, NIH Application of Microarrays to Cancer Research Identifying
TEB. Id4 p63 DAPI Merge. Id4 CK8 DAPI Merge
a Duct TEB b Id4 p63 DAPI Merge Id4 CK8 DAPI Merge c d e Supplementary Figure 1. Identification of Id4-positive MECs and characterization of the Comma-D model. (a) IHC analysis of ID4 expression in the
The quest for the identification of the genetic determinants of cancer immune responsiveness
2015 Sidra Medical and Research Center The quest for the identification of the genetic determinants of cancer immune responsiveness Francesco M Marincola - Chief Research Officer Sidra Medical and Research
Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin
Resource Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin Katherine A. Hoadley, 1,20 Christina Yau, 2,20 Denise M. Wolf, 3,20 Andrew D. Cherniack,
AIMS: Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype
AIMS: Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype Eric R. Paquet (eric.r.paquet@gmail.com), Michael T. Hallett (michael.t.hallett@mcgill.ca) 1 1 Department of Biochemistry, Breast
Nicholas Borcherding, Nicholas L. Bormann, Andrew Voigt, Weizhou Zhang 1-4
SOFTWARE TOOL ARTICLE TRGAted: A web tool for survival analysis using protein data in the Cancer Genome Atlas. [version 1; referees: 1 approved] Nicholas Borcherding, Nicholas L. Bormann, Andrew Voigt,
Urinary Bladder: WHO Classification and AJCC Staging Update 2017
Urinary Bladder: WHO Classification and AJCC Staging Update 2017 Houston Society of Clinical Pathologists 58 th Annual Spring Symposium Houston, TX April 8, 2017 Jesse K. McKenney, MD Classification
LncRNA TUSC7 affects malignant tumor prognosis by regulating protein ubiquitination: a genome-wide analysis from 10,237 pancancer
Original Article LncRNA TUSC7 affects malignant tumor prognosis by regulating protein ubiquitination: a genome-wide analysis from 10,237 pancancer patients Xiaoshun Shi 1 *, Yusong Chen 2,3 *, Allen M.
Concordance among Gene-Expression Based Predictors for Breast Cancer
The new england journal of medicine original article Concordance among Gene-Expression Based Predictors for Breast Cancer Cheng Fan, M.S., Daniel S. Oh, Ph.D., Lodewyk Wessels, Ph.D., Britta Weigelt, Ph.D.,
a) List of KMTs targeted in the shrna screen. The official symbol, KMT designation,
Supplementary Information Supplementary Figures Supplementary Figure 1. a) List of KMTs targeted in the shrna screen. The official symbol, KMT designation, gene ID and specifities are provided. Those highlighted
SSM signature genes are highly expressed in residual scar tissues after preoperative radiotherapy of rectal cancer.
Supplementary Figure 1 SSM signature genes are highly expressed in residual scar tissues after preoperative radiotherapy of rectal cancer. Scatter plots comparing expression profiles of matched pretreatment
- 1 - Reviewers' comments: Reviewer #1 (Remarks to the Author):
Reviewers' comments: Reviewer #1 (Remarks to the Author): Summary: In this manuscript, the authors characterized cellular and transcriptional heterogeneity of breast cancer using single-cell RNA sequencing.
Micropapillary urothelial carcinoma: is molecular hair-splitting on target?
Editorial Micropapillary urothelial carcinoma: is molecular hair-splitting on target? Nuzhat Husain, Azfar Neyaz Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, India Correspondence to: Prof.
Expanded View Figures
Solip Park & Ben Lehner Epistasis is cancer type specific Molecular Systems Biology Expanded View Figures A B G C D E F H Figure EV1. Epistatic interactions detected in a pan-cancer analysis and saturation
ACCME/Disclosures. Case History 4/13/2016. USCAP GU Specialty Conference Case 3. Ann Arbor, MI
USCAP GU Specialty Conference Case 3 March 2016 L. Priya Kunju, M.D. University of Michigan Health System Ann Arbor, MI University of Michigan Health System ACCME/Disclosures The USCAP requires that anyone
Molecular classification of breast cancer implications for pathologists. Sarah E Pinder
Molecular classification of breast cancer implications for pathologists Sarah E Pinder Courtesy of CW Elston Histological types Breast Cancer Special Types 17 morphological special types 25-30% of all
Predicting outcome in metastatic breast cancer
Predicting outcome in metastatic breast cancer Aleix Prat, MD, PhD Medical Oncology Department Translational Genomics and Targeted Therapeutics in Solid Tumors Monday, 15 th January, Manchester, UK Disclosures
Tumor Purity and Immune Cell Infiltration as a Prognostic Risk Predictor for Clear Cell Renal Cell Carcinoma (ccrcc)
Tumor Purity and Immune Cell Infiltration as a Prognostic Risk Predictor for Clear Cell Renal Cell Carcinoma (ccrcc) Andrew G. Winer, Yasin Senbabaoglu, Samuel D Kaffenberger, Jonathan A. Coleman, Paul
Cancer develops as a result of the accumulation of somatic
Cancer-mutation network and the number and specificity of driver mutations Jaime Iranzo a,1, Iñigo Martincorena b, and Eugene V. Koonin a,1 a National Center for Biotechnology Information, National Library
SUPPLEMENTARY APPENDIX
SUPPLEMENTARY APPENDIX 1) Supplemental Figure 1. Histopathologic Characteristics of the Tumors in the Discovery Cohort 2) Supplemental Figure 2. Incorporation of Normal Epidermal Melanocytic Signature
CoINcIDE: A framework for discovery of patient subtypes across multiple datasets
Planey and Gevaert Genome Medicine (2016) 8:27 DOI 10.1186/s13073-016-0281-4 METHOD CoINcIDE: A framework for discovery of patient subtypes across multiple datasets Catherine R. Planey and Olivier Gevaert
Postoperative Adjuvant Chemotherapies. Stefan Aebi Luzerner Kantonsspital
Postoperative Adjuvant Chemotherapies Stefan Aebi Luzerner Kantonsspital stefan.aebi@onkologie.ch Does Chemotherapy Work in Older Patients? ER : Chemotherapy vs nil Age
Nature Immunology: doi: /ni Supplementary Figure 1. RNA-Seq analysis of CD8 + TILs and N-TILs.
Supplementary Figure 1 RNA-Seq analysis of CD8 + TILs and N-TILs. (a) Schematic representation of the tumor and cell types used for the study. HNSCC, head and neck squamous cell cancer; NSCLC, non-small
Distinct cellular functional profiles in pan-cancer expression analysis of cancers with alterations in oncogenes c-myc and n-myc
Honors Theses Biology Spring 2018 Distinct cellular functional profiles in pan-cancer expression analysis of cancers with alterations in oncogenes c-myc and n-myc Anne B. Richardson Whitman College Penrose
Contemporary Classification of Breast Cancer
Contemporary Classification of Breast Cancer Laura C. Collins, M.D. Vice Chair of Anatomic Pathology Professor of Pathology Beth Israel Deaconess Medical Center and Harvard Medical School Boston, MA Outline
INTRADUCTAL LESIONS OF THE PROSTATE. Jonathan I. Epstein
INTRADUCTAL LESIONS OF THE PROSTATE Jonathan I. Epstein Topics Prostatic intraepithelial neoplasia (PIN) Intraductal adenocarcinoma (IDC-P) Intraductal urothelial carcinoma Ductal adenocarcinoma High Prostatic
Table 1 Demographic data of PD-patients. Data are represented as counts or median and full range.
Table 1 Demographic data of PD-patients. Data are represented as counts or median and full range. Parameter Number Patients 5 Diabetes mellitus 0 Previous NTX 0 Steroids 0 Patients with residual renal
Completion of The Cancer Genome Atlas, what did we learn?
Charles M. Perou, Ph.D. Departments of Genetics Lineberger Comprehensive Cancer Center University of North Carolina at Chapel Hill Completion of The Cancer Genome Atlas, what did we learn? TCGA Breast
Heterologous Tissue Culture Expression Signature Predicts Human Breast Cancer Prognosis
Heterologous Tissue Culture Expression Signature Predicts Human Breast Cancer Prognosis Eun Sung Park 1 *, Ju-Seog Lee 2, Hyun Goo Woo 2, Fenghuang Zhan 4, Joanna H. Shih 3, John D. Shaughnessy, Jr. 4,
Triple Negative Breast Cancer
Triple Negative Breast Cancer Prof. Dr. Pornchai O-charoenrat Division of Head-Neck & Breast Surgery Department of Surgery Faculty of Medicine Siriraj Hospital Breast Cancer Classification Traditional
Relationship between genomic features and distributions of RS1 and RS3 rearrangements in breast cancer genomes.
Supplementary Figure 1 Relationship between genomic features and distributions of RS1 and RS3 rearrangements in breast cancer genomes. (a,b) Values of coefficients associated with genomic features, separately
15. Supplementary Figure 9. Predicted gene module expression changes at 24hpi during HIV
Supplementary Information Table of content 1. Supplementary Table 1. Summary of RNAseq data and mapping statistics 2. Supplementary Table 2. Biological functions enriched in 12 hpi DE genes, derived from
Nature Getetics: doi: /ng.3471
Supplementary Figure 1 Summary of exome sequencing data. ( a ) Exome tumor normal sample sizes for bladder cancer (BLCA), breast cancer (BRCA), carcinoid (CARC), chronic lymphocytic leukemia (CLLX), colorectal
8/1/2017. Imaging and Molecular Biomarkers of Lung Cancer Prognosis. Disclosures. The Era of Precision Oncology
Imaging and Molecular Biomarkers of Lung Cancer Prognosis Ruijiang Li, PhD Assistant Professor of Radiation Oncology 08/01/2017 Stanford University Department of Radiation Oncology School of Medicine Disclosures
Epigenetics & Chromatin. Open Access RESEARCH
DOI 10.1186/s13072-016-0102-4 Epigenetics & Chromatin RESEARCH Open Access Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer
Updates in Urologic Pathology WHO Made Those Changes?! Peyman Tavassoli Pathology Department BC Cancer Agency
Updates in Urologic Pathology WHO Made Those Changes?! Peyman Tavassoli Pathology Department BC Cancer Agency World Health Organization Available in Feb 2016 Frame work for reporting Major contributing
Types of bladder cancer
There are three main types of bladder cancer: Urothelial bladder cancer Squamous cell cancer Adenocarcinoma of the bladder There is more information about how we treat the different types of bladder cancer