1. Identify the Key Players and Their
Regulators in Major Cancer Types
Jesse Liang, Ph.D.
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Sample & Assay Technologies
2. 8 Hallmarks of Cancer
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The 8 Hallmarks of Cancer (Cell, March 2011):
1. Sustaining proliferative signaling
2. Evading growth suppressors
3. Resisting cell death
4. Enabling replicative immortality
5. Inducing angiogenesis
6. Activating invasion and metastasis
7. Reprogramming energy metabolism
8. Escaping immune destruction
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3. Corresponding PCR Arrays to Study These Hallmarks
1. Cell Cycle
2. Apoptosis
3. Cell Death Pathway Finder
4. Telomeres and Telomerases
5. Angiogenesis
6. Extracellular Matrix (ECM) and Adhesion Molecules
7. EMT (Epithelial-Mesenchymal Transition)
8. Tumor Metastasis
9. Cell Motility
10. Energy Metabolism
11. Innate and Adaptive Immune Response
12. Cancer Pathway Finder
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http://www.sabiosciences.com/ArrayList.php
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Sample & Assay Technologies
4. Profile Key Gene Expressions –
Using RT2 Profiler PCR Array
84 Pathway-Specific
Genes of Interest
5 Housekeeping Genes
Genomic DNA
Contamination Control
Reverse Transcription
Controls (RTC)
Positive PCR Controls
(PPC)
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5. Simple Workflow of PCR Arrays
cDNA Synthesis (kit)
45 minutes
Load Plates (Use 8-Channel
Pipettors)
2 minutes
Run 40 cycle qPCR Program
2 to 2.5 hours
compatible with all major
real-time PCR instruments
Upload and Analyze Data
15 minutes
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Sample & Assay Technologies
6. Identify the Key Genetic Players in Breast Cancer
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Breast Cancer PCR Array
http://www.sabiosciences.com/rt_pcr_product/HTML/PAHS-131A.html
Breast cancer can be classified into normal breast-like, luminal, HER2-like, and basallike (also inaccurately called triple-negative) tumors.
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Tumor Classification Markers:
Luminal: ESR1 (ERa), FOXA1, GATA3, KRT8, KRT18, SLC39A6, TFF3, XBP1.
HER2-like: ERBB2 (HER2), GRB7.
Basal-like / Triple Negative: BIRC5, EGFR, KRT5, NOTCH1.
Metastasis to Lung: ID1, MMP2 (Gelatinase A), PTGS2 (COX2).
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Signal Transduction:
Steroid Receptor-Mediated: AR, BRCA1, CCNE1, CTNNB1, ESR1 (ERa), ESR2 (ERß),
IGF1, KRT19, PGR, RB1.
Hedgehog: BCL2, CCND1, GLI1, SNAI2.
Glucocorticoid: IGFBP3, NME1 (NM23A), NR3C1 (GRL).
Classical WNT: APC, CCND1, CTNNB1, SFRP1.
PI3K/AKT: AKT1, ERBB2 (HER2), IGF1, IGF1R, PTEN.
NOTCH: BIRC5, NOTCH1.
MAPK: MAPK1 (ERK2), MAPK3 (ERK1), MAPK8 (JNK1), TP73.
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Sample & Assay Technologies
7. Breast Cancer Subtypes
Subtype
These tumors tend to be
Prevalence
Luminal A
ER+ and/or PR+, HER2-, low Ki67
42-59%
Luminal B
ER+ and/or PR+, HER2+ (or HER2with high Ki67)
6-19%
Triple
negative/basal-like
ER-, PR-, HER2-, cytokeratin 5/6 +
and/or HER1(EGFR)+
14-20%
HER2+
ER-, PR-, HER2+
7-12%
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Sample & Assay Technologies
8. Identify the Key Genetic Players in Lung Cancer
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Lung Cancer PCR Array
http://www.sabiosciences.com/rt_pcr_product/HTML/PAHS-134A.html
non-small-cell lung carcinoma (NSCLC) and small-cell lung carcinoma (SCLC)
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Differentially Methylated Promoters: APBA1, APC, CADM1, CDH1, CDH13, CDKN1C,
CDKN2A, CDKN2B, CXCL12, CYP1B1, DLC1, FHIT, MGMT, MLH1, MTHFR, OPCML,
PRDM2, RASSF1, RASSF2, SFRP1, TCF21
Metastatic Potential: ANXA5, DUSP6, ERBB3, HGF, HMMR, IRF4, LCK, MET, MMD, NF1,
STAT1, STAT2
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Differentially Expressed Genes in Adenocarcinoma (AC) Versus Squamous Cell
Carcinoma (SCC):
Higher in AC than in SCC: CLCA2, DSG3, KRT5, KRT14, SPRR1A
Higher in SCC than in AC: AGR2, LGSN, NKX2-1, SFTA3, SPINK1
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Up-Regulated in Lung Cancer: CEACAM5, COL11A1, CP, CXCL13, GREM1, MKI67,
MMP1, MMP12, SPINK1, SPP1, TOP2A, TOX3
Down-Regulated in Lung Cancer: AGER, CA4, CLDN18, CLIC5, FABP4, GPM6A,
SCGB1A1, SFTPC, SOSTDC1, WIF1
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Sample & Assay Technologies
13. Methylation PCR Arrays
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1. DNA Digestion
Genomic DNA sample is aliquoted into four equal portions:
a. Mock Digest (Mo)
No enzymes are added in this reaction. The product of the mock digestion
represents the total amount of input DNA for real-time PCR detection.
b. Methylation Sensitive Digest (Ms)
Cleavage with a methylation-sensitive enzyme will digest unmethylated and
partially methylated DNA. The remaining (hyper)-methylated DNA will be
detected by real-time PCR.
c. Methylation Dependent Digest (Md)
Cleavage with a methylation-dependent enzyme will preferentially digest
methylated DNA. The remaining unmethylated DNA will be detected by realtime PCR.
d. Double Digest (Msd)
Both enzymes are added in the double digest, and all DNA molecules (both
methylated and unmethylated) will be digested. This reaction measures the
background and the fraction of input DNA refractory to enzyme digestion.
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2. Real-Time PCR
3. Data Analysis
We provide user-friendly free online data analysis tool.
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Sample & Assay Technologies
14. What Methylation PCR Array Offers – a Quick Screening Tool
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What Does Methylation PCR Array Offer?
http://www.sabiosciences.com/dna_methylation.php
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Disease or Pathway Focused: Simultaneously detect DNA
methylation of 24-96 genes on a 96-well or 384-well plate.
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Genome-Wide Coverage: DNA methylation analysis of any human,
mouse or rat genes. You can also order individual primers for an individual
gene. Ordering custom array is also welcome.
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Easy, Fast & Reliable: Simple restriction enzyme digestion followed
by optimized qPCR. No bisulfite conversion, cloning or sequencing.
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Sample & Assay Technologies
21. Important Note
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Please Note:
If you study lung cancer, for example, I greatly recommend
that you use regular Lung Cancer PCR Array and Methylation
Lung Cancer PCR Array to get corresponding results. This
applies to other cancer types, also to apoptosis, cell cycle,
DNA damage, EMT, tumor suppressors, and cancer-related
miRNAs researchers.
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Sample & Assay Technologies
22. Cancer Mutation PCR Arrays and Assays
Custom available!
We also provide over 900 individual gene assays:
http://www.sabiosciences.com/mutationproductlist.php?tab=browsebygene
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Sample & Assay Technologies
23. Overview 45-Signaling Pathway Activity in a Cell Assay
Transcription factor activity can be used as a readout for the activation status of signal
transduction pathways. Therefore, the development of reliable cell-based assays to
measure transcription factor activity is a crucial technology for fast and efficient global
functional genomics and chemical genetics studies.
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Cignal 45-Pathway Reporter Array is a novel cell-based assay for monitoring 45 cell
signaling pathways in cultured cells in a single experiment. You can observe
phenotypes and quantitate as a dual-luciferase assay.
http://www.sabiosciences.com/reporter_assay_product/HTML/CCA-901L.html
For individual assay: http://www.sabiosciences.com/reporterproductList.php
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Sample & Assay Technologies
24. We Provide Service – Send Samples to Us & Receive Results!
Whole Genome
Illumina Gene Expression Profiling
Illumina Genotyping
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Pathway / Focused Panel
Mutation Profiling
Methylation
PCR Array
miRNA PCR Array
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Individual Gene / Locus
Mutation Detection
Methylation
qPCR
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Sample Preparation – DNA, RNA Extraction and Purification
Cells, Tissue or Biofluids
Fixed Tissue
Small Sample
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http://www.sabiosciences.com/servicecore.php
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Sample & Assay Technologies