Serial Analysis of Gene Expression Velculescu, V., Zhang, L., Vogelstein, B. Kinzler, K. (1995) Science

Authors: The Wild-Types Victor Velculescu: Keyboard Ken Kinzler Drummer Bert Vogelstein Keyboard Lin Zhang Honorary member

Current Research Victor Velculescu: Dept. of Oncology, Johns Hopkins University. -New therapeutic targets for colon cancer Lin Zhang: Dept. of Pharmacology, University of Pittsburg. -genetic basis of differential sensitivity to anticancer drugs, as well as the genetic alterations in cancer cells that cause drug resistance Bert Vogelstein: Dept. of Oncology, Johns Hopkins University. -Identification and characterization of oncogenes. Ken Kinzler: Dept. of Oncology, Johns Hopkins University.

Aim of This Paper Provide researchers with a means to study expression of an entire genome rather than single genes To create a method of comparing gene expression differences between two samples with information about abundance of transcripts To illustrate effectiveness of this technique by examining pancreatic gene expression patterns To confirm the quantitative nature of the novel technique through library screening

Major Findings Developed a new technique to study gene expression that is capable of quantitative analysis of an entire genome Characterized gene expression in human pancreas Used SAGE to identify novel cDNA transcripts

SAGE: Based on 2 principles 1.A 9 bp tag is sufficient to unambiguously identify a gene 2.Concatenation (linking together) of these short DNA sequences increases the efficiency of identifying unique transcripts in a serial manner.

Methods 1.mRNA cDNA 2.Cleave with A.E 3.Isolate 3’ most transcript of each cDNA by binding to Streptavidin beads 4.Divide cDNA in half 5.Ligate to 1 of 2 linkers (each with a T.E site) 6.Ligate the two pools of tags together…. FIG. 1 SAGE protocol

Methods 7.Ligated linkers serve as primers for amplification 8.Cleave PCR products with A.E. to isolate ditags 9.Concatenate by ligation 10.Clone 11.Sequence FIG. 1 SAGE protocol

SAGE Analysis: Human Pancreas Table 1. Pancreatic SAGE tags.

Comparison of Transcript Abundance Quantitative nature of SAGE tested by construction of a pancreatic cDNA library that was screened with cDNA probes for several pancreatic genes Relative abundance of SAGE tags agreed with results from library screening

Current Applications 1.Gene Discovery 2.Analysis of Cardiovascular gene expression 3.Gene expression in carcinogenesis 4.Substance abuse studies 5.Cell, tissue and developmental stage profiles in C. elegans 6.Profiling of human diseases and more…..

Other Technologies to Study Expression 1.Expressed Sequence Tags (ESTs) 2.RT-PCR 3.RNA Blotting 4.DNA Microarray’s

Expressed Sequence Tags Short, annotated sequences at 3’ or 5’ end Can be used to determine the number of genes/genome Can be used to identify novel genes

qRT-PCR Can be used to both detect & quantify gene expression Not high-throughput Can only be used on a limited scale

RNA Blotting To quantify RNA (semi-quantitative) Can detect RNA slicing Again, not quantitative

DNA microarrays High-throughput Allows for simultaneous detection of genome-wide expression Can provide relative quantitative information about expression…

Microarray vs. SAGE

C. elegans temporal & Tissue-Specific Expression Profiling Project About 1.9 million C.elegans tags sequenced to date Several libraries have been completed, including: Embryo, all larval stages, Young and old adult, sterile adult, microdissected gut tissue, FACS-sorted muscle cells, and FACS embryonic intestinal cells Several libraries are in progress, including: FACS-sorted pan-neural cells, FACS-sorted ciliated neurons, FACS pharynx, and FACS hypodermal cells

Long SAGE vs. Short SAGE A comparison of short SAGE (14bp) vs. long SAGE (21bp) Some tags are not unambiguously assigned to a gene (similar 3’ ends due to ancestral duplications) About 12% of C. elegans tags are not unambiguously identified using 14bp tags Results of empirical data suggests that LongSAGE gives far greater resolution, but at an increased cost.

Why is this paper a landmark? 1.New technique for quantitative analysis of gene expression 2.Identified novel transcripts in pancreatic samples 3.Has allowed for the characterization of gene expression, both temporally and spatially, in several organisms 4.Currently is being used to study disease (i.e. cancer) gene expression sciencepark.mdanderson.org/ ggeg/SAGE_technique.htm

References Velculescu, V., Zhang, L., Vogelstein, B. Kinzler, K. (1995). “Serial Analysis of Gene Expression” Science 270 (5235) Reinke, V. (2002). “Functional Expolation of the C. elegans Genome Using DNA Microarrays”. Nature Genetics 32