# Presentation: 199308

## Slide 1

## DNA Sequencing of Viral Gene Therapy Vectors During Pre-Clinical and Clinical Development

## Forward Looking Statement

- During the course of this presentation, I may make projections or other forward-looking statements regarding future events. I wish to caution you that such statements are just predictions and that actual events or results may differ materially. Further information on factors that could affect Introgen’s results can be found in the Company’s filings with the Securities and Exchange Commission, including Introgen’s registration statement on Form S-1.

## Vector Sequences: Dichotomy Between Belief and Reality

-   Barring sequencing data, the predicted origins and sequence of a vector or plasmid should be considered to be tentative.
- History of sequencing for RPR/INGN 201 (Ad5CMV-*p53* )

## Method for Generating Ad5CMV-p53

- Shuttle
- Vector
- ~7 kb

- pJM17
- ~40 kb

- 0

- pBR322

- Ad-L

- Ad-R

- Ad-L

- Ad-R

- CMV-
- p53

- Ad

## Ad5CMV-p53: Starting Reagents

-  Ad5CMV-*p53* and the reagents used to make it originated from the laboratory of Dr. Jack Roth at MDACC.
-  Documentation on the constructs was from academic scientific lab notebooks.
-  Shuttle vector - maps with restriction sites.
-  pJM17 was derived from the Ad5 dl309 adenovirus.
-  Ad5 dl309 was constructed to remove several restriction sites in the Ad5 genome.
-  Ad5 dl309 was selected as a viable virus, and grows as well as wild-type Ad5.

## Ad5CMV-p53: Starting Reagents (continued)

- At this stage we knew the historic building blocks that went into Ad5CMV-*p53*, and we knew that there had been changes made to several restriction sites in the Ad5 derived part of the Ad5CMV-*p53*.

## Ad5CMV-p53 Sequence, Version 1

-  Rationale - To confirm the sequence of the expression cassette.
-  Methods - Manual sequencing of expression cassette.
-  Timing - Early in technology transfer from academic laboratory to	Introgen’s research laboratories.  Prior to initiation of Phase I trials.

## Ad5CMV-p53 Sequence, Version 1(continued)

-  Conclusions - DNA sequence of expression cassette was as expected.
-  New Information - The polylinker sequences in the expression cassette were now defined.

## Ad5CMV-p53 Sequence, Version 1(continued)

## Ad5CMV-p53 Sequence

***p53***

**E4**

**E2**

**E3**

- In November 1995 Frank Graham and colleagues published a paper regarding changes in E3 region of dl309.

## Ad5CMV-p53 Sequence, Version 2

-  Methods -	GLP sequencing of expression cassette cloned out of clinical lot of Ad5CMV-*p53* , and sequencing of flanking viral DNA sequences directly from Ad5CMV-	*p53* viral DNA.
-  Timing -	Summer of ‘96, Phase I ongoing

## Ad5CMV-p53 Sequence, Version 2(continued)

- Conclusions - The expression cassette sequence agreed with previous sequence data.
- New information -
- Fully defined sequence of polylinkers between Ad sequences and the expression cassette.
- About 300 bp of the left adenoviral flank of Ad5CMV-*p53* has more similarity to Ad2 than to Ad5.

## Ad5CMV-p53 Sequence

-  In May of ‘98 a paper was published by the group of Estuardo Aguilar-Cordova (*Gingras et al) *which had a sequence of the E3 insertion/deletion of pJM17 that was slightly different than the sequence of this region of dl309 from the Graham lab.
-  Exact sequence of the E3 insertion/deletion event was unclear.

## Ad5CMV-p53 Sequence, Version 3

-  Method - GLP sequencing of all of Ad5CMV-*p53*.
-  Rationale - Complete sequence desired prior to initiation of pivotal trials.
-  Timing - April 1999; late Phase II.

## Ad5CMV-p53 Sequence, Version 3(continued)

- Conclusions
-  p53 expression cassette - No changes.
-  E3 region - Sequence agreed with *Gingras et al*.
-  Aside from E3 region, there were 23 discrepancies between the predicted sequence, which was based on published data, and the sequence ascertained in this sequencing of Ad5CMV-*p53*.

## Ad5CMV-p53 Sequence, Version 3(continued)

- _Discrepancies between published (Genbank) sequences and actual sequence found for Ad5CMV-__*p53*_
- Non-coding/silent		10
- Amino Acid change		  9
- Change ORF extent		  4

## Ad5CMV-p53 Sequence, Version 3(continued)

- E3 Region, Ad5CMV-*p53, *predicted ORFs

- 12.5K

- 6.7

- 19K

- 11.6K

- fusion

- novel

- E3 Region, wild-type Ad5, predicted ORFs

- 12.5K

- 6.7

- 19K

- 11.6K

- 10.4K

- 14.5K

- 14.7K

## Ad5CMV-p53 Sequence, Version 3(continued)

- _Predicted changes  to E3 proteins of Ad5 vs Ad5CMV-__*p53*__._

## Ad5CMV-p53 Sequence, Version 3(continued)

- _Nature of sequences inserted into the E3 region_ :
-  High degree of similarity between a small part of the inserted sequence and a salmon DNA sequence in Genbank (92% over 135 bp).
-  From *Gingras et al*, we know that DNA from this insert hybridizes to salmon DNA and not human DNA.
-  From studies at Introgen and from *Gingras et al* we know that RT-PCR detects RNA made from this region.

- _Insertion/Deletion region of E3 (646 base pairs)_

- Novel ORF

- Homology

## Ad5CMV-p53 Sequence

## Conclusions

- Introgen has sequenced all of Ad5CMV-*p53*, prior to initiating phase III trials.
- Until sequencing is completed, there will be uncertainties about the exact identity of almost all plasmids and vectors.

## Slide 23