# Presentation: 948484

## Safety PharmacogeneticsUse of small numbers of patients with AEs to determine genetic classifiers

** **
- Allen D. Roses, MD, FRCP [Hon]
- GSK Genetics Research
***NVAC meeting, 29 November 2005***

## Overview of presentation

**Safety and efficacy PGX examples**
**Safety [AE] genetics during the blinded period of Phase III **
**	****– ****genotype confirmation when trial blind is broken**
**SAE during clinical development**** ****to determine how few subjects are needed to determine diagnostic genetic classifier profiles **
**Rare SAE during early development – ****single case ****	****diagnostic strategies**
**Efficacy hypothesis generation during a Phase IIA study {80 patients}**
**Phase IIB efficacy confirmation {~500 patients}**

## Critical definitions

**The strategy is basically the same whether small molecule therapy, biopharmaceuticals, or vaccines**
**DNA must be consented and collected – to be immediately available**
**All AEs must have a recognizable phenotype occurring at some time after treatment**

## Adverse event profiles in clinical development and surveillance

**AEs are ****a ****classic example of environmental interaction with an individual’s genetic make-up**
**To experience an AE, patient must receive the drug or vaccine and develop a defined phenotype within a recognized time period**
**AEs are personal:  “**_**Will I**_** get an adverse event?”**

## PRESTO Trial-Example of prospective AE PGx during Phase III

**Double-blind placebo trial of 11,500 patients**
**4% of patients in the trial developed hyperbilirubinemia**
**During the trial, an association study using candidate genes identified the “7” polymorphism as associated with the AE.  When the blinded trial was opened, only 7/7s who received the drug had hyperbilirubinemia.**
_***Associations can be done during a trial***_

## How few patients does it take to recognize a SNP profile related to an AE during  drug development ?

**Mathematical analysis reflects taxonomy principles**
**Also highly dependent on the number and the ethnicity of “controls”**
**Theoretical analyses suggest that differences in SNP LD patterns can be “diagnosed” **_***prospectively***_** with as few as 10-20 patients**

## Can Safety SNP profiles be identified during trials using as few as 10-20 AE patients?    Yes

-  4 **SNPs flanking UTP1A1 “6-7 repeat” locus of tranilast ****	****hyperbilirubinemia **
** ****Cases from tranilast clinical trial (US Caucasian) **
** ****3,000 White controls from Aberdeen UK (Caucasian)**
** ****Fisher’s exact test**

## What about rare SAEs in early phase studies?

**With a single ****severe adverse event**** that happened to occur in early development, can genomic methods be used for an accurate “diagnosis?”**
**Example:****	****With an early drug asset, a single case of severe hepatotoxicity with elevated bilirubin occurs, threatening the program - as would occur in major programs**

## Recognising rare SAEs early in development

**The background science of the drug target and metabolism can suggest several “candidate” hypotheses for hepatitis:**
**Example: a clinical association of hyperbilirubinemic hepatotoxicity with patients who were heterozygous for a rare specific receptor mutation – “beta 13”**
**There were also transgenic animal experiments to confirm an association of this mutation with hepatotoxicity**

## Recognising rare SAEs early in development

**DNA had already been obtained with informed consent, for pharmacogenetics**
**The patient’s extracted DNA had been stored [PGX default] and available within days.**
**Sequencing of the patient’s DNA for this gene, as well as other candidate genes, was performed within a week.**
**Diagnostic microarrays for hepatocellular toxicity, neuropathy, cardiomyopathy, etc., can be designed and ready for immediate use – validation by sequencing**

## Another example:“Drug C”  Side effects – not severe AEs  Early diarrhea and mild rash

**Studied in Phase I subjects and early Phase II patients **
**Approximately 15% of 107 treated subjects and patients had side-effects**
**Two Phase I volunteers and one Phase IIA patient withdrew from the study due to severe diarrhea**

## “Drug C” Metabolism

**Preclinical *****in vitro***** studies show that “drug C” is metabolized predominately by **
**CYP3A4 and CYP3A5 **
**and to a lesser extent by CYP2C19**
***In vitro***** data suggests that “drug C” interacts with MDR1 (ABCB1) and BCRP (ABCG2) **

## SNP Coverage per Candidate Gene

| Gene | Number of SNPs genotyped within 10 kb of gene | Size of gene (kb) | Avg spacing between SNPs (kb) | Largest gap between SNPs (kb) |
| --- | --- | --- | --- | --- |
| ABCG2 | 45 | 66.9 | 1.5 | 7.5 |
| ABCB1 | 117 | 209.6 | 1.8 | 13.7 |
| CYP2C19 | 57 | 90.2 | 1.6 | 18.3 |
| CYP3A4 | 5 | 27.2 | 5.4 | 11.2 |
| CYP3A5 | 22 | 31.8 | 1.4 | 9.9 |

## Summary of Significant Results

**Association was observed between SNPs in CYP2C19 with rash and diarrhea**
**No association with ABCG2, CYP3A4 or CYP3A5.**
** ****22 SNPs within the CYP2C19 gene showed association (p<0.01) with incidence of rash and 6 of these SNPs showed association (p<0.01) with incidence of diarrhea.**
**CYP2C19 *2/*2 genotypic p-value was p=0.001 for diarrhea and p=0.0016 for rash.**
**3 of 3 subjects **_**homozygous**_** for CYP2C19*2 had rash and diarrhea (2 healthy volunteers, one patient) and had discontinued the medicine **

## Immediate future

**In house 500k SNP chip scans for whole blood DNA to determine classifiers**
**In house tissue expression profiles of microRNA **
**In house tissue messenger RNA [mRNA] transcriptomics**
**Next steps will prepare GSK for “instant analyses for any AEs or efficacy profiles for current and future ****“drug C” ****trials**

## Can safety PGX be applied to vaccines

**Absolutely**
**Certainly possible to collect 3,000 ethnic controls**
**DNA can be banked as cheek swabs and safely transported in large numbers for storage**
**DNA can be readily accessed when AE phenotype is observed**
**Ready for single case analyses of candidate genes, or whole genome SNP classifiers**

## Benefits and risks of Pipeline PGx

**The most important benefit is the ability to discover and develop new drugs for bad diseases with a higher probability of efficacy and a lower risk of a safety concern**
**Differentiation of the marketplace will benefit  patients, health care providers and payers**
**Application of new science to a highly regulated field requires education and understanding**
**The biggest risk is the status quo [and believing pessimistic predictions]  **

## Phase IIA efficacy profiles

**Development example: **
**	****	****	****Weight loss for obesity**
**	****	****	****Measure weight gained or lost during ****	****	****clinical trial**

## 		1,1             1,2	             2,2

## Effect of genotype on absolute mean weight loss (Kg) for combined (capsule and tablet) high dose groups

## Create efficacy hypotheses as early as Phase IIA for reiterative analyses during subsequent development 
Genetic-based profiles can be applied to define  clinically responsive populations for more patient-focused trials
For the first time in pharmaceutical history, non-responders can be identified for follow-up with follow-on candidate molecules

**Genetic-based profiles can be applied to define  clinically responsive populations for ****more patient-focused trials**
**For the first time in pharmaceutical history, ****non-responders**** can be identified for follow-up with follow-on candidate ****molecules**

**Prospective Efficacy PGx during Phase IIB ****Proof of Efficacy**

## APOE4 - a susceptibility gene variant for common forms of Alzheimer disease

- 60       65       70      75       80       85

- 1.0

- 0.8

- 0.6

- 0.4

- 0.2

- 0

- Proportion of each

- genotype unaffected

- Age at onset

- 2/3

- 2/4

- 3/3

- 3/4

- 4/4

**APOE4 - a susceptibility gene variant for common forms of Alzheimer disease**

- Mean age of onset of Alzheimer disease as a function of the inheritance of the five common APOE genotypes

## Symptomatic Alzheimer Disease

- Source: Reiman _et al_ NEJM_ 334_ p752

## APOE4 non-demented homozygotesmean age = 50 years

- Source: Reiman _et al_ NEJM _334_ p752

## Phase IIB efficacy profiles

**Measuring clinical improvement in Alzheimer disease**
**	**
**	****Phase IIB dose-ranging trial of a drug based on a hypothesis involving APOE isoform-specific mitochondrial toxicity with >500 mild to moderate AD patients**
**Prospective hypothesis from small Phase IIA study:**** **
**	****	****	**
**	****	****“****Patients inheriting one or two APOE4 alleles will respond differently than patients who carry no APOE4 alleles”**

## PGX efficacy for AD with a new drug directed against a mitochondrial energy pathogenesisDrug “MITO”

**Patients selected for inclusion in clinical trial with mild to moderate AD, **_**not **_**based on any genotyping**
**Clinical status measured over a six month period using ASAS-cog, as well as other clinical scores**
**Patients were genotyped during the trial and, after analysis without these data**
**Patients were segmented into e4 allele carriers, and patients who did not carry an e4 allele**

## Model-adjusted Mean Change from Baseline in ADAS-cog by treatment week

**ITT population**

**PGx ITT population by APOE4 status***

- *Excluding subjects 364, 737 and 1027

## ADAS-cog by APOE4 carrier status* Model-adjusted Mean Change from Baseline

- ***Excluding patients 364, 737 and 1027**

## Memory Items* of ADAS-cog by APOE4 carrier status Model-adjusted Mean Change from Baseline 

- ***Sum of items 1, 7 and 8**

## New Phase III hypothesis

**Phase IIB hypothesis generated results:**
** **
**	****	****“****AD patients **_**without an APOE4 allele**_** ****	****	****responded better**** than patients who carry either 1 or ****	****2 APOE4 alleles”**
**Prospective Phase III APOE hypothesis to be tested:**
**	****	****“****Patients **_**without an APOE4 allele**_** ****will ****	****improve ****	****better**** than patients who carry an APOE4 allele”**

## PGX efficacy with Drug “MITO”

**There was no positive clinical effect of treatment in ITT population**
**In PGX analyses, patients without an e4 allele improved,  while e4+ carriers did not improve  compared to baseline on ADAS-cog and other clinical scales.**
**Design of Phase III studies will be powered using APOE genotype status**

## Intracellular distribution of various forms of apoE4 as determined by IHC and CMChang et al., PNAS, 2005, in press

**Intracellular distribution of various forms of apoE4 as determined by IHC and CM****Chang et al., PNAS, 2005, in press**

## The apoE4 receptor binding region is required to escape the secretory pathway and the lipid binding region mediates mitochondrial interaction

**The apoE4 receptor binding region is required to escape the secretory pathway and the lipid binding region mediates mitochondrial interaction**

## MITO treatment increases mitogenesis and increase in mitochondrial DNA

- Approximate 2 fold increase in mitochondria with differentiation
- and MITO treatment

## AcknowledgementsGSK R&D Executive chaired by Tachi Yamada, MDGenetics Research TeamMedical GeneticsDiscovery Pipeline GeneticsBioinformaticsGenomics & Proteomic SciencesMatrix and External InterfacesAll the Drug Discovery and Clinical Development (especially WW Regulatory) TeamsThe Gladstone Institute, UCSF for APOE collaboration

**Notes:**
Specifically, Linda, David B., David Y., Maha and Mike Moore for providing data.