Mitochondrial Haplogroups Genetics and Peripheral Neuropathy during Antiretroviral Therapy

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Mitochondrial Haplogroups (Genetics) and
Peripheral Neuropathy duringAntiretroviral
Therapy

• David W. Haas, Todd Hulgan and Jeffrey A. Canter
• Vanderbilt University School of Medicine
• Nashville, Tennessee

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Mitochondrial Haplogroups and Neuropathy
Background

• NRTIs are widely prescribed for HIV infection
• NRTIs can interact with human mitochondrial DNA
  polymerase gamma (esp. ddI, d4T, ddC)
• Peripheral neuropathy and other NRTI toxicities
  are thought to result from mitochondrial injury
• There is considerable interindividual variability
  in NRTI toxicities

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Relationships of oxidative phosphorylation
toproduction of energy, reactive oxygen species,
and initiation of apoptosis
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Mitochondrial Haplogroups and Neuropathy
Background

• Mitochondrial genome
• Encodes proteins of oxidative phosphorylation
• Maternally inherited
• Susceptible to somatic mutations (heteroplasmy)
• Stable mutations can cause rare inherited
  diseases of impaired energy production

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Mitochondrial and Cellular Model of Aging
Wallace. Annu Rev Genet 2005, 39359
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Mitochondrial Haplogroups and Neuropathy
Background

• Some heritable mutations have reached polymorphic
  frequencies
• Haplogroups defined by patterns of polymorphisms
• 9 European haplogroups
• H, I, J, K, T, U, V, W, X
• Haplogroup H most frequent in Europeans and
  Caucasian Americans

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Mitochondrial Haplogroups and Neuropathy
Background

• Some heritable mutations have reached polymorphic
  frequencies.
• Haplogroups defined by patterns of polymorphisms
• 9 European haplogroups
• H, I, J, K, T, U, V, W, X
• Haplogroup H most frequent in Europeans and
  Caucasian Americans

7028TC
10398GA
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Mitochondrial Haplogroups and Neuropathy
Background

• Some heritable mutations have reached polymorphic
  frequencies.
• Haplogroups defined by patterns of polymorphisms
• 9 European haplogroups
• H, I, J, K, T, U, V, W, X
• Haplogroup J associated with longevity,
  protection from Parkinson disease

13708GA
7028CT
10398AG
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Ten Single Nucleotide Polymorphisms Define
European Mitochondrial Haplogroups
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Mitochondrial Haplogroups and Neuropathy
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Mitochondrial Haplogroups and Neuropathy Methods

• ACTG study 384
• Multicenter, controlled clinical trial enrolled
  ART-naive volunteers in US and Italy from 1998-99
• 980 randomized to ddI/d4T or ZDV/3TC, with
  blinded efavirenz and/or nelfinavir
• Up to 3-year follow-up
• Neuropathy ascertained by symptoms/signs
• Primary results published late 2003
• Robbins NEJM 2003 Shafer NEJM 2003
• ddI/d4T arms had shorter time to neuropathy

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Peripheral Neuropathy in ACTG 384
Robbins et al N Engl J Med. 2003349, 2293
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Mitochondrial HaplogroupGenetic Association Study

• NWCS 238
• Retrospective case-control analysis of ACTG 384
• Case PN diagnosis and/or symptoms during study
• Control No PN during study
• Subjects with PN at baseline excluded
• DNA obtained under ACTG protocol A5128
• Taqman genotyping of 9 European haplogroups
• Self-reported race/ethnicity defined by federal
  categories
• White, non-Hispanic Black, non-Hispanic Hispanic

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Mitochondrial Haplogroups and Neuropathy Methods
980 ACTG study 384 participants
82 Italian subjects
372 non-genetic study participants
526 DNA available
17 baseline PN
509 included in analyses
147 PN cases
362 controls
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Baseline Characteristics
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Mitochondrial Haplogroups and Neuropathy
Results European haplogroup frequencies
13368GA
10398GA
7028CT
N 250 subjects
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Mitochondrial Haplogroups and Neuropathy
Results Initial ddId4T treatment arms (n137)
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Mitochondrial Haplogroups and Neuropathy
Results Multivariate logistic regression model
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Mitochondrial Haplogroups and NeuropathyConclusio
ns and Implications

• A common European mitochondrial haplogroup
  predicted development of NRTI-associated PN
• The relationship between mitochondrial haplogroup
  T and PN was strongest among subjects randomized
  to ddId4T
• This relationship was independent of age, EFV
  and/or NFV use, baseline CD4 or viral load

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Non-synonymous Mitochondrial SNPs and Neuropathy
during NRTI Therapy

• Objective To determine if non-synonymous mtDNA
  SNPs 4216TgtC and/or 4917AgtG were associated with
  PN in ACTG 384
• Methods Case-control study PN determined by
  patient report and/or provider assessment SNPs
  at mtDNA positions 4216 and 4917 determined
  logistic regression

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Non-synonymous SNPs and Neuropathy
ORs (95 CI)

• 4216TgtC 2.0 (1.0-3.8) P0.04
• 4917AgtG 2.9 (1.2-6.9) P0.01

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Non-synonymous SNPs and Neuropathy
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Non-synonymous SNPs and Neuropathy

• These SNPs were associated with PN after
  controlling for age, sex, baseline CD4 and HIV
  RNA, and NRTIs
• These SNPs
• change amino acid in Complex I subunits
• associated with neuro-degenerative phenotypes
  (e.g. LHON)
• may explain association between haplogroup T and
  NRTI-induced PN
• Validation and mechanistic studies needed

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13368GgtA haplogroup T
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A Pilot Study of Chip-based Whole Mitochondrial
Genome Sequencing

• Objective To determine if non-synonymous mtDNA
  SNPs were associated with PN among T haplogroup
  subjects from ACTG 384
• To begin exploring functional SNPs that may
  underlie halpogroups
• Methods Case-control study PN determined by
  patient report and/or provider assessment SNPs
  at mtDNA positions 4216 and 4917 determined
  logistic regression

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A Pilot Study of Chip-based Whole Mitochondrial
Genome Sequencing

• Full sequencing of 24 haplogroup Ts
• GeneChip Human Mitochondrial Resequencing Array
  2.0
• Coding region (15,477bp) call rate gt97
• All 24 Ts were accurately haplogrouped
• 87 coding region SNPs in 1 person
• 61 were previously reported SNPs (17
  non-synonymous and/or transversion SNPs)
• 26 previously unreported SNPs were identified

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Future Directions Ongoing StudiesWhole
Mitochondrial Sequencing for PN
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Future Directions Ongoing Studies

• Cognitive impairment
• CHARTER cohort
• Cybrid studies
• Deb Murdoch at Vanderbilt
• Additional phenotypes
• Lipoatrophy
• ACTG 384
• A5142)
• New cohorts collaborations welcome

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Acknowledgements
The many HIV-infected individuals who volunteered
for ACTG 384 and protocol A5128
Vanderbilt Center for Human Genetics
Research Cara Sutcliffe Ping Mayo

• Todd Hulgan
• Jeffrey Canter
• David Clifford
• Asha Kallianpur
• Gregory Robbins
• Robert Schafer
• Deb Murdoch
• Shawn Levy
• Marylyn Ritchie
• Marshall Summar
• Jonathan Haines

• SDAC
• Laura Smeaton
• ACTG 384 team and sponsors
• Bristol Myers Squibb
• GlaxoSmithKline
• Pfizer
• A5128 study team

Funding NIAID NCCAM NINDS Vanderbilt Meharry CFAR
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