Human Genetics Impact on Clinical Practice in Lipidology

National Lipid AssociationNew Orleans

May 19th, 2016

Muredach Reilly MB MSColumbia University

Human Genetics Impact on Clinical Practice in Lipidology

Muredach Reilly MB MS

DISCLOSURE INFORMATION: None applicable.

UNLABELED/UNAPPROVED USE:ISIS-APOCIIIRx

• Review genetic and clinical concepts

• Summarize genomic discoveries in lipids and CHD

• Highlight causal lipid pathways in CHD

• Discuss novel genome-based therapeutics

Educational Objectives

• New discoveries: new targets & biology

• Causality and directionality

• Therapeutic translation

• Precision medicine

Genetics - Impact in Clinic

Traditional Risk Factors for CHD…

– Age– Male gender– Smoking– Hypertension– Diabetes mellitus – High LDL cholesterol / apoB lipoproteins– Low HDL cholesterol

explain only about 60-70% of early heart attacks

Coronary Disease is Influenced by Genetics

If your mother or father had early-onset cardiovascular disease, your risk of early heart disease is:

Men 3.2 times average

Lloyd-Jones, JAMA 2004

Women 2.9 times average

Genomic Discovery Strategies

50%

5%

0.5%

0.05%

Allele Frequency

Effect Size Strong Moderate Weak

Common variants

Rare variants/Mendelian

Low‐frequency variants

An Exomic View of the Genome(Exome-seq Identifies Low Frequency and Rare Variants

in Protein Coding Genes)

Genome

Exome

1-2% genome encodes protein coding genes (~20K) but ~80% of genome is functional

DNA Variants

Cardiovascular risk factorsLipids and other

Cardiovascular risk factorsCoronary disease and

atherosclerosis

New biologyNew therapeutic targets

??

DNA Variants

Cardiovascular risk factorsLipids and other

Cardiovascular risk factorsCoronary disease and

atherosclerosis

New biologyNew therapeutic targets

??

Mendelian Causes of Extreme High LDL-C Levels Helped Confirm the “LDL Hypothesis”

Freq

uency (%

)

LDL cholesterol 760 mg/dL (normal < 130 mg/dL)

Inherited Syndromes of Extremes of LDL-C: PCSK9 Mutations

Freq

uency (%

)

LDL‐C

Gain of function mutations in PCSK9

Loss of function mutations in PCSK9

Gene Locus GWAS SNP Disorder and lipid phenotypeABCA1 9q31.1 rs1883025 Tangier disease: low HDLABCG5 2p21 rs4299376 Sitosterolemia: high LDLABCG8 2p21 rs4299376 Sitosterolemia: high LDLAPOA1 11q23‐q24 rs964184 ApoA‐I deficiency: low HDLAPOA5 11q23 rs964184 ApoA‐V deficiency: high VLDL and chylomicronsAPOB 2p24 rs515135 Familial hypobetalipoproteinemia: low LDL

Familial defective ApoB‐100: high LDLAPOC2 19q13 rs4420638 Familial ApoC‐II deficiency: high chylomicronsAPOE 19q13 rs4420638 Familial dysbetalipoproteinemia: high VLDL remnants 

and chylomicronsCETP 16q13 rs173539 Cholesteryl ester transfer protein deficiency: high HDLLCAT 16q22 rs2271293 Lecithin‐cholesterol acyltransferase deficiency (fish‐

eye disease): low HDLLDLR 19p13 rs6511720 Familial hypercholesterolemia: high LDL

LDLRAP1 1p36‐p35 rs12027135 Autosomal recessive hypercholesterolemia: high LDL

LIPC 15q22 rs10468017 Familial hepatic lipase deficiency: high VLDL remnants

LPL 8p21 rs12678919 Lipoprotein lipase deficiency: high chylomicronsMTTP 4q24 N/A Abetalipoproteinemia: low LDLPCSK9 1p32 rs11206510 Autosomal‐dominant hypercholesterolemia: high LDL

PCSK9 deficiency: low LDLSAR1B 5q31.1 N/A Chylomicron retention disease: low chylomicrons

Mendelian Lipid Disorders

LDL-C HDL-C TriglyceridesABCG5/8 HFE SORT1 ABCA1 HNF4A PDE3A ACSS2 GALNT2

ABO HMGCR ST3GAL4 ABCA8 IRS1 PGS1 AFF1 GCKR

ANGPTL3 HNF1A TIMD4 ADM KLF14 PLTP ANGPTL3 IRS1

APOA HPR TOP1 ANGPTL4 LACTB PPP1R3B ANKRD55 JMJD1C

APOB IDOL TRIB1 APOA LCAT SBNO1 APOA LIPC

APOE IRF2BP2 APOB LILRA/B SCARB1 APOB LPL

BRAP LDLR APOE LIPC SLC39A8 APOE LRP1

BTNL2 LDLRAP1 ARL15 LIPG STARD3 BTNL2 MLXIPL

CBLN3 LPA C6orf106 LPA TRIB1 CAPN3 MSL2L1

CETP MAFB CETP LPL TRPS1 CETP NAT2

CILP2 MOSC1 CITED2 LRP1 TTC39B CILP2 PINX1

CYP7A1 NPC1L1 CMIP LRP4 UBASH3B COBLL1 PLA2G6

DNAH11 OSBPL7 COBLL1 MACF1 UBE2L3 CTF1 PLTP

FADS PCSK9 DOCK6 MC4R ZNF648 CYP26A1 TIMD4

FRK PLEC1 FADS MLXIPL ZNF664 FADS TRIB1

GPAM PPP1R3B GALNT2 MMAB FRMD5 TYW1B

ZNF664Total Cholesterol

ERGIC3 EVI5 FUT2 RAB3GAP1 RAF1 SPTY2D1

Teslovich, et al Nature 2010

GWAS in > 100,000 Individuals: 95 Lipid Loci

The Role of PCSK9 in the Regulation of LDL Receptor Expression

TGRL Metabolism: Key Apolipoproteins

Fazio and Linton. Regulation and clearance of apoB‐continaing lipoproteina in Ballantyne. Clinical Lipidology, 2nd Ed. 

LPL activityTG

LPL activityTG

VLDL

DNA Variants

Cardiovascular risk factorsLipids and other

Cardiovascular risk factorsCoronary disease and

atherosclerosis

New biologyNew therapeutic targets

??

?

Replicated GWAS Loci for MI/CHD:Ongoing Functional Genomics

CARDIoGRAM. Nature Genet. 2011

• ~50 CHD loci at genome-wide significance

• 12 loci for lipid traits and 5 for blood pressure

• ADAMTS7, COL4A1, TCF21, PDGF implicate VSMC, matrix

• CXCL12, IL6R, IL5 implicate inflammation and immunity

• FLT1/VEGFR1, EDNRA, GUCY1A implicate endothelium

• 13 CHD loci with consistent mouse knock out model finding

• Exomes: known loci, TGRL loci (ANGPTL4), novel loci (SEVP1)

• Mega GWAS, large exome & whole genome seq on-going

Summary: GWAS, MetaboChip and Exome-seq Loci in CHD

CARDIoGRAMplusC4D Nature Genet 2013 and Nature Genet 2015; MIGen ExSeq Nature 2015

• New discoveries: new targets & biology

• Causality and directionality in CHD

• Therapeutic translation

• Precision medicine

Impact on Clinic

Exomes (dark blue)

Why Sequence Exons?

Identify Rare Functional Variants & Establish Causal Direction

Exome-seq Identifies Mutations in Protein Coding Genes

PCSK9 Mutations: Causality and DirectionalityFreq

uency (%

)

LDL‐C

Gain of function mutations in PCSK9

Loss of function mutations in PCSK9

‐15% ‐5% 5% 15%

Causality – GWAS of LDL-C (Common Variants)

Voight. Lancet 2012;380:572. Ference. JACC 2012;60:2631.

Change in LDL-C Change in MI Riskrs3798220 (LPA)rs562338 (APOB)rs6544713 (ABCG8)rs10402271 (APOE)rs7953249 (HNF1A)rs3846663 (HMGCR)rs1501908 (TIMD4)rs11591147 (PCSK9)rs4420638 (APOE)rs599839 (SORT1)rs2228671 (LDLR)rs4299376 (ABCG8)rs4420638 (HMGCR)

‐30% ‐15% 0% 15% 30%

Increased HDL‐C Increased coronary disease

SCARB1 P376L

Zanoni, Khetarpal, Larach, et al. Science 2016

SR-BI-/- mice have elevated HDL-C levels but impaired RCT and increased atherosclerosis.

What about in humans?

The HDL Function Hypothesis

Promoting HDL functions (not raising HDL-C levels)

will reduce CV events?

Mendelian Randomization Studies

Exposed: Intervention

Randomization Method

Outcomes compared between groups

Confounders equal between groups

Randomized Controlled Trial

Exposed: Variant Allele

Control:Reference Allele

Random Segregation andAssortment of Alleles

Outcomes compared between groups

Confounders equal between groups

Mendelian Randomization

Control:No intervention

e.g., Lp(a) positiveCRP and HDL‐C negative

Jansen. Eur Heart J 2014;35:1917

Genetic variant(s)Associated with triglycerides, but not with other risk factors

Unbiased approachCommon variant (GWAS)Rare mutation (WES)

Candidate gene approachDocumented or suspected association or mechanism

Coronary diseaseTriglycerides

Mendelian Randomization Studies

APOC3 LOF Mutations Reduce TG levels and Protect against CAD

Clinical EffectSequencing Apolipoprotein C-III(APOC3)

TG MI

-39% -40%

IVS1-2GA IVS2+1GA

R19X A43T

1 in 150 individualsare heterozygous for

loss-of-function mutations

Humans with very low TG

First mechanism of lowering TG shown to reduce MI risk in humans

Loss-of-function mutations in APOC3 reduceplasma TG levels and risk of CHD

APOA5: Mendelian Randomization Study

Jorgensen. Eur Heart J 2013;34:1826.

68% 1.5 1.9

LPL: Mendelian Randomization Study

Thomsen. Clin Chem 2014;60:737

HR All‐Cause Mortality

0.86

0.730.43

0.77

• New discoveries: new targets & biology

• Causality and directionality in CHD

• Therapeutic translation

• Precision medicine

Impact in Clinic

Human genetics leading to smarter and faster development of

new medicines

Unmet Medical Needs in the Treatment of Elevated LDL-C

Unable To Get LDL < 100

Statin-Intolerant

LDL > 130

LDL > 160

Apheresis-eligibleLDL > 200

HoFH

High risk and on maximal tolerated statin

Mendelian Syndromes of LowLDL-C Provide New Targets for Therapy

Freq

uency (%

)

LDL‐C

LDLRCE

BLDL

CE

VLDL

TGB

apoB

CETG

Truncation Mutations in ApoB Cause Low LDL-C Levels

X

LDLR

apoB

TG

BVLDL

BLDL

Antisense Oligonucleotide to apoB: a Strategy for Reducing LDL-C

ASO to apoB (mipomersen)

X

LDLR

LDLR

apoB

Degradation

TGMTP

BVLDL

BLDL

Loss-of-function Mutations in MTP Cause Failure to Assemble and Secrete VLDL

X

LDLR

apoB

TGMTP

BVLDL

BLDL

MTP Inhibition: a Strategy for Reducing Hepatic VLDL Secretion and LDL-C

Small molecule inhibitor (lomitapide)

X

Inhibition of PCSK9 as a Novel Strategy for Reducing LDL-C

LDLR

CEB

LDL

CE

VLDL

TGB

Pcsk9

PCSK9X

Antibody, anti‐sense oligonucleotide (ASO), siRNA, small molecule inhibitor

PCSK9: From human genetic discovery to new medicine

May 2003 July 2015

• Alirocumab (Approved July 2015)• Evolocumab (Approved August 2015)• Indications:

– Patients with heterozygous familial hypercholesterolemia on maximally tolerated statin therapy with inadequate plasma LDL levels

– Patients with a history of CHD with inadequate plasma LDL levels

http://www.fda.gov/NewsEvents/Newsroom/PressAnnouncements/ucm455883.htm

APOC3-Targeted Therapeutic: ISIS-APOCIIIRx

Gaudet. NEJM 2014;371:2200

• New discoveries: new biology & targets

• Causality and directionality

• Therapeutic translation

• Precision medicine

Impact in Clinic

• Right diagnosis in patient & family• Cascade screen, diagnose and treat• Precision public health

• Right drug - patient (genetics): efficacy• Genome based drug selection• “N=1” trials

• Avoid wrong drug: patient safety• Gene-drug interactions•“N=1” trials

Precision Medicine

• Treasure trove of discoveries for lipids and CHD• Most novel CHD loci not related to traditional RF

• Genetic inference of causality and directionality

• LDL-C (but not HDL-C) loci relate to CHD • TG loci causal in CHD

• New therapeutics in trials – lipids (not direct CHD)

• Genetics for precision medicine

Summary – Take Home Message

Reilly GroupHanrui Zhang MD PhDXuan Zhang PhDChenyi Xue MSYing Wang PhDRob Bauer PhDAnd … more

Funding Support

Cardiology, Department of Medicine

Recent “Graduates”Jane FergusonNehal MehtaRachana ShahJennie LinRachel Ballantyne

RNA Biology

Columbia: Peter Sims, Raul Rabadan, PieroDalerba, Andrea Califano, Tom Maniatis

U.Penn: Arjun Raj, Ben Garcia

Sulzberger Genome Center: Olivier Cormonne

Collaboration & Team ScienceCARDIoGRAMplusC4D

NHLBI ESP-MI

U.Penn ColleaguesDan Rader, Danish Saleheen, Marina Cuchel

Edward Morrisey (iPS Core Facility)

Biostatistics & ModelingMingyao Li (UPenn) & Andrea Foulkes (MHC)

Columbia University Medical CenterR01-DK-090505; R01-HL-113147; R01-HL-111694; K24-HL107643. U01-HG006398

Acknowledgements

Columbia CollaboratorsDavid Goldstein,

Henry Ginsberg, Tony Ferrante, Alan Tall, Ira Tabas, many more ….