Third Annual New Frontiers in Urology

Moffitt Cancer Center

James J. Hsieh, M.D. Ph.D.

Associate Member, MSK

The Panoramic View and

Clinical Implications of Large

Scale Kidney Cancer Global

Metabolomics

Histological Subtypes of Kidney Cancer

Hsieh, Tickoo et al

3

Current Signaling Targets in ccRCC

RAS

RAF

MEK

MAPK

HIF1/2

Target Genes

PI3K

AKT

mTORC1

Tumor Cell

Nucleus

HIF-1/2α

PTEN

Everolimus

Temsirolimus

Endothelial Cell

TIE2

Bevacizumab

FGF

PDGF

VEGF Sunitinib, Sorafenib,

Pazopanib, Axitinib

FGFR

PDGFR

VEGFR

Angiogenesis

mTORC2

TSC1/2

S6K

4EBP1

Rheb

HIF-1/2α

VHL

MET

Tumor Microenvironment

1992-2005

Treatment for ccRCC (Past, Now, Future)

Sorafenib

Sunitinib

Temsirolimus

High dose

interleukin-2

2005 2006 2007 2008 2009

Bevacizumab + IFN

Axitinib Interferon- Everolimus

2010

Pazopanib

2012 2014

Nivolumab

2015-2016

Dark Age Modern Age Golden Age

• Ipilimumab etc.

• Precision

• Combination Sequence

• Immunization

• Prevention

• Detection

Hsieh, Aug 2016

Cabozantinib

Single Arm Targeted Therapy 2005-2014

Lenvatinib

Cancer Hallmarks

Hanahan & Weinberg

Cell, 2011, 44, 646

Challenges of Precision Medicine

Layers of Complexity

Pan-Omics of Three Major Kidney Cancer Types

Creighton et al. Cell Reports 2016

Cancer Metabolism:

Blind Men & The Elephant

Nature, 2013

Biochemical Extraction

Metabolyzer™ UHPLC-MS/MS (+ESI)

GC-MS (+EI)

UHPLC-MS/MS (-ESI)

Instrumentation

Biochemical Analysis

Global Metabolomics Platform For Human Biospecimens

Peak Detection

Peak Integration

Library Search RT, Mass, MS/MS

QA/QC

In Collaboration with Metabolon

13

tryptophan 984,812

glutamic acid 23,387

histidine 32,597

leucine 117,683,785

cholesterol 197,866

asparagine 1,245,744

creatinine 127,611

cytidine 721,266

lactate 2,111,697

alpha-keto-glutarate 14,105,654

4-hydroxyphenylacetate 444,817

3-hydroxybutanoic acid 1,639,392

cytosine 106,032

arabinose 778,911

fructose 2,519,658

X-3370 1,101,581

mannose 2,833,397

pyruvate 250,670

uridine 135,807

Cholic acid 26,394,344

allantoin 208,938

isocitrate 5,825,474

heptadecanoic acid 913,112

inosine 1,115,331

isoleucine 452,549

alanine 462,648

threonine 208,938

tyrosine 67,989

lysine 296,740

methionine 49,879

malic acid 156,499

X-3697 46,230

n-hexadecanoic acid 298,590

octadecanoic acid 240,570

trans-4-hydroxyproline 132,151

X-9043 13,989,172

2-deoxyguanosine 5,913,519

3-hydroxyphenylacetate 7,214,406

3-phospho-d-glycerate 8,649,644

Kynurenic acid 468,663

5-s-methyl-5-thioadenosine 14,569,292

(p-Hydroxyphenyl)lactic acid 1,303,643

alphahydroxybenzeneacetic acid 450,807

ornithine 326,949

5-oxoproline 890,753

orotic acid 97,674

palmitoleic acid 4,036,188

pantothenic acid 94,772,385

salicylic acid 379,417

alpha-tocopherol 766,717

citric acid 4,245,654

X-6270 228,209

glyceric acid 8,267,905

histamine 912,667

N-acetyl-L-leucine 45,949

N-acetylneuraminic acid 2,178,243

uric acid 312,025

arginine 364,344

ascorbic acid 584,247

fumaric acid 4,459,712

n-dodecanoate 370,805

glutamine 109,597

serine 321,078

valine 2,241,354

pyridoxal 78,842

urea 437,094

riboflavine 2,520,194

proline 901,738

pyrophosphate 1,045,231

taurine 101,103,133

X-3030 5,726,735

citrulline 1,243,836

biliverdin 420,511

pyridoxamine 218,468

serotonin 5,105,113

gamma-L-glutamyl-L-glutamine 174,652

gamma-L-glutamyl-L-tyrosine 8,854,738

guanosine-5-monophosphate 82,682

3-indoxyl-sulfate 369,207

X-3100 135,999

phosphate 35,095

glycine 6,209,638

nonanate 1,936,241

DL-homocysteine 418,561

L-kynurenine 3,451,095

tartaric acid 631,615

sn-Glycerol-3-phosphate 282,554

carnitine 76,307

2-methylhippuric acid 462,487

3-methyl-2-oxovaleric acid 395,839

4-Guanidinobutanoic acid 73,352,989

4-methyl-2-oxopentanoate 272,564,647

beta-hydroxypyruvic acid 431,358

X-1656 118,271

hippuric acid 7,724,959

ethylmalonic acid 182,320

D-lyxose 267,189

maltose 27,024

S-5-adenosyl-L-methionine 216,405

2-deoxycytidine 1,151,739

L-alpha-glycerophosphorylcholine 992,513

aspartate 6,520,826

p-hydroxybenzaldehyde 106,124

X-1962 147,926

D-sphingosine 289,530

cortodoxone 58,939

DL-indole-3-lactic acid 281,085

gamma-glu-leu 177,587

glycocholic acid 725,542

taurocholic acid 3,281,189

X-10381 231,486

phenylalanine 118,902,022

taurodeoxycholic acid 29,443,151

inositol 146,593

X-10419 554,814

D-glucose 65,293,846

1,5-anhydro-D-glucitol 5,183,545

meso-erythritol 1,151,739

X-3026 992,513

2-hydroxybutyric acid 6,520,826

digalacturonic acid 106,124

3-methyl-2-oxobutyric 147,926

monopalmitin 289,530

1-stearoyl-rac-glycerol 58,939

21-hydroxyprogesterone 147,926

3-hydroxyoctanoic acid 289,530

1-methylguanidine-hydrochloride 58,939

3-hydroxydecanoic acid 281,085

3-indoleacrylic acid 177,587

DL-3-phenyllactic acid 3,281,189

DL-alpha-hydroxyisocaproic acid 231,486

DL-hexanoyl-carnitine 118,902,022

O-acetyl-L-carnitine-hydrochloride 29,443,151

EDTA 992,513

l-aspartyl-l-phenylalanine 6,520,826

Metabolyzer Software

4 5 6 7 8 9 10 11 12 13 14

Time (min)

4.01 14.43

5.84

4.38 10.66

8.46

10.18

11.76 4.55 6.52 6.73 7.74

9.34 11.79

11.03

13.05 9.47 7.50

11.21 5.34 12.89 3.17 13.30

8.01

Mass spectrum

3.17 min

Biochemical Amount

cholesterol 143,789

Database

Of

Standards

cholesterol

Biochemical ID

Automated Biochemical Identification

MSK TKCRP N=138 T/N Global Metabolomics Cohort

Hakimi et al. Cancer Cell 2016

KEGG Metabolic Pathway Analysis (T vs N)

Immunesuppressivemetabolites

5-Hydroxy-L-Tryptophan

Serotonin

5-Hydroxykynurenamine

0.00

0.50

1.00

1.50

NG1G2G3G4

Foldchange

Grade

DDC

Tryptamine Indole-3-acetaldehyde

0.00

0.50

1.00

1.50

N G1 G2 G3 G4

Foldchan

ge

Grade

MAOA

0.00

2.00

4.00

6.00

N G1 G2 G3 G4

Foldchan

ge

Grade

MAOB

0.00

0.50

1.00

1.50

NG1G2G3G4

Foldchan

ge

Grade

DDC

0.00

0.50

1.00

1.50

NG1G2G3G4

Foldchange

Grade

ALDH2

Indolepyruvate

Indoleacetamide

N-Formyl-Kynurenine

IDO

TDO

Immune suppression

0

0.5

1

1.5

N G2 G3 G4

Foldchange

Grade

Indoleacetate

0

0.5

1

1.5

N G2 G3 G4

Foldchange

Grade

Tryptophan

0

1

2

3

N G2 G3 G4

Foldchan

ge

Grade

Indolelactate

0

10

20

N G2 G3 G4

Foldchan

ge

Grade

Kynurenine

0

5

10

N G2 G3 G4

Foldchange

Grade

Quinolinate

H. Wettersten et al. Cancer Research 2015 75, 2542

0.00

0.20

0.40

0.60

0.80

1.00

1.20

N G2 G3 G4

Fold

ch

ange

Grade

L-Tryptophan

Central Carbon Metabolism of ccRCC (Tumor versus Normal)

Hakimi et al. Cancer Cell 2016

Metabolic Progression of ccRCC (Supervised)

Dipeptides

Glutathione Pathway

Hakimi et al. Cancer Cell 2016

Interconnected Metabolic Progression in ccRCC

ccRCC Pathogenesis (T vs N)

Hakimi et al. Cancer Cell 2016

Unsupervised NMF Consensus Clusteringof ccRCC

Based on Metabolites

Hakimi et al. Cancer Cell 2016

mCluster 2 (high glutathione) & mCluster 3 (high dipeptide)

have worse survival (higher metastasis)

The Lack of Clear Concordance between Transcriptomics & Metabolomics:

Based on Metabolic Pathways

RNA

Metabolites

IsoEnzymes, Allosteric Regulation, Substrate, Rx Condition

RNA

Metabologram

Integrative Metabolic Analysis to

Highlight Prominent Metabolic Shifts

http://kidneymetab.chenghsiehlab.org/

Volume 29

Number 1

Jan 11

2016

Cancer

Cell

An Integrated Metabolic Atlas of Clear Cell Renal Cell Carcinoma

Unsupervised RNA Clusters (rCluster) Based on Metabolic Genes Expression Based on KIRC TCGA RNA-Seq Data

A C B D

Hakimi et al. Cancer Cell 2016

Conclusion ccRCC exhibits broad shifts in central carbon metabolism,

one carbon metabolism, and antioxidant response

Clinical progression of ccRCC manifested with elevated

glutathione and dipeptides

Metabolomic clustering of human ccRCC identified

distinct high- and low-risk subsets

Lack of correlation between enzyme expression levels and

abundance of metabolites in ccRCC

Metabolograms visualize metabolomic, transcriptomic,

and clinical data of ccRCC

Pan-Omics including metabolomics provides integrated

insights that could be exploited for prognostic and

therapeutic purposes in ccRCC

MSKCC

TKCRP

7/2016

MSK Kidney

Cancer Core Lab

James Hsieh Dina Djesevic

Jianing Xu

Amrita Nargund

Toshinao Oyama

Jozefina Casucelli

Chelsea Ray

Maria Becerra

Yiyu Dong

Smrutiben Mehta

Emily Cheng Toru Wakamatsu

Yogesh Ganesan

Song Han

Yuchen Xie

Metabolomics Metabolon

Genomics

NYGC

Antibodies

Eureka

Cores

IGO/CMO

Metabolomics

Proteomics Surgery

Paul Russo

Ari Hakimi

J. Coleman

Brandon Manley

Comp Bio Chris Sander

Nils Weinhold Edward Reznik John Chodera

Steven Albanese Christina Leslie

Hatice Osmangeyoglu

Radiology

Hedi Hricak

Kayvan Keshari

Evis Sala

Omer Aras

Jeremy Durack

Biostatistics

Mithat Gonen

Irina Ostrovnaya

Elli Papaemmanuil

Venkat Seshan

Emily Zabor

Medicine

Bob Motzer

James Hsieh

Martin Voss

Darren Feldman

Joe Lee

Maria Carlo

Pathology

Victor Reuter

Ying-Bei Chen

Satish Tickoo

Chris Iacobuzio

Mike Berger

Lu Wang

TCGA

& KCA

& ACKC

& Rare KCA

Immunology

Ming Li