Lung Cancer Project update Schumacher - Kaiser November 17, 2006.

Lung Cancer Projectupdate

Schumacher - KaiserNovember 17, 2006

• DB sample annotations

• Univariate and multivariate analyses (definition of classes conditions biological interpretation)

• Preliminary biomedical assessment of transcriptional signatures

• Dataset integration

• Project timeline and milestones

• Ph.D. student – update

• Next steps ...

Agenda

• Novachip platform

• Biopsies with at least 10% of tumor cells (score>0)

• Definite diagnoses

• Squamous cell carcinomas, adenocarcinomas, controls

• Orthogonal Partial Least Squares Discriminant Analysis

• Two classes question OPLS-DA ranked features

• Top 500 features analyses

¬ Pubmed and other NCBI db and tools, Ingenuity Pathway Analysis, Metacore, Medgene, Pathologene, OntoExpress, ...

Transcriptional assessment of lung biopsies - approach

NSCLC: some markers for diagnosis of primary lung adenocarcinomas

from Ueno et al (2003) BJC 88:1229

NSCLC: adenocarcinoma – transcriptional signatures tumor features (1.2)

• increased levels of pulmonary adenocarcinoma markers (e.g. SFTPA2, SFPTB, SFTPC, SFTPD, NASPA, TTF1)

• increased cell migration (tumor cells?, endothelial cells,leukocytes??) tumor cell spreading (increased AREG, CLDN4, FN1, HPN, MET, MMP9, PLAU, THBS1, VCAM1)

• no significant change of APC and other leukocytes‘ markers

• chemoattraction of mononuclear leukocytes (CCL2, CCL20, CXCL13) – respiratory burst of monocytes? (increased CCL2, FN1, ICAM1, TREM1, VCAM1)

• increased cell invasiveness – cell extravasation signaling? increased cell attachment (e.g. macrophages: increased FN1, ICAM, VCAM1; tumor cells: increased IGF2, PLAU, THBS1)

• increased angiogenesis (increased ADAMTS1, FN1, SERPINE1, SPARC, THBS1)

• increased reactive stroma - myofibroblasts (e.g. SPARC, other)

• increased tumor growth (increased CCL2, CRABP2, FN1, IGF2, IL6, MET, MMP9, OLR1, PLAU, SPP1, THBS1)

• increased ECM remodelling – „wound healing“ (increased MMP1, MMP9, MMP11, MMP12, MMP13)

• decreased redox stress? (decreased GSTA1, GSTA2, GSTM1 - low proliferation? cell cycle?)

• increased neuritogenesis (increased ABL2, GEM, NFGB, PLAU)

NSCLC: adenocarcinoma – transcriptional signatures tumor features (2.2)

• tumor progression mechanisms (CTAs (MAGEs, GAGEs), TP63, TP53?)

• other oncogenes, tumor suppresors relevant markers (MYC, SRC, HER/NEU, HRAS, KRAS2, CCND1; CTNNB1, VEGFC, ERBB1-3)

• evidence of epigenetics? (HATs, HDACs, DNMTs, ...)

• markers of poor prognosis (e.g. SPARC, more to come ...)

• xenobiotic metabolism (e.g. decreased AKR1C1, GSTs, CYP4B1, ...)

• serum markers? (e.g. IL6, SPP1)

• relevant molecular pathways: e.g. inflammation-related

• stem cell –like markers, transient amplifying compartments (KIT, POU5F1, SOXs, SCF, CD33, ABCG2)

NSCLC: distinguishing pulmonary small cell carcinoma from poorly differentiated squamous cell carcinoma

from Zhang et al (2005) Modern Pathology 18:111

Small cell carcinoma Poorly differentiated squamous carcinoma

TTF1 TTF1 TP63

TP63 KRT CDKN2A CDKN2AKRT

(?)

NSCLC: poorly differentiated adenocarcinoma

from Zhang et al (2005) Modern Pathology 18:111

TTF1 TP63

KRT CDKN2A

SFTPBmucins

(?)

NSCLC: squamous cell carcinoma – transcriptional signatures tumor features (1.2)

• increased levels of epidermal markers (development and differentiation) - relate to carcinogenesis theories: e.g. „wound that never heals“

• inflammation, leukocytic infiltration (poor), reactive stroma?

• increased cell division, proliferation and survival

• increased invasiveness, ECM remodelling

• tumor progression mechanisms (MAGE, TP63, TP53?)

• no major evidence of epigenetics? (HATs, HDACs, DNMTs, ...)

• other oncogenes, tumor suppresors

• markers of poor prognosis (e.g. MAGEs. GAGE1, SPP1)

• mechanisms of tumor defense (?)

• xenobiotic metabolism in smokers, drug treatment, solute transport, CYPs,

• serum markers? (e.g. IL1A, IL6, SPP1, defensins)

• relevant molecular pathways (e.g. SHH, polyamines, Ca2+ signaling)

• other cancers, transient amplifying compartments, differentiation ...

from Proksch et al (2006) J Dermatol Sci 43(3):159

NSCLC: squamous cell carcinoma – transcriptional signatures tumor features (2.2)

MAGEs, TP53, epigenetics, TP63

Discussion ...

Datasets integration

Week 44 45 46 47 48 49 50 51 52 01 02 03 04 05 06 07 08 09 10 11 12 13

A1.1. A2.1. A2.1. A2.2. A1.2. A4.1 A4.1 A5

A2.2. A2.2. A3.2. A4.1 A4.2 A4.2

A3.1. A4.1 A3.3. A3.3.

A4.1 A3.4. A3.4.

E E E

B1. B3.1. B3.1. B3.3. B3.3. B4.1 B4.3 B4.3 B4.3 B5

B2.1. B3.2. B3.4. B3.4. B4.2 B4.4 B4.4

B2.2. DR

E E E E E E

Q4 2006 Q1 2007

Biopsies

Blood

Proposed project timeline and milestones

Next steps ...