Endometriosis gene-expression, meta-analysis

Gene-expression in Endometriosis: Chromosome 1q significantly

contributes to endometriosis gene-expression

Mehis Pold, M.D.Founder

EOMIX, Inc.

August 9, 2010

04/12/2023 [email protected]

Terms:

Ectoendometrium – endometrial tissue outside of it’s natural locationEuendometrium – endometrium in it’s natural location, uterine cavity

Endometriosis (from endo, "inside", and metra, "womb") is a medical condition in which endometrial cells are deposited in areas outside the

uterine cavity. The uterine cavity is lined by endometrial cells, which are under the influence of female hormones. Endometrial cells deposited in areas outside the uterus (endometriosis) continue to be influenced by these hormonal changes and respond similarly as do those cells found

inside the uterus. Symptoms often exacerbate in time with the menstrual cycle.

Endometriosis is typically seen during the reproductive years; it has been estimated that it occurs in roughly 5% to 10% of women.

Symptoms depend on the site of implantation. Its main but not universal symptom is pelvic pain in various manifestations. Endometriosis is a

common finding in women with infertility.

Source: Wikipedia


Diagnostics of Endometriosis:

INVASIVE - Confirmed by laparoscopyExclusion of other conditions

Systemic diagnostic markers poorly understood

Medical need for non-invasive diagnostic test

How do we find endometriosis markers?

BloodUrineSaliva

Skin biopsyHair follicles


Exper

Platf

GEO Platform

IDAuthors

Non-disease Endometrium

Endometriosis Summary

GSE7305

Affy

GPL570 Roth et al. 10 10 Normal and diseased (ovarian endometriosis) human tissues w ere profiled for gene expression

GSE7846

Affymetr

GPL570 Sha et al. 5 5

The pathogenesis of endometriosis may result from aberrant angiogenesis that occurs in eutopic

endometrium w ith retrograde menstruation. The difference in gene expression profile betw een human

endometrial endothelial cells (HEECs) from eutopic endometria

GSE5108

GE Hea

GPL2895 Klinkova et al. 11 11

Experimental design: Eutopic and ectopic endometrium w ere obtained from the same patients; for each

patient, eutopic endometrium from the uterus served as the control for her ectopic endometrial samples.

GSE6364

Affymet

GPL570 Burney et al. 16 21

Analysis of endometrial specimens from w omen w ith endometriosis. Endometrial gene expression examined

at various phases of the menstrual cycle. Results provide insight into the molecular pathogenesis of

endometriosis.

GSE4888

Affymet

GPL570 Talbi et al. 27

Analysis of the normal endometrium at distinct phases of the menstrual cycle. Results provide insight into w hether molecular profiles of the endometrium can

distinguish the different phases of the menstrual cycle.

GSE12446

Affyme

GPL570 Klaassens et al. 31

Transcriptome analysis of human endometrial tissues from healthy post-menoupausal w omen reflecting the

endometrial response to 3-w eeks treatment w ith tibolone, E2 and E2+MPA.

GSE11769

Affymetr

GPL96 Hull et al. 9 9

The pathophysiology of endometriotic lesion development remains unclear but involves a complex interaction betw een ectopic endometrium and host

peritoneal tissues.

Endometriosis database of EOMIX Inc.

(1) Meta-analysis of three independent whole-genome expression sets(2) GenMAPP pathway analysis


Roth

Klinkova

Hull

Pathway analysis by GenMAPP on genes altered in at least two of out three Endometriosis datasets

N = 2,522 = Venn diagram [2+3+4]R = 19,632

Summary Statistics of Endometriosis sets (Roth, Klinkova, Hull)


Variable Value

N 19,632

R 2,522

n 25

r 7

Z 2.265788

Mathematics of hypergeometric distribution

R – depends on cut-offs: e.g. p-value < 0.01n – specific MAPP pathway

Produces best results when• R 10 – 15% of N• n is not too small or too large

Excellent software but beware of mathematical limitations!

Results depend on Gene Ontology hierarchies and the existing pathway information

Many genes have no GO annotations and positions on currently known pathways

Z-values greater than 2 and smaller than -2 considered relevant• Z < -2 and Z > 2

GenMAPP calculates hypergeometric distributionGenMAPP is a freeware


Variable Value

N 19,632

R 2,522

n 90

r 30

Z 5.82174

Results depend on Gene Ontology hierarchies and the existing pathway information

Z-values greater than 2 and smaller than -2 considered relevant

Z < -2 and Z > 2

Examples at R/N= 0.128 (12.8%)

n = 90 pathway of 90 known members,r = 30 of which 30 are altered

r/n = 0.333 (33.3%)Z = 5.82

n = 9r = 3r/n = 0.333 (33.3%)Z = 1.83 = insignificant

GenMAPP OverviewSmall amount of information does not produce reliable results


GenMAPP pathways upregulated in endometriosisGenMAPP pathways Gene Ontology Samples KEGG converted

Cellular Processes• Focal adhesion• G13 signalin• G-protein signaling• Integrin-mediated adhesion• T -cell receptor pathway

Metabolic Processes• Prostaglandin synthesis

Molecular Function• Small ligand GPCR

Physiological Process• Adipogenesis• Calcium regulation in cardiac muscle• Circadian exercise• Complement activation by classical

pathway• Complement and coagulation cascade

KEGG• Smooth muscle contraction• Striated muscle contraction

Biological Processes• Actin cytoskeleton organization and

biogenesis• Actin filament-based process• Anion transport• Cell growth• Cell-cell adhesion• Endocytosis• Enzyme-linked receptor protein

signaling• Growth• Humoral Defense sensu Vertebrata• Humoral Immune response• I-kappa kinase NF-kappa cascade• Inflammatory response• Inorganic anion transport• Muscle contraction• Muscle development• Regulation of cell size• Transmembrane receptor PTK

signaling

Cellular Component• Actin cytoskeleton• Cytoskeleton• Extracellular matrix sensu Metazoa• Plasma membrane

Molecular Function• Actin binding• Carbohydrate binding• Enzyme activator activity• Enzyme inhibiting activity• GTPase activator activity

Nicotinate and nicotinamide metabolism


GenMAPP pathways Gene Ontology Samples KEGG converted

Cellular Processes• Androgen receptor pathway• Cell cycle G1 to S control• Delta-Notch signaling• DNA replication reactome• Hedgehog pathway• mRNA processing reactome• TNFalpha-NFkB pathway

Metabolic Processes• Electronic transport chain• Fatty acid synthesis• Nucleotide metabolism

Molecular Function• Homologous recombination• Mismatch repair

Physiological Process

Biological Processes• Cell cycle• Cytokinesis• DNA repair• DNA replication• M phase• M phase of mitotic cell cycle• Microtubule-based process• Regulation of cell cycle• Response to DNA damage stimuli• Response to endogenous stimuli

Cellular Component• Chromatin• Endomembrane system• Microtubule cytoskeleton

Molecular Function• Ligase activity• Nucleotidyltrasferase activity• Protein transporter activity

• Biotin metabolism• Glutathione metabolism• Lysine biosynhesis• Lysine degradation• Methionine metabolism• Nicotinate and nicotinamide

metabolism• One carbon pool by folate• Phe, Tyr, Trp biosynthesis• Selenoamina acid

metabolism• Sphingoglycolipid

metabolism

GenMAPP pathways downregulated in endometriosis


Endometriosis pathway analysis summary

• Inflammation and immune response upregulated in endometriosis: complement, inflammation

mediators, humoral response, T-cell response, B-cell receptor genes

• Muscle-related pathways upregulated in endometriosis: smooth and striated muscle-related

genes, calcium-regulated gene-expression.

• Cytoskeleton-related processes involved

• Metabolism and Cell cycle appear low in endometriosis as compared to normal endometrial

tissue

Connection to previously published studies

Plasma cell infiltration ~ high levels of B-cell receptor gene-expression documented in previous studies. Hever et al.

(PNAS, 2007) documented plasma-cell infiltration of ovarian endometriosis.


Variable Value

N 19,632

R 2,522

n 104

r 23

Z 2.8324

1q21Variable Value Variable Value

N 19,632 N 19,632

R 2,522 R 2,522

n 681 n 895

r 115 r 145

Z 3.207 Z 3.0701

1q21-1q32 1q12-1q44

Chromosome 1q produces substantial levels of endometriosis-specific gene-expression

Variable Value

N 19,632

R 2,522

n 156

r 32

Z 2.8731

1q32


Gene Name Gene Symbol Chromosomal locus

feline leukemia virus subgroup C cellular receptor 1 FLVCR1 chr1q32.3denticleless homolog (Drosophila) DTL chr1q32.1-q32.2TNF receptor-associated factor 5 TRAF5 chr1q32interferon regulatory factor 6 IRF6 chr1q32.3-q41TRAF3 interacting protein 3 TRAF3IP3 chr1q32.3-q41plexin A2 PLXNA2 chr1q32.2complement component (3b/4b) receptor 1 (Knops blood group) CR1 chr1q32complement component 4 binding protein, beta C4BPB chr1q32interleukin 10 I L10 chr1q31-q32SLIT-ROBO Rho GTPase activating protein 2 SRGAP2 chr1q32.1chromosome 1 open reading frame 186 C1orf186 chr1q32.1solute carrier family 41, member 1 SLC41A1 chr1q32.1RAB7, member RAS oncogene family-like 1 RAB7L1 chr1q32hypothetical protein LOC284576 LOC284576 chr1q32.1neurofascin homolog (chicken) NFASC chr1q32.1leucine rich repeat neuronal 2 LRRN2 chr1q32.1phosphoinositide-3-kinase, class 2, beta polypeptide PIK3C2B chr1q32pleckstrin homology domain containing, family A member 6 PLEKHA6 chr1q32.1golgi transport 1 homolog A (S. cerevisiae) GOLT1A chr1q32.1proline/arginine-rich end leucine-rich repeat protein PRELP chr1q32fibromodulin FMOD chr1q32jumonji, AT rich interactive domain 1B J ARID1B chr1q32.1protein phosphatase 1, regulatory (inhibitor) subunit 12B PPP1R12B chr1q32.1ubiquitin-conjugating enzyme E2T (putative) UBE2T chr1q32.1E74-like factor 3 (ets domain transcription factor, epithelial-specific ) ELF3 chr1q32.2leiomodin 1 (smooth muscle) LMOD1 chr1q32cysteine and glycine-rich protein 1 CSRP1 chr1q32kinesin family member 14 KIF14 chr1q32.1protein tyrosine phosphatase, receptor type, C PTPRC chr1q31-q32NIMA (never in mitosis gene a)-related kinase 7 NEK7 chr1q31.3asp (abnormal spindle) homolog, microcephaly associated (Drosophila) ASPM chr1q31complement factor H CFH chr1q32

UP in ECTO vs. EU

Down in ECTO vs. EU

Chromosome 1q32 genes that exhibit altered expression in endometriosis

Red font and blue font denote up- and downregulation, respectively


04/12/2023 [email protected] 13

SUMMARY

Pathways modulating host defense are activated in endometriosis

Chromosome 1q significantly contributes to endometriosis gene-expression

Endometriosis gene-expression, meta-analysis

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