The document discusses research on aberrant gene expression and promoter methylation in primordial germ cells of the rat F3 generation affected by vinclozolin exposure. It emphasizes the efficacy of PCA-based unsupervised feature extraction in identifying genes related to transgenerational epigenetics compared to traditional methods, which showed no significant enrichments. The findings indicate the potential implications of identified genes in various diseases linked to environmental factors, highlighting the need for further investigation into how transgenerational epigenetics operates.

1. Identification of aberrant gene expression Identification of aberrant gene expression
associated with aberrant promoter associated with aberrant promoter
methylation in primordial germ cells methylation in primordial germ cells
between E13 and E16 rat F3 generation between E13 and E16 rat F3 generation
vinclozolin lineagevinclozolin lineage
Y­h. Taguchi
Department of Physics
Chuo University
Tokyo
Japan
http://www.biomedcentral.com/1471­2105/16/S18/S16/http://www.biomedcentral.com/1471­2105/16/S18/S16/

2. 1. What is PCA based unsupervisedunsupervised FE?
2. What is transigenetational epigenetics?
3. Comparison of primordial germ cells
between E13 and E16 rat F3 generation
vinclozolin lineage and biological validations
of obtained gene set
4. Summary

3. What is PCA based unsupervisedunsupervised FE?
N features
Categorical
multiclasses
In contrast to usual usage of PCA, not samples but
features are embedded into Q dimensional space.
PCA
PC1
samples
M samples
N × M Matrix X (numerical values)
PC2
PC1
+
+ +
+ +
++
+
+
+
++ +
+
+
No distinction
between classes

4. Synthetic example
10 samples
10 samples
90 features 10 features
N(0)
N()
[N()+N(0)]/2
+:Top 10 outliers

Thus, extracting outliers
selects features distinct
between two classes in an
unsupervised way.
Accuracy:(100 trials)Accuracy:(100 trials)
89.5% (
52.6% (
PC1
PC2
Normal μ：mean
Distribution ½ :SD

5. The First example:
Transgenerational Epigenetics (TGE)
Phenotype transfers between generations
without DNA modification
(also focused in “Cell Best of 2014Cell Best of 2014”)
F3 generation of F0 pregnant female exposed
to endocrine disruptor
F0♀
F1♂ F2
F3
Abnormalities
without inherited
DNA exposed to
endocrine disruptor?

6. Yes!
・ male infertility
(Guerrero­Bosagna, PLoS ONE 2013)
・ anxiety behavior (Skinner, PLoS ONE, 2008)
・ mate preference (Skinner, BMC Genom., 2013)
・ various diseases (Anway, Endocrinology, 2006)
(on prostate, kidney, immune system, testis, and
tumor development)
・ reprogramming of primordial germ cells
(Skinner, PLoS ONE, 2013)
・ stress responses ( Crews, PNAS, 2012)
However, understanding how TGE takes place still lacks.

7. Authors' conclusion :
“A comparison between the germ cell
differential DNA methylation regions
and the differentially expressed genes
indicated no significant overlap”
Significant overlaps observed would be Significant overlaps observed would be
interesting....interesting....
Skinner, PLoS ONE, 2013:
Primordial germ cell in F3 generation at E13
and E16, gene expression/promoter methylation
F2♀
F3

8. N'' common
genes
Feature
Extraction
N' genes
Feature
Extraction
Promoter
methylation
Vinclozolin
treated
Control
E13 E16 E13 E16
Gene
expression
Vinclozolin
treated
Control
E13 E16 E13 E16
Our strategy.....Our strategy.....
N' ←→ N''
PP
Total N genes

9. N〜１０４
Results.....Results.....
P=0.05
T­test based feature selectionsT­test based feature selections
No overlaps
(N' 300)≦

10. N〜１０４
Results.....Results.....
P=0.05
limma based feature selectionslimma based feature selections
N''=33 genes with RefSeq ID
No significant enrichments of
GO BP, GO CC, GO MF, KEGG pathway, or PPI
using DAVID, TargetMine, g:profiler, or STRING

11. N〜１０４
Results.....Results.....
P=0.05
SAM based feature selectionsSAM based feature selections
N''=30 genes with RefSeq ID
P=10­2
No significant enrichments of
GO BP, GO CC, GO MF, KEGG pathway, or PPI
using DAVID, TargetMine, g:profiler, or STRING

12. N〜１０４
Results.....Results.....
P=0.05
P=10­3
P=10­2
PCA based PCA based unsupervisedunsupervised FE FE
N''=48 genes with RefSeq ID

13. multiple significant enrichments of GO BP, GO MF, using
DAVID and g:profiler
Seven PPIs (P=0.05) detected by STRING

14. N〜１０４
Results.....Results.....
P=0.05
P=10­3
P=10­2
PCA based PCA based unsupervisedunsupervised FE FE
N''=179 genes with RefSeq ID

15. DAVIDDAVID

16. g:profilerg:profiler

17. TargetMineTargetMine

18. We further validated that 22 genes among 48
genes selected by PCA based unsupervisedunsupervised
FE when N'=1000 are related to either
kidney, testis, prostate, tumor and immune
system whose associated diseases were
caused by TGE.
We also proposed that Chemokine signaling
pathway as well as LRR proteins are deeply
related to TGE.
Because of lack of time, we cannot discuss
about it.

19. Summary
・PCA based unsupervisedunsupervised FE identified more genes
associated with both differential gene expression
and aberrant promoter methylation between E13
and E16 rat F3 generation vinclozolin lineage
・ Genes selected by PCA based unsupervisedunsupervised FE
were associated with various enrichments of
biological terms/concepts while none were
associated with those selected by t­test, limma, or
SAM based FE.
・ These suggested definitely the superiority of
unsupervisedunsupervised method toward supervised methods.

20. This study was supported by
Chuo university joint research grant
“In silico drug discovery using FAMS”
and
KAKENHI
“Initiative for High­Dimensional Data­
driven Science through Deepening of
Sparse Modeling”