CymaBay Therapeutics : Assessment of PPAR-delta target engagement in mouse liver assessed by single nuclei sequencing following a single oral dose of seladelpar

	Assessment of PPAR target engagement in mouse liver assessed by
SAT-177	single nuclei sequencing following a single oral dose of seladelpar
Edward Cable, Yun-Jung Choi, Xia Wu, Jiangao Song, Jeff Johnson, Charles McWherter

CymaBay Therapeutics, Fremont, CA

Intro and Scientific Objectives

1. Ppard is the most widely expressed but least studied of the three PPAR isoforms.
2. Seladelpar targets Ppard and has recently completed a Ph 3 study as a second line therapy for Primary Biliary Cholangitis (PBC) and is currently under review at the FDA and EMA.
3. Target engagement by seladelapr has been described in hepatocytes with respect to FGF21 mediated reductions in bile acid synthesis.
4. Seladelapar target engagement in other liver cell types has not yet been reported.

Experimental Design and Methods

Hepatocytes

Hallmark Analysis FDR<0.25

Fatty Acid Metabolism	***	3
Peroxisomes
***	2	Normalized
Adipogenesis
***	1
Oxidative Phosphorylation	***
		Enrichment
Bile Acid Metabolism	***	0

Endothelial Cells

Hallmark Analysis FDR<0.25
Fatty Acid Metabolism
***	3
Peroxisomes
***	2
Adipogenesis
***	Normalized
Oxidative Phosphorylation
***	1
Bile Acid Metabolism	***
Xenobiotic Metabolism			Enrichment
***	0
MTORC1 Signaling	***	-1

CH3

			O					10 mg/kg PO
							or Veh 5 mL/kg
		O	S		CH3
				OH	6h
F3C		Seladelpar		O
						O

Hu et al 2022

Li et al 2020

Pan et al 2023

Internal Data

Halpern et al 2017

Su et al 2021

Wang et al 2021

Xu et al 2022

Cao et al 2023

Isolate RNA

Make Libraries

Sequence

Annotate Cell Types

n=5 male CD-1/group

Isolate Nuclei

Remove Liver

Xenobiotic Metabolism	***	-1	Score
KRAS signaling Up	***	-2
Allograft Rejection
***	-3
Coagulation	***

Cholangiocytes

Hallmark Analysis FDR<0.25

Fatty Acid Metabolism
***	3
Peroxisomes
***	2
Adipogenesis	***	Normalized
Xenobiotic Metabolism
***	1
Bile Acid Metabolism	***
Oxidative Phosphorylation			Enrichment
***	0
UV Response Down
***	-1
KRAS signaling Up
***
	Score

Heme Metabolism	***		Score
Reactuve Oxygen Species Pathway	***	-2
Estrogen Response Late
***
Unfolded Protein Response
***	-3
Allograft Rejection	***
Coagulation	***

Stellate Cells

Hallmark Analysis FDR<0.25
Fatty Acid Metabolism
***	3
Peroxisomes
***
Adipogenesis
***	2	Normalized
Oxidative Phosphorylation
***	1
Bile Acid Metabolism
***
Estrogen Response Late		Enrichment
***	0
Xenobiotic Metabolism
***	-1
Epithelial Mesenchymal Transition	***

Cluster Annotation

Estrogen Response Late	***	-2
Apical Surface	***
Coagulation	***	-3

UV Response Down			Score
***	-2
KRAS signaling Down
***

	15
	14
	13
	12
	11
	10
Identity	9
8
7
	6

_2

10

5

0

Unfolded Protein Response ***

Kupffer Cells

Unfolded Protein Response
***	-3
Coagulation
***

Summary

5
4
3
2
1
0
Alb Fabp1 Rbp4 Serpina3k	Ttr F8 Plekhg1 Ptprb Stab2 Bgn Col14a1 Dcn Ntm Reln	Arhgap15 Clec4f Ptprc Slc8a1 Vsig4 Bicc1 Krt7 Pdgfd Pkhd1
	Features

UMAP

-5

-10

-15
-15	-10	-5	0	5

UMAP_1

Hallmark Analysis FDR<0.25

Fatty Acid Metabolism	***	3
Peroxisomes
***
2
Adipogenesis
***	Normalized
Oxidative Phosphorylation
***	1

1. Seladelpar demonstrates Ppard target engagement in all five liver cell types

identified in the study

2. PDK4 and Angptl4, known Ppard targets, were induced in all liver cell types,

but outside the top 20 modulated genes

3. Major metabolic pathways induced by seladelpar include Fatty Acid

Metabolism, Peroxisomes, and Adipogenesis

4. The Unfoleded Protein Response is downregulated in all cells, except

Hepatocytes

Scan to Download

		Average Expression
		1
Identity	0

Xenobiotic Metabolism	***	0	Enrichment
Bile Acid Metabolism	***
Estrogen Response Late	***	-1

5. The number of inducible or repressed genes varies greatly

Hepatocytes 1503 repressed vs 1256 induced Cholangiocytes 16 repressed vs 26 induced Stellate cells ~4X more genes repressed than induced

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Percent Expressed

25

50

75

Alb Fabp1 Rbp4 Serpina3k	Ttr F8 Plekhg1 Ptprb Stab2 Bgn Col14a1 Dcn Ntm Reln Arhgap15 Clec4f Ptprc Slc8a1 Vsig4 Bicc1 Krt7 Pdgfd Pkhd1
	Features

Interferon Alpha Response			Score
***	-2
Unfolded Protein Response
***	-3
Coagulation	***

1. How these gene changes translate into pharmacodynamic effects requires further study
2. The study only used male mice, whether these changes will occur in female mice, or whether the same changes will occur in disease models requires further study
3. Understanding cell-type specific effects of seladelpar in the liver will be important when integrating mechanisms of action and clinically relavant effects in PBC patients