Biology subjects

Chen, P. B.

Publications and source records attributed to Chen, P. B..

4 recordsLinked to original sources

bioRxiv2026

Single-nucleus analysis reveals renal STAT1/CEBPB signaling as a modifiable relay of proinflammatory FGF23 effects in diabetic kidney disease

Background Circulating fibroblast growth factor 23 (FGF23) rises dramatically in chronic kidney disease, particularly in diabetic kidney disease (DKD). At high concentrations, and with declining Klotho, FGF23 has been linked to renal inflammation. The cell types and transcriptional programs mediating these off-target actions remain undefined. We asked whether the diseased kidney responds to FGF23 differently from the healthy kidney, and whether any disease-specific response could be targeted. Methods Male and female DBA/2J mice received streptozotocin or vehicle to induce DKD. On day 56, mice received a single dose intravenous injection of FGF23 (0.3 g) or vehicle, with tissue collected 1 h later for single-nucleus RNA sequencing, differential expression and regulon (inferred transcription factor activity) analysis. Candidate pathways were tested in precision-cut kidney slices using the CEBPB inhibitor ST-101. Results Streptozotocin-treated male mice developed early DKD with a 6-fold increase in urinary albumin/creatinine ratio and 50% higher blood urea nitrogen with preserved glomerular filtration rate. All major renal cell types were annotated. Canonical FGF23 signaling was intact in disease, with segment-specific target induction conserved in both conditions (e.g. Cyp24a1 in PT-S1 and DCT1). Superimposed on this were disease-restricted responses, including Wsb1 in DCT1 and Pdk4 in PT-S2, PST, DCT1 and DCT2. Regulon analysis revealed DKD-specific induction of CEBPB regulon activity by FGF23 across all analyzed tubular segments, and of STAT1 in several segments. Pre-treatment with a CEBPB inhibitor suppressed CEBPB activity, downstream NF-KB and pro-inflammatory gene sets, and immune-like cell abundance in diseased slices. Conclusion In the diabetic kidney, FGF23 engages a STAT1-CEBPB-NF-{kappa}B axis absent from healthy kidney and extending beyond its canonical Klotho-dependent target segments, identifying CEBPB as a potential treatment target for FGF23's pathological inflammatory actions.

physiology↗

bioRxiv2024

Complementation testing identifies causal genes at quantitative trait loci underlying fear related behavior

Knowing the genes involved in quantitative traits provides a critical entry point to understanding the biological bases of behavior, but there are very few examples where the pathway from genetic locus to behavioral change is known. Here we address a key step towards that goal by deploying a test that directly queries whether a gene mediates the effect of a quantitative trait locus (QTL). To explore the role of specific genes in fear behavior, we mapped three fear-related traits, tested fourteen genes at six QTLs, and identified six genes. Four genes, Lsamp, Ptprd, Nptx2 and Sh3gl, have known roles in synapse function; the fifth gene, Psip1, is a transcriptional co-activator not previously implicated in behavior; the sixth is a long non-coding RNA 4933413L06Rik with no known function. Single nucleus transcriptomic and epigenetic analyses implicated excitatory neurons as likely mediating the genetic effects. Surprisingly, variation in transcriptome and epigenetic modalities between inbred strains occurred preferentially in excitatory neurons, suggesting that genetic variation is more permissible in excitatory than inhibitory neuronal circuits. Our results open a bottleneck in using genetic mapping of QTLs to find novel biology underlying behavior and prompt a reconsideration of expected relationships between genetic and functional variation.

genetics↗

bioRxiv2023

Functional characterization of gene regulatory elements and neuropsychiatric disease-associated risk loci in iPSCs and iPSC-derived neurons

Genome-wide association studies (GWAS) have identified thousands of non-coding variants that contribute to psychiatric disease risks, likely by perturbing cis-regulatory elements (CREs). However, our ability to interpret and explore their mechanisms of action is hampered by a lack of annotation of functional CREs (fCREs) in neural cell types. Here, through genome-scale CRISPR screens of 22,000 candidate CREs (cCREs) in human induced pluripotent stem cells (iPSCs) undergoing differentiation to excitatory neurons, we identify 2,847 and 5,540 fCREs essential for iPSC fitness and neuronal differentiation, respectively. These fCREs display dynamic epigenomic features and exhibit increased numbers and genomic spans of chromatin interactions following terminal neuronal differentiation. Furthermore, fCREs essential for neuronal differentiation show significantly greater enrichment of genetic heritability for neurodevelopmental diseases including schizophrenia (SCZ), attention deficit hyperactivity disorder (ADHD), and autism spectrum disorders (ASD) than cCREs. Using high-throughput prime editing screens we experimentally confirm 45 SCZ risk variants that act by affecting the function of fCREs. The extensive and in-depth functional annotation of cCREs in neuronal types therefore provides a crucial resource for interpreting non-coding risk variants of neuropsychiatric disorders.

genetics↗

bioRxiv2022

Improved Version of ChETA Promotes Aggression in the Medial Amygdala

The development of optogenetic tools has significantly advanced our understanding of neural circuits and behavior. The medial amygdala, posterior dorsal subdivision (MeApd) is part of a distributed network controlling social behaviors such as mating and aggression. Previous work showed that activation of GABAergic neurons in mouse MeApd using channelrodopsin-2 (ChR2H134R) promoted aggression. In a recent study, Baleisyte et al. (2022) confirmed these findings using the same reagents (i.e. ChR2H134R), but also reported that a different ChR2 variant with faster kinetics--ChETA--inhibited rather than promoted aggression when high laser power, long duration photostimulation conditions were used. As ChETA is known to have a substantially lower photocurrent than ChR2 and other opsins, an improved version of ChETA (i.e. ChR2E123T/T159C; ChETATC) was subsequently developed. ChETATC has larger photocurrents than the original ChETA while maintaining fast kinetics and low plateau depolarization. Here we show that activating MeApd GABAergic neurons using the improved ChETATC promotes aggression, similar to ChR2H134R, suggesting that the results obtained using the original ChETA are not due to a difference in channel kinetics. Furthermore, we found that ChETATC is capable of driving a rapid onset of aggression within 200-300 milliseconds of stimulation, suggesting that this effect reflects direct activation of MeApd GABAergic neurons. We conclude that the different behavioral phenotypes observed using the original ChETA vs. ChETATC and ChR2 likely reflects the weaker photocurrents in ChETA vs. other opsins, and/or the long duration/high power photostimulation conditions used with ChETA. Consistent with this conclusion, the results obtained using ChR2 or ChETATC are complementary to findings from loss-of-functions experiments using optogenetic inhibition, chemogenetic inhibition, and neuronal ablation. These data support a positive-acting role of MeApd Vgat+ neurons in aggression. Our findings, in conjunction with studies of Berndt et al. (2011), suggest that the improved ChETATC should be used when faster kinetics than ChR2 offers are required.

neuroscience↗