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NEURONAL ACTIVATION AND INHIBITION, MAPPED IN THE SAME BRAIN

c-Fos marks neurons that were recently activated. Phosphorylated pyruvate dehydrogenase (pPDH, also called phospho-PDH), the first inverse activity marker for neurons, rises in neurons whose firing has dropped, which makes neuronal inhibition visible. We label both in one cleared mouse brain, image it by light sheet microscopy and map each signal across 800+ regions of the Perens CCF, so a single study shows where activity went up and where it went down.

2 markers, 1 brain

Activation and inhibition from the same animal.

800+ regions

Per-region counts for both markers, registered to the Perens CCF

Neuron, 2024

pPDH first described as an inverse activity marker by Yang et al.

CNS-Voyager™

Both maps delivered in 3D, in your browser 

50% off combined c-Fos + pPDH studies

Submit your study before 31 December 2026 to qualify.

Offer ends 31 December 2026

MAPPING NEURONAL INHIBITION

c-Fos sees activation clearly. Neuronal inhibition mostly stays invisible.

For four decades, immediate early genes such as c-Fos have been the standard histological readout of neuronal activation. A drop in activity does not reliably show up as a drop in c-Fos: the protein is induced over hours and clears slowly, so a region that was switched off during an experiment can look unchanged. 

Yang et al. (Neuron, 2024) found the missing counterpart in an unbiased phosphoproteomic screen of optogenetically driven neurons. Phosphorylation of pyruvate dehydrogenase at Ser293 rose as firing fell, and fell as firing rose. PDH gates pyruvate entry into the TCA cycle, so pPDH plausibly tracks how much energy a neuron is spending on firing, read in the opposite direction from c-Fos.

In mice, pPDH labeling increased with isoflurane anesthesia, chemogenetic silencing (hM4Di) of substantia nigra neurons, the end of visual stimulation, drinking after water deprivation, and refeeding after a fast. In the water deprivation model, more than 10 brain regions showed pPDH changes that c-Fos did not reveal.

c-Fos and pPDH compared. Source: Yang et al., Neuron 112, 959-971 (2024).
  c-Fos pPDH (Ser293)
Reports Recent increase in activity Recent decrease in activity
What it is Immediate early gene product, transcription factor Phosphorylated, inactive form of a metabolic enzyme
Where in the cell Nucleus, compact round signal Cytoplasm, soma and proximal dendrites
Response speed Hours to build up, hours to clear Detected within 1 h of inhibition in vivo
Track record Decades, thousands of studies Exploratory, first described in 2024
Known blind spots Misses most inhibition; slow off-kinetics High baseline outside the blood-brain barrier; unresponsive in some hippocampal fields and POMC neurons

HOW A COMBINED STUDY RUNS

Two channels, one cleared brain, one atlas

The original pPDH work used tissue sections and named whole-mount staining of cleared brains as the next step. A combined study runs both markers through the full LS-Journey™ pipeline, the same route as any of our custom endpoints.

Dual immunolabeling

c-Fos and pPDH antibodies in separate channels, iDISCO+ clearing of the whole mouse brain.

Light sheet imaging

Both channels acquired from the intact brain by light sheet microscopy at cellular resolution.

CNS-Voyager™ delivery

Activation and inhibition maps in 3D in CNS-Voyager™, with overlays of connectivity and gene expression data. Formal report available as an add-on.

Where a bidirectional map changes the answer

Feeding and obesity pharmacology

Satiety drugs switch some circuits on and others off. Yang et al. used pPDH to find orexin neurons in the lateral hypothalamus that refeeding inhibits, a population c-Fos did not flag.

Sedatives, anesthetics, antiepileptics

Compounds whose mechanism is suppression are the hardest to see with c-Fos alone. pPDH gives the suppressed regions a positive signal to count.

Circuit manipulation checks

Confirm that chemogenetic silencing worked where intended, and see which downstream regions went quiet or lit up as a result. 

Behavioral state transitions

Thirst to satiation, hunger to fullness, stimulus to rest. pPDH responds within the hour, so the offset of a state becomes measurable, a new angle for whole-brain c-Fos studies of behavior.

WHAT IS STILL OPEN

pPDH is an exploratory marker, and that is the point

Most of what is known about pPDH in vivo comes from one paper. Its authors describe the gaps plainly:

  • Baseline pPDH is high and unresponsive in regions outside the blood-brain barrier, including the area postrema, subfornical organ and parts of the arcuate nucleus. These matter for GLP-1 pharmacology.

  • Some populations, such as CA3 of the hippocampus and POMC neurons, did not change pPDH despite changes in activity.

  • Anything that acts directly on neuronal glucose metabolism could shift pPDH independently of firing.

  • Tonically active or tonically inhibited populations have not yet been characterized.

Each of these is an experiment waiting to be run alongside c-Fos in the same brain. Every combined study adds a brain-wide data point to a marker that, so far, has mostly been read one section at a time.

SfN Neuroscience 2026 collaboration offer

Run a c-Fos + pPDH study with us

We want to learn how pPDH behaves across the whole brain, in as many models as possible. Run your study with both markers and we will halve the LS-Journey™ price in return for doing the science together.

Valid for studies submitted by 31 December 2026.

You get

  • 50% off a full c-Fos + pPDH LS-Journey™ study

  • Both maps in CNS-Voyager™, per-region data for 800+ regions

  • CNS-Voyager™ access for 3 users for 6 months

  • Study design input from the team that built the Perens CCF

We ask

  • A collaboration agreement

  • Vibraint co-authorship on publications that use the study data

  • Permission to use the pPDH results to train our image analysis algorithms

FREQUENTLY ASKED QUESTIONS

c-Fos and pPDH studies: what you need to know

What is pPDH?

pPDH is pyruvate dehydrogenase E1 alpha phosphorylated at Ser293, the inactive form of the enzyme that feeds pyruvate into the TCA cycle. Yang et al. (Neuron, 2024) showed that pPDH rises when neuronal firing decreases and falls when it increases, making it the first endogenous inverse activity marker that can be stained in tissue.

Is there a marker for neuronal inhibition, like c-Fos is for activation?

pPDH is the best-characterized candidate so far. It increased in vivo after general anesthesia, chemogenetic silencing, the end of visual stimulation, drinking after thirst and refeeding after fasting. It is still exploratory, with known blind spots in some regions and cell types.

Can c-Fos and pPDH be measured in the same brain?

Yes. The two antibodies are read in separate fluorescence channels, and the signals sit in different compartments: c-Fos in the nucleus, pPDH in the cytoplasm. Vibraint labels both in one cleared mouse brain and maps each to the Perens CCF.

How quickly does pPDH respond compared with c-Fos?

Faster. In mice, pPDH was clearly elevated 1 h after anesthesia or after drinking ended a period of thirst, while c-Fos took up to 8 h to return to baseline in the same thirst model. In cultured neurons, pPDH dropped within 10 min of stimulation and recovered about 50 min after it stopped.

Where does pPDH not work well?

In regions outside the blood-brain barrier, such as the area postrema and subfornical organ, baseline pPDH is high and did not respond to anesthesia. CA3 of the hippocampus and POMC neurons also showed no pPDH change. Compounds that directly affect neuronal glucose metabolism need extra controls.

How long does a combined c-Fos + pPDH study take?

A standard LS-Journey™ study takes 2 to 2.5 months from sample receipt to data live on CNS-Voyager™. The timeline for a dual-marker study is confirmed when the study is scoped.

What does the 50% collaboration offer require?

A collaboration agreement, Vibraint co-authorship on any publication that uses data from the study, and permission to use the pPDH results to train our image analysis algorithms. The offer covers combined c-Fos + pPDH studies submitted by 31 December 2026.

REFERENCES

 Yang D, Wang Y, Qi T, et al. Phosphorylation of pyruvate dehydrogenase inversely associates with neuronal activity. Neuron 112, 959-971 (2024). doi:10.1016/j.neuron.2023.12.015

Perens J, Salinas CG, Skytte JL, et al. An optimized mouse brain atlas for automated mapping and quantification of neuronal activity using iDISCO+ and light sheet fluorescence microscopy. Neuroinformatics 19, 433-446 (2021). doi:10.1007/s12021-020-09490-8