# Proteomic insights into the biology of dopaminergic neurons

**Authors:** Claudia Cavarischia-Rega, Karan Sharma, Julia C. Fitzgerald, Boris Macek

PMC · DOI: 10.3389/fnmol.2025.1642519 · 2025-07-30

## TL;DR

This review explores how proteomics has advanced our understanding of dopaminergic neurons and their roles in brain function and disease.

## Contribution

The paper provides a comprehensive overview of recent proteomic techniques and findings specific to dopaminergic neurons.

## Key findings

- Proteomic studies have identified brain region-specific protein signatures in dopaminergic neurons.
- Mitochondrial and synaptic proteins are critical for the health and vulnerability of these neurons.
- Advanced tools like microfluidic devices and proximity labeling enhance subcellular proteome analysis.

## Abstract

Dopaminergic neurons, primarily located in the substantia nigra, hypothalamus, and ventral tegmental area of the brain, play crucial roles in motor control, reward, motivation, and cognition. Alterations in their function are associated with numerous neurological and psychiatric disorders, such as Parkinson’s disease, but also Schizophrenia, substance use disorders, and bipolar disorder. Recent advances in mass spectrometry-based proteomics have enabled the comprehensive profiling of protein expression, turnover, subcellular localization, and post-translational modifications at an unprecedented depth of analysis. This review summarizes the developments in proteomic approaches taken to study dopaminergic neurons. We cover findings from global and spatial proteomics studies that revealed brain region-specific protein signatures, as well as dynamic turnover of proteins and the importance of mitochondrial and synaptic proteins for the health and vulnerability of dopaminergic neurons. Combined with advanced molecular cell biology tools, such as growth in microfluidic devices, fluorescent-activated synaptosome sorting, and enzymatic proximity labeling, modern proteomics allows for investigation of synaptic and subcellular proteomes. Despite these advancements, the complexity of the human brain and its cell-specific characteristics remain a challenge. The continuing integration of advanced proteomic techniques with other -omics will eventually yield improved and mechanistic understanding of dopaminergic neurons in health and disease.

## Linked entities

- **Diseases:** Parkinson’s disease (MONDO:0005180), Schizophrenia (MONDO:0005090), bipolar disorder (MONDO:0004985)

## Full-text entities

- **Genes:** AGO1 (argonaute RISC component 1) [NCBI Gene 26523] {aka EIF2C, EIF2C1, GERP95, NEDLBAS, Q99, hAgo1}, ADA (adenosine deaminase) [NCBI Gene 100] {aka ADA1}, PRL (prolactin) [NCBI Gene 5617] {aka GHA1, pPRL}, Apex2 (apurinic/apyrimidinic endonuclease 2) [NCBI Gene 77622] {aka C430040P13Rik, ape2}, LRRK2 (leucine rich repeat kinase 2) [NCBI Gene 120892] {aka AURA17, DARDARIN, PARK8, RIPK7, ROCO2}, Th (tyrosine hydroxylase) [NCBI Gene 21823], MT1H (metallothionein 1H) [NCBI Gene 4496] {aka MT-0, MT-1H, MT-IH, MT1}, S100B (S100 calcium binding protein B) [NCBI Gene 6285] {aka NEF, S100, S100-B, S100beta}, SNCA (synuclein alpha) [NCBI Gene 6622] {aka NACP, PARK1, PARK4, PD1}, PLA2G4A (phospholipase A2 group IVA) [NCBI Gene 5321] {aka GURDP, PLA2G4, cPLA2, cPLA2-alpha}, RHOA (ras homolog family member A) [NCBI Gene 387] {aka ARH12, ARHA, EDFAOB, RHO12, RHOH12}, SYNC (syncoilin, intermediate filament protein) [NCBI Gene 81493] {aka SYNC1, SYNCOILIN}, Oxr1 (oxidation resistance 1) [NCBI Gene 170719] {aka 2210416C20Rik, C7, C7B}, CXCR4 (C-X-C motif chemokine receptor 4) [NCBI Gene 7852] {aka CD184, D2S201E, FB22, HM89, HSY3RR, LCR1}, Kcnd3 (potassium voltage-gated channel, Shal-related family, member 3) [NCBI Gene 56543] {aka Kncd3, Kv4.3}, DHX30 (DExH-box helicase 30) [NCBI Gene 22907] {aka DDX30, NEDMIAL, RETCOR}, GBA1 (glucosylceramidase beta 1) [NCBI Gene 2629] {aka GBA, GCB, GLUC}, APEX1 (apurinic/apyrimidinic endodeoxyribonuclease 1) [NCBI Gene 328] {aka APE, APE1, APEN, APEX, APX, HAP1}, Kif5c (kinesin family member 5C) [NCBI Gene 16574] {aka KINN, Khc, NKHC, NKHC2}, ANXA1 (annexin A1) [NCBI Gene 301] {aka ANX1, LPC1}, CST3 (cystatin C) [NCBI Gene 1471] {aka ADLDWA, ARMD11, HEL-S-2}, ADAR (adenosine deaminase RNA specific) [NCBI Gene 103] {aka ADAR1, AGS6, DRADA, DSH, DSRAD, G1P1}, PRKN (parkin RBR E3 ubiquitin protein ligase) [NCBI Gene 5071] {aka AR-JP, LPRS2, PARK2, PDJ}, Kcnj6 (potassium inwardly-rectifying channel, subfamily J, member 6) [NCBI Gene 16522] {aka BIR1, GIRK2, KATP2, KCNJ7, Kir3.2, weaver}, ALDH1A1 (aldehyde dehydrogenase 1 family member A1) [NCBI Gene 216] {aka ALDC, ALDH-E1, ALDH1, ALDH11, HEL-9, HEL-S-53e}, Atp6v1g1 (ATPase, H+ transporting, lysosomal V1 subunit G1) [NCBI Gene 66290] {aka 1810024D14Rik, ATP6J, Atp6g1, VAG1, Vma10}, GALC (galactosylceramidase) [NCBI Gene 2581], CD44 (CD44 molecule (IN blood group)) [NCBI Gene 960] {aka CDW44, CSPG8, ECM-III, ECMR-III, H-CAM, HCELL}, PINK1 (PTEN induced kinase 1) [NCBI Gene 65018] {aka BRPK, PARK6}, Slc6a3 (solute carrier family 6 (neurotransmitter transporter, dopamine), member 3) [NCBI Gene 13162] {aka DAT, Dat1}, Aldh1a1 (aldehyde dehydrogenase family 1, subfamily A1) [NCBI Gene 11668] {aka ALDH-E1, ALHDII, Ahd-2, Ahd2, Aldh1, Aldh1a2}, Mapk3 (mitogen-activated protein kinase 3) [NCBI Gene 26417] {aka Erk-1, Erk1, Ert2, Esrk1, Mnk1, Mtap2k}, PARK7 (Parkinsonism associated deglycase) [NCBI Gene 11315] {aka DJ-1, DJ1, GATD2, HEL-S-67p}, MAOA (monoamine oxidase A) [NCBI Gene 4128] {aka BRNRS, MAO-A}, SHH (sonic hedgehog signaling molecule) [NCBI Gene 6469] {aka HHG1, HLP3, HPE3, MCOPCB5, SMMCI, ShhNC}
- **Diseases:** BD (MESH:D001714), Alzheimer's disease (MESH:D000544), slowness of movement (MESH:D020754), AUD (MESH:D000437), DA (MESH:D009422), neurodegenerative and psychiatric disorders (MESH:D019636), depression (MESH:D003866), bradykinesia (MESH:D018476), Mitochondrial and synaptic dysfunctions (MESH:D028361), NMGs (MESH:C562873), dopaminergic neuron degeneration (MESH:D009410), Schizophrenia (MESH:D012559), substance abuse (MESH:D019966), resting tremor (MESH:D014202), cancer (MESH:D009369), IPD (MESH:D010300), neurological disorders (MESH:D009461), postural instability (MESH:D054972), rigidity (MESH:D009127), OUD (MESH:D009293), Neuropsychiatric disorders (MESH:D001523)
- **Chemicals:** L-DOPA (MESH:D007980), calcium (MESH:D002118), alcohol (MESH:D000438), urea (MESH:D014508), pyruvate (MESH:D019289), NADPH (MESH:D009249), carboxylic acid (MESH:D002264), lithium (MESH:D008094), neuromelanin (MESH:C014121), amino acids (MESH:D000596), PI (MESH:D010716), DA (MESH:D004298), cholesterol (MESH:D002784), LFQ (-), amide (MESH:D000577), lysine (MESH:D008239), TCA (MESH:D014238), BX795 (MESH:C579675), nucleotide (MESH:D009711), cysteine (MESH:D003545), aminopyrimidine (MESH:C012180), purine (MESH:C030985)
- **Species:** Homo sapiens (human, species) [taxon 9606], Rattus norvegicus (brown rat, species) [taxon 10116], Mus musculus (house mouse, species) [taxon 10090]
- **Mutations:** p.A53T, G2019S, I368N, N370S, G209A

## Figures

3 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12344309/full.md

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Source: https://tomesphere.com/paper/PMC12344309