# Region-resolved proteomic map of the human brain: functional interconnections and neurological implications

**Authors:** Pei-Pei Zhang, Man-Sheng Li, Jia Zhou, Chu-Hong Zhu, Rui Tang, Zhi-Cheng He, Xiao-Hong Yao, Yi-Fang Ping, Dong-Fang Xiang, Le-Yong Tan, Yu-Jie Wang, Shuai Wang, Si-Si Li, Jie Ma, Yun-Ping Zhu, Xiu-Wu Bian, Ling Leng

PMC · DOI: 10.1038/s41392-025-02554-8 · Signal Transduction and Targeted Therapy · 2026-02-04

## TL;DR

This study creates a detailed proteomic map of the human brain, revealing how different regions are functionally connected and their roles in brain function and disease.

## Contribution

The paper introduces a three-module framework for understanding brain region interconnectivity based on proteomic data.

## Key findings

- The four cerebral lobes show interconnectivity, supporting information integration via large-scale neural networks.
- The midline regulatory axis is implicated in higher-order cognitive functions and structural homeostasis.
- Proteomic and transcriptomic integration is highlighted as essential for understanding brain physiology and neurological disorders.

## Abstract

While progress has been made in transcriptomic profiling of the human brain, functional characterization of brain regions and their interactions on the basis of regional protein expression remains limited. Here, we constructed a proteomic map from thirteen anatomical brain regions of eight cadaver donors to elucidate region-specific protein expression patterns and their implications for brain function. The results underscore the interconnectivity of the four cerebral lobes, suggesting facilitated information integration through large-scale neural networks. We propose a three-module framework (cortical integration module [frontal lobe, temporal lobe, parietal lobe, occipital lobe], limbic-relay network [amygdaloid nucleus, hippocampus, thalamus/hypothalamus], and midline regulatory axis [thalamus/hypothalamus, corpus callosum, ventricles, optic chiasm]) and provide molecular evidence supporting the potential involvement of the midline regulatory axis, brainstem, and cerebellum in higher-order cognitive functions. The midline regulatory axis may play a critical but underexplored role in neurodevelopment, interregional signaling, and structural homeostasis, potentially through efficient synaptic function, energy metabolism, and extracellular matrix integrity. This analysis may enhance the understanding of brain physiology and highlight the need to integrate proteomic and transcriptomic approaches in the study of brain function and neurological disorders.

## Full-text entities

- **Genes:** MAPT (microtubule associated protein tau) [NCBI Gene 4137] {aka DDPAC, FTD1, FTDP-17, MAPTL, MSTD, MTBT1}, SIRPA (signal regulatory protein alpha) [NCBI Gene 140885] {aka BIT, CD172A, MFR, MYD-1, MYD1, P84}, Nf2 (neurofibromin 2) [NCBI Gene 18016] {aka merlin}, PLCB1 (phospholipase C beta 1) [NCBI Gene 23236] {aka DEE12, EIEE12, PI-PLC, PLC-154, PLC-I, PLC-beta-1}, Ctsb (cathepsin B) [NCBI Gene 13030] {aka APPM, CB}, EGFR (epidermal growth factor receptor) [NCBI Gene 1956] {aka ERBB, ERBB1, ERRP, HER1, NISBD2, NNCIS}, MACROH2A2 (macroH2A.2 histone) [NCBI Gene 55506] {aka H2AFY2}, PEX14 (peroxisomal biogenesis factor 14) [NCBI Gene 5195] {aka NAPP2, PBD13A, Pex14p, dJ734G22.2}, PALM (paralemmin) [NCBI Gene 5064] {aka PALM1}, Dcx (doublecortin) [NCBI Gene 13193] {aka Dbct}, Rp2 (retinitis pigmentosa 2 homolog) [NCBI Gene 19889] {aka Rp2h}, S1PR1 (sphingosine-1-phosphate receptor 1) [NCBI Gene 1901] {aka CD363, CHEDG1, D1S3362, ECGF1, EDG-1, EDG1}, Nefl (neurofilament, light polypeptide) [NCBI Gene 18039] {aka CMT2E, NF-L, NF68, Nfl}, MECP2 (methyl-CpG binding protein 2) [NCBI Gene 4204] {aka AUTSX3, MRX16, MRX79, MRXS13, MRXSL, PPMX}, Cck (cholecystokinin) [NCBI Gene 12424], KCNA2 (potassium voltage-gated channel subfamily A member 2) [NCBI Gene 3737] {aka DEE32, EIEE32, HBK5, HK4, HUKIV, KV1.2}, Itga3 (integrin alpha 3) [NCBI Gene 16400] {aka CD49C, GAPB3}, CABP1 (calcium binding protein 1) [NCBI Gene 9478] {aka CALBRAIN, HCALB_BR}, Sptbn2 (spectrin beta, non-erythrocytic 2) [NCBI Gene 20743] {aka Spnb3}, LAMB2 (laminin subunit beta 2) [NCBI Gene 3913] {aka LAMS, NPHS5, PIERS}, Dlg4 (discs large MAGUK scaffold protein 4) [NCBI Gene 13385] {aka Dlgh4, PSD-95, PSD95, SAP90, SAP90A}, LMAN2L (lectin, mannose binding 2 like) [NCBI Gene 81562] {aka MRD69, MRT52, VIPL}, EPN1 (epsin 1) [NCBI Gene 29924], SHANK1 (SH3 and multiple ankyrin repeat domains 1) [NCBI Gene 50944] {aka SPANK-1, SSTRIP, synamon}, DMD (dystrophin) [NCBI Gene 1756] {aka BMD, CMD3B, DXS142, DXS164, DXS206, DXS230}, CDC37 (cell division cycle 37, HSP90 cochaperone) [NCBI Gene 11140] {aka P50CDC37}, Tubb4b (tubulin, beta 4B class IVB) [NCBI Gene 227613] {aka 4930542G03Rik, Tubb2c, Tubb2c1}, EIF2AK2 (eukaryotic translation initiation factor 2 alpha kinase 2) [NCBI Gene 5610] {aka PKR, PPP1R83, PRKR}, SLC1A2 (solute carrier family 1 member 2) [NCBI Gene 6506] {aka DEE41, EAAT2, EIEE41, GLT-1, GLT1, HBGT}, PPARG (peroxisome proliferator activated receptor gamma) [NCBI Gene 5468] {aka CIMT1, FPLD3, GLM1, NR1C3, PPARG1, PPARG2}, IGHV3OR16-7 (immunoglobulin heavy variable 3/OR16-7 (pseudogene)) [NCBI Gene 28309] {aka IGHV3/OR16-7, IGHV3OR167}, JAM3 (junctional adhesion molecule 3) [NCBI Gene 83700] {aka JAM-2, JAM-3, JAM-C, JAMC}, BGLAP (bone gamma-carboxyglutamate protein) [NCBI Gene 632] {aka BGP, OC, OCN}, CAMSAP3 (calmodulin regulated spectrin associated protein family member 3) [NCBI Gene 57662] {aka KIAA1543, NEZHA, PPP1R80}, SYN1 (synapsin I) [NCBI Gene 6853] {aka EPILX, EPILX1, MRX50, SYN1a, SYN1b, SYNI}, TJP2 (tight junction protein 2) [NCBI Gene 9414] {aka C9DUPq21.11, DFNA51, DUP9q21.11, FHCA1, PFIC4, X104}, ARHGEF11 (Rho guanine nucleotide exchange factor 11) [NCBI Gene 9826] {aka GTRAP48, PDZ-RHOGEF}, TACR2 (tachykinin receptor 2) [NCBI Gene 6865] {aka NK2R, NKNAR, SKR, TAC2R}, Shank3 (SH3 and multiple ankyrin repeat domains 3) [NCBI Gene 58234] {aka Spank-2, proSAP2}, CDKN2A (cyclin dependent kinase inhibitor 2A) [NCBI Gene 1029] {aka ARF, CAI2, CDK4I, CDKN2, CMM2, INK4}, CAMK2A (calcium/calmodulin dependent protein kinase II alpha) [NCBI Gene 815] {aka CAMKA, CaMKIINalpha, CaMKIIalpha, MRD53, MRT63}, PAK1 (p21 (RAC1) activated kinase 1) [NCBI Gene 5058] {aka IDDMSSD, PAKalpha, alpha-PAK, p65-PAK}, Gh (growth hormone) [NCBI Gene 14599] {aka Gh1, Ghb1}, SLC27A4 (solute carrier family 27 member 4) [NCBI Gene 10999] {aka ACSVL4, FATP4, IPS}, Ntrk2 (neurotrophic tyrosine kinase, receptor, type 2) [NCBI Gene 18212] {aka GP145-TrkB/GP95-TrkB, Tkrb, trk-B, trkB}, FMNL1 (formin like 1) [NCBI Gene 752] {aka C17orf1, C17orf1B, FHOD4, FMNL, KW-13}, BMAL1 (basic helix-loop-helix ARNT like 1) [NCBI Gene 406] {aka ARNTL, ARNTL1, BMAL1c, JAP3, MOP3, PASD3}, TPBG (trophoblast glycoprotein) [NCBI Gene 7162] {aka 5T4, 5T4AG, M6P1, WAIF1}, Eif4a3 (eukaryotic translation initiation factor 4A3) [NCBI Gene 192170] {aka 2400003O03Rik, Ddx48, eIF4A-III, mKIAA0111}, LYRM4 (LYR motif containing 4) [NCBI Gene 57128] {aka C6orf149, CGI-203, COXPD19, ISD11}, Pex11g (peroxisomal biogenesis factor 11 gamma) [NCBI Gene 69129] {aka 1810022F11Rik, 1810049N02Rik, Pex11c, Pex11gamma}, POSTN (periostin) [NCBI Gene 10631] {aka OSF-2, OSF2, PDLPOSTN, PN}, Tubb1 (tubulin, beta 1 class VI) [NCBI Gene 545486] {aka 2810484G07Rik, M(beta)1}, NCK2 (NCK adaptor protein 2) [NCBI Gene 8440] {aka GRB4, NCKbeta}, HK1 (hexokinase 1) [NCBI Gene 3098] {aka CNSHA5, HK, HK1-ta, HK1-tb, HK1-tc, HKD}, EIPR1 (EARP complex and GARP complex interacting protein 1) [NCBI Gene 7260] {aka EIPR-1, TSSC1}, TSC1 (TSC complex subunit 1) [NCBI Gene 7248] {aka LAM, TSC}, BIN1 (bridging integrator 1) [NCBI Gene 274] {aka AMPH2, AMPHL, CNM2, SH3P9}, PRKCG (protein kinase C gamma) [NCBI Gene 5582] {aka PKC-gamma, PKCC, PKCG, PKCI(3), PKCgamma, SCA14}, WFS1 (wolframin ER transmembrane glycoprotein) [NCBI Gene 7466] {aka CTRCT41, WFRS, WFS, WFSL}
- **Diseases:** CC (MESH:D061085), hepatic/renal insufficiency (MESH:D048550), multiple sclerosis (MESH:D009103), brain injury (MESH:D001930), Huntington's disease (MESH:D006816), FL (MESH:D001927), myocardial infarction (MESH:D009203), synaptic dysfunction (MESH:C536122), dysfunction (MESH:D006331), OC (MESH:D009901), Parkinson's disease (MESH:D010300), systemic diseases (MESH:D034721), callosal agenesis (MESH:D058540), inflammation (MESH:D007249), metabolic (MESH:D008659), pneumonia (MESH:D011014), amyotrophic lateral sclerosis (MESH:D000690), viral toxicity (MESH:D014777), THA damage (MESH:D020263), psychosis (MESH:D011618), amyloid (MESH:C000718787), intracranial pathologies (MESH:D005598), Congenital disorders (MESH:D009358), diabetes mellitus (MESH:D003920), cytokine release syndrome (MESH:D000080424), AD (MESH:D000544), neurological disorders (MESH:D009461), atherosclerosis (MESH:D050197), VT (MESH:D002551), depression (MESH:D003866), cortical dysfunction (MESH:D054220), bipolar disorder (MESH:D001714), cognitive decline (MESH:D003072), dehydration (MESH:D003681), sleep-wake disturbances (MESH:D012893), OL (MESH:D004828), craniopharyngiomas (MESH:D003397), periventricular white matter injury (MESH:D056784), seizure (MESH:D012640), major depression (MESH:D003865), axonal degeneration (MESH:D009410), substance abuse (MESH:D019966), congenital, treatment-resistant disorders (MESH:D061218), atrophy (MESH:D001284), septo-optic dysplasia (MESH:D025962), epilepsy (MESH:D004827), inflammatory damage (MESH:D018746), autism spectrum disorder (MESH:D000067877), neurological diseases (MESH:D020271), congenital hydrocephalus (MESH:D006849), alcohol (MESH:D000437), brain atrophy (MESH:C566985), schizophrenia (MESH:D012559), neurodevelopmental delay (MESH:D006968), BS (MESH:D020295), autoimmune diseases (MESH:D001327), traumatic brain injury (MESH:D000070642), cerebral ischemic stroke (MESH:D020521), Rett syndrome (MESH:D015518), gliomas (MESH:D005910)
- **Chemicals:** Hematoxylin (MESH:D006416), Dithiothreitol (MESH:D004229), DAB (MESH:C000469), serotonin (MESH:D012701), paraffin (MESH:D010232), H2O (MESH:D014867), hydrogen peroxide (MESH:D006861), alkaloids (MESH:D000470), norepinephrine (MESH:D009638), THA (MESH:D013619), ethanol (MESH:D000431), trifluoroethanol (MESH:D014270), corticosterone (MESH:D003345), amine (MESH:D000588), ATP (MESH:D000255), amphetamine (MESH:D000661), acetonitrile (MESH:C032159), dopamine (MESH:D004298), ACN (MESH:C084683), ROS (-), catecholamine (MESH:D002395), TFE (MESH:D011138), metal (MESH:D008670), citrate (MESH:D019343), ceramide (MESH:D002518), xylene (MESH:D014992), ADP (MESH:D000244), Formalin (MESH:D005557), TFA (MESH:D014269), lipid (MESH:D008055), calcium (MESH:D002118), iodoacetamide (MESH:D007460), fatty acid (MESH:D005227), glucose (MESH:D005947), formic acid (MESH:C030544)
- **Species:** Homo sapiens (human, species) [taxon 9606], Rattus norvegicus (brown rat, species) [taxon 10116], Mus musculus (house mouse, species) [taxon 10090], Danio rerio (leopard danio, species) [taxon 7955]

## Full text

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## Figures

6 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12868004/full.md

## References

2 references — full list in the complete paper: https://tomesphere.com/paper/PMC12868004/full.md

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Source: https://tomesphere.com/paper/PMC12868004