CSF proteomic analysis of Alzheimer's disease subtypes

Classification

• five different subtypes of AD identified by CSF proteomics of 1038 proteins

subtype 1

• characterized by proteins related to neuronal hyperplasticity
  • enriched with TREM2 R47H
  • longest average survival time 8.9 years
  • enrichment in TREM2 & variants in LILRB2, RHOH & APP
  • 3 of 4 PSEN1 carriers, 3 of 4 NCK2 carriers
    • LILRB2 mediates TREM2 signaling
    • RHOH & NCK2 encode signaling molecules downstream from TREM2 that influence cytoskeletal rearrangement of microglia

subtype 2

• characterized by innate immune activation & neuronal hypoplasticity
  • along with subtype 5, highest risk of MCI progression to dementia
  • many proteins increased in subtype 2 are specific to microglia
    • these proteins are associated with innate immune activation
      • complement proteins: C1QA, C1QB, C1QC, C1S, C1R
      • APOE, LPL
    • increased microglial Tyro3, Axl, MER, MERTK, GAS6
    • increased PYCARD specific to subtype 2
      • released by microglia with NLRP3 inflammasome activation
      • can form ASC specs, fibrils that worsen amylid aggregation & induce tau phosphorylation
    • proteins related to neuron-microglial signaling increased in subtype 2
      • CSF1, CSF1R, CX3CL1
    • AD variants associated with subtype 2 are involved in immune processes
      • IDUA, CLNK, SCIMP

subtype 3

• characterized by RNA dysregulation*
  • shortest average survival time 5.6 years
  • proteins with increased CSF levels are associated with cytoskeletal organization, axonal transport & proteosome & protein folding
  • specifically increased in subtype 3
    • heterologous nuclear ribonucleoproteins & other RNA-binding protein
  • decreased in subtype 3: STMN2
  • increased in subtype 3: KLF4, TAF1, MYC
  • genetic risk factors: BIN1, TREM2(R62H), SPDYE3, SNX1, KAT8

subtype 4

• characterized by choroid plexus dysfunction
  • choroid plexus dysfunction may lead to diminished clearance mechanisms
  • lowest risk of MCI progression to dementia
  • worse cerebral atrophy than subtypes 1,3 & 5 with specific involvement of anterior cingulate areas
  • many proteins increased in subtype 4 are specific to microglia or other immune cells
    • subset of these increased proteins is found in the choroid plexus of the lateral ventricles
      • TTR, SPARC
      • extracellular matrix proteins: DCN, LUM, COLA12
  • proteins increased in subtype 4 are enriched in fibroblasts that produce extracellular matrix proteins & provide support for the choroid plexus
  • other proteins increased in subtype 4 include cytokines CCL2, CCL21 & CCL15 chemotactic for monocytes & T-cells
  • proteins decreased in subtype 4 are related to axonal outgrowth & synaptic plasticity (example BDNF) suggesting decreased neuroplasticity
  • processes include cell adhesion & BMP & SMAD pathways involved in choroid plexus development
  • genetic risk variants: ABCA7, PICALM, IL-34, CLNK enriched in subtype 4
    • ABCA7 & IL-34 are expressed in choroid plexus
    • PICALM is expressed in blood-CSF barrier
    • ABCA7 & PICALM play a role in lipid metabolism & may be associated with amyloid clearance in connection with LRP1

subtype 5

• characterized by blood-CSF barrier dysfunction
  • along with subtype 2, highest risk of MCI progression to dementia
  • increased CSF levels of proteins that leak into the CSF when the blood-CSF barrier is compromised: albumin, fibrinogen, plasminogen, prothrombin, immunoglobulins
  • pathways associated with increased proteins include coagulation, humoral immunity, acute inflammation
  • no increase in transcription factors for increased CSF proteins
  • highest level of MRI microbleeds of the 5 subtypes
  • 61% of proteins with decreased levels associated with neuroplasticity & the transcription factors SUZ12 & REST suggesting decreased neuroplasticity like subtype 4
  • neuroplasticity can be impaired by leakage of blood protein including fibrin, specifically elevated in subtype 5
  • additional proteins altered in subtype 5 are associated with pericytes,
    • diminished levels of PDGFRB, CDH2, MFGE8, HTRA1, LAMB1, EDN1, LRP1, JAM3
    • increased levels of CDH5, ANXA3, ICAM1, AMBPP, VWF, PTPRB
    • all associated with deposition of blood proteins in brain parenchyma
    • diminished PDGFRB may be associated with loss of pericytes, cells that normally cover capillaries
    • PDGFRB is also expressed in arterial smooth muscle cells
  • genetic risk characterized by enrichment in IL-34, ECHDC3 & APP variants
    • IL-34 also associated with subtype 4 suggesting it contributes to AD pathogenesis through mechanisms associated with the blood-CSF barrier
    • ECHDC3 is associated with lipid metabolism
    • APP variants are associated with cerebral amyloid angiopathy & loss of vascular integrity *

* RNA dysregulation has been observed in frontotemporal dementia

Expression

• CSF protein expression in Alzheimer's disease subtypes

Protein	Controls	subtype 1	subtype 2	subtype 3	subtype 4	subtype 5
total tau	199	592	765	882	301	469
p-tau 181	0	3.4	5.1	5.0	0.6	2.1
BACE1	1930	2200	2480	2190	1390	1820
Abeta40	7140	7830	8520	6820	4610	5940
NRGN	317	488	634	561	244	371
NEFL	360	447	620	630	454	594
VMAP2	162	196	233	189	100	142

* values in pg/mL

* NRGN = neurogranin, NEFL = neurofilament light polypeptide, VAMP2 = synaptobrevin-2

Pathology

• microbleed count on MRI

Controls	subtype 1	subtype 2	subtype 3	subtype 4	subtype 5
0.91	1.89	1.16	1.65	2.07	4.40

Management

• CSF proteomic subtyping may be useful to select patients for specific therapeutic treatment if & when such clinically useful treatment becomes available

More general terms

• proteomic analysis (proteomics)
• laboratory evaluation of Alzheimer's disease