Table 2 Antibiotic treatment significantly reduces neural proteomic expression at 4-Weeks post-implantation

ATG12

autophagy related 12

Autophagy: autophagosome protein (KEGG:04140)^111,112,113

-

-

-

-

-

-

ATG5

autophagy related 5

Autophagy: autophagosome protein (KEGG:04140)^111,112,113

-

BAG3

BCL2-associated athanogene 3

Autophagy: promotes autophagy through increasing glutamine consumption¹¹⁴

-

-

-

-

CD11b

integrin alpha M

Microglia, macrophages, peripheral immune: expressed in activated microglia, macrophages, and dendritic cells; plays a role in cell-cell adhesion during inflammation^115,116

-

CD163

CD163 antigen

M2 Macrophage, Macrophage, Myeloid, Myeloid Suppression: Marker that indicates transition from pro-inflammatory M1 to M2 anti-inflammatory macrophage phenotype⁴²

-

CD31

platelet/endothelial cell adhesion molecule 1

Endothelial cell marker, mediates BBB permeability, specifically permeability to immune cells¹¹⁶

-

-

-

-

-

CD39

ectonucleoside triphosphate diphosphohydrolase 1

Myeloid Suppression: Expressed by microglia and involved in both innate and adaptive immunity¹¹⁷

-

CD40

CD40 antigen

.General marker for myeloid cells and myeloid activation. Also plays a role in neuronal development, maintenance, and protection^118,119

-

-

-

CD45

protein tyrosine phosphatase, receptor type, C

Microglia, macrophages, peripheral immune: Expressed highly in macrophages, less so in microglia, involved in adhesion and T-cell activation¹²⁰

-

-

CD68

CD68 antigen

Macrophage, Microglia, Myeloid: Highly expressed in macrophages and myeloid cells. General marker for inflammation¹²¹

-

-

-

-

-

-

-

CSF1R

colony stimulating factor 1 receptor

Microglia: A major regulator of microglial development and homeostasis¹²².

-

-

-

-

CTSD

Cathepsin D

Astrocytes, microglia, macrophage, peripheral immune: Regulates proteolysis in lysosomes; expressed in neurons, astrocytes, microglia, and macrophages^{123,124,125,126}

-

GPNMB

glycoprotein (transmembrane) nmb

Disease-Associated Microglia: Highly expressed in microglia and macrophages during neuroinflammation and neurodegenerative disease states¹²⁷

-

-

-

-

ITGAX

Integrin alpha x

Microglia, macrophages, peripheral immune: integrin protein found in microglia, macrophages, dendritic cells, and T-cells¹¹⁶; hypothesized to be neuroprotective^128,129

-

Ki-67

N/A

Astrocytes, microglia, macrophages, peripheral immune: Marker of cell proliferation^116,130

-

MAP2

microtubule-associated protein 2

Neuronal health: Cytoskeletal/microtubule structure¹³¹

-

-

-

-

-

-

-

MerTK

MER proto-oncogene tyrosine kinase

Astrocytes, microglia, macrophages, peripheral immune: anti-inflammatory, involved in phagocytosis of apoptotic cells; also plays a role in maintaining BBB integrity^132,133,134

-

NeuN

RNA binding protein, fox-1 homolog (C. elegans) 3

Neuronal health: Binds to DNA in mature neurons, serves as a marker for neuronal nuclei¹³⁵

-

-

NfL

neurofilament, light polypeptide

Neuronal health: Cytoskeletal protein found in neurons¹³⁶

-

-

-

OLIG2

oligodendrocyte transcription factor 2

Neuronal health: Promotes myelin production in oligodendrocytes and differentiation¹³⁷

-

-

-

P62

sequestosome 1

Autophagy: Tags protein inclusion bodies and delivers them to autophagosomes for degradation¹³⁸

-

-

-

-

PLA2G6

phospholipase A2, group VI

Autophagy: Associated with Parkinson’s and other neurodegenerative diseases. Essential for metabolism of phospholipids, proper mitochondrial function, inhibition of apoptosis^139,140.

-

-

-

-

SYP

synaptophysin

Neuronal health: synaptic vesicle protein¹⁴¹

-

-

-

-

-

-

TFEB

transcription factor EB

Autophagy: promotes transcription of genes that lead to autophagosome formation¹⁴²

-

-

TMEM119

transmembrane protein 119

Microglia: Marker for microglia, specifically resting¹¹⁵

-

-

-

-

ULK1

unc-51 like kinase 1

Autophagy: forms protein complex that initiates autophagosome formation¹⁴³

-

-

-

-

-

-

-

VIM

vimentin

Astrocytes: Intermediate filament protein regulating astrocyte structure during gliosis, also expressed in endothelial cells^144,145,146

-

-

-

-

VPS35

Vacuolar protein sorting 35

Autophagy: forms protein complex that initiates autophagosome formation¹⁴³

-

-