TABLE 4.

Upregulated genes and their potential pro-osseointegration roles under basal conditions.

Gene	Role	Pro-osteointegrative role in early phase
MMP1	Matrix metalloproteinase involved in ECM degradation	Promotes extracellular matrix remodeling, facilitating cell migration and early bone–implant interface adaptation
MMP3	Stromelysin involved in ECM turnover and growth factor activation	Supports matrix remodeling and release of bioactive factors enhancing tissue integration
CXCL1	Chemokine involved in neutrophil recruitment and inflammatory signaling	Modulates early immune signaling and chemotactic environment at the implant interface
CXCL5	Chemokine involved in angiogenesis and leukocyte recruitment	Promotes vascular and immune cell recruitment supporting early healing responses
CXCL6	Chemokine with pro-inflammatory and angiogenic activity	Contributes to immune modulation and early regenerative microenvironment formation
BUB1	Mitotic checkpoint kinase regulating chromosome segregation	Indicates controlled proliferation supporting early tissue expansion and repair
TOPBP1	DNA replication and damage response factor	Ensures genomic stability during active cell cycling in early adaptation phase
CHEK2	DNA damage checkpoint kinase	Regulates stress response and controlled proliferation under biomaterial-induced stress
RAD17	DNA damage checkpoint loading factor	Supports genome integrity during early proliferative response
FANCM	DNA repair and replication stress response protein	Maintains genomic stability during increased cellular activity
TXN	Thioredoxin, redox regulator	Maintains redox balance and supports survival in early oxidative microenvironment
ERO1L	Oxidoreductase involved in disulfide bond formation	Supports protein folding and oxidative metabolism during adaptation
HIGD1A	Mitochondrial stress response protein	Promotes mitochondrial adaptation and cell survival under stress
RAB8B	Vesicle trafficking and membrane transport regulator	Supports intracellular trafficking and membrane remodeling at cell–material interface
RAB27B	Regulates exosome secretion and vesicular transport	Contributes to intercellular communication via extracellular vesicle release
SEC62	Protein translocation into endoplasmic reticulum	Supports protein processing and secretory pathway activation
COG5	Golgi trafficking and glycosylation complex component	Ensures proper protein processing and extracellular matrix organization
COG6	Golgi trafficking and vesicle transport	Supports secretion and ECM-related protein maturation
SUZ12	Epigenetic regulator (PRC2 complex component)	Regulates gene silencing and early lineage commitment programs
HMGA1	Chromatin architectural regulator	Facilitates transcriptional reprogramming and stem cell plasticity
HMGA2	Stemness and proliferation-associated chromatin factor	Promotes early proliferative and undifferentiated cellular state favorable to repair
METTL14	RNA methylation (m6A modification) regulator	Modulates post-transcriptional regulation of genes involved in differentiation and adaptation