ADC	Antibody–drug conjugate
AKT	Protein kinase B
AP-1	Activator protein 1
APOBEC3A	Apolipoprotein B mRNA editing enzyme catalytic subunit 3A
CAF	Cancer-associated fibroblast
CDK2	Cyclin-dependent kinase 2
CDK4/6	Cyclin-dependent kinases 4 and 6
CDK4/6i	CDK4/6 inhibitor(s)
CITUP	Clonal inference in tumors using phylogeny
CODEX	CO-Detection by indEXing
CSC	Cancer stem cell
ctDNA	Circulating tumor DNA
DCIS	Ductal carcinoma in situ
DNA	Deoxyribonucleic acid
DNMT	DNA methyltransferase
DTP	Drug-tolerant persister
ECM	Extracellular matrix
EGFR	Epidermal growth factor receptor
EMT	Epithelial-to-mesenchymal transition
ER	Estrogen receptor
ER+	Estrogen receptor-positive
ET	Endocrine therapy
EZH2	Enhancer of zeste homolog 2
FAD	Flavin adenine dinucleotide
FAO	Fatty acid oxidation
FGFR	Fibroblast growth factor receptor
GPX4	Glutathione peroxidase 4
H3K4me3	Histone H3 lysine 4 trimethylation
H3K27me3	Histone H3 lysine 27 trimethylation
H4K20me3	Histone H4 lysine 20 trimethylation
HDAC	Histone deacetylase
HER2	Human epidermal growth factor receptor 2
HER2+	HER2-positive
HGF	Hepatocyte growth factor
HIF-1α	Hypoxia-inducible factor 1 alpha
HLA-G	Human leukocyte antigen G
HMOX1	Heme oxygenase 1
ICI	Immune checkpoint inhibitor
IGF-1R	Insulin-like growth factor 1 receptor
IL-6	Interleukin 6
IL-10	Interleukin 10
IMC	Imaging mass cytometry
ISR	Integrated stress response
ITH	Intra-tumoral heterogeneity
JAK	Janus kinase
KDM5A/B	Lysine demethylase 5A/B (JARID1A/B)
KDM6A/B	Lysine demethylase 6A/B
KRT5/14/17	Keratin 5/14/17
LAM	Lipid-associated macrophage
LSD1	Lysine-specific demethylase 1 (KDM1A)
MAPK	Mitogen-activated protein kinase
MDR1	Multidrug resistance protein 1 (P-glycoprotein)
MERFISH	Multiplexed error-robust fluorescence in situ hybridization
MET	Mesenchymal–epithelial transition factor (hepatocyte growth factor receptor)
MHC	Major histocompatibility complex
MOFA+	Multi-Omics Factor Analysis
MPC	Metastatic precursor cell
mTOR	Mechanistic target of rapamycin
NF-κB	Nuclear factor kappa-light-chain-enhancer of activated B cells
NRF2	Nuclear factor erythroid 2-related factor 2 (NFE2L2)
OXPHOS	Oxidative phosphorylation
PD-1	Programmed cell death protein 1
PD-L1	Programmed death-ligand 1
PDX	Patient-derived xenograft
P-gp	P-glycoprotein (MDR1/ABCB1)
PI3K	Phosphatidylinositol 3-kinase
PINK1	PTEN-induced kinase 1
PIK3CA	Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha
PRC2	Polycomb repressive complex 2
RB1	Retinoblastoma protein 1
RNA	Ribonucleic acid
ROS	Reactive oxygen species
RTK	Receptor tyrosine kinase
SAM	S-adenosylmethionine
scATAC-seq	Single-cell assay for transposase-accessible chromatin sequencing
scCUT&Tag	Single-cell cleavage under targets and tagmentation
scRNA-seq	Single-cell RNA sequencing
SLC7A11	Solute carrier family 7 member 11 (xCT)
ST	Spatial transcriptomics
STAT3	Signal transducer and activator of transcription 3
TAM	Tumor-associated macrophage
TCA	Tricarboxylic acid
T-DXd	Trastuzumab deruxtecan
TER	Tumor clonal evolution rate
TGF-β	Transforming growth factor beta
TIGIT	T-cell immunoreceptor with Ig and ITIM domains
TIM-3	T-cell immunoglobulin and mucin domain-containing protein 3
TME	Tumor microenvironment
TNBC	Triple-negative breast cancer
VAF	Variant allele frequency
WNN	Weighted nearest neighbor
xCT	Cystine/glutamate antiporter (SLC7A11)
α-KG	Alpha-ketoglutarate