Table 2.
Markers to label the TME of cleared tumors.
| Antibody | RRID/clone | Clearing | Target | Tumor |
|---|---|---|---|---|
| α-SMA | AB_476977 | CUBIC | Perivascular cells | A549 orthotopic lung tumors (36), OS-RC-1 brain metastases in whole cleared mice (41) |
| α-SMA | AB_476746 | Fructose | Perivascular cells | MMTV-Her2/Neu mammary tumor (38) |
| CD3 | Clone LN10 | CLARITY | T cells | Breast cancer (39) |
| CD3 | AB_389323 | ECi | T cells | HNSCC (40) |
| CD8 | Clone 2.43 | Fructose | T cells | Mammary tumor (38) |
| CD31 | AB_726362 | Glycerol, TDE | Blood endothelium | Orthotopic glioblastoma (42) Melanoma xenografts (43) |
| CD31 | AB_312909 | Fructose | Blood vessel endothelium | MMTV-Her2/Neu and 4T1 mammary tumors (38) |
| CD31 | AB_61339 | FocusClear | Blood vessel endothelium | Human colon adenocarcinoma biopsies (14) |
| CD34 | Clone QBEnd/10 | FocusClear | Blood vessel endothelium | Human colon adenocarcinoma biopsies (14) |
| CD42c | Cat. no. X649 Emfret Analytics | CUBIC | Platelets | A549 orthotopic lung tumors (36) |
| CD66b | AB_2893284 | ECi | Neutrophils | Human HNSCC (40) |
| Factor VIII | Agilent | CUBIC, BABB, TDE | Coagulation cascade | Melanoma xenografts (43) |
| GFAP | AB_10013382 | THF+nycodenz, CUBIC, iDISCO | Astrocytes | U251-MG orthotopic GBM (28, 29) |
| Iba-1 | AB_2687911 | CUBIC | Macrophages | Lung adenocarcinoma (A549 IV) (36) |
| K5 | AB_869890 | iDISCO | Myoepithelial cells | Prostate DCIS (22) |
| K7 | Clone EPR1619Y | CUBIC | Luminal and glandular epithelia | Uterine adenomyosis (26) |
| K8/18 | AB_141750 | iDISCO | Luminal cells | Prostate DCIS (22) |
| K8 | AB_531826 | FLASH | Tumor cells, airways, alveolar cells | Lungs with MMTV-PyMT metastases (23) |
| K19 | AB_2133570 | FLASH | Ductal epithelia | Pancreas, lung and liver biliary tree with transformed cells (27) |
| Lyve-1 | AB_881387 | DCM DBE | Lymphatic vessels | Human bladder cancer FFPE (44) |
| Lyve-1 | AB_301509 | RapiClear 1.52 | Lymphatic vessels | Mouse and human PanIN and PDAC (45) |
| MBP | AB_956157 | CUBIC, iDISCO | Myelin | GBM (29) |
| MECA-79 | AB_395099 | Dent bleach and BABB | High endothelial venules | Fibrosarcoma and 4T1 xenografts (46) |
| Podoplanin | AB_2565183 | RapiClear 1.52 | Lymphatic vessels | Mouse and human PanIN and PDAC (45) |
| Podoplanin | AB_2268062 | FLASH | Alveolar cells | Lungs with MMTV-PyMT metastases (11) |
| SFTPC | AB_1857425 | FLASH | Alveolar type I cells | Lungs with MMTV-PyMT metastases (11) |
| VEGFR | AB_2167245 | CUBIC | Angiogenesis | A549 orthotopic lung tumors (36) |
| Vimentin | AB_11212377 | RapiClear | Glioma cell processes | Glioma invasion assay in brain slices in vitro ( 31, 32 ) |
α-SMA, alpha-smooth muscle actin; CUBIC, clear, unobstructed brain/body imaging cocktails and computational analysis; CD, cluster of differentiation; MMTV, murine mammary tumor virus; CLARITY, clear lipid-exchanged acrylamide-hybridized rigid imaging / immunostaining / in situ-hybridization-compatible tissue hydrogel; ECi, ethyl cynammate; HNSCC, head and neck squamous cell carcinoma; TDE, thiodiethanol; BABB, benzyl alcohol/benzyl benzoate; THF, tetrahydrofuran; iDISCO, immunolabeling-enabled imaging of solvent-cleared organs; GFAP, glial fibrillary acidic protein; GBM, glioblastoma; Iba-1, allograft inflammatory factor 1; IV, intravenous; K, cytokeratin; DCIS, ductal carcinoma in situ; FLASH, fast light-microscopic analysis of antibody-stained whole organs; PyMT, polyomavirus middle-T; Lyve-1, link domain-containing hyaladherin; DCM, dichloromethane; DBE, dibenzyl ether; FFPE, formalin-fixed paraffin-embedded; PanIN, pancreatic intraepithelial neoplasia; PDAC, pancreatic ductal adenocarcinoma; MBP, myelin basic protein; MECA-79, peripheral node addressin antibody; SFTPC, surfactant protein C; VEGFR, vascular endothelial growth factor. Clone or catalog number and/or provider were indicated for antibodies for which RRID identifier was not available.