Article Figures & Data
Figures
- Figure 1.
Proportion and diversity of infiltrated T lymphocytes in breast tumor and other tissues. A, Comparison of infiltration proportion of T lymphocytes in tumor and nontumor breast tissue of 14 patient samples analyzed by IHC (P = 0.0023). B, Shannon diversity index of LN, nontumor, and tumor tissue. *p < 0.01, ***p < 0.001 according to Mann-Whitney U test.
- Figure 2.
Shared clones between different tissues. The percentage was calculated by dividing the total clones of each tissue by the shared clones. A, The proportion of shared clones between LN and nontumor tissue. B, The proportion of shared clones between LN and tumor tissue. ***p < 0.001 according to Mann-Whitney U test.
- Figure 3.
Percentage of T-cell clones of tumor and LN tissue in different degree of expansion for each patient. Colored bars represent the percentage of T-cell clones in each proportion. (Expanded clone: > 0.1%; medium clone: 0.01%–0.1%; small clone: < 0.01%). A, Total T-cell clones of LN tissue. B, Total T-cell clones of tumor tissue. C, T-cell clones of LN shared with tumor tissue. D, T-cell clones of tumor tissue shared with LN tissue. # Node-positive patients with high LNR (>70%). The patients were ordered in sequence of their percentage of expanded clones for the total T cells in the LNs, from the smallest to the largest.
- Figure 4.
Correlation of node positivity with T lymphocyte ratio in tumor and expansion in LN. A, Comparison of infiltration proportion of T lymphocytes in tumor tissue of LN-positive patients and LN-negative patients (P = 0.1416). B, Comparison of infiltration proportion of T lymphocytes in tumor tissue of patients with high LNR and LN-negative patients (P = 0.00022). C, Comparison of T-cell expansion in LN for node-negative, node-positive, and high LNR patients (*, P < 0.05; **, P < 0.01; ***, P < 0.001, according to the Mann–Whitney U test; LNR, lymph node ratio).
- Figure 5.
The Pearson correlation coefficients between tumor and nontumor in luminal-like and basal-like breast cancer subtypes. A, The comparison in the main cohort. B, The comparison combining the main cohort with the validation cohort (*, P < 0.05 according to the Mann–Whitney U test).
Tables
- Table 1.
The pathological data of the discovery cohort in the study
Patient ID ER HER2 PR Ki-67 Lymph node ratio Tumor subtype Tumor infiltration (%) Nontumor infiltration (%) BC0001A 3+ — 2+ 20% 0/16 Luminal B NA NA BC0002A 1+ + — 35% 0/6 Luminal B 10 2 BC0003A — — — 30% 1/14 Basal-like 20 0.1 BC0004A 3+ — 3+ 10% 0/16 Luminal A 8 1 BC0005A 3+ + 2+ 5% 1/18 Luminal B 0.3 0.1 BC0006A — — — 95% 0/5 Basal-like 25 0.5 BC0007A — — — 20% 0/23 Basal-like 2 1 BC0008A — + — 40% 0/29 HER2 enriched NA NA BC0009A 1+ — — 30% 14/18 Luminal B 30 0.1 BC0010A — — — 50% 15/15 Basal-like 40 0.2 BC0011A 3+ — 2+ 5% 0/20 Luminal A 8 0.1 BC0012A 2+ + 1+ 28% 0/16 Luminal B 3 1 BC0013A — — — 50% 0/18 Basal-like 2 0.2 BC0014A 3+ — 3+ 28% 0/23 Luminal B 0.2 2 BC0015A — — — 60% 0/5 Basal-like 15 3 BC0016A 3+ — 2+ 10% 1/10 Luminal A 12 0.1 NOTE: NA means this sample was not analyzed.
- Table 2.
Public TRB CDR3 clones among tumor tissues of all 16 patients
Clone_CDR3 Sample number V gene J gene ID (%) CSARSPGYEQYF 3 TRBV20-1 TRBJ2-7 BC0002A(0.0035) BC0007A(0.0163) BC0012A(0.0196) CAISESTQAYEQYF 3 TRBV10-3 TRBJ2-7 BC0005A(0.0044) BC0007A(0.0229) BC0009A(0.0200) CASSLGQSSYGYTF 3 TRBV5-1 TRBJ1-2 BC0002A(0.0038) BC0004A(0.0101) BC0011A(0.0243) CATSRDSGGLGTTDTQYF 3 TRBV15 TRBJ2-3 BC0002A(0.0006) BC0005A(1.0582) BC0006A(0.0107) CSVDAGGGGNTIYF 2 TRBV29-1 TRBJ1-3 BC0012A(0.0291) BC0013A(0.0481) CSARVGLAGADTQYF 2 TRBV20-1 TRBJ2-3 BC0005A(0.0134) BC0014A(0.0116) CASSGTGGSSNQPQHF 2 TRBV6-3 TRBV6-2 TRBJ1-5 BC0001A(0.0166) BC0009A(0.0524) CSVAGTSGRNTGELFF 2 TRBV29-1 TRBJ2-2 BC0013A(0.0160) BC0015A(0.1018) CSAREIGGGGQPQHF 2 TRBV20-1 TRBJ1-5 BC0003A(0.0204) BC0008A(0.0135) CSASPGLAGRETQYF 2 TRBV20-1 TRBJ2-5 BC0004A(0.0131) BC0013A(0.0102) CSVEEAYEQYF 2 TRBV29-1 TRBJ2-7 BC0005A(0.0453) BC0007A(0.0135) CSANFRERNSPLHF 2 TRBV20-1 TRBJ1-6 BC0005A(0.8711) BC0006A(0.0107) CASSLFQGPSYEQYF 2 TRBV7-8 TRBJ2-7 BC0001A(0.0188) BC0010A(0.0837) CSASQTDTQYF 2 TRBV20-1 TRBJ2-3 BC0002A(0.0278) BC0008A(0.0358) CASSFAASKHYEQYF 2 TRBV12-4 TRBV12-3 TRBJ2-7 BC0016A(0.0152) BC0008A(0.0352) CSASRRDGTDTQYF 2 TRBV20-1 TRBJ2-3 BC0015A(0.0171) BC0008A(0.0149) CATSLAGGETQYF 2 TRBV24/OR9-2 TRBV24-1 TRBJ2-5 BC0011A(0.0100) BC0015A(0.1671) CATSDINEQFF 2 TRBV24/OR9-2 TRBV24-1 TRBJ2-1 BC0002A(0.0123) BC0010A(0.0211) CAWSPSGGLPQYF 2 TRBV30 TRBJ2-3 BC0005A(0.4246) BC0006A(0.0113) CATSRENNEQFF 2 TRBV15 TRBJ2-1 BC0003A(0.0113) BC0005A(0.0115) CSAPGQGSGNTIYF 2 TRBV20-1 TRBJ1-3 BC0001A(0.0108) BC0013A(0.0109) CASSLVGRGDYGYTF 2 TRBV7-2 TRBJ1-2 BC0003A(0.0141) TRBV5-1 TRBJ1-2 BC0004A(0.0177) CASSATGTGANSPLHF 2 TRBV5-1 TRBJ1-6 BC0001A(0.0147) TRBV2 TRBJ1-6 BC0003A(0.1580) CASTTNTDTQYF 2 TRBV12-4 TRBV12-3 TRBJ2-3 BC0010A(0.0182) TRBV19 TRBJ2-3 BC0009A(0.0301) Note: All these clones were filtered with a TRB database of 661 healthy individuals.
Supplementary Data
- Supplementary Figure S1 - Amplification bias assessment across multiplex PCR primer mix.
- Supplementary Figure S2 - TRB repertoire diversity of lymph node, non-tumor and tumor tissue.
- Supplementary Figure S3 - Comparison of TRBV or TRBJ segment usage between tumor tissue and other two tissues.
- Supplementary Figure S4 - Shared clone frequency between lymph node and tumor tissue in lymph node and tumor tissue.
- Supplementary Figure S5 - Expanded clones (>0.1%) percentage in tumor tissue and lymph node.
- Supplementary Figure S6 - The similarity between paired lymph node, non-tumor and tumor tissue.
- Supplementary Figure Legends and Supplementary Tables 1 through 3 - Supplementary Figure Legends. Table S1. The reproducibility of IHC scoring of infiltrated T cells. Table S2. The infiltration level of CD4+ and CD8+ T cells in tumors and non-tumors. Table S3. The clinical characteristics of 49 patients.
Volume 5, Issue 2
