Tissue Collection and Patient Cohort
100 TNBC cases were reviewed and selected from the Yale University Pathology archives. Specifically, treatment-naïve cases were selected by the pathologist if there was an abundance of tumor present in the blocks for future study. Areas of invasive tumor were identified by a pathologist and circled on the whole tissue section, giving careful attention to avoid areas with admixed in situ and/or benign tissue. Patients’ demographic characteristics are described in Table 1. The Yale Human Investigation Committee approved the patient consent forms or in some cases a waiver of consent all in accordance with the ethical guidelines of the US Common Rule (protocol #9505008219).
Table-1
AA and Non-AA patient information
Characteristic
|
African American, N=491
|
Non-African American, N=511
|
p-value 2
|
Age
|
59 (47,66)
|
55 (49,66)
|
0.8
|
Ethnicity
Hispanic or Latino
Non-Hispanic
Unknown
|
1 (2%)
40 (82%)
8 (16%)
|
0(0%)
38 (75%)
13 (25%)
|
0.3
|
BMI
Unknown
|
31.0 (27.0, 35.3)
12
|
26.6 (24.0, 31.9)
12
|
0.009
|
Stage (AJCC 8th edition)
IA
IIA
IIB
IIIA
IIIB
|
17 (35%)
17 (35%)
13 (27%)
2 (4.1%)
0 (0%)
|
18 (35%)
19 (37%)
8 (16%)
4 (7.8%)
2 (3.9%)
|
0.5
|
Grade
2
3
|
6 (12%)
43 (88%)
|
10 (20%)
41 (80%)
|
0.3
|
Histology
AdenoSquamous
Fibromatoid Nodule
IDC
IDC-medullary
IDC-micropapillary
ILC
IMC
Metaplastic
Squamoid
Unknown
|
1 (2.2%)
1 (2.2%)
40 (87%)
1 (2.2%)
1 (2.2%)
0 (0%)
2 (4.3%)
0 (0%)
0 (0%)
3
|
0 (0%)
0 (0%)
44 (86%)
0 (0%)
3 (5.9%)
1 (2.0%)
1 (2.0%)
1 (2.0%)
1 (2.0%)
0
|
0.6
|
Chemotherapy
Unknown
|
37 (76%)
0
|
38 (81%)
7
|
0.5
|
XRT
Unknown
|
41 (84%)
0
|
31 (70%)
7
|
0.13
|
Follow up (years)
Unknown
|
6.1 (2.9, 11.0)
1
|
5.4 (1.9, 10.2)
0
|
0.2
|
1 Median (IQR); n (%)
2 Wilcoxon rank sum test; Fisher's exact test; Pearson's Chi-squared test
|
Experimental Design
Characterization of T cell subsets in resected tissues was performed using multiplexed quantitative immunofluorescence. We used CD45 positivity as a marker of all immune cells, including lymphoid and myeloid cells. CD14 further distinguished myeloid from lymphoid cells. Among myeloid-derived cells we sought to identify macrophages (CD68+) and more specifically alternatively activated macrophages or CD206+ cells, which may alter the disease outcome [18].
Similarly, we investigated the different immune cell types that belong to lymphoid cells; T-cells (CD3+) and B-cells (CD20+). CD3+ T-cells, were subsequently, divided into helper T-cells (CD4+) and cytotoxic T-cells (CD8+). After phenotyping typical CD3+ cells, we selected activated CD3+ cells, as high expressors of Ki67 and Granzyme B (GZMB). We used median Automated quantitative analysis (AQUA) score as the cutoff to determine high versus low Ki67/ GZMB expression and active vs dormant CD3+ cells, respectively [19]. Regulatory T-cells (Tregs) were defined by CD4 and FOXP3 a double-positive phenotype.
In order to evaluate cancer-associated fibroblasts we utilized different mesenchymal phenotype markers. Thy1+FAP+a-SMA+ phenotype represented stromal fibroblasts [20]. Since smooth muscle surrounds both breast ducts and endothelial cells, we used a CD34+COL4+vWF+ phenotype to exclude these a-SMA+ cell types that could skew our results.
Finally, we examined the level of expression of the Programmed Death-Ligand 1 (PD-L1) in tumor cells (Cytokeratin positive, CK+), stroma cells (CK-) and macrophages (CD68+). PD-L1 has a key role in tumor immune evasion and more specifically in TNBC, where incorporation of immunotherapy in the neoadjuvant setting and metastatic disease has been recently pproved [21, 22].
Antibodies, Quantitative Immunofluorescence (QIF)
Antibodies
Expression of CD45, CD14, CD8, CD20, CD68, CD206, PD-L1, THY1, FAP, CD3, Ki67, GZMB, CD4,FOXP3, a-SMA, CD34, COL4/vWF was evaluated using monoclonal antibodies as follows; for CD45: monoclonal mouse IgG1 antihuman 2B11 + PD7/26 (DAKO, Carpinteria, CA), for CD14: monoclonal rabbit antihuman D7A2T (Cell Signaling Technology/CST, Danvers, MA), for CD8: monoclonal mouse IgG1 antihuman C8/144B (DAKO, Carpinteria, CA), for CD20: monoclonal mouse IgG2a antihuman L26, for CD68: monoclonal mouse antihuman IgG3 PG-M1 (DAKO, Carpinteria, CA), for CD206: monoclonal rabbit antihuman EPR22489-7 (Abcam, Cambridge, UK), for PD-L1: monoclonal rabbit antihuman SP142 (Abcam, Cambridge, UK), for THY1: monoclonal mouse IgG1 7E1B11 (Abcam, Cambridge, UK), for FAP: monoclonal rabbit antihuman EPR20021 (Abcam, Cambridge, UK), for CD3: monoclonal rabbit antihuman SP7 (Littleton, CO), for Ki67: monoclonal mouse IgG1 antihuman MIB-1 (DAKO, Carpinteria, CA), for GZMB: monoclonal mouse IgG2a antihuman GZB01 (LSBio, Seattle, WA), for CD4: monoclonal rabbit antihuman EPR6855 (Abcam, Cambridge, UK), for FOXP3: monoclonal rabbit antihuman D2W8E (CST, Danvers, MA), for a-SMA: monoclonal mouse IgG2a antihuman 1A4 (DAKO, Carpinteria, CA), for CD34: monoclonal rabbit antihuman EP373Y (Abcam, Cambridge, UK), for COL4: monoclonal mouse IgG1 antihuman COL-94 (Abcam, Cambridge, UK), and for vWF: monoclonal mouse IgG1 antihuman F8/86 (DAKO, Carpinteria, CA).
Cytokeratin at 1:100 dilution (polyclonal rabbit anti-cow cytokeratin, wide spectrum screening, DAKO, Carpinteria, CA) or (monoclonal mouse IgG1 antihuman Clone AE1/AE3, DAKO Carpinteria, CA) was used to identify the tumor cells. Rabbit EnVision reagent (DAKO,neat), Goat Anti-Mouse IgG2a heavy chain (Horseradish peroxidase, HRP) (Abcam), Rat anti-Mouse IgG1 Secondary Antibody, HRP, eBioscience (ThermoFisher Scientific, Waltham, MA USA), Goat Anti-Mouse IgG3 heavy chain (Horseradish peroxidase, HRP) (Abcam), Alexa 546 conjugated goat antirabbit secondary antibody (Molecular Probes, Eugene, OR) were used as secondary antibodies. Tyramide-bound fluorophores were added after each secondary antibody to bind to the HRPs. Cyanine 5 (Cy5) directly conjugated to tyramide (Akoya, Waltham, MA, USA), Alexa Fluor 750 streptavidin (Cy7) (ThermoFisher Scientific, Waltham, MA USA) and Tyramide Signal Amplification (TSA) fluorescein (Fluorescein isothiocyanate (FITC)) (AKOYA, Marlborough, MA 01752, USA) were used for target antibody detection.
Staining of Whole Tissue Sections
Formalin-Fixed Paraffin-Embedded whole tissue sections were deparaffinized with xylene. Rehydration was performed using ethanol. Antigen retrieval was performed using EDTA buffer pH 8.0 at 97°C for 20 minutes in a pressure-boiling container (PT Module, Lab Vision, Thermo Scientific, Waltham, MA). 2.5% hydroxyl peroxide in methanol for 30 minutes was used to block endogenous peroxidase activity, followed by 0.3% bovine serum albumin in 0.1mol/L of Tris-buffered saline for 30 minutes at room temperature. This was followed by incubation of the slides with the primary antibodies and cytokeratin. Slides were then incubated at 1-hour room temperature with the primary antibodies and with cytokeratin. Secondary antibodies and tyramide-bound fluorophores were used for target antibody detection. 4,6-diamidino-2-phenyl-indole (DAPI) was used to stain nuclei and mounted with Prolong Gold antifade mounting reagent (P36394, Life Technologies). All staining was performed using the Lab Vision Autostainer 720 (Thermo Scientific).
Fluorescence Measurement and Scoring
Quantitative immunofluorescence (QIF) was assessed using two platforms: image collection was performed on either the PM2000 (HistoRx) or Vectra Polaris (Perkin Elmer) automated fluorescence microscopy platforms. The final images were analyzed and quantified using the AQUAnalysis Software (Navigate Biopharma) or the InForm Software (Perkin Elmer), respectively.
Image analysis with AQUA method of QIF was used initially for all the markers CD45, CD14, CD8, CD20, CD68, CD206, PD-L1, THY1, FAP, CD3, Ki67, GZMB, CD4, FOXP3, a-SMA, CD34, COL4/vWF. A QIF score was generated by dividing the sum of target pixel intensities by the area of the molecularly designated compartment, as previously described {Camp, 2002 #53}. In order to distinguish tumor from tissue stroma and other components, an epithelial tumor “mask” was created by binarizing the cytokeratin signal and creating an epithelial compartment. Stromal “mask” is created by subtracting tumor mask from the nuclear mask and is representative of tumor microenvironment. The expression level of a maximum of 3 targets can be measured in the above molecular compartments.
For the whole sections, using a × 20 objective, a series of image fields of view (FOV) were captured within the circled invasive tumor to ultimately cover the tissue of interest. Depending on the size of the tumor, 40–200 fields were captured per section. QIF scores were normalized to the exposure time and bit depth at which the images were captured, to compensate for any variability. All acquired histospots were visually assessed and cases with staining artifacts or less than 2% tumor (cytokeratin staining) were omitted from the analysis. Since the expression of Tregs was low in our samples, we quantified Tregs, which are characterized by the expression of CD4 and FOXP3, using the InForm Software, as previously described [23]. Multispectral images were captured by Vectra Polaris in three channels on all tumor tissues. With the trainable feature-recognition InForm software, Tregs and tissue types were identified. Cell nuclei were visualized by the signal from DAPI stain; cytokeratin was visualized with Alexa 546 fluorophore; and the proteins of interest were visualized with the Cy5, Cy7 and FITC dye.
The cell count for phenotype of interest (CD4 and FOXP3 double-positive phenotype) was calculated in both tumor and stromal tissue for final analysis, using the segmentation software, InForm Tissue Finder (PerkinElmer, Waltham, MA, USA). The area of each tissue category, tumor and stroma, was evaluated to assess the density of Tregs, represented by (number of Tregs) / (pixel area) in each FOV.
Validation of staining and protein expression
Yale-Tissue microarray (YTMA) 405, a cell-line tissue microarray for immune cells, was used as positive control and for day-to-day standardization of assays. It revealed the expected levels and expression patterns of the immune cell biomarkers. YTMA 417, a random breast cancer tissue microarray was used as a second control. QIF scores for each marker, showed high concordance and remained reproducible, among control slides stained in different batches indicating limited inter-batch variation.
To show specificity and reproducibility, all antibodies were validated using an antibody validation protocol described previously [24]. Briefly, we have tested the antibodies in different conditions and chose the one that maximizes their dynamic range and the signal to noise ratio. Once the optimal conditions and concentrations have been determined, we proceeded with the tissue staining and further analysis.
Statistical Analysis
We used the median QIF scores of every marker from all FOV in each section to represent marker expression at the section level. Statistical comparisons between AA and NAA population were made using the Mann–Whitney U test except for comparison of T-cell status for which Fisher’s exact test was used. Statistical analyses were performed using the GraphPad Prism v6.0 for Windows (GraphPad Software, Inc, San Diego, CA, USA). Significance is defined as p<0.05.