In vivo model set-up for optimal CAFs isolation
The injection of 105 4T1-luc cells into the mammary fat pad of female BALB/c mice leads to the growth of a detectable tumor mass at 5 days after implantation. By measuring the tumor volume by calipers and the tumor cell viability by BLI, tumor growth was monitored for one month after implantation. To find a sacrifice window that is adequate for CAFs isolation, an optimal compromise was sought between higher tumor size and BLI on the one hand and an emerging tumor ulceration and necrosis on the other hand (Figure 1). As a necrotic core appears 20 days after implantation, and it enlarges at 25 and 30 days (as documented by BLI images in Figure 1C), day 20 was set as the time point to optimize cell recovery after the isolation process. Even after carefully removing all visible necrotic areas during the first steps of tumor handling ex vivo, a high percentage of dead cells was found at the end of dissociation into single cells (Table 1). As this percentage may be relevant, especially with the increase in tumor size, dead cell removal is always necessary when working with the 4T1 model.
Optimization of CAFs isolation procedure, culture, and characterization
Two more passages are needed to isolate the population of CAFs (CD90.2+ CD45-) from the panel of collected viable cells: the depletion of non-tumor-associated fibroblasts and the enrichment of tumor-associated fibroblasts (Figure 2). The depletion bead cocktail efficiently removes CD45+ cells (accounting for 67.35% and 0.69% of total cells pre- and post-depletion, respectively, Table 2), and was always used to process one single tumor in every column. As shown in Table 1, the number of eluted cells dropped from an average of 3 × 106 to 1 × 105 after the depletion step. Due to this massive decrease in total cell number, it is convenient to pool the collected cells from at least 2 to a maximum of 4 tumors in a single tube before proceeding with the enrichment step. By doing so, an adequate number of cells was obtained for incubation with tumor-associated fibroblast beads and passed through a single separation column to obtain a final average of 93% of CD90.2+ CD45- cells (Table 2).
Once seeded onto tissue culture plates, these recovered cells attached to the plastic and revealed a large spindle-shaped morphology typical of fibroblasts (Figure 3A,B) and different from 4T1 tumor cells (Figure 3D). Not pooling tumors after depletion causes the cellular yield with tumor-associated fibroblast microbeads to be too low to establish a culture. In other cases, when the duration and temperature of the incubations with microbeads are not carefully maintained, some non-specific binding may occur. In such cases, the enrichment steps were less efficient and higher percentages of CD90.2- CD45+ and CD90.2- CD45- cells were recovered along with the CD90.2+ CAFs (5.97 ± 1.5 and 16.75 ± 1.1, respectively) (Figure 4 and Table 3). These contaminant cells were likely to be responsible for the presence in culture of small clones with different morphology (Figure 4B, black arrowheads) that grew faster than CAFs and prevailed over the primary CAF culture (Figure 4C). These suboptimal results confirmed the importance of always double-checking both CD90.2 and CD45 expression, as well as cell morphology at the end of the enrichment process and during cell growth in culture.
Use of isolated cells to evaluate CAF-targeting potential of engineered nanodrugs
The freshly isolated CAFs can be used for several applications ranging from basic research to pharmacological studies. This group’s aim is to develop HFn nanocages that can specifically target CAFs. HFn was functionalized with a specific anti-FAP antibody fragment (HFn-FAP) at two different protein:antibody ratios (a lower 1:1 and a higher 1:5), and their binding with CAFs was tested. As FAP was used as a surface biomarker of pro-tumorigenic CAFs, it was of fundamental importance to check FAP expression on isolated CAFs (Figure 3C). FAP expression was followed over 5 passages in culture to confirm that the primary CAF culture maintained its original characteristics.
FAP functionalization on HFn was found to contribute to a significant shift toward CAF targeting as compared to bare HFn, and the lower amount of antibody (1:1) was enough to observe this effect (Figure 5A). However, this was not observed with the tumor 4T1 cells used to set up the in vivo tumor model, wherein bare HFn showed higher binding than functionalized HFn (Figure 5B). This was most likely due to the absence of FAP overexpression in 4T1 cells and the preferential interaction of HFn with TfR1, which regulates HFn uptake in cells, as widely reported by this group27,33. These results confirm the usefulness of using primary cultures of breast CAFs to preliminarily screen the targeting capability of nanoparticles designed to tackle the tumor microenvironment.

Figure 1: Establishment of the 4T1 tumor model. Cells (105 cells/mouse) were injected into the mammary fat pad. Tumor growth was followed at days 5, 10, 15, 20, 25, and 30 after implantation (A) by measuring tumor volume with calipers and (B) by bioluminescence imaging. Tumor volumes and BLI are expressed as mm3 and counts, respectively. Results are reported as average ± SEM (n=6). (C) BLI representative images obtained 5, 10, 15, 20, 25, and 30 days after cell implantation confirm tumor growth until day 25, when it seems to reach a plateau. At the last time point of analysis (30 days), the BLI does not increase as compared to day 25. Starting at day 20, areas of necrosis and ulceration start to become visible in the central part of the tumor. Color Scale: Min = 1,194, Max = 20,462. Abbreviations: BLI = bioluminescence imaging; SEM = standard error of the mean. Please click here to view a larger version of this figure.

Figure 2: Tumor sample preparation and flow cytometry characterization of isolated CAFs. Tumors were excised and reduced into (A) small pieces of approximately 1–2 mm with the help of a scalpel; (B) single cell suspension after tissue digestion and mechanical dissociation of an excised tumor; (C) cell pellet obtained after lysis of red blood cells; (D) flow cytometry analysis of CD45 and CD90.2 expression in cells obtained after removal of red blood cells and dead cells, (E) after depletion of non-cancer-associated fibroblasts, and (F) after enrichment of cancer-associated fibroblasts, where the majority of cells are CD90.2+ CD45- (blue rectangle). Abbreviations: CAFs= cancer-associated fibroblasts; CD = cluster of differentiation; PE-A = area of phycoerythrin; FITC-A = areas of fluorescein isothiocyanate. Please click here to view a larger version of this figure.

Figure 3: Morphological analysis of CAFs and FAP expression. (A, B) CAFs morphology was checked throughout all passages of culture by optical microscopy (different levels of confluence at passage 2 and passage 5) and compared to (D) 4T1 tumor cells; scale bars = 10 µm. (C) Fibroblast activation protein (FAP) expression was evaluated by flow cytometry at the end of the isolation process on the collected CD90.2+ CD45- cells to confirm their molecular characteristics. A fluorescence threshold was set on unstained control cells (red graph) to quantify mean fluorescence intensity and the percentage of positive cells (FAP+) among antibody-stained cells (blue graph). Abbreviations: CAFs= cancer-associated fibroblasts; FAP = fibroblast activation protein; CD = cluster of differentiation; MFI = mean fluorescence intensity; Ab = antibody; FITC-A = area of fluorescein isothiocyanate; FAP+ = FAP-positive cells. Please click here to view a larger version of this figure.

Figure 4: Example of a sub-optimal CAFs isolation process. (A) Flow cytometry evaluation after the final isolation step revealed the presence of contaminant CD90.2- CD45+ and CD90.2- CD45- cells. (B) These cells can be seen as clones with small round morphology upon seeding (black arrowheads and inset in the bottom left corner of the panel) that (C) prevailed over CAFs after the third passage in culture. Scale bars = 10 µm. Abbreviations: CAF = cancer-associated fibroblast; CD = cluster of differentiation; PE-A = area of phycoerythrin; FITC-A = areas of fluorescein isothiocyanate. Please click here to view a larger version of this figure.

Figure 5: Binding of HFn nanocages on CAFs and 4T1. HFn nanocages were fluorescently labeled with FITC, functionalized with an anti-FAP antibody fragment (HFn-FAP) at two different protein-antibody ratios (1:1 and 1:5), and incubated with (A) target CAFs and (B) 4T1 cells at 4 °C for 2 h. Binding was evaluated by flow cytometry. (A) HFn-FAP binding with CAFs is significantly increased at both antibody fragment concentrations by three-fold as compared to bare HFn. (B) in contrast, a significantly higher binding of bare HFn was observed in 4T1 cells, where binding is not enhanced by FAP recognition. Results are reported as average ± standard deviation of three independent experiments. *** p = 0.0003; °° p = 0.0021 ; °°° p = 0.0008. Abbreviations: CAFs= cancer-associated fibroblasts; FAP = fibroblast activation protein; HFn = recombinant variant of human ferritin heavy chain used as bare nanoparticle or conjugated; HFN-FAP = HFn nanoparticles functionalized with the variable portion of an anti-FAP antibody prepared at two HFn:Fab@FAP molar ratios, 1:1 and 1:5. Please click here to view a larger version of this figure.
| Cell Number (average ± SD) | Extraction Yield Total (per passage) |
| Excised tumor (Post red blood cell removal) | 1.27 x 108 ± 9.81 x 107 | 100% |
| Excised tumor (Post dead cell removal) | 3.01 x 106 ± 9.61 x 105 | 2.38% |
| Post depletion cocktail | 1.15 x 105 ± 4.95 x 104 | 0.11% (3.82%) |
| Post enrichment | 3.00 x 104 ± 1.2 x 104 | 0.027% (26.09%) |
Table 1: Total cell count after each step of isolation of cancer-associated fibroblasts.
| Cell Distribution (%) | CD90.2+ CD45- | CD90.2+ CD45+ | CD90.2- CD45+ | CD90.2- CD45- |
| Excised tumor (Post dead cell removal) | 1.81 ± 0.98 | 10.78 ± 4.51 | 56.57 ± 14.05 | 28.20 ± 17.57 |
| Post depletion cocktail | 69.33 ± 16.75 | 0.14 ± 0.13 | 0.55 ± 0.63 | 39.89 ± 30.31 |
| Post enrichment | 93.14 ± 3.3 | 0.09 ± 0.1 | 0.09 ± 0.08 | 6.69 ± 3.4 |
Table 2: Cell distribution according to expression of CD90.2 and CD45 after each passage of isolation of cancer-associated fibroblasts.
| Cell Distribution (%) | CD90.2+ CD45- | CD90.2+ CD45+ | CD90.2- CD45+ | CD90.2- CD45- |
| Post Enrichment (no pooling) | 75.80 ± 2.9 | 1.49 ± 0.4 | 5.97 ± 1.5 | 16.75 ± 1.1 |
Table 3: CD90.2 and CD45 expression of cells collected after a sub-optimal cancer-associated fibroblast isolation experiment.