Apoptosis and JUN signaling gene signatures are upregulated within the tumor-nerve microenvironment of KPC mice. To investigate tumor-nerve interactions which occur during PDAC, we utilized the KPC genetic mouse model, in which pancreas specific expression of oncogenic Kras and mutant p53 drives development of PDAC. Mice begin to develop pancreatic intraepithelial neoplasia (PanIN) at 8-10wks of age and disease progression to PDAC typically occurs within 16-20wks (Rhim et al., 2013). Once tumors reached 1 cm in diameter, measured by palpation, mice were sacrificed, and immunofluorescence was performed on the frozen fixed tumors using markers for nerves (TH), epithelial cells (PanCK) and macrophages (F4/80). High magnification images resolved differences in tumor associated nerve structures where axon fibers and larger caliber bundles could be found (Fig. 1A). The labeled cryosections were loaded onto the GeoMx nanostring instrument and a representative diagram of the pipeline is shown (Fig. 1B). Regions of interest (ROI) were collected from the tumor tissue and barcoded by the instrument in a plate for next generation sequence analysis. Principal component analysis was performed on 10 ROIs containing either axon fibers, or larger nerve bundles (Fig. 1C). We found that larger nerve bundles clustered together (red), while axonal ROIs clustered separately (blue). A heatmap was generated from the expression values, which revealed two large distinct clusters which separated the axonal gene signatures from the nerve bundle gene signatures. To note, axon # 81 ROI, clustered more closely with the nerve bundle ROIs (Fig. 1D). Differential expression analysis was performed, and a volcano plot (Fig. 1E, top) was created to show the most significant upregulated and downregulated genes in nerve bundles, as well as an MA plot to show the amplitude of expression (Fig. 1E, bottom). Amongst the most upregulated genes included BMP4, BMP7 and BDNF. Gene ontology analysis was performed, which revealed upregulation of numerous pathways related to MAPK, JUN kinase, as well as apoptosis gene signatures (Fig. 1F). Based on the GO gene signatures, we selected genes from pathways enriched for apoptosis, JUN kinase, as well as SMAD/BMP signaling, which was highly upregulated in Kegg Pathways (Fig. 1G). Interestingly MT2 was the most downregulated gene in large nerve bundles: it has shown to be highly expressed in healthy nerves, but not in painful neuromas (13), and is lost during chemotherapy induced neuropathic pain (14). These results reveal a unique transcriptional program in cancer associated nerve bundles marked by upregulation of MAPK, apoptosis and JUN gene signatures. This molecular signature has been observed in Schwann cell regeneration, in non-cancer contexts (15, 16). As a check for the fidelity of our analysis, we performed internal controls comparing spleen, acinar tissues (Supplemental Fig. 1) and sequential regions in tumor tissues, compared to non-paired regions (Supplemental Fig. 2). Regions of acinar tissues and spleen showed independent clustering and enrichment for genes involved in pancreatic digestion. Additionally, sequentially matched regions clustered together using PCA analysis. Lastly, the top differentially expressed genes in our data provide insight into tissue type differences that were resolved by nanostring analysis (TH + fibers, bundles, spleen, and acinar) (Supplemental Table 1 and Table 2). Quality control of the data analyzed revealed high quality UMIQ30 values, as well as read correlations with nuclei counts (Supplemental Fig. 3). Taken together, these molecular data indicate a nerve repair program is activated by repair Schwann cells in PDAC associated nerves.
Nerve associated macrophage express signatures reflective of a role in phagocytosis. Tissue resident macrophages have unique functions based on their origin and tissue location. For instance, cardiac resident macrophages participate in electoral conduction via gap junction communication with cardiac myocytes (17). While numerous reports have described tumor associated macrophages (TAMs) to function as pro- or anti tumorigenic (18–20), only a few studies have been reported on the function of endoneurial macrophages within PDAC. In these studies, nerve associated macrophages (NAMs) have been shown to secrete neurotrophic factors (21), as well as express inflammatory regulators such as LIF and CTSB (22, 23). However, to our knowledge a molecular characterization of these resident immune cells in-situ has not been performed. Here we performed digital spatial sequencing analysis of PDAC nerve bundles in regions devoid of- or containing F4/80 + macrophages (Fig. 2A-2B). Principal component analysis revealed distinct clustering of bundles with and without macrophages (Fig. 2C). Differential expression showed an enrichment for macrophage type associated genes including Csf1r, Cd68 and AIF1, enriched in F4/80 + bundles and did not contain upregulated epithelial or fibroblast signatures (Fig. 2D). Macrophage genes reached significance (p = .049 for Csf1r and p = .043 for AIF1; students t-test). Differential expression analysis was performed, and a volcano plot (Fig. 2E, top) was created to reveal the most significantly upregulated and downregulated genes in nerve bundles, as well as an MA plot to show the amplitude of expression (Fig. 2E, bottom). Amongst the most upregulated genes included Marcks and Fcgr2b, and Psap. Gene ontology analysis revealed upregulation of pathways involved in antigen presentation, phagocytosis and lysosome compartments (Fig. 2F). Based on the GO gene signatures enriched in KeggPathways, we highlighted selected genes from enriched pathways for apoptosis, as well as chemokine ligands/receptors and TAM receptor/ligands, which play pivotal roles in macrophage function (Fig. 2G). We found that CCL7, Cxcl12 and Cxcl13 were amongst the most differentially expressed genes enriched in 5 TH+, F4/80 + ROIs. Interestingly, the aforementioned chemokines have been shown to be important for macrophage chemotaxis to damaged nerves (CCL7) (24, 25), and neuropathic pain (Cxcl12, Cxcl13) (26, 27). To note, many interleukin genes were not included as they were detected at low frequency (Supplemental Table 3). These transcriptomic signatures strongly suggest that local F4/80 + macrophages within nerve bundles have phagocytic function. While their role in PDAC biology has not been described, in the context of nerve injury, nerve associated macrophages have been shown to play a key role in phagocytosis, antigen presentation and clearance of damaged axons during Wallerian degeneration (28).
Local neuroglia proliferate within the tumor nerve microenvironment. Our findings that transcriptomic signatures of non-myelinating repair-type Schwann cells (BMPs, JUN kinases and BDNF) are upregulated in PDAC associated nerve bundles along with nerve-associated macrophage upregulation of phagocytic gene signatures, resembles changes found in damaged nerves during traumatic non-cancer related injuries. In such settings, neuroglial (neural supportive cell types; macrophage, Schwann cells) undergo a functional transformation and proliferate locally to support the repair and regeneration of a damaged nerve (29–31). As such, we hypothesized that during PDAC local neuroglial would actively proliferate at sites of neural damage. To test this, when a palpable tumor was detected, we enrolled mice into daily intraperitoneal injections of EdU (50 mg/kg), which allowed tracking of cell proliferation over multiple days. We performed colocalization analysis in TH + nerves, in acinar regions (remote from the tumor) as well as intra-tumoral TH + nerve bundles. We found in non-tumor tissues, nerve fibers did not colocalize with EdU + nuclei (DAPI) independent of neural density, while in intra-tumoral regions EdU + nuclei were found within TH + bundles (Fig. 3A-3E). Proliferative nuclei were quantified and were significantly increased in TH + regions within tumors compared to TH + regions in acinar tissues, which we did not detect in our analysis (Fig. 3F). These results indicate that neuroglial have functional responses (increased proliferation), based on their proximity to a growing tumor. Given that paracrine signaling factors secreted by the pancreatic cancer TME, such as LIF, SLIT2, and NGF (5, 22, 32), have been shown to promote Schwann cell proliferation in-vitro, we sought to determine whether increased proliferation rates were found in nearby epithelial cells (less than 50 microns), compared to distant TH + bundles (greater than 50 microns). After stratification of intra-tumor TH staining into near epithelial or distant epithelial cells (PanCK+), we did not find a significant difference in TH+, EdU + nerves based on tumor cell location (Fig. 3G-3I). These data indicate that the proliferative phenotype of local neuroglia in the setting of the tumor-nerve microenvironment does not require direct contact with epithelial cells.
The tumor nerve microenvironment of human PDAC and other gastrointestinal malignancies express markers of non-myelinating Schwann cell phenotypes. Given our functional and transcriptomic data in our mouse models, we sought to identify how the transcriptional state of Schwann cells differs in ‘healthy’ acinar tissue and within pancreatic tumors. As we identified transcriptional and functional gene signatures of non-myelinating repair Schwann cells within tumor tissues, we hypothesized that adjacent healthy acinar tissue enriched for TH + axons would have gene signatures of Schwann cells, which did not present a de-differentiated, non-myelinating phenotype. As such, we compared core Schwann single cell transcriptomic signatures defined by Panglao DB, as well as non-myelinating Schwann cells defined by OnClass (CL:0002376), and previously published characterized in PDAC (10, 33). In regions containing TH + staining independently of tumor location (acinar, TH + fibers, TH + Bundles), we identified core Schwann cell transcriptomic signatures (Cryab, MPZ, GFAP) in all locations, however only in tumor TH + regions (TH + fibers, and bundles), did we identify enriched gene sets characteristic of non-myelinating Schwann cells (15/19 genes in bundles and 17/19 genes in axons) (Fig. 4A). Notably, acinar genes were also highly enriched in acinar regions (Fig. 4A; right panel). No genes were removed from OnClass (CL:0002376) signatures in our comparative analysis, however, 6 genes did not meet the minimum threshold for analysis. Using gene ontology analysis, we compared axons in healthy and tumor regions and identified enrichment scores involved in spinal cord injury and complement pathway activation (Fig. 4B). As these are pathways that occur upon activation of damaged nerves, we hypothesized that a common pathway might be present across multiple tumor models, whereby tumors damage nerves, and promote a non-myelinating Schwann cell transcriptional program (Figs. 4C-4D). To investigate whether this phenotype was present across multiple tumor types, we utilized the human protein atlas to interrogate the tumor-nerve microenvironment across multiple organs and tumor types. Using protein markers c-JUN and JUND which control the repair-Schwann cell phenotype (11, 16), we sought to determine whether these transcription factors were upregulated within PDAC nerve bundles compared to healthy tissues. Using the JUND antibody CAB005628, we identified low protein expression in the normal pancreas (Fig. 4E) while high expression was present in nerve bundles from PDAC (Fig. 4F-4G). These results were highly concordant to nerve bundles found during stomach cancer, and liver cancer (Fig. 4H-4L). While, perineural invasion has been reported in many tumor types; reviewed in (34), our data suggest repair-Schwann cells and JUN kinase upregulation in nerve bundles is common across multiple tumor types, and identifies it as a cardinal feature of perineural invasion.