Multimodal profiling of chordoma immunity reveals distinct immune contextures

BACKGROUND

Chordomas are rare cancers from the axial skeleton which present a challenging clinical management with limited treatment options due to their anatomical location. In recent years, a few clinical trials demonstrated that chordomas can respond to immunotherapy. However, an in-depth portrayal of chordoma immunity and its association with clinical parameters is still lacking.

METHODS

We present a comprehensive characterization of immunological features of 76 chordomas through application of a multimodal approach. Transcriptomic profiling of 20 chordomas was performed to inform on the activity of immune-related genes through the immunologic constant of rejection (ICR) signature. Multidimensional immunophenotyping through imaging mass cytometry was applied to provide insights in the different immune contextures of 32 chordomas. T cell infiltration was further evaluated in all 76 patients by means of multispectral immunofluorescence and then associated with clinical parameters through univariate and multivariate Cox proportional hazard models as well as Kaplan-Meier estimates. Moreover, distinct expression patterns of human leukocyte antigen (HLA) class I were assessed by immunohistochemical staining in all 76 patients. Finally, clonal enrichment of the T cell receptor (TCR) was sought through profiling of the variable region of TCRB locus of 24 patients.

RESULTS

Chordomas generally presented an immune "hot" microenvironment in comparison to other sarcomas, as indicated by the ICR transcriptional signature. We identified two distinct groups of chordomas based on T cell infiltration which were independent from clinical parameters. The highly infiltrated group was further characterized by high dendritic cell infiltration and the presence of multicellular immune aggregates in tumors, whereas low T cell infiltration was associated with lower overall cell densities of immune and stromal cells. Interestingly, patients with higher T cell infiltration displayed a more pronounced clonal enrichment of the TCR repertoire compared with those with low T cell counts. Furthermore, we observed that the majority of chordomas maintained HLA class I expression.

CONCLUSION

Our findings shed light on the natural immunity against chordomas through the identification of distinct immune contextures. Understanding their immune landscape could guide the development and application of immunotherapies in a tailored manner, ultimately leading to an improved clinical outcome for patients with chordoma.

Neoantigen Targetability in Progressive Advanced Melanoma

PURPOSE

The availability of (neo)antigens and the infiltration of tumors by (neo)antigen-specific T cells are crucial factors in cancer immunotherapy. In this study, we aimed to investigate the targetability of (neo)antigens in advanced progessive melanoma and explore the potential for continued T-cell-based immunotherapy.

EXPERIMENTAL DESIGN

We examined a cohort of eight patients with melanoma who had sequential metastases resected at early and later time points. Antigen-presenting capacity was assessed using IHC and flow cytometry. T-cell infiltration was quantified through multiplex immunofluorescence. Whole-exome and RNA sequencing were conducted to identify neoantigens and assess the expression of neoantigens and tumor-associated antigens. Mass spectrometry was used to evaluate antigen presentation. Tumor recognition by autologous T cells was assessed by coculture assays with cell lines derived from the metastatic lesions.

RESULTS

We observed similar T-cell infiltration in paired early and later metastatic (LM) lesions. Although elements of the antigen-presenting machinery were affected in some LM lesions, both the early and later metastasis-derived cell lines were recognized by autologous T cells. At the genomic level, the (neo)antigen landscape was dynamic, but the (neo)antigen load was stable between paired lesions.

CONCLUSIONS

Our findings indicate that subsequently isolated tumors from patients with late-stage melanoma retain sufficient antigen-presenting capacity, T-cell infiltration, and a stable (neo)antigen load, allowing recognition of tumor cells by T cells. This indicates a continuous availability of T-cell targets in metastases occurring at different time points and supports further exploration of (neo)antigen-specific T-cell-based therapeutic approaches for advanced melanoma.

CD103 and CD39 coexpression identifies neoantigen-specific cytotoxic T cells in colorectal cancers with low mutation burden

BACKGROUND

Expression of CD103 and CD39 has been found to pinpoint tumor-reactive CD8⁺ T cells in a variety of solid cancers. We aimed to investigate whether these markers specifically identify neoantigen-specific T cells in colorectal cancers (CRCs) with low mutation burden.

EXPERIMENTAL DESIGN

Whole-exome and RNA sequencing of 11 mismatch repair-proficient (MMR-proficient) CRCs and corresponding healthy tissues were performed to determine the presence of putative neoantigens. In parallel, tumor-infiltrating lymphocytes (TILs) were cultured from the tumor fragments and, in parallel, CD8⁺ T cells were flow-sorted from their respective tumor digests based on single or combined expression of CD103 and CD39. Each subset was expanded and subsequently interrogated for neoantigen-directed reactivity with synthetic peptides. Neoantigen-directed reactivity was determined by flow cytometric analyses of T cell activation markers and ELISA-based detection of IFN-γ and granzyme B release. Additionally, imaging mass cytometry was applied to investigate the localization of CD103⁺CD39⁺ cytotoxic T cells in tumors.

RESULTS

Neoantigen-directed reactivity was only encountered in bulk TIL populations and CD103⁺CD39⁺ (double positive, DP) CD8⁺ T cell subsets but never in double-negative or single-positive subsets. Neoantigen-reactivity detected in bulk TIL but not in DP CD8⁺ T cells could be attributed to CD4⁺ T cells. CD8⁺ T cells that were located in direct contact with cancer cells in tumor tissues were enriched for CD103 and CD39 expression.

CONCLUSION

Coexpression of CD103 and CD39 is characteristic of neoantigen-specific CD8⁺ T cells in MMR-proficient CRCs with low mutation burden. The exploitation of these subsets in the context of adoptive T cell transfer or engineered T cell receptor therapies is a promising avenue to extend the benefits of immunotherapy to an increasing number of CRC patients.

Transcriptomic and immunophenotypic profiling reveals molecular and immunological hallmarks of colorectal cancer tumourigenesis

OBJECTIVE

Biological insights into the stepwise development and progression of colorectal cancer (CRC) are imperative to develop tailored approaches for early detection and optimal clinical management of this disease. Here, we aimed to dissect the transcriptional and immunologic alterations that accompany malignant transformation in CRC and to identify clinically relevant biomarkers through spatial profiling of pT1 CRC samples.

DESIGN

We employed digital spatial profiling (GeoMx) on eight pT1 CRCs to study gene expression in the epithelial and stromal segments across regions of distinct histology, including normal mucosa, low-grade and high-grade dysplasia and cancer. Consecutive histology sections were profiled by imaging mass cytometry to reveal immune contextures. Finally, publicly available single-cell RNA-sequencing data was analysed to determine the cellular origin of relevant transcripts.

RESULTS

Comparison of gene expression between regions within pT1 CRC samples identified differentially expressed genes in the epithelium (n=1394 genes) and the stromal segments (n=1145 genes) across distinct histologies. Pathway analysis identified an early onset of inflammatory responses during malignant transformation, typified by upregulation of gene signatures such as innate immune sensing. We detected increased infiltration of myeloid cells and a shift in macrophage populations from pro-inflammatory HLA-DR⁺CD204^- macrophages to HLA-DR^-CD204⁺ immune-suppressive subsets from normal tissue through dysplasia to cancer, accompanied by the upregulation of the CD47/SIRPα 'don't eat me signal'.

CONCLUSION

Spatial profiling revealed the molecular and immunological landscape of CRC tumourigenesis at early disease stage. We identified biomarkers with strong association with disease progression as well as targetable immune processes that are exploitable in a clinical setting.

The identification of the anthracycline aclarubicin as an effective cytotoxic agent for pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal types of cancer, mainly due to its delayed diagnosis and lack of effective therapeutic options. Therefore, it is imperative to find novel treatment options for PDAC. Here, we tested a series of conventional chemotherapeutics together with anthracycline compounds as single agents or in combination, determining their effectivity against established commercial and patient-derived, low-passage PDAC cell lines. Proliferation and colony formation assays were performed to determine the anticancer activity of anthracyclines; aclarubicin and doxorubicin, on commercial and patient-derived, low-passage PDAC cell lines. In addition, the effect of standard-of-care drugs gemcitabine and individual components of FOLFIRINOX were also investigated. To evaluate which mechanisms of cell death were involved in drug response, cleavage of poly(ADP-ribose)polymerase was evaluated by western blot. Aclarubicin showed superior antitumor activity compared to other anthracyclines and standard of care drugs (gemcitabine and individual components of FOLFIRINOX) in a patient-derived, low-passage PDAC cell line and in commercial cell lines. Importantly, the combination of gemcitabine and aclarubicin showed a synergistic effect at a dose range where the single agents by themselves were ineffective. In parallel, evaluation of the antitumor activity of aclarubicin demonstrated an apoptotic effect in all PDAC cell lines. Aclarubicin is cytotoxic for commercial and patient-derived low-passage PDAC cell lines, at doses lower than peak serum concentrations for patient treatment. Our findings support a (re)consideration of aclarubicin as a backbone of new combination regimens for pancreatic cancer patients.

673 (Re-) Solving the biology of colorectal cancer onset and progression to improve treatment and prevention

Background

Colorectal cancer (CRC) development is accompanied by the gradual accumulation of genetic alterations in epithelial cells of the colon and rectum.1 2 The paradigm of the adenoma-carcinoma sequence was originally centered around cancer cells; however, it is now clear that the tumor microenvironment plays a substantial role in cancer progression and patient outcome.3 In recent years, technologies have evolved rapidly, allowing the multiplexed quantification of gene expression while preserving spatial context.4 Furthermore, some spatial transcriptomic technologies also allow the parallel interrogation of different cell populations in the tumor microenvironment. Here, we performed digital spatial profiling on early-stage CRC samples to elucidate the biological processes that are at the basis of malignant transformation and to identify novel therapeutic targets and (immune) biomarkers.

Methods

Endoscopically resected early-stage CRC samples were obtained at Leiden University Medical Center. In total, 144 areas of illumination were interrogated with GeoMx digital spatial profiling using the Cancer Transcriptome Atlas (>1,800 genes). In each of eight samples, nine regions of interest with different levels of cancer progression were selected, including normal epithelium, transition areas, low-, and high-grade dysplasia, and invasive carcinoma (figure 1A). We segmented each region based on cytokeratin and vimentin protein expression (figure 1B). Immunohistochemical detection was performed on these samples and 26 additional samples to validate targets associated with disease progression.

Results

Digital spatial profiling allowed us to dissect transcriptional alterations in epithelial and stromal fractions between different regions from healthy tissue, different degrees of dysplasia, and cancer. Gene expression data revealed a clear separation of profiled areas by histologic category. Interestingly, gene expression features in the stromal compartment provided a better data-driven separation of histologic categories than the epithelial fraction (figure 1C). Substantial changes in immune-related pathways were identified, including differential expression of specific immunomodulators. We validated the expression of several candidate biomarkers/targets that demonstrated consistent alterations from normal tissue to cancer by immunohistochemistry. Several proteins were identified that could clearly discriminate benign from malignant tissue.

Conclusions

We here demonstrated the unique biological insights that are provided by spatial examination of early-stage CRC by digital spatial profiling. We identified specific genes that were altered during CRC tumorigenesis, in epithelial and stromal/immune fractions. Furthermore, our results indicate an essential role for innate immunity in colorectal cancer onset and progression. The genes identified by this approach could potentially serve as novel biomarkers and targets for early interception or prevention of CRC development.

Acknowledgements

This work was supported by the European Research Council (ERC) Starting grant awarded to Dr. Noel F. de Miranda and the Stichting Management Apothekers en de Gezondheidszorg (STIMAG) Research grant awarded to Jessica Roelands.

Trial Registration

N/A

References

Fearon ER, Vogelstein B. A genetic model for colorectal tumorigenesis. Cell 1990;61(5):759–767. doi: 10.1016/0092-8674(90)90186-I.

Nowell PC. The clonal evolution of tumor cell populations. Science 1976;194(4260):23–28. doi: 10.1126/science.959840.

Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell 2011;144(5):646–674. doi: 10.1016/j.cell.2011.02.013.

Merritt CR, et al. Multiplex digital spatial profiling of proteins and RNA in fixed tissue. Nat Biotechnol 2020;38(5):586–599. doi: 10.1038/s41587-020-0472-9.

Ethics Approval

This study was approved by the METC Leiden-Den Haag-Delft (protocol B20.039). Patient samples were anonymised and handled according to the medical ethical guidelines described in the Code of Conduct for Proper Secondary Use of Human Tissue of the Dutch Federation of Biomedical Scientific Societies.

Abstract 673 Figure 1

Transcriptional alterations in early-stage colorectal cancer. Digital spatial profiling defines transcriptional alterations in early-stage colorectal cancer. (A) Schematic representation of an early-stage CRC sample containing regions with different levels of cancer progression, including normal epithelium, transition areas, low-, and high-grade dysplasia, and invasive carcinoma. (B) Segmentation based immunofluorescent labelling with antibodies directed against PanCK and Vimentin in one of the early-stage CRC samples. Artificial overlay of implemented segmentation is indicated for each ROI, visualizing Vimentin+ (pink) and PanCK+ (orange) segments. Inset: higher magnification of an individual ROI. (C) Dimension reduction of expression of all quantified genes by t-Distributed Stochastic Neighbor Embedding (tSNE). tSNE plots are annotated by segment (left), and histological region (right).

Neoantigen-specific immunity in low mutation burden colorectal cancers of the consensus molecular subtype 4

Background

The efficacy of checkpoint blockade immunotherapies in colorectal cancer is currently restricted to a minority of patients diagnosed with mismatch repair-deficient tumors having high mutation burden. However, this observation does not exclude the existence of neoantigen-specific T cells in colorectal cancers with low mutation burden and the exploitation of their anti-cancer potential for immunotherapy. Therefore, we investigated whether autologous neoantigen-specific T cell responses could also be observed in patients diagnosed with mismatch repair-proficient colorectal cancers.

Methods

Whole-exome and transcriptome sequencing were performed on cancer and normal tissues from seven colorectal cancer patients diagnosed with mismatch repair-proficient tumors to detect putative neoantigens. Corresponding neo-epitopes were synthesized and tested for recognition by in vitro expanded T cells that were isolated from tumor tissues (tumor-infiltrating lymphocytes) and from peripheral mononuclear blood cells stimulated with tumor material.

Results

Neoantigen-specific T cell reactivity was detected to several neo-epitopes in the tumor-infiltrating lymphocytes of three patients while their respective cancers expressed 15, 21, and 30 non-synonymous variants. Cell sorting of tumor-infiltrating lymphocytes based on the co-expression of CD39 and CD103 pinpointed the presence of neoantigen-specific T cells in the CD39⁺CD103⁺ T cell subset. Strikingly, the tumors containing neoantigen-reactive TIL were classified as consensus molecular subtype 4 (CMS4), which is associated with TGF-β pathway activation and worse clinical outcome.

Conclusions

We have detected neoantigen-targeted reactivity by autologous T cells in mismatch repair-proficient colorectal cancers of the CMS4 subtype. These findings warrant the development of specific immunotherapeutic strategies that selectively boost the activity of neoantigen-specific T cells and target the TGF-β pathway to reinforce T cell reactivity in this patient group.