Research Highlight: Basal Cell Carcinoma’s Low Immunogenicity Linked to Antigen Presentation Suppression from Its Cellular Origin

Basal cell carcinoma (BCC) sits at a fascinating crossroads in cancer biology: despite being the most mutated human cancer, it paradoxically exhibits remarkably low immunogenicity, rendering it resistant to many immune-based therapies. This perplexing phenomenon has puzzled oncologists and immunologists alike. A groundbreaking study led by Dr. Shawn Demehri at Massachusetts General Hospital, recently published in Cell Reports, illuminates the epigenomic underpinnings of BCC’s immune evasion, revealing new avenues for improving therapeutic outcomes in this ubiquitous yet insidious form of skin cancer.

The immune system’s ability to recognize and eliminate cancer cells hinges on effective antigen presentation, a process primarily mediated by the human leukocyte antigen class I (HLA-I) complex. Tumor antigens are processed and presented on HLA-I molecules on the cancer cell surface, flagging aberrant cells for destruction by CD8+ cytotoxic T lymphocytes. Paradoxically, BCC cells suppress the expression of HLA-I, effectively cloaking themselves in immunological invisibility. This suppression results from a sophisticated epigenomic mechanism connected to the tumor’s cell of origin and its intrinsic stemness programs.

Dr. Demehri’s team meticulously compared BCC samples to cutaneous squamous cell carcinomas (SCCs), which exhibit higher responsiveness to immune checkpoint inhibitors. Through single-cell RNA sequencing and histological analyses, they demonstrated that BCCs harbor an “immune-excluded” microenvironment, characterized by minimal infiltration of CD4+ and CD8+ T cells within tumor foci. This contrasts sharply with SCCs, where immune cells readily penetrate the tumor stroma. The immune exclusion observed in BCC correlates tightly with the downregulation of antigen presentation machinery (APM), evident even at early disease stages, suggesting an inherent, developmental basis for immune evasion.

Central to this suppression is the transcription factor Foxc1, which is normally involved in maintaining quiescence of hair follicle stem cells — the presumptive cell of origin for BCC. Foxc1 directly represses genes encoding key components of the APM, including HLA-I and interferon regulatory factor 1 (IRF1), through epigenomic modifications that silence their expression. This pharmacologically reversible epigenetic repression provides a molecular explanation for why BCCs, despite their heavy mutational load, remain largely undetected and refractory to immune attack.

The clinical implications of these discoveries are profound. Dr. Demehri’s research shows that topical application of entinostat, a histone deacetylase inhibitor, can epigenetically reverse APM suppression in BCC cells in vivo. When used in combination with imiquimod, a topical immune response modifier approved for skin cancers, entinostat significantly enhances antigen presentation and stimulates immune cell infiltration, producing a synergistic antitumor effect. This dual-regimen effectively overcomes the immune exclusion barrier, transforming BCC from an immunologically “cold” tumor into one more amenable to immune-mediated clearance.

Such findings challenge the existing paradigm that high tumor mutational burden necessarily predicts immunotherapy success. Instead, they emphasize the pivotal role of a cancer’s cellular and epigenetic context, particularly the intrinsic stemness programs inherited from their cell of origin, in dictating immunogenicity. By targeting these epigenomic regulators, it may be possible to sensitize otherwise resistant tumors to immune-based treatments, broadening the therapeutic horizon beyond BCC.

Beyond immediate treatment strategies, this work raises critical questions about how tissue-specific stemness pathways modulate tumor-immune interactions more broadly. Could similar epigenetic constraints on antigen presentation operate in other cancers arising from quiescent stem cell populations? If so, unraveling these intrinsic immunosuppressive mechanisms may unlock new generalizable approaches to cancer immunotherapy.

Furthermore, these insights offer hope for organ transplant recipients and immunosuppressed patients, who are disproportionately susceptible to SCC yet relatively spared from BCC development. This differential risk underscores the clinical relevance of BCC’s low immunogenicity and may inform personalized surveillance and therapeutic strategies for high-risk populations.

In essence, this study elegantly combines molecular immunology, epigenomics, and clinical oncology to redefine our understanding of tumor immune evasion. The identification of Foxc1 as a master regulator of antigen presentation heralds a new chapter in skin cancer research and immunotherapy, anchored in the biology of the tumor’s origin rather than mutation burden alone.

Looking forward, Dr. Demehri and colleagues advocate for clinical trials testing the efficacy and safety of entinostat-primed immunotherapy in patients with BCC. Such trials could validate this novel combination as a frontline or adjunct treatment, potentially improving outcomes for thousands of patients afflicted with this common yet challenging cancer.

This research exemplifies the power of combining cutting-edge single-cell technologies with translational oncology to unravel the complex interplay between cancer cell states and immune recognition. As the field of cancer immunotherapy continues to evolve, studies like this underscore the importance of considering tumor cell origin and epigenetic regulation when designing effective treatments.

In conclusion, the elucidation of epigenomic mechanisms governing stemness and immune suppression opens promising avenues not only for the treatment of basal cell carcinoma but also for a broader understanding of cancer immunobiology. By leveraging these insights, the oncology community stands poised to overcome longstanding barriers in combating immune-resistant tumors, heralding a new era of precision medicine and immunotherapy.

Subject of Research: Cells

Article Title: Epigenomic regulation of stemness contributes to the low immunogenicity of the most mutated human cancer

News Publication Date: 17-Apr-2025

Web References:

https://www.cell.com/cell-reports/fulltext/S2211-1247(25)00332-8
http://dx.doi.org/10.1016/j.celrep.2025.115561

Image Credits: Shawn Demehri, Massachusetts General Hospital

Keywords: Skin cells, Immunogenicity, Combination therapies, Cancer immunotherapy

Tags: antigen presentation in cancerBasal cell carcinoma immunogenicitycancer immune evasion strategiesCD8+ T lymphocytes and cancerepigenomic mechanisms in BCCHLA-I suppression in tumorsimmune checkpoint inhibitors in skin cancerMassachusetts General Hospital studyoncological research advancementsskin cancer immune resistancetherapeutic outcomes in BCCtumor cell origin and immunity