HLA-I aberrations in cutaneous T-cell lymphoma

In this issue of Blood, Kwang et al present a comprehensive genetic analysis of class I of HLA (HLA-I) in advanced-stage cutaneous T-cell lymphoma (CTCL).¹ The authors explore the prevalence, biological consequences, and potential therapeutic implications of HLA-I genetic defects, and highlight their subclonal nature and dynamic changes over the treatment course.

CTCL encompasses a heterogeneous group of non-Hodgkin lymphomas, with mycosis fungoides (MF) and Sézary syndrome (SS) being the most prevalent subtypes. Advanced CTCL is associated with limited therapeutic options and poor outcomes. Recent advances in immunotherapy, particularly immune checkpoint inhibitors (ICIs), have revolutionized cancer treatment. However, the overall response rate in mycosis fungoides and Sézary syndrome remains modest at 38%.² Furthermore, acquired resistance after initial response to ICIs poses another challenge. Although the escape mechanisms are not yet fully characterized, increasing evidence from other lymphomas and solid tumors suggests that abnormalities in HLA-I expression and neoantigen presentation play a crucial role. The HLA-I complex presents tumor antigens to T cells, thereby facilitating immune recognition. It is comprised of a polymorphic α-heavy chain encoded by HLA-A, -B, or -C genes, paired with β2-microglobulin (β2M), which stabilizes the complex. HLA-I molecules are also recognized by killer cell immunoglobulin-like receptors on natural killer (NK) cells, inhibiting the HLA-independent cytotoxic activity of NK cells. Given its critical role in immune surveillance, HLA-I alterations are likely to result in immune evasion and resistance to immunotherapy. HLA-I defects can be categorized into irreversible and reversible, depending on whether HLA-I expression can be restored through pharmaceutical intervention. Irreversible alterations include loss of heterozygosity at 6p21.3, causing haplotype loss; changes affecting HLA-A, -B, or -C alleles, leading to allele-specific loss; or disruption to B2M, resulting in complete HLA-I loss. Genetic changes in the antigen-presentation machinery, interferon pathway, or JAK/STAT pathway are also irreversible. In contrast, reversible defects arise from epigenetic, transcriptional, and translational modifications of HLA-I or related genes.³ Although HLA-I abnormalities are well documented in some lymphomas, their prevalence, biological roles, and clinical implications in CTCL remain underexplored.^4,5 Furthermore, there is a notable lack of data on how tumor HLA-I expression dynamically evolves over the treatment course in CTCL.

In their study, Kwang et al address these gaps by investigating genetic alterations in HLA-I in 51 patients with advanced CTCL, employing targeted DNA sequencing and single-cell RNA sequencing. Their findings reveal HLA-I aberrations, including loss of heterozygosity and allele-specific mutations, in 49% of the patients. Single-cell RNA sequencing showed that these abnormalities were subclonal and dynamic, with some alleles disrupted or restored over time, indicating ongoing immune selection. A particularly novel observation was that these abnormalities tended to selectively target HLA alleles presenting the most neoantigens, while maintaining normal or elevated total HLA-I expression. This contrasts sharply with other lymphomas, where complete HLA-I loss is common. Consistent with this finding, B2M mutations, which typically lead to complete loss of HLA-I presentation, are common in other lymphomas but rare in CTCL.⁵ Notably, HLA-I abnormalities were associated with shorter progression-free survival; however, prospective studies on HLA-I events at diagnosis are needed to accurately delineate their prognostic significance.

The study reveals novel aspects of CTCL pathogenesis. First, tumor cells notably maintained total HLA-I expression despite disruption of multiple HLA-I alleles. This paradox indicates a balance between 2 competing selective pressures: allele-specific HLA-I disruption allows tumor cells to evade neoantigen-evoked T-cell recognition, whereas retaining sufficient total HLA-I expression inhibits NK-cell–mediated cytotoxicity. This raises the possibility that therapeutically disrupting this balance could enhance antitumor immunity. Second, the subclonal nature of HLA-I aberrations may suggest that they occur as late events in tumor evolution. However, their high prevalence indicates they are not merely random epiphenomena of genomic instability but represent meaningful adaptive mechanisms. This adaptation is particularly significant given the genomic complexity of advanced CTCL, which increases neoantigen formation. Furthermore, the higher prevalence of mutations in immune surveillance genes (but not other pathways) in samples with HLA abnormalities suggests a coordinated evasion strategy. Likely, tumors with HLA abnormalities continue to face immune pressure from other immune components---evidenced by the dynamic nature of HLA-I abnormalities observed---driving the acquisition of additional mutations to enhance tumor survival.

The findings prompt questions about the predictive role of HLA-I genetic disruption in immunotherapy response in CTCL. HLA expression is undoubtedly indispensable for antigen presentation. However, effective antigen presentation relies on the coordinated interplay of myriad mechanisms operating across different levels, including genetic, epigenetic, transcriptional, posttranscriptional, and tumor microenvironmental regulation. This complexity provides tumor cells with various mechanisms to disrupt antigen presentation, and genetic defects in HLA-I may represent only the tip of the iceberg. Accordingly, HLA-I genetic defects, particularly in isolation, have limitations as predictive biomarkers, which may explain some counterintuitive observations in the study. For instance, reduced antigen presentation is an established mechanism of resistance to ICI therapy in solid tumors.^6,7 However, in patient 8, the subclone containing the HLA-B splice variant responded to pembrolizumab, whereas a related subclone with fully intact HLA expression was resistant. This paradox may be explained by retained total surface HLA-I expression or cross-presentation, allowing the subclone with allele-specific HLA-I loss to remain responsive to pembrolizumab. If true, combining ICIs with strategies to increase general HLA-I expression---such as interferon or epigenetic modulators---may reduce treatment resistance in CTCL.⁸ 

Kwang et al’s findings underscore the need for appropriate HLA-I assessment methods. Despite nearly all immunotherapies relying on functional surface HLA-I, routine assessment of HLA-I is not commonly implemented in immune oncology, partly due to the absence of standardized protocols. Immunohistochemistry is used most often, but its inability to capture allele-specific losses limits its effectiveness in diseases like CTCL, where such losses are common. In this context, targeted sequencing offers more precise and comprehensive detection of HLA-A, -B, and -C alleles.

Overall, the study has conceptual and practical implications and raises intriguing questions that warrant future exploration. Ultimately, broader adoption of in-depth immune profiling beyond HLA-I analysis may be necessary to understand immune evasion, establish reliable biomarkers, and tailor individual treatment. It is hoped that this important study will inspire continued research in this area.

Conflict-of-interest disclosure: The authors declare no competing financial interests.