Melanoma is the fifth most common cancer in the United Kingdom and one of the most dangerous forms of skin cancer when it spreads beyond the skin. Surgery can be curative when the disease is detected early, while advanced melanoma may be treated with targeted drugs or immunotherapy. Checkpoint inhibitors have transformed care by releasing molecular brakes that normally restrain T cells, allowing these immune cells to recognise and attack tumour cells. Yet the treatment is far from universally effective: nearly half of patients do not obtain meaningful benefit, while some develop serious inflammatory side effects as the immune system attacks healthy tissues.

The new study focused on the adaptive immune system, the branch of immunity that develops highly specific responses to foreign or abnormal targets. T cells can directly kill cancer cells or coordinate broader immune activity, while B cells produce antibodies and can also present tumour-related antigens to T cells. Although B cells have historically received less attention in cancer immunology than T cells, growing evidence suggests that they can influence whether immunotherapy succeeds. The King’s-led team examined both cell types together, tracking how their activation states changed during treatment.

Researchers analysed blood samples from 24 people with stage 2 to stage 4 melanoma who were receiving checkpoint inhibitor immunotherapy at Guy’s and St Thomas’ NHS Foundation Trust. Samples were collected before treatment and at two time points during therapy, including within the first six weeks. Blood from 25 healthy volunteers was also assessed for comparison. Instead of examining only broad cell categories, the scientists used mass cytometry, a highly multiplexed technology that measures numerous proteins and other characteristics on individual cells simultaneously.

Mass cytometry enabled the team to distinguish rare immune-cell populations that would be difficult to identify using conventional methods. The researchers could determine whether B and T cells displayed signs of activation, maturation, proliferation or impaired function, then follow those features over time. This approach revealed substantial variation between patients even before treatment began, suggesting that the immune system’s starting condition may influence how an individual responds to immunotherapy.

Patients with favourable outcomes tended to show renewed activation and expansion of both B-cell and T-cell populations during the early stages of treatment. This pattern was interpreted as evidence of immune reinvigoration: checkpoint inhibitors appeared to restore or amplify immune responses that had been suppressed by the tumour or by chronic exposure to tumour antigens. The coordinated behaviour of the two cell types was particularly important, because effective anti-cancer immunity often depends on communication between antibody-producing B cells, antigen-presenting cells and tumour-killing T cells.

In contrast, patients whose blood continued to contain immature or poorly functioning B-cell populations during treatment generally experienced less favourable outcomes. Weaker baseline B-cell and T-cell anti-cancer responses were also associated with poorer survival after therapy. Certain T-cell subtypes appeared to be linked with treatment-related toxicity, indicating that the same immune activation that can damage tumours may sometimes trigger inflammation in healthy organs. However, the researchers emphasised associations rather than definitive proof that these cell populations directly cause treatment success or side effects.

The results are promising because blood sampling is substantially less invasive than repeated tumour biopsies. A future immune-monitoring test could potentially measure B-cell maturation, T-cell activation and changes in immune-cell abundance before and shortly after therapy begins. Such information might help oncologists decide which patients should continue a treatment, receive intensified surveillance or be assessed early for immune-related complications. Nevertheless, the study was small, and the findings must be validated in larger patient groups before they can be used to guide clinical decisions. Immune profiles may also differ between cancer types, treatment combinations and disease stages.

Lead author Lucy Booth, a PhD student at King’s College London’s St John’s Institute of Dermatology, said the work highlights the importance of studying B cells alongside T cells. Professor Sophia Karagiannis, Professor of Translational Cancer Immunology and Immunotherapy at King’s, said that analysing the two adaptive immune-cell populations over time showed how they simultaneously change during treatment. The group previously identified blood-based B-cell markers associated with immunotherapy toxicity and treatment response, and now plans to investigate how B and T cells behave inside tumours themselves. The researchers also hope to repeat the analysis in larger cohorts and in other cancers, including triple-negative breast cancer, where treatment options remain limited.

Subject of Research: People

Article Title: Circulating B cell and T cell activation states predict clinical outcomes in melanoma and reveal dynamic immune reinvigoration with checkpoint inhibitor immunotherapy

Web References: Journal for ImmunoTherapy of Cancer study; King’s College London research background

References: DOI: 10.1136/jitc-2026-015585

Keywords: melanoma, immunotherapy, checkpoint inhibitors, B cells, T cells, immune profiling, mass cytometry, cancer immunology, treatment response, immune-related side effects

At the core of this investigation lies a novel Multi-Patient-Targeted (MPT) single-cell DNA sequencing approach. Unlike previous studies that have often relied on bulk sequencing methods, this technique integrates bulk exome sequencing with the high-resolution capabilities of Tapestri single-cell DNA sequencing. By designing a patient-specific targeted mutation panel, the researchers achieved an unprecedented sensitivity in detecting rare clonal mutations that drive tumor progression. The application of MPT sequencing thus represents a significant advance in the molecular characterization of heterogenous tumor populations within individual CSCC patients.

The study focused on a cohort of Chinese CSCC patients, and the genomic profiles revealed a diverse array of somatic mutations. Missense mutations emerged as the predominant mutational type across tumor samples. Among the most frequently mutated genes were NOTCH1, TP53, NOTCH2, and others involved in critical cellular pathways such as cell-cycle regulation, DNA damage repair, and signal transduction. The mutational patterns bore remarkable resemblance to those previously reported in Korean and Caucasian cohorts, underscoring certain conserved genomic features of CSCC across ethnicities.

However, the researchers also discovered significant population-specific variations. Notably, mutation frequencies in genes like HRAS, TTN, MUC16, and MUC4 deviated markedly from those observed in non-Chinese populations. These findings highlight the necessity of considering ethnic diversity when designing mutation panels and therapeutic approaches, as distinct mutational signatures may influence tumor biology and treatment response differentially.

The analytic strength of single-cell DNA sequencing transcended the identification of mutations; it provided a window into clonal architecture and tumor evolution. By dissecting individual cancer cells, the study traced dynamic clonal trajectories within tumors, revealing how distinct subclones emerge, expand, or diminish over time. Such clonal evolution patterns elucidate the heterogeneity underpinning tumor aggressiveness and metastatic potential, offering prognostic value and aiding in the anticipation of therapy resistance.

Intriguingly, the MPT scDNA-seq approach uncovered two low-frequency mutation clones involving the genes NLRP5 and HMMR. Though these clones existed in minor proportions within tumors, their influence on clonal evolution and tumor behavior appears substantial. NLRP5 and HMMR have been implicated in regulatory pathways associated with cellular proliferation and immune responses, suggesting that even rare clonal populations could orchestrate critical oncogenic processes.

Further comparative analyses probed the relationships between specific gene mutations and clinical parameters such as tumor stage and patient sex. The study illuminated previously unappreciated associations, indicating that certain mutational profiles may predispose tumors to more advanced stages or may exhibit sex-based prevalence. These correlation patterns pave the way toward more nuanced risk stratification frameworks tailored to individual genetic contexts.

The broader implications of this study lie in its provision of a robust framework for personalized oncology in CSCC. By integrating high-resolution scDNA-seq data with clinical phenotypes, the research generates actionable insights that can guide precision medicine efforts. Custom-designed mutation panels, based on comprehensive bulk and single-cell sequencing data, foster the identification of subclonal populations that might escape conventional detection yet drive disease progression.

From a technical standpoint, the collaborative use of bulk exome sequencing and the Tapestri platform for scDNA-seq exemplifies innovative cross-method integration. Bulk sequencing acted as a foundation to identify prevalent and patient-specific mutations, which then informed panel design for targeted single-cell interrogation. This layered approach optimizes resource efficiency while maximizing the depth and accuracy of mutational discovery.

The study also forms a critical comparative reference by juxtaposing mutational data derived from Chinese patients with those from Korean and Caucasian populations. This comparative genomics angle not only advances the understanding of CSCC’s ethnic variability but also calls attention to the limitations of one-size-fits-all diagnostic and therapeutic tools. Ethnic-specific panels and treatment regimens might be necessary to achieve optimal outcomes in diverse patient populations.

Interestingly, the identification of clonal mutations such as those in NOTCH1 and TP53 corroborates their established roles as key drivers in squamous cell carcinomas. Their persistent presence across populations underscores the potential for these genes to serve as universal therapeutic targets. Meanwhile, the discovery of novel mutation clones invites further research to elucidate their biological functions and therapeutic potential.

The insights gained from this study are expected to catalyze downstream clinical research, including the exploration of targeted therapies that disrupt clonal evolution pathways. By interrupting the emergence or dominance of aggressive tumor subclones, clinicians may be able to forestall metastasis and improve patient survival. Moreover, monitoring clonal dynamics through repeated single-cell sequencing could enable real-time evaluation of treatment efficacy.

This groundbreaking research not only charts the complex genomic terrain of CSCC but also exemplifies the transformative power of next-generation sequencing technologies when applied in a patient-tailored manner. The MPT scDNA-seq methodology stands poised to become a valuable tool in both basic cancer biology and clinical oncology, enabling the disentangling of tumor heterogeneity and the tailoring of personalized interventions.

In summary, the study presents a compelling paradigm shift in how cutaneous squamous cell carcinoma is studied and understood at the molecular level. It bridges technologic innovations with clinical imperatives, laying the groundwork for mutation-informed diagnostics and treatments. As genomic medicine continues its rapid evolution, such approaches hold promise for controlling a cancer that has long been notorious for its unpredictability and resistance.

Going forward, the integration of genomic data with transcriptomic and proteomic profiles could deepen the understanding of how genetic alterations translate into phenotypic behaviors. Combined multi-omics analyses at the single-cell level may unravel the full complexity of CSCC and unveil novel biomarkers for early detection, prognosis, and therapy selection.

Ultimately, this research epitomizes how methodical, high-resolution genomic investigations can reveal the underpinnings of cancer heterogeneity and evolution, which are pivotal to overcoming the challenges of metastatic and treatment-resistant skin cancers. By illuminating the mutational landscapes and clonal architectures, the study charts a path toward more effective and individualized management of cutaneous squamous cell carcinoma.

Subject of Research: Genomic heterogeneity and mutational landscape in cutaneous squamous cell carcinoma (CSCC) using multi-patient-targeted single-cell DNA sequencing.

Article Title: Analysis of genomic heterogeneity and the mutational landscape in cutaneous squamous cell carcinoma through multi-patient-targeted single-cell DNA sequencing.

Article References:
Chen, W., Xu, J., Yu, C. et al. Analysis of genomic heterogeneity and the mutational landscape in cutaneous squamous cell carcinoma through multi-patient-targeted single-cell DNA sequencing. BMC Cancer 25, 1362 (2025). https://doi.org/10.1186/s12885-025-14585-z

Image Credits: Scienmag.com

DOI: https://doi.org/10.1186/s12885-025-14585-z