How Restoring Immune Function Cured Treatment-Resistant Skin Cancer

Table of Contents

• Background: Understanding Skin Cancer and HPV
• The Patient's Story: A Complex Medical History
• How Researchers Investigated This Case
• Detailed Analysis of the Skin Cancer
• Genetic and Immune System Discoveries
• The Comprehensive Treatment Strategy
• Treatment Outcomes and Immune Recovery
• What This Means for Patients
• Study Limitations and Considerations
• Source Information

Background: Understanding Skin Cancer and HPV

Skin cancers, including cutaneous squamous-cell carcinoma (SCC), are the most common cancers in the United States and worldwide. While most skin cancers have good outcomes, approximately 3-5% of patients develop locally advanced or metastatic disease that can be life-threatening. Researchers have well understood the roles of ultraviolet (UV) exposure, skin type, age, and sex in skin cancer development, but the contribution of certain viruses and immune surveillance has remained unclear.

Cutaneous β-human papillomaviruses (β-HPVs) were previously believed to only facilitate early cancer development in a "hit-and-run" model, where they help accumulate UV-induced DNA damage but then become unnecessary for maintaining the cancer. This differs from mucosal HPVs (like those causing cervical cancer), where the virus directly drives cancer development through continuous expression of viral oncogenes. The role of immune escape—how cancers evade the immune system—in skin cancer development has also been uncertain, though we know immunocompromised patients have higher rates of skin cancer.

The Patient's Story: A Complex Medical History

The study patient was a 34-year-old woman with a history of cryptococcal meningitis (a serious fungal infection affecting the brain and eyes) who developed progressively worsening HPV-related diseases. She had:

• Oral condylomas (wart-like growths)
• Diffuse verrucous lesions (extensive wart-like skin changes)
• Multiple recurrent cutaneous SCCs on sun-exposed skin
• 43 different biopsy-proven lesions or sites affected

Her susceptibility to infections and skin cancers was initially attributed to a combined immunodeficiency and radiation-sensitivity caused by ZAP70 deficiency and biallelic RNF168 variants. The defect in UV-mediated DNA repair caused by RNF168 mutations in skin cells was believed to substantially increase risks and reduce benefits of hematopoietic-cell transplantation (HCT, also known as bone marrow transplant).

The development of a recurrent, invasive cutaneous SCC on her forehead that resisted multiple courses of aggressive surgical resection and checkpoint-inhibitor immunotherapy prompted referral to the National Institutes of Health for advanced evaluation and treatment.

How Researchers Investigated This Case

The patient provided written informed consent for enrollment in three clinical studies and was evaluated at the NIH Clinical Center. Researchers used multiple advanced techniques to understand her condition:

1. Flow cytometric analysis for T-cell immunophenotyping
2. Functional analysis of T-cell activation and proliferation
3. Analysis of HPV-specific T-cell responses
4. Assessment of DNA repair capabilities
5. Western blot analysis of ZAP70 signaling
6. Histologic and molecular analysis of the cutaneous SCC
7. HPV genotyping and identification of somatic variants in cancer-relevant genes

All experimental methods and clinical protocols were approved by the institutional review board at the NIH to ensure ethical research standards.

Detailed Analysis of the Skin Cancer

The forehead SCC showed concerning features indicating high risk for recurrence and spread:

• Large size: 5.2 cm
• Deep invasion: 6 mm depth
• Prominent desmoplastic stromal reaction (dense fibrous tissue surrounding cancer cells)
• Perivascular and perineural invasion (cancer cells invading blood vessels and nerves up to 3 mm in size)
• Moderate to poor differentiation (more aggressive cancer cells)

Despite previous reports suggesting β-HPVs aren't expressed in advanced cutaneous SCC, RNA sequencing revealed high levels of HPV19 transcription—a β1-HPV variant associated with cutaneous cancers. The analysis showed:

• Two internal junctions within the HPV19 genome suggesting recombined viral DNA
• Five host-virus junctions across four chromosomes indicating multiple integration events
• Active transcription of HPV19 products in the SCC

DNA sequencing identified no somatic driver mutations commonly associated with cutaneous SCC (TP53, NOTCH1/2, or CDKN2A genes) and no microsatellite instability. The tumor mutational burden was only 5.7 mutations per megabase—well below the average 50 mutations per megabase typically seen in cutaneous SCC.

Analysis of mutational signatures showed only modest ultraviolet exposure signatures (26% compared to 77% average in sporadic cutaneous SCC), along with signatures of aging, alkylating agents (25%), and approximately 50% unknown mutational patterns.

Genetic and Immune System Discoveries

Whole-exome sequencing confirmed a homozygous RNF168 missense variant (p.D103N) that had been previously proposed to confer radiation hypersensitivity. However, this variant had an elevated minor allele frequency (0.14) in the admixed American population and was predicted to be benign in computer models.

Functional testing showed normal DNA repair response to double-strand breaks after irradiation, with normal protein phosphorylation-dephosphorylation kinetics and levels of apoptosis and cell death within reference limits—supporting a lack of genetic radiation sensitivity.

The critical finding was compound ZAP70 heterozygous missense variants (c.733G→A, p.G245R; and c.1505C→T, p.P502L) that alter highly conserved residues in the carboxyterminal-SH2 domain and kinase domain of ZAP70. These variants were predicted to be damaging and segregated with the disease phenotype in the family.

ZAP70 is crucial for T-cell receptor (TCR) signaling. When T-cells encounter their specific target, signal transduction occurs through a complex process involving multiple proteins. The patient's CD4 and CD8 T cells showed:

• Reduced levels of phosphorylated ZAP70 after TCR stimulation
• Minimal downstream phosphorylated PLC-γ1 and ERK (key signaling molecules)
• Profound impairment of T-cell activation and proliferation in response to stimulation
• Minimal response to β1-HPV19 E6-peptide pools

The Comprehensive Treatment Strategy

After ruling out underlying ultraviolet hypersensitivity, researchers attributed a causative role to the ZAP70-mediated TCR defect for the recurrent mucocutaneous HPV-related diseases, including the β1-HPV19-related cutaneous SCC.

Since this invasive, unresectable, high-risk cutaneous SCC with β1-HPV19 genomic integration was resistant to standard treatments due to the underlying TCR-signaling defect, an integrated management plan was developed after ruling out distant metastasis by positron-emission tomography.

The treatment approach included:

1. Combination therapy with cetuximab, 5-fluorouracil, and cisplatin
2. Cutaneous SCC prophylaxis with capecitabine and nicotinamide
3. Haploidentical hematopoietic-cell transplantation (HCT) from a ZAP70 wild-type donor to definitively treat the underlying immunodeficiency

Treatment Outcomes and Immune Recovery

The patient experienced no clinical complications throughout treatment. Stable resolution of all HPV skin-related diseases was achieved after HCT and maintained up to the most recent follow-up at 35 months after transplantation.

After engraftment of the ZAP70 wild-type haploidentical donor:

• TCR signaling function and integrity was completely restored
• T-cell activation and proliferation normalized
• Robust expansion of HPV19-specific T cells occurred
• Gene-expression patterns in resting and TCR-stimulated CD4 and CD8 T cells became similar to those observed in healthy controls

The complete resolution included all facial skin lesions, verruca vulgaris and flat warts on the left leg and hand, and the recurrent invasive cutaneous SCC that had previously resisted multiple treatments.

What This Means for Patients

This case demonstrates that β-HPVs can play a direct oncogenic role in cutaneous SCC maintenance, not just as early facilitators as previously believed. The research shows that:

• Certain immune deficiencies (specifically ZAP70 defects affecting TCR signaling) can create permissive environments for HPV-driven cancers
• Comprehensive genetic and immunologic evaluation can identify treatable underlying causes of treatment-resistant cancers
• Restoring proper immune function through HCT can resolve even advanced, treatment-resistant HPV-related diseases
• HPV vaccination and immune-based therapies may have broader applications than previously recognized

For patients with recurrent or treatment-resistant skin cancers, particularly those with other immune-related issues, this research suggests that comprehensive immune evaluation might reveal underlying treatable conditions. The success of this approach highlights the importance of considering the immune environment in cancer treatment and the potential for immunotherapeutic approaches even in advanced cases.

Study Limitations and Considerations

While this case provides groundbreaking insights, several limitations should be considered:

• This is a single case study, and results may not apply to all patients with similar conditions
• The specific genetic mutations in this patient are rare, and most skin cancer patients won't have this exact immune deficiency
• Hematopoietic-cell transplantation carries significant risks and is not appropriate for all patients
• The long-term outcomes beyond 35 months are still being monitored
• The approach requires highly specialized medical centers with expertise in both immunology and oncology

Further research is needed to understand how common similar mechanisms are in other patients with treatment-resistant skin cancers and whether less invasive immunotherapies might achieve similar results in patients with different types of immune deficiencies.

Source Information

Original Article Title: Resolution of Squamous-Cell Carcinoma by Restoring T-Cell Receptor Signaling

Authors: Stefania Pittaluga, Roshini S. Abraham, Peiying Ye, Jenna R.E. Bergerson, Isaac Brownell, Gabriel J. Starrett, Megan V. Anderson, Triscia Martin, Derek MacMath, Hye Sun Kuehn, Jyothi Padiadpu, Siqi Zhao, Sergio D. Rosenzweig, Roxane Tussiwand, Warren J. Leonard, Mark Raffeld, Danielle E. Arnold, Andrea Lisco

Publication: New England Journal of Medicine, 2025;393:469-78

DOI: 10.1056/NEJMoa2502114

Funding: National Institutes of Health

This patient-friendly article is based on peer-reviewed research originally published in the New England Journal of Medicine. It maintains all significant findings, data points, and clinical details from the original study while making the information accessible to patients and caregivers.