small molecules

2026-03-30 | Rare internal malignancies in xeroderma pigmentosum: A report of two cases from Tunisia and analysis of driver mutations.

Xeroderma pigmentosum (XP)-associated internal malignancies are characterized by their rarity, early onset, atypical histological presentations, and poorly characterized genomic landscape. In this study, we report the clinical, pathological, and molecular features of two rare XP-associated internal malignancies, focusing on their somatic mutation profiles. These tumors represented rare histological variants at their respective anatomical sites: an ovarian high-grade sex cord-stromal tumor (HG-SCST) with heterologous rhabdomyosarcomatous differentiation diagnosed in an 18-year-old female, harboring a homozygous XP Complementation Group C (XPC): NM_004628.5:c.1643_1644delTG (p.Val548Alafs∗25) mutation and a renal leiomyosarcoma diagnosed in a 14-year-old male carrying a homozygous XPC: NM_004628.5:c.850G>T (p.Glu284∗) mutation. Neither patient had a documented history of cutaneous malignancies. The patient with the ovarian tumor exhibited no response to chemotherapy and succumbed six months after diagnosis, whereas the patient with the renal leiomyosarcoma initially achieved a complete response but subsequently relapsed and died after five years and eight months of follow-up. The literature review identified only one previously reported case of renal leiomyosarcoma in a patient with XP and seven cases of XP-associated malignant ovarian tumors, including four SCSTs. In this study, targeted next-generation sequencing using the AmpliSeq for Illumina Cancer HotSpot Panel identified pathogenic mutations in canonical cancer driver genes: tumor protein p53 (TP53) NM_000546.6:c.730G>T (p.Gly244Cys) and platelet-derived growth factor receptor alpha (PDGFRA) NM_006206.6:c.2525A>T (p.Asp842Val) mutations in renal leiomyosarcoma and NRAS proto-oncogene, GTPase (NRAS) NM_002524.5:c.35G>T (p.Gly12Val) mutation in the ovarian tumor. These findings suggest a potential benefit of personalized therapies for XP patients with internal malignancies.

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2025-08-12 | Uncovering the Role of DNA Repair Impairment in UVA-Induced Mutagenesis in Human Xeroderma Pigmentosum Variant Cells.

Ultraviolet A (UVA) radiation induces DNA damage both directly, by forming cyclobutane pyrimidine dimers (CPDs), and indirectly, by generating oxidative stress. Cells rely on nucleotide excision repair (NER) and translesion synthesis (TLS) to tolerate these lesions. Xeroderma pigmentosum variant (XP-V) cells, deficient in DNA polymerase eta (pol eta), exhibit a heightened risk of skin cancer due to impaired TLS. While XP-V patients are considered NER-proficient, our findings challenge this assumption by demonstrating that UVA-induced oxidative stress impaired NER activity, leading to increased C > T transitions at CPD sites. Whole-exome sequencing of UVA-irradiated XP-V cells revealed a substantial rise in mutations, with a distinct C > T signature characteristic of defective CPD repair. Notably, pretreatment with the antioxidant N-acetylcysteine (NAC) mitigated this effect, reducing C > T transitions through enhanced NER function and decreasing C > A transversions via its antioxidant properties. These results redefine the mutagenic landscape of XP-V cells, revealing that oxidatively generated damage to NER proteins-rather than TLS deficiency alone-contributes to their elevated mutation burden. Our findings suggest that antioxidant strategies may partially protect XP-V patients from UVA-driven mutagenesis enhancing the cells' DNA repair capacity, ultimately reducing skin cancer and contributing to better overall health outcomes.

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2025-01-01 | Structural and function impact of ERCC2 gene variants in Xeroderma pigmentosum: An integrative computational and docking analysis

Xeroderma pigmentosum (XP) is a rare inherited disorder that causes extreme sensitivity to sunlight, leading to early-onset skin lesions, eye complications, and a higher risk of developing tumors. The disease occurs due to defects in the DNA repair system, especially in the ERCC2 gene, which encodes a helicase enzyme essential for repairing ultraviolet-induced DNA damage. This study aimed to identify genetic variations in ERCC2 that may contribute to XP and to examine how these changes affect the structure and function of the encoded protein through detailed in-silico analysis. Nonsynonymous SNPs were collected from the dbSNP, UniProt, and Ensembl databases and evaluated using several prediction tools, including SIFT, PolyPhen-2, PredictSNP, PROVEAN, and MutPred2. Protein stability and structural alterations were assessed through I-Mutant 3.0, MUpro, DynaMut2, and SWISS-MODEL. Three highly deleterious and novel missense mutations R112H, R450C, and R658H were identified as potentially damaging. Structural modeling indicated that the R658H mutation disturbs hydrogen bonding and changes the α-helical arrangement near the ATP-binding site, possibly reducing helicase activity. Molecular docking and 100 ns molecular dynamics simulations with Loniflavone and Palbociclib showed stable binding interactions. Analyses of RMSD, RMSF, radius of gyration, hydrogen bonds, and MM-PBSA free energy confirmed stronger affinity for Loniflavone (−72.3 kJ mol−1) than Palbociclib (−64.8 kJ mol−1). Density Functional Theory further supported their chemical reactivity, while StopTox predicted low toxicity. The computationally derived insights in this study lay a strong foundation for subsequent in-vitro and in-vivo validation. While this work focuses on in-silico modeling and molecular simulation, the proposed drug-like candidates warrant future biochemical and cellular assays to confirm their biological relevance.

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2024-10-21 | Cutaneous Squamous Cell Carcinoma and Multiple Basal Cell Carcinomas in Xeroderma Pigmentosum-Variant Type Treated with Imiquimod 5% Cream and Radiotherapy: A Case Report.

Xeroderma pigmentosum (XP) is a rare DNA repair disorder characterized by sensitivity to sunlight and predisposition to cutaneous malignancies. There are various types, including the Variant type, which does not manifest with acute sunburn reactions. This results to the development of multiple malignancies that are often discovered at late stages, making management more challenging. This is a case of a 54-year-old Filipino female presenting with multiple basal cell carcinomas (BCCs) on several areas of the face and advanced cutaneous squamous cell carcinoma (cSCC) on the right zygomatic area, treated with imiquimod 5% cream and external beam radiation therapy, respectively. There was an excellent response of the BCCs to imiquimod 5% cream and good tumoral response of the SCC to radiation therapy, with tolerable side effects, highlighting the use of these palliative treatment modalities for XP patients with multiple, unresectable, or difficult-to-treat cutaneous malignancies.

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2024-08-20 | Cell cycle arrest combined with CDK1 inhibition suppresses genome-wide mutations by activating alternative DNA repair genes during genome editing.

Cells regularly repair numerous mutations. However, the effect of CRISPR/Cas9-induced dsDNA breaks on the repair processes of naturally occurring genome-wide mutations is unclear. In this study, we used TSCE5 cells with the heterozygous thymidine kinase genotype (TK+/-) to examine these effects. We strategically inserted the target sites for guide RNA (gRNA)/Cas9 and I-SceI into the functional allele and designed the experiment such that deletions of > 81 bp or base substitutions within exon five disrupted the TK gene, resulting in a TK-/- genotype. TSCE5 cells in the resting state exhibited 16 genome-wide mutations that affected cellular functions. After gRNA/Cas9 editing, these cells produced 859 mutations, including 67 high-impact variants that severely affected cellular functions under standard culture conditions. Mutation profile analysis indicated a significant accumulation of C to A substitutions, underscoring the widespread induction of characteristic mutations by gRNA/Cas9. In contrast, gRNA/Cas9-edited cells under conditions of S∼G2/M arrest and cyclin-dependent kinase 1 inhibition showed only five mutations. Transcriptomic analysis revealed the downregulation of DNA replication genes and upregulation of alternative DNA repair genes, such as zinc finger protein 384 (ZNF384) and dual specificity phosphatase, under S∼G2/M conditions. Additionally, activation of nucleotide and base excision repair gene, including O-6-methylguanine-DNA methyltransferase and xeroderma pigmentosum complementation group C, was observed. This study highlights the profound impact of CRISPR/Cas9 editing on genome-wide mutation processes and underscores the emergence of novel DNA repair pathways. Finally, our findings provide significant insights into the maintenance of genome integrity during genome editing.

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proteins

2026-02-06 | [Clinical characterization and genetic analysis of a patient with Xeroderma pigmentosum in conjunct with basal cell carcinoma and melanoma due to variants of XPC gene].

To explore the clinical presentation and genetic etiology of a case with Xeroderma pigmentosum in conjunct with basal cell carcinoma and melanoma. A male patient with Xeroderma pigmentosum treated at Xinxiang Central Hospital in October 2022 was selected as study subject. Whole exome sequencing (WES) was carried out. Candidate variants were verified by Sanger sequencing of his family members. This study was approved by the Ethics Committee of the hospital (Ethics No.: 2021-167). Magnetic resonance imaging showed that the patient has a solid soft tissue mass in the anterior and lower part of his right eyeball and a small nodule on the left nasal wing. Histopathological biopsy showed that the periocular tumor was basal cell carcinoma in conjunct with malignant melanoma, and the nasal wing tumor was basal cell carcinoma. WES and Sanger sequencing revealed that he has harbored compound heterozygous variants of the XPC gene, namely c.2391delT (p.F797Lfs*11) and IVS1+1G>A, which were inherited from his father and mother, respectively. Based on the guidelines from the American College of Medical Genetics and Genomics (ACMG), the variants were rated as likely pathogenic (PVS1+PM2_Supporting+PM3) and pathogenic (PVS1+PM2_Supporting+PM3+PP5), respectively. The c.2391delT variant was unreported previously. Bioinformatic analysis suggests that it could significantly affect the tertiary structure of XPC protein. The c.2391delT(p.F797Lfs*11) and IVS1+1G>A compound heterozygous variants probably underlay the pathogenesis in this patient. The detection of the novel variant has enriched the mutational spectrum of the XPC gene.

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2025-11-17 | Expanding the landscape of nucleotide excision repair disorders: from discovery to therapy.

DNA damage and repair are central to the onset of cancer, aging, and aging-related diseases. Rare genetic defects in the nucleotide excision repair pathway, such as those causing the cancer-prone disorder xeroderma pigmentosum (XP) or the progeroid condition Cockayne syndrome, highlight the dramatic consequences of unrepaired DNA lesions. In this issue of the JCI, two related papers from Ogi and coworkers - Fassihi et al. and Nakazawa et al. - describe a new XP clinical entity, XP-J, linked to a pathogenic variant in the p52 subunit of the transcription-repair complex TFIIH. The studies' characterization of XP-J and the p52ΔC variant opened unexpected possibilities to ameliorate the molecular defect in another subunit of TFIIH that causes a different, more severe repair syndrome: trichothiodystrophy. This commentary provides a broader historical, medical, and molecular context for the intricate genotype-phenotype relationship between compromised repair and its clinical consequences and discusses next steps for the advances reported.

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2025-04-30 | Prevalence of NER DNA repair gene XPG rs17655 C>G polymorphism among Saudi Populations: A Comparative Study with Global population

Environmental toxins damage DNA, increasing the risk of cancer if not repaired. Xeroderma pigmentosum group G (XPG) is essential for nucleotide excision repair (NER). The XPG exon 15 C>G polymorphism may influence this process, increasing the risk of cancer. We examined the frequency of the XPG exon 15 C>G polymorphism in the Saudi population and compared it with that in other populations. By conducting a PUBMED search, we identified epidemiological studies across different ethnic groups. Allele and genotype frequencies were determined, and statistical analysis was performed using the SPSS 21 software. In Saudi Arabia, the frequency of the mutant allele G was 57%, which was higher than that reported in the USA, Brazil, and China. However, higher frequencies of G alleles were found in Germany (79%), India (65%), Italy (75%), Romania (78%), Spain (75%), and Tunisia (61%). The frequency of the GG genotype in Saudi Arabia was 32%, which was higher than that in the USA (5%), Brazil (12%), and other countries but lower than that in Germany, India, Italy, Romania, Spain, and Tunisia. It was found that the XPG exon 15 C>G polymorphism has a unique frequency pattern in Saudi Arabia, probably due to ethnic differences. This study provided insights into the role of GG variants in the progression and therapeutic response of cancer, leading to improved treatments for the Saudi population.

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2025-04-20 | Identification of a novel pathogenic XPC:c.2420 + 1 G>C variant in a patient with xeroderma pigmentosum.

Xeroderma Pigmentosum group C (XP-C) is a rare, inherited autosomal recessive genetic disorder characterized by extreme sensitivity to ultraviolet (UV) radiation, caused by mutations in the XPC gene. Among the eight XP complementation groups, XP-C is the most prevalent worldwide. Here, we present an 8-year-old girl with multiple discrete hyperpigmented and depigmented macules on her face, neck, upper chest, and arms. Her skin abnormalities first appeared around the age of one as dark patches on the face and neck, progressively worsening with sun exposure. The patient was also diagnosed with bilateral blepharoconjunctivitis and severe dry eye syndrome. Histopathological examination revealed hyperkeratinization of stratified squamous epithelium. Moreover, the proband also exhibited increased expression of PCNA, p53, and cleaved-caspase 3. Genetic analysis identified a novel homozygous pathogenic variant in the XPC gene at c.2420 + 1 G>C. We also demonstrated that the mutant can localize to the site of DNA damage, but it is defective in CPD repair. Among all reported intronic XPC variants, the XPC:c.2420 + 1 G>C mutation seems to have a significant impact as it results in a one-base-pair deletion at the splice donor site of exon 13. This leads to a frameshift, triggering nonsense-mediated decay and causing a premature stop codon in exon 14 of the XPC gene. Thus, the patient is advised to undergo regular examinations to monitor the progression of the disease and the development of precancerous lesions.

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2024-09-24 | Germline Variants in Patients Affected by Both Uveal and Cutaneous Melanoma.

Uveal melanoma (UM) and nonacral cutaneous melanoma (CM) are distinct entities with varied genetic landscapes despite both arising from melanocytes. There are, however, similarities in that they most frequently affect people of European ancestry, and high penetrance germline variants in BAP1, POT1 and CDKN2A have been shown to predispose to both UM and CM. This study aims to further explore germline variants in patients affected by both UM and CM, shedding light on the underlying genetic mechanism causing these diseases. Using exome sequencing we analysed germline DNA samples from a cohort of 83 Australian patients diagnosed with both UM and CM. Eight (10%) patients were identified that carried pathogenic mutations in known melanoma predisposition genes POT1, MITF, OCA2, SLC45A2 and TYR. Three (4%) patients carried pathogenic variants in genes previously linked with other cancer syndromes (ATR, BRIP1 and MSH6) and another three cases carried monoallelic pathogenic variants in recessive cancer genes (xeroderma pigmentosum and Fanconi anaemia), indicating that reduced penetrance of phenotype in these individuals may contribute to the development of both UM and CM. These findings highlight the need for further studies characterising the role of these genes in melanoma susceptibility.

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oligonucleotides

2023-06-28 | Deep intronic founder mutations identified in the ERCC4/XPF gene are potential therapeutic targets for a high-frequency form of xeroderma pigmentosum.

Xeroderma pigmentosum (XP) is a genodermatosis defined by cutaneous photosensitivity with an increased risk of skin tumors because of DNA repair deficiency. The worldwide prevalence of XP is ~1 to 4 in million, with higher incidence in some countries and regions including Japan (1 in 22,000) and North Africa due to founder mutations and a high degree of consanguinity. Among XP, the complementation group F (XP-F), is a rare form (1% of worldwide XP); however, this is underdiagnosed, because the ERCC4/XPF gene is essential for fetal development and most of previously reported ERCC4/XPF pathogenic variants are hypomorphs causing relatively mild phenotypes. From the largest Japanese XP cohort study, we report 17 XP-F cases bearing two pathogenic variants, both identified in deep intronic regions of the ERCC4/XPF gene. The first variant, located in intron 1, is a Japanese founder mutation, which additionally accounts for ~10% of the entire Japanese XP cases (MAF = 0.00196), causing an aberrant pre-mRNA splicing due to a miss-binding of U1snRNA. The second mutation located in intron eight induces an alternative polyadenylation. Both mutations cause a reduction of the ERCC4/XPF gene expression, resulting in XP clinical manifestations. Most cases developed early-onset skin cancers, indicating that these variants need critical attention. We further demonstrate that antisense oligonucleotides designed for the mutations can restore the XPF protein expression and DNA repair capacity in the patients' cells. Collectively, these pathogenic variants can be potential therapeutic targets for XP.

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2013-01-25 | Catalytic DNAs That Harness Violet Light To Repair Thymine Dimers in a DNA Substrate

UV1C is an in vitro selected catalytic DNA that shows efficient photolyase activity, using light of <310 nm wavelength to photo-reactivate CPD thymine dimers within a substrate DNA. We show here that a minimal mutational strategy of substituting a guanine analogue, 6MI, for single guanine residues within UV1C extends the DNAzyme's activity into the violet region of the spectrum. These 6MI point mutant DNAzymes fall into three distinct functional classes, which photo-reactivate the thymine dimer along different pathways. Cumulatively, they reveal the modus operandi of the original UV1C DNAzyme to be a surprisingly versatile one. The interchangeable properties of no less than six of the G→6MI point mutants highlight UV1C's built-in functional flexibility, which may serve as a starting point for the creation of efficient, visible light-harnessing, photolyase DNAzymes for either the prophylaxis or therapy of UV damage to human skin.

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2011-01-01 | A novel phosphatase modulating the DNA damage response and the tumor suppressor p53

The cellular genome is constantly exposed to harmful endogenous and exogenous factors. Unrepaired DNA lesions and mismatches promote genomic instability, a major cause of cancer. Therefore, the prompt recognition and repair of damaged DNA, and the senescence or elimination of cells with persistent damage, are crucial to preserve genomic stability and suppress transformation. These processes depend on a cascade of phosphorylations known as the DNA damage response. The phosphorylation of histone H2Ax on Ser139 is one of the earliest events upon activation of the cascade, and the phosphorylated histone, γH2Ax, serves as a marker of the damaged chromatin areas. Several kinases initiate the signal from the sites of the damage and transduce it to effector proteins, such as the tumor suppressor p53. The activation of p53 induces cell cycle arrest via the increased transcription of the Cdk inhibitor p21, and it promotes apoptosis mainly via the transcription of proapoptotic genes. The balance of phosphorylated versus unphosphorylated proteins regulate most of the known steps in the DNA damage response. Thus phosphatases are expected to act as modulators of this cascade; however, our knowledge regarding their precise role is very limited. To identify novel phosphatases that modulate the response to genotoxic stress, a high-throughput screen was performed using an siRNA library targeting the human phosphatase subunits. UVC irradiation was used to induce DNA damage in siRNA-transfected U2OS cells, an osteosarcoma-derived cell line with wild-type p53. The levels of p53 and γH2Ax were quantified by immunofluorescence in cells previously exposed or non-exposed to UVC irradiation. In this way, 39 phosphatase subunits were identified as potential regulators of the early DNA damage response and the tumor suppressor p53. Among them, the dual specificity phosphatase 18 (Dusp18) was a prominent negative regulator of p53. The depletion of Dusp18 induced the accumulation and activation of p53 and p21 in several cell lines. Dusp18 knockdown did not detectably increase the post-translational modifications of p53, nor did it abolish its interaction with its negative regulator Mdm2. The induction of p21 was p53-dependent, and chromatin immunoprecipitation showed an increased amount of p53 bound to the p21 promoter in cells transfected with siRNAs against Dusp18. Interestingly, Dusp18 depletion alone could induce apoptosis that was not dependent on p53, but was augmented in cells with wild-type p53. In addition, it promoted the activation of the DNA damage response cascade, as detected by the enhanced phosphorylation of Chk2 and H2Ax. Analysis of the cell cycle profile of Dusp18-depleted cells revealed an arrest in G1 and S phases, which was accompanied by reduced proliferation of these cells. Finally, the siRNAs against Dusp18 increased the sensitivity of tumor cells to the S phase specific genotoxic drug gemcitabine. Hence, the depletion of Dusp18 inhibits the proliferation and promotes the apoptotic death of tumor cells. Furthermore, the knockdown of Dusp18 can enhance the cytotoxic effect of therapeutic drugs like gemcitabine. These results identify Dusp18 as a novel phosphatase needed for the survival and proliferation of cancer cells, and as a suppressor of the DNA damage response and the p53 pathway, potentially identifying Dusp18 as a cancer drug candidate.

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2005-09-25 | Triplex targeted genomic crosslinks enter separable deletion and base substitution pathways

We have synthesized triple helix forming oligonucleotides (TFOs) that target a psoralen (pso) interstrand crosslink to a specific chromosomal site in mammalian cells. Mutagenesis of the targeted crosslinks results in base substitutions and deletions. Identification of the gene products involved in mutation formation is important for developing practical applications of pso-TFOs, and may be informative about the metabolism of other interstrand crosslinks. We have studied mutagenesis of a pso-TFO genomic crosslink in repair proficient and deficient cells. Deficiencies in non homologous end joining and mismatch repair do not influence mutation patterns. In contrast, the frequency of base substitutions is dependent on the activity of ERCC1/XPF and polymerase ζ, but independent of other nucleotide excision repair (NER) or transcription coupled repair (TCR) genes. In NER/TCR deficient cells the frequency of deletions rises, indicating that in wild-type cells NER/TCR functions divert pso-TFO crosslinks from processes that result in deletions. We conclude that targeted pso-TFO crosslinks can enter genetically distinct mutational routes that resolve to base substitutions or deletions.

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2004-04-01 | Chemical Tools for Targeted Mutagenesis of DNA Based on Triple Helix Formation

The development of methods for targeted mutagenesis shows promise as an alternative form of gene therapy. Triple helix-forming oligonucleotides (TFOs) provide an attractive strategy for inducing mutations. Especially, alkylation of nucleobases with functionalized TFOs would have potential for site-directed mutation. Several studies have demonstrated that treatment of mammalian cells with TFOs can be exploited to introduce desired sequence changes and point mutations. This review summarizes targeted mutagenesis using reactive TFOs, including studies with photo reactive psolaren derivatives as well as a new reactive derivative recently developed by our group.

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antibodies

2026-05-23 | Synergistic enhancement of PD-L1 expression from DNA repair dysfunction and UV exposure in xeroderma pigmentosum: Potential therapeutic role of PD-L1 inhibitors.

Xeroderma pigmentosum (XP) is a rare genetic disorder caused by defective nucleotide excision repair, leading to extreme UV sensitivity and early-onset skin cancers. Although PD-1/PD-L1 inhibitors have shown benefit in XP-associated tumors, the mechanisms that underpins these therapeutic responses remains unclear. To elucidate the molecular basis of XP pathogenesis in a 4-year-old Filipino girl and to investigate the potential role of PD-L1 inhibitors in treating XP-associated squamous cell carcinoma (SCC). A 4-year-old girl with XP underwent germline whole-exome sequencing. Transcriptomic profiling and immunochemistry validation were performed on XP-SCC and non-XP SCC tissues. In vitro assays using HaCaT keratinocytes evaluated DNA damage and PD-L1 expression following XPA knockdown and UV radiation. A Jurkat-HaCaT co-culture system, incorporating a PD-L1 neutralizing antibody, assessed T-cell attachment. A homozygous splice-site variant in XPA (c.556-1 C>G) was identified. RNA-seq revealed marked up-regulation of CD274 (PD-L1), PDCD1 (PD-1), and STAT1 in XP-SCC. In vitro, XPA-deficient keratinocytes exhibited increased UV-induced DNA damage and synergistic PD-L1 induction. Jurkat T-cell attachment was elevated in UV-exposed, XPA-deficient groups; crucially, this enhanced attachment was significantly abolished by PD-L1 blockade. XPA deficiency and UV-induced stress jointly enhance PD-L1 expression in XP-associated cSCC. These molecular and functional data provide biologic rationale for PD-L1-targeted therapy in XP and support further evaluation of immune checkpoint inhibitors in this population.

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2023-10-25 | Retrospective study of efficacy and adverse events of immune checkpoint inhibitors in 22 xeroderma pigmentosum patients with metastatic or unresectable cancers

Xeroderma pigmentosum (XP), a rare disease with defects in DNA repair genes, has >1,000-fold increased risk of ultraviolet-induced skin cancers. Immune checkpoint inhibitors (ICIs) are used for treating cancers with large numbers of mutations but may also promote adverse events (AEs). Deficient DNA repair in XP patients may lead to increased numbers of mutations, leading to enhanced efficacy of cancer response or, alternatively, to increased AE in response to ICI. We sought to compare the efficacy and AE of ICI in XP patients with metastatic or unresectable cancers to that of ICI-treated patients in the general population.In this retrospective study, we reviewed medical records of XP patients treated in the United States and in London (UK). We also reviewed published reports of ICI-treated XP patients and patients in the general population.Metastatic or unresectable cancers in all 22 (100%) XP patients showed regression or remission in response to ICI. The types and frequencies of AE in XP patients were similar to those reported among ICI-treated patients in the general population. However, two XP patients had concurrent additional cancers that did not respond to ICI, two XP patients had cancer recurrence or progression after initial response, and eight XP patients developed new skin cancers during or after ICI treatment.In this retrospective study with small sample size, XP patients demonstrated positive responses to ICI and the treatment was well tolerated but some patients developed new skin cancers while being treated. ICIs can be considered in treating metastatic or unresectable cancers in XP patients.

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2022-08-01 | Mutational signatures and increased retrotransposon insertions in Xeroderma Pigmentosum variant skin tumors

Abstract Xeroderma Pigmentosum variant (XP-V) is an autosomal recessive disease with an increased risk to develop cutaneous neoplasms in sunlight exposed regions. These cells are deficient in the translesion synthesis DNA polymerase eta. Eleven skin tumors from a genetic cluster of XP-V patients had their exome sequenced. Mutational signatures identified for most tumors were related to ultraviolet exposure, such as C>T transitions targeted to pyrimidine dimers. However, four samples carry different mutational signatures, with C>A mutations associated with tobacco usage. Basal cell carcinomas showed a distinct C>A mutation spectra reflecting a novel mutational signature. Higher levels for retroposon insertions were detected in the XP-V tumors, compared to non-XP skin tumors. The results reveal other possible causes for XP-V tumors and the involvement of polymerase eta in suppressing retrotransposition. The expected high mutation burden, found in most of these tumors, renders these XP patients good candidates for immunotherapy with checkpoint blockers.

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2022-06-25 | The landscape of genetic alterations of UVB‐induced skin tumors in DNA repair‐deficient mice

Non-melanoma skin cancer (NMSC) is mainly caused by ultraviolet (UV)-induced somatic mutations and is characterized by UV signature modifications. Xeroderma pigmentosum group A (Xpa) knockout mice exhibit extreme UV-induced photo-skin carcinogenesis, along with a photosensitive phenotype. We performed whole-exome sequencing (WES) of squamous cell carcinoma (SCC) samples after repetitive ultraviolet B (UVB) exposure to investigate the differences in the landscape of somatic mutations between Xpa knockout and wild-type mice. Although the tumors that developed in mice harboured UV signature mutations in a similar set of cancer-related genes, the pattern of transcriptional strand asymmetry was largely different; UV signature mutations in Xpa knockout and wild-type mice preferentially occurred in transcribed and non-transcribed strands, respectively, reflecting a deficiency in transcription-coupled nucleotide excision repair in Xpa knockout mice. Serial time point analyses of WES for a tumor induced by only a single UVB exposure showed pathogenic mutations in Kras, Fat1, and Kmt2c, which may be driver genes for the initiation and promotion of SCC in Xpa knockout mice. Furthermore, the inhibitory effects on tumor production in Xpa knockout mice by the anti-inflammatory CXCL1 monoclonal antibody affected the pattern of somatic mutations, wherein the transcriptional strand asymmetry was attenuated and the activated signal transduction was shifted from the RAS/RAF/MAPK to the PIK3CA pathway.

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2019-10-01 | Dramatic response of metastatic cutaneous angiosarcoma to an immune checkpoint inhibitor in a patient with xeroderma pigmentosum: whole-genome sequencing aids treatment decision in end-stage disease

“Mutational signatures” are patterns of mutations that report DNA damage and subsequent repair processes that have occurred. Whole-genome sequencing (WGS) can provide additional information to standard diagnostic techniques and can identify therapeutic targets. A 32-yr-old male with xeroderma pigmentosum developed metastatic angiosarcoma that was unresponsive to three lines of conventional sarcoma therapies. WGS was performed on his primary cancer revealing a hypermutated tumor, including clonal ultraviolet radiation-induced mutational patterns (Signature 7) and subclonal signatures of mutated DNA polymerase epsilon ( POLE ) (Signature 10). These signatures are associated with response to immune checkpoint blockade. Immunohistochemistry confirmed high PD-L1 expression in metastatic deposits. The anti-PD-1 monoclonal antibody pembrolizumab was commenced off-label given the POLE mutation and high mutational load. After four cycles, there was a significant reduction in his disease with almost complete resolution of the metastatic deposits. This case highlights the importance of WGS in the analysis, interpretation, and treatment of cancers. We anticipate that as WGS becomes integral to the cancer diagnostic pathway, treatments will be stratified to the individual based on their unique genomic and/or transcriptomic profile, enhancing classical approaches of histologically driven treatment decisions.

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other

2024-01-25 | Generation and characterization of CRISPR-Cas9-Mediated XPC Gene Knockout in Human Skin Cells

Xeroderma pigmentosum group C (XPC) is a versatile protein, crucial for sensing DNA damage in the global genome nucleotide excision repair (GG-NER) pathway. This pathway is vital for mammalian cells, acting as their essential approach for repairing DNA lesions stemming from interactions with environmental factors, such as exposure to ultraviolet (UV) radiation from the sun. Loss-of-function mutations in the XPC gene confer a photosensitive phenotype in XP-C patients with the accumulation of unrepaired UV induced DNA damage. This remarkable increase in DNA damage tends to elevate by 10,000-fold the risk of developing melanoma and non-melanoma skin cancers. To date, creating accurate and reproducible models to study human XP-C disease has been an important challenge. To tackle this, we used CRISPR-Cas9 technology in order to knockout XPC gene in various human skin cells (keratinocytes, fibroblasts, and melanocytes). After validation of the XPC knockout in these edited skin cells, we showed that they recapitulate the major phenotypes of XPC mutations: photosensitivity and the impairment of UV induced DNA damage repair. Moreover, these mutated cells demonstrated a reduced proliferative capacity compared to their respective wild-type controls. Finally, to better mimic the disease environment, we built a 3D reconstructed skin using these XPC knockout skin cells. This model exhibited an abnormal behavior, showing an extensive remodeling of its extracellular matrix compared to normal skin. Analyzing the composition of the fibroblasts secretome revealed a significant augmented shift in the inflammatory response following XPC knockout. Our innovative (disease on a dish) approach can provide valuable insights into the molecular mechanisms underlying XP-C disease, paving the way to design novel preventive and therapeutic strategies to alleviate the disease phenotype. Also, given the high risk of skin cancer onset in XP-C disease, our new approach can also serve as a link to draw novel insights towards this elusive field.

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2022-12-01 | 267 Generation and Characterization of a CRISPR-Cas9-Mediated XPC gene Knockout in Human Skin Cells

Xeroderma pigmentosum group C (XPC) is a multifunctional DNA damage recognition protein involved in the global genome nucleotide excision repair (GG-NER) pathway. Mammalian cells employ this pathway to eliminate bulky DNA lesions that induce double helix distortion caused by mutagens such as UV radiation or cisplatin. Loss-of-function mutations in the XPC gene lead to various malignancies, including skin cancers. Photosensitivity and the buildup of DNA damage can both define the phenotype of XPC patients' cells. To date, there is no relevant and reproducible cellular model available that can mimic the course of the human XPC disease. We carried out, for the first time, XPC gene editing in several immortalized skin cells (keratinocytes, fibroblasts, and melanocytes) using RNP (ribonucleoprotein) CRISPR-Cas9 technology where we had a tremendous editing efficacy. Characterization of the XPC gene mutation was validated at the mRNA and protein expression levels via qRT-PCR, western blot, and immunofluorescence and at the DNA level via automated Sanger sequencing. The viability of XP-C cells post UV radiation was further quantified by Presto Blue staining and the repair activity of DNA damage was assessed by Immunocytochemistry (ICC) via single-cell analysis. We showed that skin cells edited for the XPC gene recapitulate the major phenotypes of XPC mutations: photosensitivity and impairment of UV-damage repair. These cells will be used to investigate the etiology of skin cancers linked to XPC disease, unravel new protein biomarkers required for skin cancer genesis, and eventually design an innovative treatment or preventative measures for this disease. Finally, we will develop, for the first time, full XP-C skin organoids using the 3 cell types (keratinocytes, fibroblasts, and melanocytes) harboring XPC gene mutation.

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2021-09-27 | Novel pathogenic frameshift mutation in the POLH gene contributes to xeroderma pigmentosum variant type in a 16‐year‐old girl

Xeroderma pigmentosum (XP) is a rare, autosomal recessive disease. Based on a defect of DNA-repair mechanisms, patients suffer from increased photosensitivity and develop ultraviolet (UV) light-induced skin damage such as poikiloderma, early skin ageing and skin cancer at a young age.1 Here, we present an uncommon clinical XP presentation and the associated mutational status. A 16-year-old girl with Fitzpatrick skin type 2 presented with multiple erythematous, nodular skin lesions and substantial actinic damage of the face and upper chest (Fig. 1). The patient did not experience severe sun sensitivity. She denied any other medical conditions. Cognitive, neurological and motor development were normal. The family history was unremarkable for skin cancer, and her parents were not consanguineous. Skin biopsies confirmed multiple basal cell carcinomas and invasive squamous cell carcinomas on the grounds of actinic keratoses. We aimed to investigate a cancer-prone genetic disorder: Panel analysis including analysis of copy number variation of DDB1, DDB2, ERCC2, ERCC3, ERCC4, ERCC5, POLH, XPA, XPC revealed two different heterozygous pathogenic variants in POLH (NM_006502.2): c.(660+1_661-1)_(764+1_765-1)del, p.? and c.1189_1196del; p.(His397Ilefs*8), confirming the clinical diagnosis of xeroderma pigmentosum, variant type. Both, the previously reported deletion of Exon 6 and the novel frameshift variant, were classified as pathogenic.2 XP subtypes are divided into different complementation groups based on the affected gene. These complementation groups (XP-A to XP-G) and the XP variant (XP-V) feature different biochemical defects and clinical presentation as shown in Table 1. In contrast to all other complementation groups, XP-V cells show a normal nucleotide excision repair, but DNA polymerase eta is either absent or inactivated resulting in a defective postreplication, responsible for error-free translesion synthesis across DNA photoproducts. Thus, the ability to repair UV-induced DNA damage is drastically reduced. Predominant Skin tumours Previous analyses suggested a broad spectrum of different mutations; the novel frameshift variant of POLH found in our patient combined with a deletion of exon 6, previously published in the context of POLH-associated XP,3 led to a clinical presentation matching XP-V. Compared to all other complementation groups with a median onset of 8 years, XP-V patients typically show a late median onset of 24 years. Our patient developed rather early symptoms at 16 years: These differences may be explained by the patient’s skin type 2, high UV exposure growing up in a rural area and lack of awareness of an increased UV sensitivity. The type of mutation alone is not sufficient to individually predict the severity of disease.3 Presently, curative XP therapies are unavailable. Thus, preventive measures (e.g. sunscreen; UV shades for windows) and avoidance strategies (e.g. long clothing, avoiding midday sun) are essential. We recommended regular quarterly skin checks and performed micrographically controlled excisions, representing the treatment of choice for XP-induced skin cancer. Systemic treatment with immune checkpoint inhibitors may provide a viable option in more advanced stages of the disease.4 In the future, ex vivo gene editing of epidermal stem cells using vector-based techniques to repair defective XP genes may offer a perspective for causal treatment, yet currently experimental.5 None. The authors declare that the patient and her parents gave written informed consent for the publication of clinical information and photographic images in a publication intended for health professionals.

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2016-07-01 | Descemet Stripping Automated Endothelial Keratoplasty for Endothelial Dysfunction in Xeroderma Pigmentosum: A Clinicopathological Correlation and Review of Literature

Abstract: Xeroderma pigmentosum (XP) mainly affects the ocular surface; however, endothelial damage may also occur. We would like to report changes in the endothelial–Descemet layer and review the literature on similar findings in patients with XP, including the role of Descemet stripping automated endothelial keratoplasty (DSAEK) in the management of a 21-year-old man who presented with nonresolving corneal edema in the right eye after excision biopsy for conjunctival intraepithelial neoplasia. His best-corrected visual acuity (BCVA) was 20/200 in the right eye and 20/20 in the left eye. On general examination, there was patchy hyperpigmentation of the exposed areas of skin suggestive of XP. On examination of the right eye, there was stromal edema involving the exposed half of cornea. The left eye appeared normal. Pachymetry readings were 860 and 600 μm in the right and left eye, respectively. Descemet stripping automated endothelial keratoplasty was performed for endothelial dysfunction and the stripped endothelium, and Descemet membrane (DM) was sent for histopathologic evaluation. Postoperatively, the donor lenticule was well apposed and the overlying stromal edema resolved. The patient achieved a BCVA of 20/30 in the right eye without progression of corneal scarring at 1-year follow-up. In the meanwhile, however, the left eye developed corneal edema. Histopathology revealed gross attenuation of endothelial cells with uniform thickness of the DM. Corneal endothelial dysfunction in XP is amenable to treatment with DSAEK.

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2016-05-20 | Distinctive features of single nucleotide alterations in induced pluripotent stem cells with different types of DNA repair deficiency disorders

Disease-specific induced pluripotent stem cells (iPSCs) have been used as a model to analyze pathogenesis of disease. In this study, we generated iPSCs derived from a fibroblastic cell line of xeroderma pigmentosum (XP) group A (XPA-iPSCs), a rare autosomal recessive hereditary disease in which patients develop skin cancer in the areas of skin exposed to sunlight. XPA-iPSCs exhibited hypersensitivity to ultraviolet exposure and accumulation of single-nucleotide substitutions when compared with ataxia telangiectasia-derived iPSCs that were established in a previous study. However, XPA-iPSCs did not show any chromosomal instability in vitro, i.e. intact chromosomes were maintained. The results were mutually compensating for examining two major sources of mutations, nucleotide excision repair deficiency and double-strand break repair deficiency. Like XP patients, XPA-iPSCs accumulated single-nucleotide substitutions that are associated with malignant melanoma, a manifestation of XP. These results indicate that XPA-iPSCs may serve a monitoring tool (analogous to the Ames test but using mammalian cells) to measure single-nucleotide alterations, and may be a good model to clarify pathogenesis of XP. In addition, XPA-iPSCs may allow us to facilitate development of drugs that delay genetic alteration and decrease hypersensitivity to ultraviolet for therapeutic applications.

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