Probes for TP53

Esophageal verrucous carcinoma (VSCC) is a rare and morphologically distinct type of esophageal squamous cell carcinoma (SCC). Diagnosing VSCC on biopsy material is challenging given the lack of significant atypia and the presence of keratinizing epithelium and exophytic growth. The molecular pathogenesis of VSCC remains unclear. The aim of this study was to characterize the genomic landscape of VSCC in comparison to conventional esophageal SCC. Three cases of VSCC from the Brigham and Women's Hospital pathology archive were identified. Formalin-fixed, paraffin-embedded (FFPE) tumor tissue was used for p16 immunohistochemistry (IHC), high-risk HPV in situ mRNA hybridization (ISH), and DNA isolation. Tumor DNA was sequenced using a targeted massively parallel sequencing assay enriched for cancer-associated genes. Three additional cases of VSCC were identified by image review of The Cancer Genome Atlas (TCGA) esophageal SCC cohort. VSCC cases were negative for p16 IHC and high-risk HPV ISH. TP53 mutations (p<0.001) and copy number variants (CNVs) for CDKN2A (p<0.001), CDKN2B (p<0.01) and CCND1 (p<0.01) were absent in VSCC and significantly less frequent in comparison to conventional SCC. Five VSCC cases featured SMARCA4 missense mutations or inframe deletions compared to only 4/88 conventional SCC cases (p<0.001). VSCC featured driver mutations in PIK3CA, HRAS, and GNAS. Recurrent CNVs were rare in VSCC. VSCC is not only morphologically but also genetically distinct from conventional esophageal SCC, featuring frequent SMARCA4 mutations and infrequent TP53 mutations or CDKN2A/B CNVs. Molecular findings may aid in establishing the challenging diagnosis of VSCC. This article is protected by

Full size image [/article/10.1007/s42764-021-00038-x/figures/1] The findings described above support the statement that HPV infection is common, but, in comparison, cervical cancer is quite rare, leading to the conclusion that HPV infection alone is not sufficient to produce cancer, as tumor development and progression require the contribution of multiple factors. Among the risk factors for cancer development and progression in women infected with HR HPV are the determinants of persistent infection, as it is well established that only women in whom HR HPV infection persists are at risk for cervical lesions that may progress to cancer (Banister et al. 2015 and references therein). HPV persistence has also been linked to HPV-mediated disease in men (Bettampadi et al. 2020 [/article/10.1007/s42764-021-00038-x#ref-CR16]). This is an important area of study, because in principle, if we were able to determine at a single visit whether or not an incident HR HPV infection will persist, we could target HPV-mediated cancer surveillance resources to the people who present with persistent infection. Our own (unpublished) findings support the concept that women with persistent HPV infection fail to mount a strong immune response to HPV. In turn, immune responses to HPV are likely to be influenced by HLA and SNP profiles, both of which have been linked with cervical cancer susceptibility (Chen et al. 2014; Das Gosh et al. 2017). Among the many SNPs that have relevance for cervical cancer development, the Arg/Pro TP53 polymorphism at codon 72 has received considerable attention, as the homozygote Arg/Arg phenotype is associated with a higher risk of developing cervical cancer, at least in certain populations (Ojeda et al. 2003; Chuery et al. 2017). TP53 codon 72 polymorphism has been connected with higher HPV E6/E7 expression, which appears to correlate with the Arg/Arg genotype (Chuery et al. 2017). Despite the continuing controversies in this area, there is evidence that this particular polymorphism plays a role in cervical cancer development, albeit with additional intervening factors that may modulate its impact in different populations.

The genomic alterations contributing to the pathogenesis of conjunctival squamous cell carcinomas (SCCs) and their precursor lesions are poorly understood and hamper our ability to develop molecular therapies to reduce the recurrence rates and treatment-related morbidities of this disease. We aimed to characterize the somatic DNA alterations in human papillomavirus (HPV)-positive and HPV-negative conjunctival SCC.Patients diagnosed with conjunctival SCC in situ or SCC treated in ocular oncology referral centers in Denmark were included. HPV detection (HPV DNA PCR, p16 immunohistochemistry, and mRNA in situ hybridization) and targeted capture-based next-generation sequencing of 523 genes frequently involved in cancer were performed to describe the mutational profile based on HPV status.Tumor tissue was available in 33 cases (n = 8 conjunctival SCCs in situ, n = 25 conjunctival SCCs), constituting 25 male and 8 female patients. Nine cases were HPV positive. The HPV-positive SCCs in situ and SCCs were characterized by transcriptionally active high-risk HPV (types 16 and 39) within the tumor cells, frequent mutations in PIK3CA (n = 5/9), and wild-type TP53, CDKN2A, and RB1, while the HPV-negative counterparts harbored frequent mutations in TP53 (n = 21/24), CDKN2A (n = 7/24), and RB1 (n = 6/24).Our findings have delineated two potentially distinct distributions of somatic mutations in conjunctival SCC based on HPV status-pointing to different biological mechanisms of carcinogenesis. The present findings support a causal role of HPV in a subset of conjunctival SCC.

Neuroendocrine neoplasms (NENs) of the cervix are rare aggressive tumors associated with poor prognosis and only limited treatment options. Although there is some literature on molecular underpinnings of cervical small cell neuroendocrine carcinomas (SCNECs), detailed morphologic and associated molecular characteristics of cervical NENs remains to be elucidated. Herein, 14 NENs (SCNEC: 6, large cell neuroendocrine carcinoma [LCNEC]: 6, neuroendocrine tumor [NET]: 2), including 5 admixed with human papillomavirus (HPV)-associated adenocarcinoma (carcinoma admixed with neuroendocrine carcinoma) were analyzed. All except 3 SCNECs were HPV16/18 positive. TP53 (3) and/or RB1 (4) alterations (3 concurrent) were only seen in SCNECs (4/6) and were enriched in the HPV16/18-negative tumors. The other most common molecular changes in neuroendocrine carcinomas (NECs) overlapping with those reported in the literature for cervical carcinomas involved PI3K/MAPK pathway (4) and MYC (4) and were seen in both SCNECs and LCNECs. In contrast, the 2 NETs lacked any significant alterations. Two LCNECs admixed with adenocarcinoma had enough material to sequence separately each component. In both pathogenic alterations were shared between the 2 components, including ERBB2 amplification in one and an MSH6 mutation with MYC amplification in the other. Overall, these findings suggest that cervical HPV-associated NETs are genomically silent and high-grade NECs (regardless of small or large cell morphology) share molecular pathways with common cervical carcinomas as it has been reported in the endometrium and are different from NECs at other sites. Molecular analysis of these highly malignant neoplasms might inform the clinical management for potential therapeutic targets.

While P16 immunohistochemistry (IHC) is a well-established surrogate marker of Human Papillomavirus (HPV) in oropharyngeal squamous cell carcinoma (OSCC), Retinoblastoma 1 (RB1) loss may lead to p16 overexpression in the absence of HPV. We determined the proportion of p16-positive/HPV-negative OSCC with RB1 loss and other alterations in RB1/p16 pathway, and tested RB1 IHC as a prognostic biomarker for OSCC, along with the 8th edition of AJCC staging manual. P16 and RB1 IHC and HPV DNA in situ hybridization (ISH) were performed on 257 OSCC. High risk HPV RNA ISH, RB1 fluorescence in situ hybridization (FISH), and next generation sequencing (NGS) were done on p16-positive/HPV DNA ISH-negative OSCC. Disease free survival (DFS) was used as an endpoint. In the entire cohort and in p16-positive (n = 184) and p16-negative (n = 73) subgroups, AJCC 8th edition staging correlated with DFS (p < 0.01). RB1 IHC showed RB1 loss in p16-positive OSCC only (79/184, 43%). RB1 loss by IHC is associated with a better DFS, without providing additional prognostic information for patients with p16-positive OSCC. HPV RNA ISH was positive in 12 of 14 HPV DNA ISH-negative cases. RB1 IHC showed loss in 10 of 15 HPV DNA ISH-negative cases and in 1 of 2 HPV RNA ISH-negative cases. Overall, only one case of p16-positive/HPV RNA ISH-negative OSCC showed RB1 loss by IHC (1/184, 0.5%). Of the 10 p16-positive and HPV DNA ISH-negative cases with RB1 loss by IHC, 2 had RB1 hemizygous deletion and 3 showed Chromosome 13 monosomy by FISH. No RB1 mutations were detected by NGS. Other molecular alterations in p16-positive/HPV DNA ISH-negative cases included TP53 and TERT mutations and DDX3X loss. HPV-independent RB1 inactivation rarely results in false positive p16 IHC. RB1 inactivation by high risk HPV E7 oncoprotein may co-exist with RB1 deletion. RB1 loss is a favorable prognosticator and occurs exclusively in p16-positive OSCC. The 8th edition of the AJCC staging manual satisfactorily predicts DFS of OSCC patients.

Gastric-type mucinous adenocarcinoma (GAS) is an uncommon cervical adenocarcinoma, which is not associated with human papillomavirus (HPV) infection. Compared with HPV-associated cervical adenocarcinoma, GAS has characteristics of larger volume, deep invasion, and easy to metastasize to distant sites. Also, GAS is typically resistant to chemo/radiotherapy. Few studies have reported the molecular genetic characteristics of GAS. In order to investigate the molecular genetic characteristics of GAS and reveal its possible pathogenesis, 15 GAS patients were enrolled from Peking University People's Hospital (2009-2019) and examined with next-generation sequencing (NGS). Based on the clinicopathologic feature analysis, we found that the presence of lymph node metastasis and extensive lymphovascular invasion were associated with poor survival outcomes of GAS (p = 0.0042 and p = 0.005, respectively). Based on the NGS testing, our results showed that the most frequently mutated gene was TP53 (8/15, 53.3%), followed by STK11, CDKN2A, and ARID1A. STK11 mutations were more frequent in well-differentiated GAS (33.3% vs. 0.0%, p = 0.026) and patients with extensive lymphovascular invasion (33.3% vs. 0.0%, p = 0.044). Survival analysis revealed that STK11 mutations were significantly associated with the poor prognosis of GAS (p = 0.01). Our results also showed that mutations in the target drug were detected in 53.3% of GAS patients. Patients with ERBB2 amplification (13.3%) presented the highest level of evidence according to OncoKB recommendations. These results indicate that the genomic alterations of GAS mainly involved the cell cycle and PI3K/AKT signaling pathways, and some therapeutic candidates were identified in GAS patients.

Background Following a dose-escalation study, a dose-expansion study for ISU104 (monotherapy and combination therapy with CET) has been conducted in R/M HNSCC (Ann Oncol, abst #928P, 2020). Here we report updated final safety, clinical efficacy and biomarker analysis results from the dose-expansion study. Methods Eighteen R/M HNSCC pts excluding nasopharyngeal cancer, were enrolled and allocated to Mono (ISU104, 20 mg/kg/day, Q3W; N=6) or Combo groups (ISU104 20 mg/kg, Q3W and CET, initially 400 mg/m2 followed by 250 mg/m2, Q1W; N=12). Tumor response assessments (RECIST 1.1), safety and occurrence of anti-drug antibodies (ADA) were determined. Immunohistochemistry, RNAscope™ Assay-based in situ hybridization (ISH) and next generation sequencing were performed on sections of biopsy samples. Results Most common treatment emergent adverse events (AEs) included decreased appetite (66.7%) and stomatitis (50%) in Mono, and diarrhea (75.0%) and dermatitis acneiform (50%) in Combo. Serious AEs were reported 16.7% in Mono and 58.33% in Combo, but no AEs led to treatment discontinuation. One patient (1/18, 5.56%) developed ADA, which did not have neutralizing activity. Four pts in Combo were responsive to treatment (1 CR and 3 PR out of 11 analyzed pts; 36.36%); one patient remained CR up to now. Duration of responses were 46, 62, 163+ and 449+ days in Combo, and median progression-free survival was 54 and 99 days in Mono and Combo groups, respectively, in median follow-up period of 480 days (as of 30th April 2021). H-scores of potential biomarkers including EGFR-ISH at pre-treatment were correlated with tumor size changes following combination therapy. Potential implication of TP53 mutations and EGFR amplification in patient selection was also noted. Conclusions ISU104 alone or in combination with CET were safe and tolerable in R/M HNSCC pts. Encouraging clinical efficacies and potential biomarkers were demonstrated from combination therapy. A phase II study of ISU104 (Q3W, 20 mg/kg/day) in combination with CET (Q1W) is planned to further strengthen the clinical utility of ISU104.