Host Nuclear Genome Copy Number Variations Identify High-Risk Anal Precancers in People Living With HIV

BACKGROUND

People living with HIV (PLWH) have substantially increased incidence of anal precancer and cancer. There are very little data regarding genomic disturbances in anal precancers among PLWH. In this study, specific chromosomal variants were identified in anal squamous intraepithelial lesions.

METHODS

Overall, 63 anal biopsy specimens (27 low-grade intraepithelial lesions [LSIL] and 36 high-grade intraepithelial lesions [HSIL]) were collected from PLWH obtained as part of anal cancer screening in our NYC-based health system. Data on patient demographics, anal cytological, and high-risk human papillomavirus (HR-HPV) diagnoses were collected. Specimens were tested for a panel of chromosomal alterations associated with HPV-induced oncogenesis using fluorescence in situ hybridization, and analyses compared the associations of these alterations with clinical characteristics.

RESULTS

Gains of 3q26, 5p15, 20q13, and cen7 were detected in 42%, 31%, 31%, and 19% of HSIL compared with 7%, 0%, 4%, and 0% of LSIL, respectively. If at least 1 abnormality was observed, 89% had a 3q26 gain. In lesions with 5p15 gains, 20q13 gains co-occurred in 91% of cases, while cen7 gain only co-occurred with the other 3 alterations. The sensitivity and specificity of any alteration to predict HSIL were 47% (95% CI: 30%-65%) and 93% (95% CI: 76%-99%), respectively.

CONCLUSIONS

Genomic alterations seen in HPV-associated cancers may help distinguish anal LSIL from HSIL. 3q26 amplification may be an early component of anal carcinogenesis, preceding 5p16, 20q13, and/or chr7.

IMPACT

Insights into potential genomic biomarkers for discriminating high-risk anal precancers are shared.

Whole Genome Assembly of Human Papillomavirus by Nanopore Long-Read Sequencing

Human papillomavirus (HPV) is a causal agent for most cervical cancers. The physical status of the HPV genome in these cancers could be episomal, integrated, or both. HPV integration could serve as a biomarker for clinical diagnosis, treatment, and prognosis. Although whole-genome sequencing by next-generation sequencing (NGS) technologies, such as the Illumina sequencing platform, have been used for detecting integrated HPV genome in cervical cancer, it faces challenges of analyzing long repeats and translocated sequences. In contrast, Oxford nanopore sequencing technology can generate ultra-long reads, which could be a very useful tool for determining HPV genome sequence and its physical status in cervical cancer. As a proof of concept, in this study, we completed whole genome sequencing from a cervical cancer tissue and a CaSki cell line with Oxford Nanopore Technologies. From the cervical cancer tissue, a 7,894 bp-long HPV35 genomic sequence was assembled from 678 reads at 97-fold coverage of HPV genome, sharing 99.96% identity with the HPV sequence obtained by Sanger sequencing. A 7904 bp-long HPV16 genomic sequence was assembled from data generated from the CaSki cell line at 3857-fold coverage, sharing 99.99% identity with the reference genome (NCBI: U89348). Intriguingly, long reads generated by nanopore sequencing directly revealed chimeric cellular-viral sequences and concatemeric genomic sequences, leading to the discovery of 448 unique integration breakpoints in the CaSki cell line and 60 breakpoints in the cervical cancer sample. Taken together, nanopore sequencing is a unique tool to identify HPV sequences and would shed light on the physical status of HPV genome in its associated cancers.

Human Papillomavirus (HPV69/HPV73) Coinfection associated with Simultaneous Squamous Cell Carcinoma of the Anus and Presumed Lung Metastasis

Background: Human papillomaviruses (HPVs) have been linked to a variety of human cancers. As the landscape of HPV-related neoplasia continues to expand, uncommon and rare HPV genotypes have also started to emerge. Host-virus interplay is recognized as a key driver in HPV carcinogenesis, with host immune status, virus genetic variants and coinfection highly influencing the dynamics of malignant transformation. Immunosuppression and tissue tropism are also known to influence HPV pathogenesis. Methods: Herein, we present a case of a patient who, in the setting of HIV positivity, developed anal squamous cell carcinoma associated with HPV69 and later developed squamous cell carcinoma in the lungs, clinically presumed to be metastatic disease, associated with HPV73. Consensus PCR screening for HPV was performed by real-time PCR amplification of the L1 gene region, amplification of the E6 regions with High-Resolution Melting Curve Analysis followed by Sanger sequencing confirmation and phylogenetic analysis. Results: Sanger sequencing of the consensus PCR amplification product determined that the anal tissue sample was positive for HPV 69, and the lung tissue sample was positive for HPV 73. Conclusions: This case underscores the importance of recognizing the emerging role of these rare “possibly carcinogenic” HPV types in human carcinogenesis.

Combined assessment of 3q26 amplification and promoter methylation in patients with high grade cervical lesions show age specific differences

A considerable proportion of high grade cervical intraepithelial lesions (CIN2/3) are known to resolve on their own especially among young women. However, since reliable prognostic markers are still lacking, the diagnosis "CIN3" is still an indication for surgery which may result in overtreatment. It is conceivable that a combination of different, ideally independent molecular markers may provide more reliable results. In the present cross-sectional study two established triage markers, 3q26 amplification and a methylation signature, were evaluated in an age-dependent manner. The patient cohort comprised 60 patients with histologically confirmed CIN2/3 in two equally sized age groups (<30 years, ≥30 years). Cervical scrapes were analyzed by interphase fluorescence in situ hybridization for 3q26 amplification and methylation specific PCR (GynTect®) for six different genome regions. Both assays showed a significantly different pattern of test outcome independent of age (P = .001). Moreover, the combination of both assays differed significantly for double positive and double negative cases when comparing the two age groups: In patients <30 years there were clearly less cases with positive methylation signature and amplification of 3q26 as in women ≥30 years (23% vs 63%, Bonferroni adjusted P = .016). Of particular interest is the finding that double negative results were exclusive for the young age group (0% vs 27%, Bonferroni adjusted P = .020). Since regression of CIN2/3 characteristically occurs among young women it is tempting to speculate that a double negative test result could be prognostic for regression of CIN2/3. This will have to be investigated further in a prospective longitudinal intervention study.

Molecular approaches for HPV genotyping and HPV-DNA physical status

Persistent infection with high-risk human papillomavirus (HPV) genotypes is the leading cause of cervical cancer development. To this end several studies have focused on designing molecular assays for HPV genotyping, which are considered as the gold standard for the early diagnosis of HPV infection. Moreover, the tendency of HPV DNA to be integrated into the host chromosome is a determining event for cervical oncogenesis. Thus, the establishment of molecular techniques was promoted in order to investigate the physical status of the HPV DNA and the locus of viral insertion into the host chromosome. The molecular approaches that have been developed recently facilitate the collection of a wide spectrum of valuable information specific to each individual patient and therefore can significantly contribute to the establishment of a personalised prognosis, diagnosis and treatment of HPV-positive patients. The present review focuses on state of the art molecular assays for HPV detection and genotyping for intra-lesion analyses, it examines molecular approaches for the determination of HPV-DNA physical status and it discusses the criteria for selecting the most appropriate regions of viral DNA to be incorporated in HPV genotyping and in the determination of HPV-DNA physical status.

Cervical FISH Testing for Triage and Support of Challenging Diagnoses: A Case Study of 2 Patients

PATIENTS

A 29-year-old Caucasian woman (patient 1) and a 23-year-old Caucasian woman (patient 2).Chief Complaints: Abnormal Pap tests with high risk HPV positivity.

HISTORY OF PRESENT ILLNESS

PATIENT 1

In June 2014, this patient was diagnosed with atypical squamous cells of uncertain significance (ASCUS) after a routine screening cervical Papanicolaou (Pap) test. Reflex high risk human papilloma virus (HPV) testing was performed; the results were positive (genotyping was not performed). Subsequent endocervical curettage showed a small focus of immature, atypical squamous cells with abnormally positive p16 staining and an abnormally increased proliferative index staining pattern (evaluated with Ki-67) (Images 1A-1C). These findings strongly suggested a high-grade lesion; nevertheless, due to the minute and focal nature of these findings, a diagnosis was rendered of squamous dysplasia, cannot exclude high grade dysplasia. Additional follow-up was recommended, and the option of a fluorescent in situ hybridization (FISH) assay (HPV-4C, using reagent manufactured by Cancer Genetics Italia S.r.l.) was also suggested as a method of triage to be performed using the same Thinprep collection media used to create the Pap test. The results of the FISH assay were positive, with 6.6% of cells showing gain of the 3q26 region (Image 1D). With this knowledge, the gynecologist performed a cervical loop electrosurgical excision procedure (LEEP), which revealed moderate squamous dysplasia (cervical intraepithelial neoplasia grade 2 [CIN 2]) supported by strong and abnormal p16/Ki-67 co-expression (Images 1E-1G). PATIENT 2: In June 2013, this patient was diagnosed with atypical glandular cells (AGUS) and was shown to have high-risk human papillomavirus (HPV) positivity. (Again, genotyping was not performed.) The subsequent biopsy showed mild reactive atypia of the glandular cells, which did not completely correlate with the atypical cells revealed by the Papanicolaou (Pap) test. Therefore, further follow-up was recommended. A fluorescent in situ hybridization (FISH) assay was performed on the specimen assayed via the AGUS Pap test; the FISH assay yielded positive results, showing many cells with a gain of 3q26 and 5p15 regions above the established cutoff values. A repeat Pap test was performed, which also was interpreted as indicating AGUS. Results of a second HPV-4C FISH assay showed numerous (14.6%) cells with a gain of 3q26 and 5p15 regions (Image 2A). Repeat cervical and endocervical biopsies showed scant atypical glands in otherwise-generous biopsies (Image 2B). Supported by abnormal p16 and Ki-67 immunohistochemical staining results (Image 2C and 2D) and the knowledge of the abnormal FISH assay results, the pathologist diagnosed the patient with endocervical adenocarcinoma in situ (AIS). The results of a subsequent LEEP confirmed the diagnosis of endocervical adenocarcinoma in situ with negative resection margins.

LABORATORY FINDINGS

Abnormal Papanicolaou (Pap) test results with high risk of human papilloma virus (HPV) positivity and scant lesional tissue, as revealed by cervical/endocervical biopsies.