Identification and Validation of Human Papillomavirus Encoded microRNAs

Peer reviewe

Pleomorphic adenoma in the nasal cavity : a clinicopathological study of ten cases in Finland

The objective of the study was to investigate the nationwide occurrence of sinonasal pleomorphic adenoma in Finland. A retrospective study was conducted at The Departments of Otorhinolaryngology-Head and Neck Surgery, and Pathology at the five university hospitals in Finland. Data were obtained by searching for sinonasal pleomorphic adenoma cases in the clinical and histopathological registries at these institutions for the past two to four decades. All patients who had had a histologically proven pleomorphic adenoma in the sinonasal area were included as participants. Ten cases with pleomorphic adenoma of the nasal cavity were found. The majority of these tumours originated in the septum, and there were no malignant transformations. Pleomorphic adenomas of the nasal cavity were found to be extremely rare in this nationwide investigation.Peer reviewe

Evaluation of in vitro and in vivo personalized cancer treatment assays for oral squamous cell carcinoma

Abstract Background: Oral squamous cell carcinoma (OSCC) is a common cancer with a high heterogeneity and few approved treatments. OSCC is one of the least explored areas for precision oncology. In this study, we aimed to test the reliability of our three established rapid cancer systemic treatment-testing assays: human tumour-derived matrix (Myogel)-coated well-plates, zebrafish xenografts, and 3D microfluidic chips. Methods: Chemo-, radio- and targeted-therapy testing in Myogel-coated wells and zebrafish xenografts was conducted nine times using five samples; two primary and three metastatic lymph node samples from three OSCC patients. Peripheral blood mononuclear cells (PBMNCs) were isolated from the patients’ blood. The response of the tumour cells to radio-, chemo-, and targeted therapy was tested using Myogel-coated wells and zebrafish larvae xenografts. The tumour cells’ response to immunotherapy was tested using 3D microfluidic chips. The cells’ sensitivity to the treatments was compared with the patients’ clinical response. Primary and metastatic lymph node tissue-derived DNA samples from two patients underwent whole exome sequencing to compare the mutational profiles of the samples. Results: Test results were in line with patients’ responses in 7/9 (77%) zebrafish xenograft assays and 5/9 (55%) Myogel-coated wells assays. Immunotherapy testing was done using one metastatic patient sample which matched the patients’ response. Differences in responses to treatments between primary and metastatic samples of the same patient were detected in 50% of the zebrafish larvae assays. Conclusions: Our results show the potential of using personalized cancer treatment testing assays — specifically zebrafish xenografts that revealed promising results — in OSCC patient samples

<i>In situ</i> hybridization for HPV16-miR-H1-1 and HPV16-miR-H2-1.

<p>(A) Hematoxylin-eoxin (HE) staining, immunohistochemical staining for p16, and <i>in situ</i> (italics) hybridization for scramble (negative control), U6 (positive control), human miR-205 (positive control for cervical tissue), HPV16-miR-H1-1 (16-miR-H1-1) and HPV16-miR-H2-1 (16-miR-H2-1). Shown are two cervical intraepithelial neoplasia grade 1 (CIN 1) samples (samples 10 and 28), one squamous cell carcinoma (SCC) (sample 102), as well as normal squamous epithelium (SE) (sample 104) and normal columnar epithelium (CE) (sample 104). Arrows point to positive signals. (B) Areas of selected picture fields shown in higher magnification to depict localization and positive hybridization signal. Same numbering is used as in (A).</p

Locations and putative target sites of HPV 16 encoded microRNAs.

<p>Locations of HPV16-miR-H1-1 and HPV16-miR-H2-1 in the viral genome are shown as black bars and the predicted secondary structures are given next to the bars. For each miRNA, the seed sequences and predicted target sequences in the HPV genome are shown.</p

Exome sequencing reveals germline NPAT mutation as a candidate risk factor for Hodgkin lymphoma

A strong clustering of Hodgkin lymphoma in certain families has been long acknowledged. However, the genetic factors in the background of familial Hodgkin lymphoma are largely unknown. We have studied a family of 4 cousins with a rare subtype of the disease, nodular lymphocyte predominant Hodgkin lymphoma. We applied exome sequencing together with genome-wide linkage analysis to this family and identified a truncating germline mutation in nuclear protein, ataxia-telangiectasia locus (NPAT) gene, which segregated in the family. We also studied a large number of samples from other patients with Hodgkin lymphoma, and a germline variation leading to the deletion of serine 724 was found in several cases suggesting an elevated risk for the disease (odds ratio = 4.11; P = .018). NPAT is thus far the first gene implicated in nodular lymphocyte predominant Hodgkin lymphoma predisposition. (Blood. 2011;118(3):493-498

Summary of miRNA <i>in situ</i> hybridization (ISH), DNA PCR and p16 staining results.

<p>Expression of HPV16-miR-H1-1 was shown in all disease tissues. Expression of HPV16-miR-H2-1 was shown in only one carcinoma sample 102. CIN1-3, cervical intraepithelial neoplasia 1-3; SCC, squamous cell carcinoma; AIS, adenocarcinoma <i>in situ</i>; AC, adenocarcinoma; SE, squamous epithelium; CE, columnar epithelium. NA, not analyzed.</p

Mapped results of the twelve small RNA sequencing libraries.

<p>For each library, total reads from SOLiD small RNA sequencing and reads mapped to the papillomavirus reference genome are presented. Names of cell lines or histology of tissue samples are given in library description. Percentage of reads mapped to human miRNAs and to the human genome, respectively, are given. CIN, cervical intraepithelial neoplasia.</p

Summary of TaqMan miRNA qPCR, DNA PCR and p16 staining results, as well HPV detection and/or genotyping results by LDR, Luminex and Hybrid Capture 2.

<p>Obtained positive results in TaqMan qPCR out of performed runs are given. HPV6-miR-H1 did not give any positive results. Positive signals were obtained for HPV16-miR-H1, HPV16-miR-H2, HPV38-miR-H1 and HPV68-miR-H1 from cell lines and patient samples. Positive control U6 gives positive result in every reaction. The presence of pre-miRNA coding regions for HPV16-miR-H1 and HPV16-miR-H2 was confirmed by DNA PCR in all cell lines and many tissue samples. Results of p16 tissue staining, as well as results of HPV genotyping by LDR or Luminex, and high risk HPV detection by Hybrid Capture 2 are given. NA, not analyzed. ND, not done (inadequate sample). CIN1-3, cervical intraepithelial neoplasia 1–3; Cond pl, condyloma planum; SCC, squamous cell carcinoma; AIS, adenocarcinoma <i>in situ</i>; AC, adenocarcinoma; SE, squamous epithelium; CE, columnar epithelium; LDR, ligase detection reaction based HPV genotyping assay; Luminex, Luminex based HPV genotyping assay; HC2, Hybrid Capture 2 HPV detection assay; *, numbers are HPV types; NA, not analyzed; ND, no data (not enough material for testing).</p

Predicted viral miRNA candidate.

<p>Each row presents one candidate miRNA with name, reference genome, pre-miRNA location in the genome, total read counts of pre-miRNA, viral gene annotation in corresponding region, strand information and mature miRNA sequence. Some miRNAs were shown in more than one isolate/subtype papillomavirus genomes. ^§ Prediction results from second round.</p