p63 Expression in olfactory neuroblastoma and other small cell tumors of the sinonasal tract

Top 10 Basaloid Neoplasms of the Sinonasal Tract

BACKGROUND

Basaloid neoplasms of the sinonasal tract represent a significant group of tumors with histological overlap but often with different etiologies (i.e., viral, genetics), clinical management, and prognostic significance.

METHODS

Review.

RESULTS

"Basaloid" generally refers to cells with coarse chromatin in round nuclei and sparse cytoplasm, resembling cells of epithelial basal layers or imparting an "immature" appearance. Tumors with this characteristic in the sinonasal tract are represented by a spectrum of benign to high-grade malignant neoplasms, such as adenoid cystic carcinoma, NUT carcinoma, sinonasal undifferentiated carcinoma, SWI/SNF complex-deficient carcinomas, and adamantinoma-like Ewing sarcoma.

CONCLUSION

In some instances, histology alone may be sufficient for diagnosis. However, limited biopsy material or fine-needle aspiration specimens may be particularly challenging. Therefore, often other diagnostic procedures, including a combination of histology, immunohistochemistry (IHC), DNA and RNA testing, and molecular genetics are necessary to establish an accurate diagnosis.

Undifferentiated and dedifferentiated head and neck carcinomas

Undifferentiated carcinomas arising at salivary gland and head and neck mucosal sites may originate either de novo or through a process of dedifferentiation of a differentiated carcinoma. While in the latter group the diagnosis is largely dependent on the identification of the differentiated component or recognition of a specific genotype, the classification of undifferentiated carcinomas that lack a differentiated component is mainly based on the identification of specific genetic drivers, like for example the NUTM1 fusions in NUT carcinoma. A further category is represented by virus associated carcinomas (mainly HPV and EBV), that frequently displays an undifferentiated morphology. Overall, these tumors often represent a diagnostic challenge, especially in small biopsies. This review summarizes and discuss the diagnostic approach to the main head and neck carcinoma types that frequently or occasionally display an undifferentiated appearance, with a focus on salivary gland, oropharyngeal, nasopharyngeal and sinonasal subsites.

p63 Is a Promising Marker in the Diagnosis of Unusual Skin Cancer

Skin cancer is the most common type of cancer worldwide. Ozone depletion and climate changes might cause a further increase in the incidence rate in the future. Although the early detection of skin cancer enables it to be treated successfully, some tumours can evolve and become more aggressive, especially in the case of melanoma. Therefore, good diagnostic and prognostic markers are needed to ensure correct detection and treatment. Transcription factor p63, a member of the p53 family of proteins, plays an essential role in the development of stratified epithelia such as skin. In this paper, we conduct a comprehensive review of p63 expression in different types of skin cancer and discuss its possible use in the diagnosis and prognosis of cutaneous tumours.

Nasal NK/T cell lymphoma mimicking mucosa-associated lymphoid tissue lymphoma in morphology: A case report

The objective of the present study was to describe the clinicopathological features of a patient with nasal NK/T cell lymphoma that was similar in morphology to mucosa-associated lymphoid tissue lymphoma (MALToma). The clinicopathological data of a patient diagnosed with nasal NK/T cell lymphoma mimicking MALToma was collected, and the clinicopathological characteristics were discussed. The female patient was 43 years old and had suffered from persistent congestion for ten days. The mucosa in the left nasal cavity was inflamed, resulting in congestion and it was also purulent on the surface, as observed by nasal endoscopy. The disease was considered to be inflammatory based on CT scan. A biopsy after operation showed that the tumor consisted of small lymphoid cells that resembled MALToma in morphology. On the basis of the immunohistochemistry and in situ hybridization laboratory tests, a diagnosis of left nasal NK/T cell lymphoma was made. The patient received chemotherapy and radiotherapy, and remission was achieved six months after diagnosis. The patient was in a good condition at 16 months follow-up. In conclusion, NK/T cell lymphoma composed of small cells may be a type of indolent lymphoma with special characteristics of clinical presentation, image, pathology and prognosis. This case highlights that more attention is required by radiologists, pathologists and hematologists to diagnose this type of lymphoma.

Epstein-Barr Virus Gene BARF1 Expression is Regulated by the Epithelial Differentiation Factor ΔNp63α in Undifferentiated Nasopharyngeal Carcinoma

Epstein-Barr Virus (EBV) BamHI-A rightward frame 1 (BARF1) protein is considered a viral oncogene in epithelial cells and has immune-modulating properties. During viral lytic replication BARF1 is expressed as an early gene, regulated by the immediate early EBV protein R. However, in viral latency BARF1 is exclusively expressed in epithelial tumors such as nasopharyngeal (NPC) and gastric carcinoma (GC) but not in lymphomas, indicating that activation of the BARF1 promoter is cell type specific. Undifferentiated NPC is characterized by high expression of ΔNp63 isoforms of the epithelial differentiation marker p63, a member of the p53 family of transcription factors. Transcription factor binding site analysis indicated potential p53 family binding sites within the BARF1 promoter region. This study investigated ability of various p53 family members to transactivate the BARF1 promoter. Using BARF1 promoter luciferase reporter constructs we demonstrate that only p63 isoform ΔNp63α is capable of transactivating the BARF1 promoter, but not the TAp63 isoforms, p53 or p73. Direct promoter binding of ΔNp63α was confirmed by Chromatin Immune Precipitation (ChIP) analysis. Deletion mutants of the BARF1 promoter revealed multiple ΔNp63 response elements to be responsible for BARF1 promoter transactivation. However, ΔNp63α alone was not sufficient to induce BARF1 in tumor cells harboring full EBV genomes, indicating that additional cofactors might be required for full BARF1 regulation. In conclusion, in EBV positive NPC and GC, BARF1 expression might be induced by the epithelial differentiation marker ΔNp63α, explaining BARF1 expression in the absence of lytic reactivation.

Small round blue cell tumors of the sinonasal tract: a differential diagnosis approach

One of the most challenging diagnostic categories within tumors of the sinonasal tract is the small round blue cell tumors. Biopsies are usually small and limited, resulting in considerable diagnostic difficulty for practicing surgical pathologists. These tumors share several overlapping histologic and immunophenotypic findings while also showing considerable variation within and between cases. Specific tumor site of origin, imaging findings, and clinical findings must be combined with the histology and pertinent ancillary studies if the correct diagnosis is to be reached. Discrimination between neoplasms is critical as there are significant differences in therapy and overall outcome. It is important to have a well developed differential diagnosis for this category of tumors, where each of the diagnoses is considered, evaluated, and either confirmed or excluded from further consideration. In an undifferentiated tumor, showing a small round blue cell morphology, using the mnemonic 'MR SLEEP' helps to highlight tumors to consider: melanoma, mesenchymal chondrosarcoma, rhabdomyosarcoma, sinonasal undifferentiated carcinoma, squamous cell carcinoma (including NUT carcinoma), small cell osteosarcoma, lymphoma, esthesioneuroblastoma (olfactory neuroblastoma), Ewing sarcoma/primitive neuroectodermal tumor, pituitary adenoma, and plasmacytoma. A panel of pertinent immunohistochemistry studies, histochemistries and/or molecular tests should aid in reaching a diagnosis, especially when taking the pattern and intensity of reactions into consideration.

Sinonasal Small Round Blue Cell Tumors: An Immunohistochemical Approach

Although clinical history and morphologic appearance should be the initial considerations when evaluating small round blue cell tumors of the sinonasal tract, the final diagnosis often hinges on immunohistochemical findings. Unfortunately, interpretation of stains in these tumors is fraught with numerous pitfalls and limitations. This article presents an approach to sinonasal small round blue cell tumors based on four common immunohistochemical patterns: cytokeratin positivity, squamous marker positivity, neuroendocrine marker positivity, and cytokeratin negativity.

Meta-analysis of 701 published cases of sinonasal neuroendocrine carcinoma: The importance of differentiation grade in determining treatment strategy

The aim of this meta-analysis was to provide treatment guidelines for sinonasal neuroendocrine carcinoma (SNC) by combining all available data in the literature. A literature search for all studies concerning SNC was performed against the MEDLINE and EMBASE databases. Available clinical data was normalized, pooled, and statistically analyzed. A total of 701 cases of SNC were available for analysis, comprising 127 well or moderately differentiated sinonasal neuroendocrine carcinomas (SNEC), 459 sinonasal undifferentiated carcinoma (SNUC) and 115 sinonasal small cell carcinoma (SmCC). Tumor type was the most important predictor of survival, with a 5-year disease-specific survival (DSS) of 70.2% for SNEC, 35.9% for SNUC and 46.1% for SmCC. Tumor stage on presentation was of limited value in predicting survival or response to treatment. Overall, the application of surgery yielded significantly better results (5-year DSS 52.2% versus 30.1%, p<0.001). In SNUC, radiotherapy was a beneficial supplement to surgery (5-year DSS 54.7% versus 15.7%, p=0.027), while radiotherapy as monotherapy performed poorly (5-year DSS 17.9%). Chemotherapy did not appear to contribute to survival. Based on these findings, we can conclude that the most important predictors of survival in SNC are differentiation grade and the associated choice of treatment modality. In contrast to other head and neck cancers, tumor staging appears of limited value in predicting survival or deciding on a treatment strategy. Surgery should be the cornerstone of treatment, supplemented by radiotherapy in poorly differentiated subtypes (SNUC, SmCC). Chemotherapy does not appear to contribute to survival.

An Update on Sinonasal Round Cell Undifferentiated Tumors

The sinonasal cavities host a wide variety of undifferentiated malignancies with round cell morphology, including neoplasms of epithelial, mesenchymal, neuroectodermal, and hematolymphoid lineage. The differential diagnosis may be difficult, especially in small biopsy material, due to overlapping morphology, but their correct classification is clinically relevant. The aim of this review is to provide practical guidelines for the differential diagnosis of these malignancies, with emphasis on recently described entities and special reference to the role of ancillary techniques.

Sinonasal small round blue cell tumors: An approach to diagnosis

The differential diagnosis for small round cell tumors in the sinonasal tract is diverse and as the body of literature documenting not only uncommon presentations but also availability of ancillary studies grows, so does the need for a reminder to take a conservative and thorough approach before rendering a diagnosis. Small tissue samples are particularly problematic, with limitations that include volume of tumor cells available for studies, lack of architectural context and a non-specific gross description. Incorporation of patient history and presentation, radiologic findings, clinical impression and concurrent studies often guide the course of studies performed by the pathologist. If these are non-specific, the pathologist may need to perform ancillary studies, including a broad panel of immunohistochemical stains and molecular studies. If tissue is limited, a precise classification may not be achievable. Although the expectation to render a definitive diagnosis is high, the pathologist should never feel compelled to go further with a diagnosis than the tissue itself supports.

Squamous cell carcinoma variants of the upper aerodigestive tract: a comprehensive review with a focus on genetic alterations

CONTEXT

Squamous cell carcinoma of the upper aerodigestive tract is a heterogenous entity. Although conventional squamous cell carcinomas are easily recognized, the morphologic variants of squamous cell carcinoma can present a diagnostic challenge. Familiarity with these variants is necessary because many are associated with unique risk factors and are characterized by specific molecular alterations (eg, nuclear protein in testis midline carcinomas). Perhaps the most important distinction is in identifying viral-related from nonviral-related carcinomas. The accurate diagnosis of these variants is necessary for prognostic and therapeutic reasons.

OBJECTIVES

To provide a clinicopathologic overview and summary of the molecular alterations of the common squamous cell carcinoma variants, including verrucous, spindle cell, acantholytic, adenosquamous, basaloid, and papillary squamous cell carcinoma, as well as nuclear protein in testis midline carcinoma, and to discuss the distinguishing features of human papillomavirus- and Epstein-Barr virus-related squamous cell carcinomas.

DATA SOURCES

Published peer-reviewed literature.

CONCLUSIONS

Familiarity with squamous cell carcinoma variants is essential for proper diagnosis and to guide appropriate clinical management. Further insight into the molecular alterations underlying those variants may lead to alterations in existing treatment approaches and to evolution of novel treatment modalities.

Diagnostic value of next-generation sequencing in an unusual sphenoid tumor

Extraordinary advancements in sequencing technology have made what was once a decade-long multi-institutional endeavor into a methodology with the potential for practical use in a clinical setting. We therefore set out to examine the clinical value of next-generation sequencing by enrolling patients with incurable or ambiguous tumors into the Personalized OncoGenomics initiative at the British Columbia Cancer Agency whereby whole genome and transcriptome analyses of tumor/normal tissue pairs are completed with the ultimate goal of directing therapeutics. First, we established that the sequencing, analysis, and communication with oncologists could be completed in less than 5 weeks. Second, we found that cancer diagnostics is an area that can greatly benefit from the comprehensiveness of a whole genome analysis. Here, we present a scenario in which a metastasized sphenoid mass, which was initially thought of as an undifferentiated squamous cell carcinoma, was rediagnosed as an SMARCB1-negative rhabdoid tumor based on the newly acquired finding of homozygous SMARCB1 deletion. The new diagnosis led to a change in chemotherapy and a complete nodal response in the patient. This study also provides additional insight into the mutational landscape of an adult SMARCB1-negative tumor that has not been explored at a whole genome and transcriptome level.

Role of p40 and cytokeratin 5/6 in the differential diagnosis of sinonasal undifferentiated carcinoma

Sinonasal undifferentiated carcinoma (SNUC) is an epithelial neoplasm of sinonasal region which does not exhibit a squamous or glandular differentiation. The challenge in diagnosis of this entity is the rarity of the disease, the varying morphology of the tumor which leads to gamut of differential diagnosis and the paucity of consistent immunohistochemical markers except pancytokeratin. Forty-one cases of sinonasal epithelial neoplasm consisting of 11 cases of SNUC and 10 cases each of high-grade (grade 3 and 4) esthesioneuroblastoma, undifferentiated nasopharyngeal carcinoma, and poorly differentiated squamous cell carcinoma of the sinonasal region were analyzed for morphology and immunoexpression of CK5/6 and p40. It was found that SNUC did not exhibit immunohistochemical expression of p40 and CK 5/6, suggesting that these could be useful negative immune markers for diagnosis of SNUC.

Utility of p40 in the Differential Diagnosis of Small Round Blue Cell Tumors of the Sinonasal Tract

The sinonasal tract may give rise to a broad range of neoplasms that share a "small round blue cell" tumor (SBRCT) appearance on routine histology, but treatment strategies depend on precise tumor classification. Immunohistochemistry for p63 is often employed in the sinonasal SRBCT differential diagnosis because it is highly sensitive for squamous cell carcinoma (SCC). However, p63 staining may be observed in other tumor types, a potential diagnostic pitfall. P40 is a more squamous-specific isoform of p63, and it may be more useful in distinguishing poorly differentiated SCC from its mimickers in the sinonasal tract. Immunohistochemistry for p40 and p63 was performed on 171 sinonasal neoplasms with SRBCT morphology: 73 SCCs (67 poorly differentiated, non-keratinizing, or basaloid types and 6 nasopharyngeal carcinomas), 46 esthesioneuroblastomas, 11 sinonasal undifferentiated carcinomas (SNUCs), 11 lymphomas, 9 melanomas, 7 alveolar rhabdomyosarcomas, 4 solid adenoid cystic carcinomas, 4 NUT midline carcinomas, 4 primitive neuroectodermal tumors (PNETs), and 2 small cell carcinomas. P40 was positive in 72 of 73 SCCs, and showed a diffuse distribution in all but one positive case. P40 immunoexpression was also observed in 13 of 46 (28 %) esthesioneuroblastomas, 6 of 11 (55 %) SNUCs, 2 of 4 (50 %) adenoid cystic carcinomas, 3 of 4 (75 %) NUT midline carcinomas, 1 of 2 (50 %) small cell carcinomas, and 1 of 4 (25 %) PNETs; in the non-SCC tumors, p40 staining was focal in most cases. P63 was positive in every p40-positive tumor. In addition, a p63+/p40- phenotype was seen 5 of 11 (45 %) lymphomas, 4 of 7 (57 %) alveolar rhabdomyosarcomas, 1 of 4 (25 %) PNETs, and 3 of 46 (7 %) esthesioneuroblastomas. All sinonasal melanomas were negative for both markers. In the sinonasal SRBCT differential diagnosis, both p40 and p63 are highly sensitive for SCC, but p40 is more specific. Notably, p40 is consistently negative in lymphomas and alveolar rhabdomyosarcomas, two tumors that are frequently p63-positive. It must be remembered, however, that even diffuse p40 immunostaining is not entirely specific for the squamous phenotype, and therefore it should be utilized as part of an immunohistochemical panel.

The small round blue cell tumors of the sinonasal area: histological and immunohistochemical findings

Background

Primary Small round blue cell tumors (SRBCT) in sinonasal comprise histogenetically diverse entities with overlapping morphologic features. Because of the limited initial biopsy tissue materials, differential diagnostic difficulties may arise, and as they have different management, exact diagnosis and classification are very important.

Objectives

In this study, we analyzed the immunohistochemical expression of a panel of markers in the classification and diagnosis of sinonasal SRBCTs.

Material and Methods

This cross sectional study was performed on 36 paraffin embedded tissue samples. Histologic and immunohistochemical slides from 36 patients with SRBCT were analyzed retrospectively. The patients were admitted in Khalili hospital, Shiraz from 1383 to 1388.

Results

There were 13 women and 23 men with the mean age of 53 ±12.1. There were 9 malignant melanoma, seven poorly differentiated SCC; six lymphoma (DLBL); 4 SCNEC; three SNUC; two ON; two Ewing/PNET; two embryonal rhabdomyosarcoma, and one plasmacytoma. Pan-cytokeratin was strongly expressed poorly differentiated SCC and all cases of SNUC. Coexpression of desmin and nuclear myoD1 was only detected in rhabdomyosarcoma. HMB45 was only expressed in sinonasal melanoma. CD99 expression was identified only in Ewing/PNET. FLI-1 was detected in 50% of PNET. P63 was expressed in poorly differentiated SCC (2/7) and SNUC (1/3).

Conclusions

The results of our study indicate that the integration of histopathologic findings with application of limited but highly specific markers led to the separation of carcinomas, lymphoma and melanomas from other small cell tumors. Using a panel of keratin, LCA, desmin, and HMB45 is the most practical and economic approach to accurately classify these tumors.

p63 is an alternative p53 repressor in melanoma that confers chemoresistance and a poor prognosis

p63 is up-regulated in melanoma and prevents nuclear accumulation of p53.

The role of apoptosis in melanoma pathogenesis and chemoresistance is poorly characterized. Mutations in TP53 occur infrequently, yet the TP53 apoptotic pathway is often abrogated. This may result from alterations in TP53 family members, including the TP53 homologue TP63. Here we demonstrate that TP63 has an antiapoptotic role in melanoma and is responsible for mediating chemoresistance. Although p63 was not expressed in primary melanocytes, up-regulation of p63 mRNA and protein was observed in melanoma cell lines and clinical samples, providing the first evidence of significant p63 expression in this lineage. Upon genotoxic stress, endogenous p63 isoforms were stabilized in both nuclear and mitochondrial subcellular compartments. Our data provide evidence of a physiological interaction between p63 with p53 whereby translocation of p63 to the mitochondria occurred through a codependent process with p53, whereas accumulation of p53 in the nucleus was prevented by p63. Using RNA interference technology, both isoforms of p63 (TA and ΔNp63) were demonstrated to confer chemoresistance, revealing a novel oncogenic role for p63 in melanoma cells. Furthermore, expression of p63 in both primary and metastatic melanoma clinical samples significantly correlated with melanoma-specific deaths in these patients. Ultimately, these observations provide a possible explanation for abrogation of the p53-mediated apoptotic pathway in melanoma, implicating novel approaches aimed at sensitizing melanoma to therapeutic agents.

Establishment and characterization of novel cell lines from sinonasal undifferentiated carcinoma

PURPOSE

Sinonasal undifferentiated carcinoma (SNUC) is a rare and aggressive cancer. Despite the use of multimodality treatment, the overall prognosis remains poor. To better understand the biologic features of SNUC and help develop new therapies for the disease, we established SNUC cell lines and characterized their biologic behaviors.

EXPERIMENTAL DESIGN

Cell lines were established from a patient with a T4N0M0 SNUC of the right maxillary sinus who was treated with surgical resection at our center. Tumor colonies were harvested and were sequentially replated onto larger plates. Two populations were developed and labeled MDA8788-6 and MDA8788-7. These cell lines were characterized with molecular, biomarker, functional, and histologic analyses.

RESULTS

Short tandem repeat genotyping revealed that the cell line is isogenic to the parental tumor, and cytogenetic analysis identified 12 chromosomal translocations. The SNUC cell lines do not form colonies in soft agar but are tumorigenic and nonmetastatic in an orthotopic mouse model of sinonasal cancer. Western blot analysis revealed that both MDA8788 cell lines express epithelial markers but do not express mesenchymal markers or the endocrine marker synaptophysin.

CONCLUSIONS

This is the first report of the establishment of stable human-derived SNUC cell lines. The lines were highly tumorigenic and maintain the histologic and molecular features of the original tumor. These cell lines should serve as useful tools for the future study of SNUC biology and the development and testing of novel therapies for this deadly disease.

NUT midline carcinomas of the sinonasal tract

NUT midline carcinoma (NMC) is a highly lethal tumor defined by translocations involving the NUT gene on chromosome 15q14. NMC involves midline structures including the sinonasal tract, but its overall incidence at this midline site and its full morphologic profile are largely unknown because sinonasal tumors are not routinely tested for the NUT gene translocation. The recent availability of an immunohistochemical probe for the NUT protein now permits a more complete characterization of sinonasal NMCs. The archival files of The Johns Hopkins Hospital Surgical Pathology were searched for all cases of primary sinonasal carcinomas diagnosed from 1995 to 2011. Tissue microarrays were constructed, and NUT immunohistochemical analysis was performed. All NUT-positive cases underwent a more detailed microscopic and immunohistochemical analysis. Among 151 primary sinonasal carcinomas, only 3 (2%) were NUT positive. NUT positivity was detected in 2 of 13 (15%) carcinomas diagnosed as sinonasal undifferentiated carcinoma and in 1 of 87 (1%) carcinomas diagnosed as squamous cell carcinoma. All occurred in men (26, 33, and 48 y of age). The NMCs grew as nests and sheets of cells with a high mitotic rate and extensive necrosis. Two were entirely undifferentiated, and 1 tumor showed abrupt areas of squamous differentiation. Each case had areas of cell spindling, and 2 were heavily infiltrated by neutrophils. Immunohistochemical staining was observed for cytokeratins (3 of 3), epithelial membrane antigen (3 of 3), p63 (2 of 3), CD34 (1 of 3), and synaptophysin (1 of 3). All patients died of the disease (survival time range, 8 to 16 mo; mean, 12 mo) despite combined surgery and chemoradiation. NMC represents a rare form of primary sinonasal carcinoma, but its incidence is significantly increased in those carcinomas that exhibit an undifferentiated component. Indiscriminant analysis for evidence of the NUT translocation is unwarranted. Instead, NUT analysis can be restricted to those carcinomas that demonstrate undifferentiated areas. The availability of an immunohistochemical probe has greatly facilitated this analysis and is helping to define the full demographic, morphologic, and immunohistochemical spectrum of sinonasal NMC.

Clinicopathological significance of NUT rearrangements in poorly differentiated malignant tumors of the upper respiratory tract

Nuclear protein in testis (NUT) midline carcinoma (NMC) is a highly malignant carcinoma originating from the midline of the body. This study investigated the clinicopathological significance of NUT rearrangements in poorly differentiated malignant tumors (PDMTs) of the upper-respiratory tract (URT) in China. The clinical and pathological features of 155 PDMTs of the URT were reviewed. Epstein-Barr virus (EBV)-encoded RNA and NUT were investigated by in situ hybridization and immunohistochemistry (IHC), respectively. NUT-positive cases were examined by fluorescence in situ hybridization (FISH) and immunohistochemical staining with a set of cytokeratins (CKs) and neuroendocrine markers. One case was observed by transmission electron microscopy. Four cases of poorly differentiated squamous cell carcinomas and sinonasal undifferentiated carcinomas were diffuse positive for NUT by IHC and also stained for antibodies to CKs and P63 but were negative for neuroendocrine markers. Only 2 of these 4 cases showed rearrangements of the NUT and BRD4 genes by FISH; both these patients died within 12 months. The remaining 2 patients showed no NUT rearrangement by FISH and did not have an aggressive clinical course. NMC is a rare, poorly differentiated carcinoma, which occurs most often in midline organs, and in this first series from China, affected the sinonasal tract of older adults and was not associated with EBV infection. Determination of NUT protein expression and gene rearrangement can allow the differentiation of NMC from other URT PDMTs. The authors suggest that molecular determination of NUT gene rearrangements should therefore represent the gold standard for NMC diagnosis.

Discovering biological connections between experimental conditions based on common patterns of differential gene expression

Background

Identifying similarities between patterns of differential gene expression provides an opportunity to identify similarities between the experimental and biological conditions that give rise to these gene expression alterations. The growing volume of gene expression data in open data repositories such as the NCBI Gene Expression Omnibus (GEO) presents an opportunity to identify these gene expression similarities on a large scale across a diverse collection of datasets. We have developed a fast, pattern-based computational approach, named openSESAME (Search of Expression Signatures Across Many Experiments), that identifies datasets enriched in samples that display coordinate differential expression of a query signature. Importantly, openSESAME performs this search without prior knowledge of the phenotypic or experimental groups in the datasets being searched. This allows openSESAME to identify perturbations of gene expression that are due to phenotypic attributes that may not have been described in the sample annotation included in the repository.

To demonstrate the utility of openSESAME, we used gene expression signatures of two biological perturbations to query a set of 75,164 human expression profiles that were generated using Affymetrix microarrays and deposited in GEO. The first query, using a signature of estradiol treatment, identified experiments in which estrogen signaling was perturbed and also identified differences in estrogen signaling between estrogen receptor-positive and -negative breast cancers. The second query, which used a signature of silencing of the transcription factor p63 (a key regulator of epidermal differentiation), identified datasets related to stratified squamous epithelia or epidermal diseases such as melanoma.

Conclusions

openSESAME is a tool for leveraging the growing body of publicly available microarray data to discover relationships between different biological states based on common patterns of differential gene expression. These relationships may serve to generate hypotheses about the causes and consequences of specific patterns of observed differential gene expression. To encourage others to explore the utility of this approach, we have made a website for performing openSESAME queries freely available at http://opensesame.bu.edu.

Immunohistochemical characterization of human olfactory tissue

OBJECTIVES/HYPOTHESIS

The pathophysiology underlying human olfactory disorders is poorly understood because biopsying the olfactory epithelium (OE) can be unrepresentative and extensive immunohistochemical analysis is lacking. Autopsy tissue enriches our grasp of normal and abnormal olfactory immunohistology and guides the sampling of the OE by biopsy. Furthermore, a comparison of the molecular phenotype of olfactory epithelial cells between rodents and humans will improve our ability to correlate human histopathology with olfactory dysfunction.

STUDY DESIGN

An immunohistochemical analysis of human olfactory tissue using a comprehensive battery of proven antibodies.

METHODS

Human olfactory mucosa obtained from 21 autopsy specimens was analyzed with immunohistochemistry. The position and extent of olfactory mucosa was assayed by staining whole mounts (WMs) with neuronal markers. Sections of the OE were analyzed with an extensive group of antibodies directed against cytoskeletal proteins and transcription factors, as were surgical specimens from an esthesioneuroblastoma.

RESULTS

Neuron-rich epithelium is always found inferior to the cribriform plate, even at advanced age, despite the interruptions in the neuroepithelial sheet caused by patchy respiratory metaplasia. The pattern of immunostaining with our antibody panel identifies two distinct types of basal cell progenitors in human OE similar to rodents. The panel also clarifies the complex composition of esthesioneuroblastoma.

CONCLUSIONS

The extent of human olfactory mucosa at autopsy can easily be delineated as a function of age and neurologic disease. The similarities in human versus rodent OE will enable us to translate knowledge from experimental animals to humans and will extend our understanding of human olfactory pathophysiology.

Role of p63 in cancer development

Since their initial identification p53 homologues p63 and p73 have been expected to play a role in cancer development due to their close homology to p53, notoriously one of the most mutated genes in cancer. However soon after their discovery the awareness that these genes were rarely mutated in cancer seemed to indicate that they did not play a role in its development. However a large number of data collected in the following years indicated that altered expression rather than mutation could be found in different neoplasia and play a role in its biology. In particular p63 due to its fundamental role in epithelial development seems to play a role in a number of tumors of epithelial origin. In this review we summarize some of the evidence linking p63 to carcinogenesis.

Current diagnostic strategies for undifferentiated tumours of the nasal cavities and paranasal sinuses

Several malignant tumours occurring in the sinonasal tract may present with an undifferentiated morphology. Overall, these lesions pose significant diagnostic difficulties for the surgical pathologist, especially in limited biopsy material, but their correct classification is becoming increasingly important for an appropriate treatment strategy. This review deals with the criteria for differential diagnosis of these neoplasms, with emphasis on recent advances in immunohistochemistry and molecular biology, as well as with previous progress in electron microscopy. Through careful microscopic examination of haematoxylin and eosin-stained sections, in the light of clinical information and imaging data, a list of differential diagnoses can be made and an appropriate panel of antibodies can be chosen to further categorize the tumour. An initial panel including cytokeratins, synaptophysin, S100 protein, desmin and CD45 may allow the classification of most lesions or may help to narrow the list of differential diagnoses. Further refinement can be obtained through second-line markers, including in-situ hybridization for Epstein-Barr virus, other neuroendocrine markers, melanocytic markers, myogenin, CD99, other lymphocyte markers, and CD138 and light chains. Finally, molecular analysis can further assist in the recognition of specific entities such as nuclear protein in testis midline carcinoma, Ewing's sarcoma/peripheral neuroectodermal tumour, alveolar rhadbomyosarcoma, and poorly differentiated synovial sarcoma.

A review of NUT midline carcinoma

Nut midline carcinomas are uncommon carcinomas characterized by chromosomal rearrangements that involve the gene encoding the nuclear protein of the testis (NUT). This article reviews the clinicopathologic features of these malignancies. Ancillary testing is discussed as well as the pathologic differential diagnosis.

Sinonasal carcinomas: recent advances in molecular and phenotypic characterization and their clinical implications

Sinonasal carcinomas are rare tumors with an aggressive clinical behaviour which frequently pose a number of problems regarding the interpretation of diagnostic findings and the treatment. In addition, in comparison with other malignancies of the head and neck region, an elevated fraction of sinonasal carcinomas can be attributed to occupational exposure. This review is focused on the recent advances in the molecular and phenotypic characterization of sinonasal carcinomas, and their possible implications for the interpretation of epidemiological data, as well as for the diagnosis and treatment of these rare malignancies. The increasing knowledge on their phenotypic and genotypic features is progressively leading to a refinement in diagnosis, especially for poorly differentiated and undifferentiated lesions, as well as to the identification of markers which can be potentially useful to identify the early phases of carcinogenesis, to detect subclinical disease, to predict the response to therapy, and finally, that may represent potential targets for alternative treatments.

Increased invasiveness and aggressiveness in breast epithelia with cytoplasmic p63 expression

Our previous studies revealed that pregnancy associated breast cancer (PABC) had significantly reduced nuclear p63 expression in myoepithelia, while intense cytoplasmic p63 expression in associated epithelia. Our current study assessed these epithelia using immunohistochemistry with a panel of aggressiveness and invasiveness related markers and comparative genomic hybridization (array-CGH) with over 30,000 DNA probes. These epithelia showed several unique alterations, including (1) immunohistochemical and morphological resemblance to invasive cancer, (2) significant gain in copy numbers of DNA coding genes for morphogenesis, angiogenesis, and metastasis, and (3) significant loss in copy numbers of DNA coding genes for tumor suppressors, cell adhesion, and macromolecular complex assembly or intra-cellular trafficking. Detected array-CGH alterations correlated well with in vivo expression of a number of corresponding proteins tested. These findings suggest that aberrant sub-cellular localization of p63 expression in normal or hyperplastic appearing epithelial cells may significant contribute to increased invasiveness and aggressiveness of these cells.

Basaloid squamous cell carcinoma of the esophagus: assessment for high-risk human papillomavirus and related molecular markers

Basaloid squamous cell carcinoma (BSCC) of the esophagus is rare, historically confused for adenoid cystic carcinoma, and recently shown to behave similar to conventional, keratinizing esophageal squamous cell carcinoma. At other sites (eg, oropharynx, anogenital tract) the basaloid phenotype is frequently associated with the presence of high-risk human papillomavirus (HPV). HPVs role in esophageal squamous cell carcinomas is less certain, and to our knowledge, a direct examination of esophageal BSCC for high-risk HPV has not been performed earlier. Nine cases of esophageal BSCC were retrieved from our surgical pathology files. Twenty-two cases of keratinizing esophageal squamous cell carcinoma served as controls. In situ hybridization (ISH) for high-risk HPV and immunohistochemistry for related molecular markers including p53, cyclin D1, and p16 (scored 0 to 4+ based on percentage of cells staining; p53 additionally scored for intensity) were performed. HPV ISH was nonreactive in all tested cases. Compared with controls, BSCC showed less immunoreactivity for p16 and p53 (P=0.003, 0.009). Esophageal BSCC is negative for high-risk HPV by ISH, distinguishing these lesions from other BSCCs. Differential p16 and p53 expression in BSCC suggests that these tumors are molecularly distinct from conventional esophageal squamous cell carcinomas.

[Undifferentiated malignant round cell tumors of the sinonasal tract and nasopharynx]

Undifferentiated malignant round cell tumors of the sinonasal tract and nasopharynx comprise of aggressive malignant neoplasms with overlapping morphologic features, which yet are very different and can be identified as carcinoma, lymphoma, sarcoma, melanoma or olfactory neuroblastoma. Differentiating these tumors is important because their treatment and prognosis are quite different. Because of the limited initial biopsy tissue materials, major differential diagnostic difficulties may arise. The use of a panel of immunohistochemical markers and the identification, in some cases, of specific chromosomal translocations are most often required. We describe clinical, morphological, immunohistochemical and molecular features as well as therapeutic management and prognosis of rhabdomyosarcoma (RMS), Ewing sarcoma/primitive neuroectodermic tumor (EWS/PNET), nonkeratinizing nasopharyngeal carcinoma, undifferentiated subtype (UCNT), olfactory neuroblastoma (ONB), small cell carcinoma, neuroendocrine type (SCCNET), sinonasal undifferentiated carcinoma (SNUC) and mucosal melanoma. Mesenchymal chondrosarcoma, small round cell synovialosarcoma, lymphomas and plasmocytoma are not introduced. The most important features of diagnosis will be summarized in two tables.

Olfactory neuroblastoma: a review and update

Olfactory neuroblastoma (ONB) is a malignant neuroectodermal tumor that typically occurs in the superior nasal cavity. It is a distinct entity with features that include nesting, low-grade stippled nuclei, and neurofibrillary stroma with formation of pseudorosettes. It has a distinctive immunoprofile that includes keratin negativity, neuroendocrine marker positivity, and S100 positive sustentacular cells, which surround the nests of tumor in a supportive manner. Although the typical clinicopathologic features leave little room for misinterpretation, the wide variability in this tumor may cause diagnostic difficulty. This includes immunophenotypic diversity or patchy staining with immunomarkers, wide spectrum of grade and histology, posttreatment changes, and occasional divergent differentiation. In addition, problems in sampling, preservation, and clinical localization may make the diagnosis more challenging. A large group of tumors may show morphologic overlap with ONB, with some mimicking low-grade tumors, whereas others mimic high-grade tumors. This differential diagnosis has important treatment and prognostic implications. Further complicating the issue is that many of the mimics themselves may show great morphologic and immunophenotypic variability. This manuscript will review the typical clinical and pathologic features of ONB, address the great variability of ONB in our experience, will focus on the differential diagnosis and report on recent findings in these tumors including molecular genetics where applicable.

Carcinomas of the upper aerodigestive tract with rearrangement of the nuclear protein of the testis (NUT) gene (NUT midline carcinomas)

This manuscript reviews carcinomas of the upper aerodigestive tract associated with genetic rearrangements of the nuclear protein of the testis (NUT) gene, also known as NUT midline carcinomas. The literature is reviewed regarding all reported cases of NUT midline carcinomas and the clinicopathologic features are discussed. Our current understanding of the molecular pathogenesis of the disease is also discussed, along with the differential diagnosis for undifferentiated or poorly differentiated malignancy of the upper aerodigestive tract.