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Biomedical subjects

Mark W Lingen

Publications and source records attributed to Mark W Lingen.

11 recordsLinked to original sources
PubMed2025

Analytical and clinical performance validation of HPV-SEQ, a novel NGS-based liquid biopsy platform for detection and quantification of human papilloma virus circulating tumor DNA.

BACKGROUND: Human papillomavirus (HPV) is the primary causative driver of oropharyngeal squamous cell carcinoma (OPSCC). Accurate detection of HPV-DNA is critical for risk stratification and management of OPSCC. However, assays designed to detect HPV in primary tumors do not allow monitoring of HPV-DNA over time, whereas commercially available droplet digital PCR-based methods for assessment of circulating cell free (cf)HPV-DNA in plasma remain suboptimal, hindering adaptation into clinical practice. We have developed HPV-SEQ, a novel next-generation-sequencing (NGS) based method for detection and quantification of HPV16/18 DNA in plasma of patients with OPSCC. METHODS: The assay uses primers targeting the L1 gene of HPV16 and HPV18 viral genomes and strain specific calibrators at a defined concentration to determine the ratio of native HPV to a known standard, enabling accurate reporting of patient-derived HPV16/18 viral load in a sample. This study was conducted using two different patient populations in addition to healthy donors and contrived material. All experiments were performed to fulfill several applicable analytical, performance and validation guidelines. RESULTS: A thorough analytical characterization and clinical validation of this platform demonstrates that HPV-SEQ detects cfHPV-DNA with exceptional limit of quantification and high precision, providing a foundation for integrating this platform into clinical settings. CONCLUSIONS: This ultra-sensitive HPV profiling method with optimal analytical performance may represent a significant advancement in risk stratification, treatment management, and post-treatment surveillance for patients with OPSCC.

Humans↗
PubMed2003

Plasminogen activator inhibitor-2: a molecular biomarker for head and neck cancer progression.

Head and neck squamous cell carcinoma (HNSCC) is an aggressive epithelial malignancy in which the early diagnosis of premalignant lesions is known to directly correlate with increased survival. However, only a portion of biopsies showing dysplasia will progress to cancer, and there are no currently accepted criteria for predicting which lesions will progress. Therefore, diagnostic protocols that can identify the lesions that are likely to become HNSCC are required. RNA was isolated from normal keratinocytes, the immortalized but nontumorigenic HaCat cell line, and the tumor cell lines SCC-4, SCC-9, SCC-25, and OSCC-3. The RNA was then labeled and used to probe nylon microarray filters that contained a total of 9184 genes (5295 named and 3889 Expression Sequence Tags). Genes whose expression demonstrated a 3-fold or greater change were considered significant. Comparison of expression profiles from normal, HaCat, and four tumor cell lines revealed changes in gene expression in a total of 508 genes. Of these, 16 genes showed a consistent loss of expression when comparing normal to immortalized keratinocytes. In addition, 10 genes demonstrated a consistent loss of expression in the tumor cell lines only. In this latter group of genes, plasminogen activator inhibitor-2 (PAI-2), a gene whose expression has been linked to cell invasion, was additionally investigated. Altered expression of PAI-2 in the different cultured cells was validated via real-time quantitative-PCR. In addition, immunohistochemical evaluation of biopsy samples revealed a high expression of PAI-2 in both normal and dysplastic epithelium with a marked decrease of expression in areas of the biopsies containing HNSCC. These data demonstrate that genomic profiling can then be used to identify potential genotypic/phenotypic biomarkers that may predict which dysplastic lesions are most likely to progress to HNSCC.

Biomarkers, Tumor↗
PubMed2003

Classification and identification of genes associated with oral cancer based on gene expression profiles. A preliminary study.

Oral squamous cell carcinoma (OSCC) is an aggressive malignancy. The five-year survival rate remains largely unchanged for the past 40 years. Early diagnosis has been shown to correlate with increased survival, based on cytologic changes. In order to improve our current treatment strategies for OSCC, it is necessary to understand the genetic and molecular networks underlying this disease. In this preliminary study, we illustrate the application of DNA microarrays to study OSCC. Using computational and statistical algorithms, we were able to differentiate (or classify) "cancer" and "normal" samples based on the behavior of the gene expression profiles. We found 651 genes to be associated with cancer. This article describes a preliminary study of current developments from the Human Genome Project (HGP) and its application to OSCC.

Carcinoma, Squamous Cell↗
PubMed2002

Prediction of in vivo synergistic activity of antiangiogenic compounds by gene expression profiling.

Angiogenesis, an essential phenotype for tumor formation, requires the interaction of many cells within the tumor microenvironment. Therefore, successful antiangiogenic therapies must be able to block all of the different mechanisms tumors use to induce neovascularization. A major challenge for developing such protocols is determining which agents are likely to have the highest degree of synergistic activity in vivo. We treated human microvascular endothelial cells with six inhibitors of angiogenesis and used microarrays to seek divergent patterns of gene expression suggestive of potential synergies. The expression profiles of a thrombospondin-mimetic peptide (DI-TSPa) and TNP-470 (TNP) were very similar, whereas endostatin had a dramatically different profile. In vitro, endostatin was synergistically antiangiogenic with either TNP-470 or DI-TSPa. In vivo, mice bearing Lewis lung carcinoma cells treated with a combination of endostatin and either DI-TSPa or TNP-470, at doses that were ineffective when used alone, resulted in a marked inhibition of tumor growth and decreased tumor angiogenesis. Conversely, animals treated with both DI-TSPa and TNP-470 demonstrated a modest effect on both tumor growth and angiogenesis. These results suggest that even in the absence of a complete mechanistic understanding of how these inhibitors work, gene expression profiling may be used to predict synergistic antiangiogenic activity and thus maximize their antitumor efficacy.

Angiogenesis Inhibitors↗
PubMed2002

Retinoic acid modulates the ability of macrophages to participate in the induction of the angiogenic phenotype in head and neck squamous cell carcinoma.

Angiogenesis, an essential step in the development of neoplasia, is a complex process that involves the interaction of tumor cells with stromal cells. Tumor-associated macrophages (TAMs) can participate in the induction of angiogenesis and are of prognostic value in some neoplasms. Specimens from head and neck squamous cell carcinomas (HNSCC) often contain large numbers of TAMs. In addition, experimental evidence has demonstrated that HNSCC tumor cells can attract and activate macrophages to participate in the expression of the angiogenic phenotype. These findings suggest that antiangiogenic therapies for HNSCC must include strategies that will block the recruitment of macrophages into the tumor microenvironment. We investigated the ability of retinoic acid (RA) to modulate the ability of tumor cells to recruit and activate monocytes for participation in tumor angiogenesis. Owing to a decrease in the secretion of MCP-1 and transforming growth factor-beta 1 (TGF-beta 1), tumor cells treated with RA were unable to induce peripheral blood monocyte (PBM) chemotaxis. Also, as a result of the decrease in TGF-beta 1 secretion, RA-treated tumor cells were unable to activate macrophages for secretion of vascular endothelial growth factor (VEGF) and interleukin-8 (IL-8). In addition to its affects on tumor cells, RA also directly altered the ability of monocytes to participate in the tumor angiogenesis process. PBM exposed to RA were unable to migrate toward inducers of PBM such as MCP-1 and TGF-beta 1. Finally, RA decreased the ability of tumor-activated macrophages to secrete IL-8 and VEGF. These data demonstrate alternative mechanisms by which RA may modulate angiogenesis in the tumor microenvironment. In addition, it underscores the necessity to develop antiangiogenic treatment protocols that can block each of the ways in which new blood vessel growth is induced in tumor microenvironments.

Carcinoma, Squamous Cell↗
PubMed2002

Synchronous benign and malignant salivary gland tumors in ipsilateral glands: a report of two cases and a review of literature.

BACKGROUND: Ipsilateral salivary gland tumors of different histologic types are rare and make up less than 0.3% of all salivary gland neoplasms. Only nine cases of synchronous benign and malignant ipsilateral parotid gland tumors have been described in the literature. METHODS: Two additional cases of synchronous benign and malignant neoplasms in the parotid gland are reported and discussed with a review of literature. RESULTS: Our first case describes a pleomorphic adenoma and a salivary duct carcinoma, an entity not previously reported in the literature. The second case documents the most common benign and malignant ipsilateral parotid gland neoplasm reported in this case series, a Warthin's tumor and a mucoepidermoid carcinoma. CONCLUSIONS: Synchronous salivary gland tumors exhibiting both benign and malignant components are uncommonly observed, with only nine cases published to date. We describe two additional cases of a synchronous benign and malignant ipsilateral parotid gland tumor.

Adenolymphoma↗
PubMed2002

Neuropilin-1 participates in wound angiogenesis.

Angiogenesis, the formation of new capillaries from existing vasculature, plays an essential role in tissue repair. The rapid onset and predominance of proangiogenic factors optimizes healing in damaged tissues. One factor that directly mediates wound vessel angiogenesis is vascular endothelial growth factor (VEGF). Although much is known about the biology of VEGF and its cognate receptors, VEGFR1 and VEGFR2, the role of a recently identified co-receptor for VEGF, neuropilin-1, is not well understood. Using a murine model of dermal wound repair, we found that neuropilin-1 was abundantly expressed on new vasculature in healing wounds. Moreover, mice treated with anti-neuropilin-1 antibodies exhibited a significant decrease in vascular density within these wounds (67% decrease, P = 0.0132). In in vitro assays, VEGF induced formation of endothelial cord-like structures on collagen gel and endothelial cell migration toward VEGF was inhibited by antibodies directed against neuropilin-1. These results provide both in vitro and in vivo evidence for a critical role of neuropilin-1 in wound angiogenesis.

Animals↗
PubMed2002

Gene expression profiling using laser capture microdissection.

Human disease is governed by a complex array of cellular populations and sub-population. Gene expression profiling is proving an important means of understanding and classifying pathophysiologic processes by identifying genes, gene pathways and pathway networks not previously known to be associated with particular diseases. However, disease-associated gene expression can be obscured by surrounding 'normal' tissue. Laser capture microdissection allows gene expression analysis of pooled single cells, cell subpopulations and cell populations. Analysis of laser capture microdissection-procured cells will allow a better understanding of the cellular components of disease.

DNA, Complementary↗
PubMed2002

Acellular dermal matrix allografts to achieve increased attached gingiva. Part 2. A histological comparative study.

BACKGROUND: In part 1 of this study, we compared the clinical efficacy of freeze-dried acellular dermal matrix (ADM) allograft in 6 patients with autogenous free gingival graft (FGG) in 6 patients for increasing the width of attached gingiva in the mandibular anterior area. The purpose of the present study was to histologically compare the microstructure of ADM and FGG treated sites from the same group. METHODS: Biopsies were harvested from all 12 patients at 6 months postsurgery. The biopsies included the grafted sites with adjacent alveolar mucosa and gingiva propria and also donor palatal mucosa saved at the time of surgery. The 5 microm thick, neutral buffered formalin fixed, paraffin-embedded tissue sections were stained with hematoxylin and eosin (H&E), Masson's trichrome, and Verhoeff-van Gieson stains in order to investigate the density of collagen and elastic fibers. Additional sections were stained with periodic acid-Schiff (PAS) and Papanicolaou's stain to identify the presence of glycogen granules in the epithelial layer and to highlight the keratin layer respectively. RESULTS: The unique appearance of ADM-derived tissue did not parallel any known oral mucosa. The connective tissue portion contained dense to extremely dense collagen fibers along with scattered elastic fibers. The demarcations between the ADM graft and the coronal gingiva as well as the apical alveolar mucosa were usually not very defined. A moderate to thin epithelial layer, with heterogeneous expression of keratinization and flat epithelium-connective tissue interface, covered the lamina propria. Both the thickness of the epithelium and the degree of keratinization decreased in apical direction, being mostly para- or orthokeratinized in the area close to gingiva and non-keratinized adjacent to the alveolar mucosa. In the FGG-treated sites, the density of collagen fibers was less than in ADM-derived tissue, palatal mucosa, and gingiva. Elastic fibers were very sparse, comparable to gingiva, but much less than in ADM-derived tissue. The epithelium was moderate, somewhat thinner but the shape of the rete ridges resembled that of palatal mucosa. Similar to gingiva epithelium, the epithelium of the FGG-treated area was relatively uniform in both thickness and keratinization, mostly para-keratinized with a well defined border to the non-keratinized alveolar mucosa. Underneath the FGG-alveolar mucosa junction, a scar band composed of extremely dense collagen fibers consistently existed. CONCLUSIONS: The results of this 6-month histological evaluation suggest that: 1) the resultant tissue types of ADM grafts were similar to "scar" tissue; 2) the non-vital dermal matrix of ADM allograft lacked the capability of directing cyto-differentiation of the covering epithelium; 3) autogenous FGG-derived tissue was neither identical to donor palatal mucosa nor to adjacent gingiva propria; 4) the connective tissue of donor palatal mucosa only partially contributed to the differentiation of the epithelium covering the FGG-treated area; and 5) the epithelium/connective tissue microenvironment surrounding the recipient site influenced the epithelial differentiation of the graft; this may play a more critical role in ADM grafting than in the grafting of autogenous FGG.

Adult↗
PubMed2002

Gene expression levels in different stages of progression in oral squamous cell carcinoma.

Oral squamous cell carcinoma (OSCC) is one of the most common cancer types worldwide. The prognosis for patients with this disease is generally poor and little is known about its progression. Gene expression studies may provide important insights to the molecular mechanisms of this disease. We analyzed gene expression data from a small panel of patients diagnosed with OSCC. Even with only 13 patient samples we were able to find genes with significant differences in expression levels between normal, dysplasia, and cancer samples. The largest differences in expression were generally found between normal and cancer samples, but significant differences were also found for several genes between dysplasia and the other two sample types. We also represent the significance levels of differentially expressed genes on the chromosome domain. The genes and genetic features we examine are potentially important factors on the molecular level in the progression of OSCC.

Carcinoma, Squamous Cell↗