Spatially distinct molecular patterns of gene expression in idiopathic pulmonary fibrosis.

BACKGROUND: Idiopathic pulmonary fibrosis (IPF) is a heterogeneous disease that is pathologically characterized by areas of normal-appearing lung parenchyma, active fibrosis (transition zones including fibroblastic foci) and dense fibrosis. Defining transcriptional differences between these pathologically heterogeneous regions of the IPF lung is critical to understanding the distribution and extent of fibrotic lung disease and identifying potential therapeutic targets. Application of a spatial transcriptomics platform would provide more detailed spatial resolution of transcriptional signals compared to previous single cell or bulk RNA-Seq studies. METHODS: We performed spatial transcriptomics using GeoMx Nanostring Digital Spatial Profiling on formalin-fixed paraffin-embedded (FFPE) tissue from 32 IPF and 12 control subjects and identified 231 regions of interest (ROIs). We compared normal-appearing lung parenchyma and airways between IPF and controls with histologically normal lung tissue, as well as histologically distinct regions within IPF (normal-appearing lung parenchyma, transition zones containing fibroblastic foci, areas of dense fibrosis, and honeycomb epithelium metaplasia). RESULTS: We identified 254 differentially expressed genes (DEGs) between IPF and controls in histologically normal-appearing regions of lung parenchyma; pathway analysis identified disease processes such as EIF2 signaling (important for cap-dependent mRNA translation), epithelial adherens junction signaling, HIF1α signaling, and integrin signaling. Within IPF, we identified 173 DEGs between transition and normal-appearing lung parenchyma and 198 DEGs between dense fibrosis and normal lung parenchyma; pathways dysregulated in both transition and dense fibrotic areas include EIF2 signaling pathway activation (upstream of endoplasmic reticulum (ER) stress proteins ATF4 and CHOP) and wound healing signaling pathway deactivation. Through cell deconvolution of transcriptome data and immunofluorescence staining, we confirmed loss of alveolar parenchymal signals (AGER, SFTPB, SFTPC), gain of secretory cell markers (SCGB3A2, MUC5B) as well as dysregulation of the upstream regulator ATF4, in histologically normal-appearing tissue in IPF. CONCLUSIONS: Our findings demonstrate that histologically normal-appearing regions from the IPF lung are transcriptionally distinct when compared to similar lung tissue from controls with histologically normal lung tissue, and that transition zones and areas of dense fibrosis within the IPF lung demonstrate activation of ER stress and deactivation of wound healing pathways.

Relationship between gene expression and lung function in Idiopathic Interstitial Pneumonias.

BACKGROUND: Idiopathic interstitial pneumonias (IIPs) are a group of heterogeneous, somewhat unpredictable diseases characterized by progressive scarring of the interstitium. Since lung function is a key determinant of survival, we reasoned that the transcriptional profile in IIP lung tissue would be associated with measures of lung function, and could enhance prognostic approaches to IIPs. RESULTS: Using gene expression profiling of 167 lung tissue specimens with IIP diagnosis and 50 control lungs, we identified genes whose expression is associated with changes in lung function (% predicted FVC and % predicted DLCO) modeled as categorical (severe vs mild disease) or continuous variables while adjusting for smoking status and IIP subtype; false discovery rate (FDR) approach was used to correct for multiple comparisons. This analysis identified 58 transcripts that are associated with mild vs severe disease (categorical analysis), including those with established role in fibrosis (ADAMTS4, ADAMTS9, AGER, HIF-1α, SERPINA3, SERPINE2, and SELE) as well as novel IIP candidate genes such as rhotekin 2 (RTKN2) and peptidase inhibitor 15 (PI15). Protein-protein interactome analysis of 553 genes whose expression is significantly associated with lung function when modeled as continuous variables demonstrates that more severe presentation of IIPs is characterized by an increase in cell cycle progression and apoptosis, increased hypoxia, and dampened innate immune response. Our findings were validated in an independent cohort of 131 IIPs and 40 controls at the mRNA level and for one gene (RTKN2) at the protein level by immunohistochemistry in a subset of samples. CONCLUSIONS: We identified commonalities and differences in gene expression among different subtypes of IIPs. Disease progression, as characterized by lower measures of FVC and DLCO, results in marked changes in expression of novel and established genes and pathways involved in IIPs. These genes and pathways represent strong candidates for biomarker studies and potential therapeutic targets for IIP severity.

Immunological and metabolic characterization of environmental Mycobacterium chimaera infection in a murine model.

Mycobacterium chimaera causes pulmonary disease, but little is known of gradations in isolate virulence. Previously, 17 M. chimaera isolates were screened for survival in THP1 macrophages. "M. chimaera 1" was categorized as "more virulent" because it showed the greatest survival in macrophages, whereas "M. chimaera 2" was categorized as "less virulent" with reduced survival. Herein, we infected C3HeB/FeJ mice to compare the in vivo immune responses to M. chimaera 1 and 2. Unlike macrophages, significantly lower M. chimaera 1 counts were recovered from mouse lung tissue and BAL cells with less lung histopathologic changes compared to M. chimaera 2. Compared to M. chimaera 2, significantly more IL-1ß, IL-6, and TNFα was produced early after M. chimaera 1 infection. LC-MS metabolomics analyses of BAL fluid revealed divergence in sphingolipid, phospholipid metabolism between M. chimaera 1 versus M. chimaera 2 mice. From pan-GWAS analyses, virulence and organizing DNA/molecular structure genes were associated with more virulent M. chimaera isolates. Vigorous lung-specific immune responses to M. chimaera 1 may influence effective bacterial control, but for a different isolate M. chimaera 2, subvert immune control. Continued studies of the gradations in virulence among the same NTM species will advance our understanding of NTM pathogenesis.

IgA Antibodies Directed Against Citrullinated Protein Antigens Are Elevated in Patients With Idiopathic Pulmonary Fibrosis.

BACKGROUND: The etiology of idiopathic pulmonary fibrosis (IPF) is unknown. Because it shares genetic, histopathologic, and radiographic features with the fibrosing interstitial lung disease seen in rheumatoid arthritis (RA), the goal of this study was to investigate RA-related autoantibodies in IPF. METHODS: The study included patients with IPF from two separate cohorts at National Jewish Health and Brigham Women's Hospital (n = 181), general population control subjects (n = 160), and control subjects with disease (n = 86 [40 with RA-usual interstitial pneumonia and 46 with hypersensitivity pneumonitis]). Serum was tested for RA-associated antibodies (including IgG and IgA) to citrullinated protein antigens (ACPA). Lung tissue in 11 patients with IPF was examined for ectopic lymphoid aggregates. RESULTS: An increased prevalence of ACPA positivity was found in two separate IPF cohorts. In particular, positivity for IgA-ACPA was increased in these two IPF cohorts compared with general population control subjects (21.3% and 24.8% vs 5.6%; P < .01). Patients with IPF were more likely to be IgA-ACPA-positive than IgG-ACPA-positive (23.2% vs 8.3%; P < .01), whereas patients with RA were more likely to be IgG-ACPA-positive than IgA-ACPA-positive (72.5% vs 52.5%; P = .04). There was a strong correlation between IgA-ACPA level and the number of ectopic lymphoid aggregates on lung histologic examination in IPF (r = 0.72; P = .01). CONCLUSIONS: In this study, IgA-ACPA was elevated in patients with IPF and correlated with lymphoid aggregates in the lung, supporting the theory that IgA-ACPA may play a role in lung disease pathogenesis in a subset of individuals with IPF. Future studies are needed to determine whether this subset of ACPA-positive patients with IPF is distinct from patients with IPF but without antibodies.

Electrical Properties of Ultrathin Platinum Films by Plasma-Enhanced Atomic Layer Deposition.

The ability to deposit thin and conformal films has become of great importance because of downscaling of devices. However, because of nucleation difficulty, depositing an electrically stable and thin conformal platinum film on an oxide nucleation layer has proven challenging. By using plasma-enhanced atomic layer deposition (PEALD) and TiO2 as a nucleation layer, we achieved electrically continuous PEALD platinum films down to a thickness of 3.7 nm. Results show that for films as thin as 5.7 nm, the Mayadas-Shatzkes (MS) model for electrical conductivity and the Tellier-Tosser model for temperature coefficient of resistance hold. Although the experimental values start to deviate from the MS model below 5.7 nm because of incomplete Pt coverage, the films still show root mean square electrical stability better than 50 ppm over time, indicating that these films are not only electrically continuous but also sufficiently reliable for use in many practical applications.

Frequency of recurrence of atrial fibrillation within 48 hours after ablation and its impact on long-term outcome.

Because of delayed structural and electrophysiologic effects of radiofrequency ablation of atrial fibrillation (AF), early recurrence of AF after ablation does not necessarily indicate long-term ablation failure. This study was intended to assess the prognostic value of early recurrence of AF within 48 hours after ablation. The study included 234 patients (aged 23 to 80 years; 72% men) with symptomatic drug-resistant paroxysmal (n = 165) or persistent AF (n = 69) who underwent either Lasso-guided segmental pulmonary vein isolation (n = 83) or CARTO-guided left atrial circumferential ablation (n = 151). After a median follow-up of 12.7 months, 64% of patients with paroxysmal and 45% of patients with persistent AF were AF free. Early recurrence of AF occurred in 43% of patients and was more frequently observed in the persistent-AF group (paroxysmal vs persistent 39% vs 54%; p = 0.037). Early recurrence of AF was a significant predictor of long-term ablation failure in univariate (hazard ratio [HR] 2.29, p <0.001) and multivariate (HR 2.17. p <0.001) Cox regression analysis. Nevertheless, 46% of patients with early recurrence of AF were AF free during long-term follow-up compared with 68% of patients without early recurrence of AF. The prognostic value of early recurrence of AF was found in patients with paroxysmal (HR 2.05, p = 0.005) and persistent AF (HR 2.35, p = 0.013). In conclusion, early recurrence of AF within 48 hours after ablation was a significant predictor of a poor long-term ablation outcome. However, because nearly half the patients with early recurrence of AF remained AF free during long-term follow-up, early recurrence of AF should not automatically result in an early repeated procedure.

B7-h4 is highly expressed in ductal and lobular breast cancer.

PURPOSE: This study was designed to investigate the expression of B7-H4 protein, a member of the B7 family that is involved in the regulation of antigen-specific immune responses, in normal breast and in primary and metastatic breast carcinomas. EXPERIMENTAL DESIGN: Archival formalin-fixed tissue blocks from breast cancers and normal somatic tissues were evaluated for B7-H4 expression by immunohistochemistry with manual and automated image analysis. The proportion of B7-H4-positive cells and the intensity of B7-H4 staining were compared with histologic type, grade, stage, hormone receptor status, and HER-2/neu status. RESULTS: B7-H4 was detected in 165 of 173 (95.4%) primary breast cancers and in 240 of 246 (97.6%) metastatic breast cancers. B7-H4 staining intensity was greater in invasive ductal carcinomas [24.61 relative units (RU)] and in invasive lobular carcinomas (15.23 RU) than in normal breast epithelium (4.30 RU, P = 0.0003). Increased staining intensity was associated with negative progesterone receptor status (P = 0.014) and history of neoadjuvant chemotherapy (P = 0.004), and the proportion of B7-H4-positive cells was associated with negative progesterone receptor (P = 0.001) and negative HER-2/neu (P = 0.024) status. However, there was no statistically significant relationship between the proportion of B7-H4-positive cells or staining intensity and grade, stage, or other clinicopathologic variables. Low levels of B7-H4 expression were also detected in epithelial cells of the female genital tract, lung, pancreas, and kidney, but B7-H4 was generally absent in most other normal somatic tissues. CONCLUSIONS: The nearly ubiquitous expression of B7-H4 in breast cancer, independent of tumor grade or stage, suggests a critical role for this protein in breast cancer biology.

Analysis of telomerase as a diagnostic biomarker of cervical dysplasia and carcinoma.

Telomerase expression is a potentially important marker of high-grade cervical dysplasia and squamous cell carcinoma (SCC). The routine practice of cervical cytology is limited by problems of false negative diagnoses as well as by poor specificity for clinically significant lesions in patients with low-grade cytologic abnormalities. Telomerase is widely expressed in most SCCs as well as in a high proportion of high-grade squamous intraepithelial lesions. Histochemical studies have confirmed that telomerase is expressed in the lower portions of normal or metaplastic squamous mucosa but that telomerase positive cells extend into the upper epithelial layers in cases of high-grade dysplasia. Since the cervical smear samples the uppermost cell layers of the cervical mucosa, but does not normally include cells derived from the lower layers of the squamous mucosa, the detection of telomerase in exfoliated cells of the cervical smear may have specificity for clinically significant lesions. The analysis of hTR, hTERT, and telomerase activity are complicated by a number of technical factors that may lead to either false negative or false positive test results. Thus, the practical application of telomerase analysis as a diagnostic adjunct for cervical cytopathology may depend on the development of more reliable and sensitive assay systems, possibly formatted for cytochemical applications.

Telomerase and human papillomavirus as diagnostic adjuncts for cervical dysplasia and carcinoma.

Telomerase and human papillomavirus (HPV) DNA were evaluated as potential markers of high-grade dysplasia in cervical cytological specimens. Cytology specimens were collected from patients at the time of colposcopic evaluation for management of a previous abnormal cytology test result. Telomerase activity was evaluated by the telomeric repeat amplification protocol (TRAP), and HPV DNA was detected by polymerase chain reaction with L1 consensus-sequence primers and filter hybridization genotyping. Telomerase was detected in 8 of 97 (8.2%) cases with normal cytology or benign cellular changes, in 7 of 98 (7.1%) cases of atypical squamous cells of undetermined significance (ASCUS), in 3 of 95 (3.2%) cases of low-grade squamous intraepithelial lesion (LSIL), and in 17 of 48 (35.4%) cases with high-grade squamous intraepithelial lesion (HSIL). High-risk HPVs were detected in 23 of 97 (23.7%) cases with normal/reactive cellular changes (RCC) cytology, in 28 of 98 (28.6%) cases of ASCUS, in 69 of 95 (72.6%) cases of LSIL, and in 35 of 48 (72.9%) cases of HSIL. Telomerase expression did not correlate with the detection of high-risk HPVs in any cytological diagnostic categories. Telomerase and HPV test results of cytological specimens were correlated with the histological diagnoses of concurrent cervical biopsy specimens. Telomerase showed a sensitivity of 29.9% and a specificity of 94.0% for biopsy-confirmed cervical intraepithelial neoplasia (CIN) II/III. In contrast, high-risk HPVs were detected in 70.1% of cases with underlying CIN II/III, with a specificity of 62.5%. A relatively high proportion of normal/RCC or ASCUS cases with telomerase-positive test results had underlying high-grade dysplasia on cervical biopsy. Thus, technical and practical limitations of the TRAP assay in cervical cytology specimens limit the practical application of telomerase as a diagnostic adjunct in cervical cytopathology.

Evaluation of p16INK4a and pRb expression in cervical squamous and glandular neoplasia.

p16(INK4a) is known to play a critical role as a negative regulator of cell cycle progression and differentiation by controlling the activity of the tumor-suppressor protein pRb. The present study evaluated the expression of p16(INK4a) and pRb in cervical squamous and glandular neoplasia. Immunohistochemical staining was performed for p16(INK4a) and pRb in formalin-fixed, paraffin-embedded tissue sections of the uterine cervix using an indirect immunoperoxidase method. p16(INK4a) staining was detected in 7 of 108 sections (6.5%) of normal squamous mucosa, in scattered ciliated columnar cells in 33 of 88 sections (37.5%) of normal endocervical glands, in 9 of 30 sections (30%) with Nabothian cysts, and in 4 of 4 areas (100%) of tubal metaplasia. In contrast, strong p16(INK4a) staining was found in 13 of 18 cases (72.2%) of cervical intraepithelial neoplasia (CIN) I and in all cases of CIN II/III (n = 46), squamous cell carcinoma (n = 18), endocervical glandular dysplasia (n = 10), adenocarcinoma in situ (n = 23), and invasive adenocarcinoma (n = 12). pRb expression was detected in each diagnostic category; however, the proportion of pRb-positive cells was relatively decreased in high-grade premalignant and malignant lesions of the squamous and endocervical mucosa and showed a generally inverse correlation with the expression of p16(INK4a) at the tissue level. These findings confirm a correlation between the expression of p16(INK4a) and pRb in cervical neoplasias and indicate that p16(INK4a) is a specific marker for premalignant and malignant lesions of the squamous and endocervical mucosa.

The use of a combination of galectin-3 and thyroid peroxidase for the diagnosis and prognosis of thyroid cancer.

In this retrospective histologic study, galectin-3 had a sensitivity of 92% (22/24) for papillary thyroid carcinoma and 44% (4/9) for follicular thyroid carcinoma. Thyroid peroxidase (TPO) had a sensitivity of 50% (12/24) for papillary and 11% (1/11) for follicular carcinoma. The combination of galectin-3 and TPO had a sensitivity of 96% (23/24) for papillary and 44% (4/9) for follicular carcinoma. From a prognostic standpoint, of patients whose papillary carcinomas expressed both markers, all became free of disease. Of those whose papillary carcinomas expressed galectin-3 but not TPO, 57% (4/7) became free of disease, 29% (2/7) had persistent disease, and 14% (1/7) had progressive disease. This study confirms previous observations that galectin-3 alone is highly sensitive for papillary carcinoma but not adequately sensitive for follicular carcinoma. TPO alone is not adequately sensitive for the evaluation of any thyroid lesion. The combination of galectin-3 and TPO is complementary as a diagnostic and prognostic tool for patients with papillary carcinoma.

Analysis of survivin expression in a spectrum of benign to malignant lesions of the breast.

Survivin, a novel inhibitor of apoptosis, is expressed in a variety of human cancers, with reports of prognostic significance in some neoplasms. The authors' aim was to evaluate survivin expression in a spectrum of breast lesions to determine differential expression in malignant versus benign lesions and its potential role as a diagnostic or prognostic marker. The authors found that survivin is expressed in breast tissue in the full spectrum of normal to invasive carcinoma. It is predominantly nuclear with a faint cytoplasmic blush. Survivin expression was independent of patient age and tumor size. Benign breast tissue showed survivin expression in a lower percentage of cells (45%) than malignant lesions. The median values for the percentage of cells that stained for survivin were statistically different among the categories of invasive carcinoma, DCIS, LCIS, and benign breast tissue (P < or = 0.001). The highest percentage of positive-staining cells was seen in high-grade DCIS (95%). The authors found a trend toward a higher percentage of cells staining for survivin in breast carcinoma cases that were ER negative, PR negative, or Her2/neu positive, although this was not statistically significant. Survivin expression was preserved in biopsies from recurrent tumors without loss of nuclear survivin expression. In conclusion, survivin is overexpressed in malignant breast lesions relative to benign lesions or normal breast tissue and in high-grade DCIS relative to nonhigh-grade DCIS. Therefore, survivin may have a role, albeit a limited one, as a prognostic marker in breast lesions.

Increased lymphatic vessel length is associated with the fibroblast reticulum and disease severity in usual interstitial pneumonia and nonspecific interstitial pneumonia.

BACKGROUND: Lymphangiogenesis responds to tissue injury as a key component of normal wound healing. The development of fibrosis in the idiopathic interstitial pneumonias may result from abnormal wound healing in response to injury. We hypothesize that increased lymphatic vessel (LV) length, a marker of lymphangiogenesis, is associated with parenchymal components of the fibroblast reticulum (organizing collagen, fibrotic collagen, and fibroblast foci), and its extent correlates with disease severity. METHODS: We assessed stereologically the parenchymal structure of fibrotic lungs and its associated lymphatic network, which was highlighted immunohistochemically in age-matched samples of usual interstitial pneumonia (UIP), nonspecific interstitial pneumonia (NSIP) with FVC < 80%, COPD with a Global Initiative for Obstructive Lung Disease stage 0, and normal control lungs. RESULTS: LV length density, as opposed to vessel volume density, was found to be associated with organizing and fibrotic collagen density (P < .0001). Length density of LVs and the volume density of organizing and fibrotic collagen were significantly associated with severity of both % FVC (P < .001) and diffusing capacity of the lung for carbon monoxide (P < .001). CONCLUSIONS: Severity of disease in UIP and NSIP is associated with increased LV length and is strongly associated with components of the fibroblast reticulum, namely organizing and fibrotic collagen, which supports a pathogenic role of LVs in these two diseases. Furthermore, the absence of definable differences between UIP and NSIP suggests that LVs are a unifying mechanism for the development of fibrosis in these fibrotic lung diseases.

Evaluation of left atrial function by multidetector computed tomography before left atrial radiofrequency-catheter ablation: comparison of a manual and automated 3D volume segmentation method.

INTRODUCTION: The purpose of this study was to compare a manual and automated 3D volume segmentation tool for evaluation of left atrial (LA) function by 64-slice multidetector-CT (MDCT). METHODS AND MATERIALS: In 33 patients with paroxysmal atrial fibrillation a MDCT scan was performed before radiofrequency-catheter ablation. Atrial function (minimal volume (LAmin), maximal volume (LAmax), stroke volume (SV), ejection fraction (EF)) was evaluated by two readers using a manual and an automatic tool and measurement time was evaluated. RESULTS: Automated LA volume segmentation failed in one patient due to low LA enhancement (103HU). Mean LAmax, LAmin, SV and EF were 127.7 ml, 93 ml, 34.7 ml, 27.1% by the automated, and 122.7 ml, 89.9 ml, 32.8 ml, 26.3% by the manual method with no significant difference (p>0.05) and high Pearsons correlation coefficients (r=0.94, r=0.94, r=0.82 and r=0.85, p<0.0001), respectively. The automated method was significantly faster (p<0.001). Interobserver variability was low for both methods with Pearson's correlation coefficients between 0.98 and 0.99 (p<0.0001). CONCLUSIONS: Evaluation of LA volume and function with 64-slice MDCT is feasible with a very low interobserver variability. The automatic method is as accurate as the manual method but significantly less time consuming permitting a routine use in clinical practice before RF-catheter ablation.

Morphological changes in the chicken ductus arteriosi during closure at hatching.

The chicken embryo has two functioning ductus arteriosi (DA) during development. These blood vessels connect the pulmonary arteries to the descending aorta providing a right-to-left shunt of blood away from the nonrespiring lungs and to the systemic circuit and chorioallanotic membrane. The DA consists of two distinct tissue types along its length, a muscular proximal portion and an elastic distal portion. During hatching, the DA must close for proper separation of systemic and pulmonary circulation. We examined the morphological changes of the chicken DA before, during, and after hatching. Occlusion of the proximal DA began during external pipping and was complete at hatching. Anatomical remodeling began as early as external pipping with fragmentation of the internal elastic lamina and smooth muscle actin appearing in the neointimal zone. By day 2 posthatch, the proximal DA lumen was fully occluded by endothelial cells and smooth muscle actin positive cells. In contrast, the distal DA was not fully occluded by day 2 posthatch. Increases in Po(2) of the blood serves as the main stimulus for closure of the mammalian DA. The responsiveness of the chicken proximal DA to oxygen increased during hatching, peaking during external pipping. This peak correlated with an increase in blood gas Po(2) and the initial occlusion of the vessel. The distal portion remained unresponsive to oxygen throughout hatching. In conclusion, the chicken DA begins to close during external pipping when arterial Po(2) increases and vessel tone is most sensitive to oxygen.

Validation of a novel immunocytochemical assay for topoisomerase II-alpha and minichromosome maintenance protein 2 expression in cervical cytology.

BACKGROUND: Cervical cytopathology has limited specificity for the detection of underlying clinically significant lesions in cases with low-grade cytologic abnormalities. The current study evaluated the performance of a novel immunocytochemical test (ProEx C) for topoisomerase II alpha (TOP2A) and minichromosome maintenance protein 2 (MCM2) in normal versus high-grade squamous intraepithelial lesion (HSIL) and positive control (SiHa) pooled cytology preparations and in a pilot series of prospectively collected patient specimens. METHODS: TOP2a and MCM2 were detected as markers of aberrant S-phase induction in SurePath cervical cytology specimens by an indirect polymer-based immunoperoxidase method (ProEx C, TriPath Oncology, Burlington, NC). Slides were scored based on specimen adequacy, the presence of nuclear stain in epithelial cells, and the association of nuclear staining with cytologic atypia (>/=atypical squamous cell of undetermined significance [ASC-US] or atypical glandular cells [AGC]). RESULTS: Intense nuclear staining was detected in cytologically abnormal cells but not in most normal squamous and glandular cells. Slides were scored positive in pooled samples in 1 of 40 (2.5%) cases that were negative for intraepithelial neoplasia or malignancy (NIL), in 40 of 40 (100%) SiHa-spiked NIL, and in 40 of 40 (100%) HSILs. There was 100% concordance in test classification of 20 slides between 2 pathologists. Subsequent evaluation of prospectively collected patient specimens was positive for ProEx C in none of 10 NIL (0%), 2 of 10 ASC-US (20%), 5 of 10 low-grade SIL (LSIL) (50%), and in 10 of 10 (100%) HSILs. CONCLUSIONS: The ProEx C test showed almost no variability with regard to scoring and staining reproducibility and was consistently positive in HSIL. Further studies are indicated to evaluate the potential role of ProEx C as a diagnostic adjunct for the triage of ASC-US/LSIL.

Correlation of p16 and pRb expression with HPV detection in Bowen's disease.

BACKGROUND: Bowen's disease is a form of cutaneous squamous cell carcinoma which may be caused by ultraviolet radiation, human papilloma virus (HPV) infection, or other causes. Although p16 over-expression is a surrogate marker of HPV E7-mediated catabolism of pRb in premalignant and malignant lesions of the cervical mucosa, the correlation of p16 and pRb expression with HPV detection in Bowen's disease has not been well characterized. METHODS: A retrospective study on formalin-fixed tissues was performed. Immunohistochemistry for p16 and pRb was performed on 32 cases. DNA was successfully extracted from 20 cases, and polymerase chain reaction was performed to amplify a highly conserved region of the HPV L1 open reading frame. RESULTS: Twenty-eight of 32 (88%) cases showed strong diffuse staining for p16 but were negative for pRb; two of 32 cases (6%) were negative for p16 but were diffusely positive for pRb; one case was strongly positive for both p16 and pRb, and one case was negative for both p16 and pRb. Three of 20 cases (15%) contained HPV DNA. All three of these cases showed strong p16 expression and lack of pRb staining. CONCLUSIONS: Most cases of Bowen's disease strongly express p16 but not pRb. In contrast to HPV-associated lesions of the cervical mucosa, p16 overexpression in cutaneous Bowen's disease appears to be unrelated to HPV status. The p16 overexpression in Bowen's disease may reflect disruption of the G1/S checkpoint, resulting in unregulated cell cycle progression.

B7-H4 overexpression in ovarian tumors.

OBJECTIVES: Despite great advances in therapeutic management, the mortality rate for ovarian cancer has remained relatively stable over the past 50 years. This study was designed to evaluate the expression of B7-H4 protein, recently identified as a potential molecular marker of breast and ovarian cancer by quantitative PCR analysis, in benign tumors, tumors of low malignant potential and malignant tumors of the ovary. METHODS: Archival formalin-fixed tissue blocks from serous, mucinous, endometrioid and clear cell ovarian tumors were evaluated by immunohistochemistry for the distribution of B7-H4 expression, and staining intensity was measured by automated image analysis. Univariate analyses were used to test for statistically significant relationships. RESULTS: B7-H4 cytoplasmic and membranous expression was detected in all primary serous (n = 32), endometrioid (n = 12), and clear cell carcinomas (n = 15), and in all metastatic serous (n = 23) and endometrioid (n = 7) ovarian carcinomas. By contrast, focal B7-H4 expression was detected in only 1/11 mucinous carcinomas. The proportion of positive cells and median staining intensity was greater in serous carcinomas than in serous cystadenomas or serous tumors of low malignant potential, and the differences were statistically significant (P < 0.0001 and P = 0.034, respectively). The median staining intensity was also significantly greater in endometrioid carcinomas than in endometriosis (P = 0.005). CONCLUSIONS: The consistent overexpression of B7-H4 in serous, endometrioid and clear cell ovarian carcinomas and the relative absence of expression in most normal somatic tissues indicates that B7-H4 should be further investigated as a potential diagnostic marker or therapeutic target for ovarian cancer.

Quantitative and qualitative differences in protein expression between papillary thyroid carcinoma and normal thyroid tissue.

In order to better understand basic mechanisms of tumor development and identify potential new biomarkers, we have performed difference gel electrophoresis (DIGE) and peptide mass fingerprinting on pooled protein extracts from patients with papillary thyroid carcinoma (PTC) compared with matched normal thyroid tissue. Image analysis of DIGE gels comparing PTC and matched normal thyroid tissue protein indicated that 25% of the protein spots were differentially expressed at a 2.5-fold cutoff and 35% at two-fold. Comparison between two different pools of protein from normal thyroid tissues revealed differential protein expression of only 4% at 2.5-fold and 6% at two-fold cutoff. One hundred ninety-two protein spots were identified by MALDI-TOFMS, representing 90 distinct proteins. Excluding albumin, globins and thyroglobulin, imaging software determined 31 proteins to be differentially expressed at the two-fold (or greater) level. Individual gel comparisons (PTC vs. matched normal) from five patients established that 15/31 (48%) of these proteins exhibited statistically significant differential expression. Previously identified molecular markers in this group of proteins include cathepsin B, cytokeratin 19, and galectin-3. Novel differentially expressed proteins include S100A6, moesin, HSP70 (BiP), peroxiredoxin 2, protein phosphatase 2, selenium binding protein 1, vitamin D binding protein, and proteins involved in mitochondrial function. The use of two-dimensional gel electrophoresis (2DGE) revealed a significantly altered protein mass and/or pI in 10%-15% of proteins, suggesting alternatively spliced forms and other posttranslational modification of proteins revealed by this approach. We confirmed S100A6 as a potentially useful biomarker using immunohistochemical analysis (85% sensitivity and 69% specificity for distinguishing benign from malignant thyroid neoplasms). In summary, proteomic analysis of PTC using DIGE and mass spectrometry has confirmed several known biomarkers, uncovered novel potential biomarkers, and provided insights into global pathophysiologic changes in PTC. Many of the differences observed would not have been detected by genomic or other proteomic approaches.