Intérêt pronostique à cours et à long terme du scanner thoracique chez les patients atteints de COVID-19

Introduction

Le scanner thoracique a une place importante dans le diagnostic positif et l’évaluation de l’étendue des lésions pulmonaires chez les patients ayant une infection respiratoire au SARS-COV2. L’objectif est d’évaluer les facteurs pronostiques et évolutives à l’imagerie thoracique à l’admission et après 3 mois chez les patients COVID-19.

Méthodes

Il s’agit d’une étude rétrospective réalisée entre octobre 2020 et juillet 2021 au service de pneumologie – Covid19 à l’hôpital Hedi-Chaker de Sfax incluant des patients atteints de COVID-19 confirmé par PCR et ayant bénéficié d’un scanner thoracique à l’admission. La quantification des lésions pulmonaires, a été réalisée de manière visuelle par un radiologue pour permettre de classer les patients selon le degré de l’atteinte : scanner normal, atteinte minime ou modérée (1–25 %), importante (26–50 %), sévère (51–75 %) ou critique (> 75 %).

Résultats

Quatre-cent vingt-trois patients ont été inclus dans l’étude. L’âge moyen était de 64 ± 16 ans. Quarante-cinq pour cent des patients étaient de sexe masculin. L’atteinte scannographique a été minime ou modérée (18,6 %), importante (35,2 %), sévère (31,2 %) et critique (13,7 %). La majorité des patients avait des lésions en verre dépoli (92,1%) et des lésions de condensations (14,8 %). Au total, 28 % des patients ont présenté une forme sévère de COVID-19. L’extension des lésions au scanner était corrélée au risque de mortalité (p < 0,01). Il n’y avait pas de différence en termes d’âge ou de comorbidités selon le degré d’atteinte au scanner. Les patients ayant une atteinte > 50 % avaient un ratio PNN/lymphocytes significativement plus élevée que ceux avec des lésions ≤ 25 % (p -0,05). Soixante-quinze patients ont consulté après 3 mois d’infection SARS-COV2. Un scanner thoracique a été réalisé chez 50 % d’entre eux. Des séquelles à l’imagerie thoracique ont été notées dans 40 % des cas à type de des lésions de verre dépoli (25 %), de condensations (9 %) et de distorsions bronchiques (66 %). L’extension des lésions au scanner initial était corrélée à la présence des séquelles à l’imagerie thoracique de contrôle (p -0,02). Aucune corrélation n’a été notée entre l’âge, les comorbidités et la présence de séquelles.

Conclusion

Le scanner thoracique est un bon outil pronostique à court terme par l’évaluation de l’atteinte pulmonaire qui semble corrélée à une forme sévère, et à long terme par la recherche de séquelles en post Covid-19.

Biospecimen Collection During the COVID-19 Pandemic

Objectives

Millions of biospecimens will be collected during the coronavirus disease 2019 (COVID-19) pandemic. As learned from severe acute respiratory syndrome (SARS), proper biospecimen handling is necessary to prevent laboratory-related infections.

Methods

Centers for Disease Control and Prevention and World Health Organization severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) interim biosafety guidelines continue to be updated. Presented here are additional considerations intended to complement the interim guidance. These considerations draw on prior SARS recommendations and recent COVID-19 reports.

Results

SARS-CoV-2 viral RNA has been detected in various biospecimen types; however, studies are needed to determine whether viral load indicates viable virus. Throughout the pandemic, biospecimens will be collected for various purposes from COVID-19 known and suspected cases, as well as presymptomatic and asymptomatic individuals. Current data suggest the pandemic start may be as early as October 2019; thus, all biospecimens collected since could be considered potentially infectious.

Conclusions

All entities handling these biospecimens should do risk assessments in accordance with institutional policies and adhere to any guidance provided. The scientific community has a responsibility to safely handle and maintain all biospecimens collected during the COVID-19 pandemic. Soon, it will be imperative to convene expert working groups to address the current and long-term storage and use of these biospecimens. Ideally, worldwide guidelines will be established to protect the personnel handling these biospecimens and communities at large.

Abstract PO-065: National Clinical Trials Network biobanking during the COVID-19 pandemic

The National Cancer Institute (NCI) has a large portfolio of ongoing cancer clinical trials that involve biospecimen collection and are supported by the NCI-funded National Clinical Trials Network (NCTN) Biospecimen Banks located across the United States and Canada. At the start of the COVID-19 pandemic, NCTN biobanks rapidly responded to staffing consequences of state- and institution-issued stay-at-home orders. Many of the NCTN biobanks were deemed essential by their institutions, allowing for limited and/or socially distanced operations. NCTN biobanks quickly worked with NCI and their respective groups to advise participating sites of changes to usual biospecimen collection procedures in order to accommodate limited staffing at the biobanks. In many instances, participating sites were navigating their own institutional process change due to the pandemic. NCTN cancer clinical trials experienced an approximate 40% decrease in enrollment from March 11 to May 19, 2020, compared to the same time frame in 2019. Likewise, NCTN biobanks saw an approximate 40% and 60% decrease in biospecimen receipt and distribution, respectively. The decrease in biospecimen receipt was likely due to two factors: (1) participating site COVID-19 policies limiting patient enrollment on NCI cancer clinical trials and/or biospecimen collection for those trials, and (2) NCTN biobank requests for participating sites to hold nonurgent and/or nonmandatory biospecimens during the initial phase of the pandemic. Decrease in biospecimen distributions was mainly due to receiving laboratory closures as dictated by their institutional COVID-19 policies. On May 20, 2020, all states had begun initial reopening phases to some extent. At this time, several, but not all, NCTN biobanks had begun measured return to full operations, following institutional guidance. NCTN biobanks are making numerous considerations toward returning to full operations and will continue to work with NCI and their respective groups to responsibly collect and distribute biospecimens collected during the COVID-19 pandemic. Likely, some patients enrolled on NCTN cancer clinical trials may have had clinical or subclinical COVID-19 at the time of biospecimen collection. Additionally, biospecimens will be collected on two recently activated NCI COVID-19 studies: (1) the NCI COVID-19 in Cancer Patients Study (NCCAPS): A Longitudinal Natural History Study (NCT04387656), and (2) a tocilizumab treatment trial for COVID-19-related acute respiratory distress syndrome in cancer patients (NCT04370834). Retrospective annotation of these biospecimens may provide a unique resource for translational research efforts and will also be a needed caveat for interpreting biomarker studies conducted using these biospecimens, as the impact of COVID-19 on various biomarkers is currently unknown.

Citation Format: Heather A. Lankes, Mark A. Watson, Richard C. Jordan, Nilsa C. Ramirez, Ignacio I. Wistuba, Lois Shepherd, Irina A. Lubensky, Hala Makhlouf. National Clinical Trials Network biobanking during the COVID-19 pandemic [abstract]. In: Proceedings of the AACR Virtual Meeting: COVID-19 and Cancer; 2020 Jul 20-22. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(18_Suppl):Abstract nr PO-065.

NADPH oxidase 1 is highly expressed in human large and small bowel cancers

To facilitate functional investigation of the role of NADPH oxidase 1 (NOX1) and associated reactive oxygen species in cancer cell signaling, we report herein the development and characterization of a novel mouse monoclonal antibody that specifically recognizes the C-terminal region of the NOX1 protein. The antibody was validated in stable NOX1 overexpression and knockout systems, and demonstrates wide applicability for Western blot analysis, confocal microscopy, flow cytometry, and immunohistochemistry. We employed our NOX1 antibody to characterize NOX1 expression in a panel of 30 human colorectal cancer cell lines, and correlated protein expression with NOX1 mRNA expression and superoxide production in a subset of these cells. Although a significant correlation between oncogenic RAS status and NOX1 mRNA levels could not be demonstrated in colon cancer cell lines, RAS mutational status did correlate with NOX1 expression in human colon cancer surgical specimens. Immunohistochemical analysis of a comprehensive set of tissue microarrays comprising over 1,200 formalin-fixed, paraffin-embedded tissue cores from human epithelial tumors and inflammatory disease confirmed that NOX1 is overexpressed in human colon and small intestinal adenocarcinomas, as well as adenomatous polyps, compared to adjacent, uninvolved intestinal mucosae. In contradistinction to prior studies, we did not find evidence of NOX1 overexpression at the protein level in tumors versus histologically normal tissues in prostate, lung, ovarian, or breast carcinomas. This study constitutes the most comprehensive histopathological characterization of NOX1 to date in cellular models of colon cancer and in normal and malignant human tissues using a thoroughly evaluated monoclonal antibody. It also further establishes NOX1 as a clinically relevant therapeutic target in colorectal and small intestinal cancer.

Toward Improving Practices for Submission of Diagnostic Tissue Blocks for National Cancer Institute Clinical Trials

OBJECTIVES

The National Cancer Institute (NCI) National Clinical Trials Network performs phase II and III clinical trials, which increasingly rely on the submission of diagnostic formalin-fixed, paraffin-embedded tissue blocks for biomarker assessment. Simultaneously, advances in precision oncology require that clinical centers maintain diagnostic specimens for ancillary, standard-of-care diagnostics. This has caused tissue blocks to become a limited resource for advancing the NCI clinical trial enterprise and the practice of modern molecular pathology.

METHODS

The NCI convened a 1-day workshop of multidisciplined experts to discuss barriers and strategic solutions to facilitate diagnostic block submission for clinical trial science, from the perspective of patient advocates, legal experts, pathologists, and clinical oncologists.

RESULTS

The expert views and opinions were carefully noted and reported.

CONCLUSIONS

Recommendations were proposed to reduce institutional barriers and to assist organizations in developing clear policies regarding diagnostic block submission for clinical trials.

Abstract A050: Validation of β-catenin as a tumor segmentation marker for delineating tumor from stromal tissues in quantitative multiplex immunofluorescence analysis of formalin-fixed, paraffin-embedded biopsy specimens

Background: Immunofluorescence assay (IFA) analysis of pharmacodynamic biomarkers in tumor biopsy tissue is limited by lack of a tumor histology–agnostic methodology for segmenting tumor tissue from the surrounding stroma. We have developed a tumor segmentation methodology utilizing β-catenin staining in combination with cell morphology to manually segment tumor regions from surrounding mesenchyme. Here, we show extensive validation of the use of β-catenin as a general tumor segmentation marker through the examination of various tumor tissue microarrays (TMAs), including both carcinoma and sarcoma specimens. Methods: We examined TMAs comprised of tumors from 4 different histologies: colorectal carcinoma (CRC), non-small cell lung cancer (NSCLC), breast cancer, and sarcoma. For each TMA specimen, we quantified tumor content via hematoxylin and eosin (H&E) staining and then assessed tumor expression of β-catenin and other established phenotypic markers of tumor differentiation by IFA and immunohistochemical (IHC) analysis, respectively. To assess b-catenin expression in tumor vs. stroma, we used a pathologist-guided annotation of specific tumor marker staining to segment tumor from stroma on sections adjacent to those stained with an immunofluorescence-conjugated β-catenin antibody; tissue overlay and area reconciliation enabled determination of the ratio of β-catenin expression in tumor vs. stroma in regions of interest (ROIs) within each tumor core. The tumor markers utilized for each histology were: carcinoembryonic antigen (CEA) and pan-cytokeratin (pan-CK) for CRC and NSCLC; MUC1, CEA, and pan-CK for breast; and desmin and pan-CK for sarcoma. Results: We detected β-catenin immunofluorescence in 169 of the 185 (91%) carcinoma TMA tumors (58/61 CRC, 57/62 NSCLC, 54/62 breast). The mean β-catenin fluorescence intensity threshold ratios in tumor vs. stroma were: CRC (3.6), NSCLC (1.5) and breast (1.1). Although IHC staining of pan-CK was detected in 183/185 (99%) carcinoma tumors (59/61 CRC, 61/62 NSCLC, 61/62 breast), pan-CK immunofluorescence is more diffuse and cytoplasmic in nature compared to β-catenin and therefore less robust as a marker for IFA-based automated tumor tissue segmentation. In addition, we examined β-catenin expression in sarcoma TMAs, detecting β-catenin in 45 of 98 sarcoma TMAs examined (46%), which was superior to both pan-CK (9 of 98; 9%) and the known sarcoma marker desmin (37 of 98 (38%). Conclusions: Together, these results demonstrate that our β-catenin–based tumor segmentation method is useful for the majority of carcinoma specimens and allows automated co-registration of tumor and pharmacodynamic biomarkers defined by tumor versus stromal areas. The same approach worked for certain sarcoma specimens. We have since developed a Definiens-based algorithm that allows automated β-catenin–based tumor segmentation for specimens from entire biopsy cohorts of NCI-sponsored clinical trials, including those examining DNA damage response and immuno-oncology biomarkers. Funded by NCI Contract No HHSN261200800001E.

Citation Format: Tony Navas, Robert J. Kinders, Hala Makhlouf, Scott M. Lawrence, Rodrigo Chuaqui, Krisitin Fino, Angie Dull, Katherine Ferry-Galow, Deborah Wilsker, Alice P. Chen, Shivaani Kummar, Ralph E. Parchment, James H. Doroshow. Validation of β-catenin as a tumor segmentation marker for delineating tumor from stromal tissues in quantitative multiplex immunofluorescence analysis of formalin-fixed, paraffin-embedded biopsy specimens [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr A050. doi:10.1158/1535-7163.TARG-19-A050

IL-4 and IL-17A Cooperatively Promote Hydrogen Peroxide Production, Oxidative DNA Damage, and Upregulation of Dual Oxidase 2 in Human Colon and Pancreatic Cancer Cells

Dual oxidase 2 (DUOX2) generates H₂O₂ that plays a critical role in both host defense and chronic inflammation. Previously, we demonstrated that the proinflammatory mediators IFN-γ and LPS enhance expression of DUOX2 and its maturation factor DUOXA2 through STAT1- and NF-κB‒mediated signaling in human pancreatic cancer cells. Using a panel of colon and pancreatic cancer cell lines, we now report the induction of DUOX2/DUOXA2 mRNA and protein expression by the T_H2 cytokine IL-4. IL-4 activated STAT6 signaling that, when silenced, significantly decreased induction of DUOX2. Furthermore, the T_H17 cytokine IL-17A combined synergistically with IL-4 to increase DUOX2 expression in both colon and pancreatic cancer cells mediated, at least in part, by signaling through NF-κB. The upregulation of DUOX2 was associated with a significant increase in the production of extracellular H₂O₂ and DNA damage-as indicated by the accumulation of 8-oxo-dG and γH2AX-which was suppressed by the NADPH oxidase inhibitor diphenylene iodonium and a DUOX2-specific small interfering RNA. The clinical relevance of these experiments is suggested by immunohistochemical, microarray, and quantitative RT-PCR studies of human colon and pancreatic tumors demonstrating significantly higher DUOX2, IL-4R, and IL-17RA expression in tumors than in adjacent normal tissues; in pancreatic adenocarcinoma, increased DUOX2 expression is adversely associated with overall patient survival. These data suggest a functional association between DUOX2-mediated H₂O₂ production and induced DNA damage in gastrointestinal malignancies.

Residual tissue repositories as a resource for population-based cancer proteomic studies

BACKGROUND

Mass spectrometry-based proteomics has become a powerful tool for the identification and quantification of proteins from a wide variety of biological specimens. To date, the majority of studies utilizing tissue samples have been carried out on prospectively collected fresh frozen or optimal cutting temperature (OCT) embedded specimens. However, such specimens are often difficult to obtain, in limited in supply, and clinical information and outcomes on patients are inherently delayed as compared to banked samples. Annotated formalin fixed, paraffin embedded (FFPE) tumor tissue specimens are available for research use from a variety of tissue banks, such as from the surveillance, epidemiology and end results (SEER) registries' residual tissue repositories. Given the wealth of outcomes information associated with such samples, the reuse of archived FFPE blocks for deep proteomic characterization with mass spectrometry technologies would provide a valuable resource for population-based cancer studies. Further, due to the widespread availability of FFPE specimens, validation of specimen integrity opens the possibility for thousands of studies that can be conducted worldwide.

METHODS

To examine the suitability of the SEER repository tissues for proteomic and phosphoproteomic analysis, we analyzed 60 SEER patient samples, with time in storage ranging from 7 to 32 years; 60 samples with expression proteomics and 18 with phosphoproteomics, using isobaric labeling. Linear modeling and gene set enrichment analysis was used to evaluate the impacts of collection site and storage time.

RESULTS

All samples, regardless of age, yielded suitable protein mass after extraction for expression analysis and 18 samples yielded sufficient mass for phosphopeptide analysis. Although peptide, protein, and phosphopeptide identifications were reduced by 50, 20 and 76% respectively, from comparable OCT specimens, we found no statistically significant differences in protein quantitation correlating with collection site or specimen age. GSEA analysis of GO-term level measurements of protein abundance differences between FFPE and OCT embedded specimens suggest that the formalin fixation process may alter representation of protein categories in the resulting dataset.

CONCLUSIONS

These studies demonstrate that residual FFPE tissue specimens, of varying age and collection site, are a promising source of protein for proteomic investigations if paired with rigorously verified mass spectrometry workflows.

Abstract A002: Evidence of pazopanib-induced epithelial-mesenchymal transition (EMT) in human tumors

Background: VEGFR inhibition by pazopanib slows tumor growth through vascular pruning, although compensatory factors associated with angiogenic inhibitors (e.g., induced HIF1-α from increased hypoxia) can lead to enhanced tumor invasion and metastasis by triggering EMT in some preclinical models (Sennino et al., 2012, Cancer Discovery 2(3);270-87). The development of a clinically suitable, validated assay for EMT has made possible the analysis of EMT in a clinical trial of the VEGFR inhibitor pazopanib. Methods: Paired tumor biopsies were obtained at baseline and on cycle 1, day 7 during a phase I trial (NCT01468922) of single-agent pazopanib (800 mg/day, PO). Biopsies were formalin fixed and paraffin embedded, and tissue sections were evaluated for EMT using a multiplex immunofluorescence assay (EMT-IFA) to quantify E-cadherin (E) and vimentin (V) expression and co-localization in tumor-segmented β-catenin+ regions of interests (ROIs) using Definiens software (Navas et al., NCI-EORTC 2015). EMT-IFA quantitative data were calculated from a minimum of 8 ROIs and 2 tissue sections per biopsy. Results: Paired biopsies from 7 patients (pts) with advanced cancer were evaluable for EMT based on H&E pathologist evaluation. As expected, the mesenchymal phenotype of a patient with chondrosarcoma was stable during treatment, but 4 of 6 carcinomas exhibited significant levels of drug-associated EMT towards more transitional (E+V+) or mesenchymal (V+) phenotypes (increased ratio of V+ to E+ area, log10 V:E; P = 0.0030 to &lt; 0.0001). Two of 4 pts with drug-induced EMT additionally displayed significant increases in the area of V+E+ co-localization (um2/cell) in individual tumor cells (P &lt;0.0001), while the other 2 pts did not show evidence of active transitional cells, but only showed increased E+ or decreased V+ tissue areas (um2/cell) within tumor regions. These results indicate that EMT occurs in some carcinoma of pts treated with pazopanib, consistent with results from preclinical models (Navas et al., 2017, AACR). Conclusions: We report for the first time pazopanib-induced EMT and direct evidence of tumor adaptation to anti-angiogenic therapy in clinical samples. Funded by NCI Contract No. HHSN261200800001E.

Citation Format: Tony Navas, Apurva K. Srivastava, Katherine Ferry-Galow, Hala Makhlouf, Rodrigo Chuaqui, Robert J. Kinders, Donald P. Bottaro, Alice P. Chen, Ralph E. Parchment, Shivaani Kummar, James H. Doroshow. Evidence of pazopanib-induced epithelial-mesenchymal transition (EMT) in human tumors [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr A002.

Nonalcoholic steatofibrosis independently predicts mortality in nonalcoholic fatty liver disease

Nonalcoholic steatohepatitis (NASH) is the progressive form of nonalcoholic fatty liver disease (NAFLD). The minimal pathologic criteria for NASH include hepatic steatosis, ballooning degeneration, and lobular inflammation. The resolution of NASH, which relies on the loss of ballooning degeneration, is subject to sampling and observer variability in pathologic interpretation. Ballooning is associated with advanced hepatic fibrosis in cross‐sectional studies but is not a predictor of mortality in NAFLD. Fibrosis staging, while still subject to some sampling variability, has less observer variability and is a robust predictor of liver‐related mortality in NAFLD. In this study, we hypothesize that, regardless of the diagnosis of NASH, the presence of steatofibrosis (steatosis accompanied by fibrosis) regardless of other pathologic features can also be a robust predictor of mortality in NAFLD. We used our previously reported cohort of patients with NAFLD with liver biopsies and long‐term mortality follow‐up. Cox proportional hazard models were used to determine the predictors of overall and liver‐related mortality. Of 209 enrolled NAFLD subjects, 97 can be classified as having steatofibrosis. During follow‐up (median 150 months), 64 (30.6%) patients died, with 18 (8.6%) from liver‐related causes. Adjusted for age, both diagnostic categories of NASH and steatofibrosis were significantly and similarly associated with liver‐related mortality (adjusted hazard ratio [aHR], 9.9; 95% confidence interval (CI), 1.3‐74.9; P = 0.027; aHR, 6.7; 95% CI, 1.5‐29.8; P = 0.013, respectively). However, only steatofibrosis showed independent association with overall mortality (aHR, 1.76; 95% CI, 1.02‐3.05; P = 0.043). Conclusion: Steatofibrosis and NASH are similarly associated with liver‐related mortality, but only steatofibrosis is associated with overall mortality in patients with NAFLD. Given the inherent observer variability in ballooning degeneration, a key diagnostic component of NASH, we suggest that steatofibrosis should be considered a viable diagnostic classification for NAFLD subjects at risk or adverse outcomes and provides a simpler endpoint for clinical trials of therapeutic agents. (Hepatology Communications 2017;1:421–428)

Hepatic small vessel neoplasm, a rare infiltrative vascular neoplasm of uncertain malignant potential

Characteristic but rare vascular neoplasms in the adult liver composed of small vessels with an infiltrative border were collected from an international group of collaborators over a 5-year period (N=17). These tumors were termed hepatic small vessel neoplasm (HSVN), and the histologic differential diagnosis was angiosarcoma (AS). The average age of patients was 54years (range, 24-83years). HSVN was more common in men. The average size was 2.1cm (range, 0.2-5.5cm). Diagnosis was aided by immunohistochemical stains for vascular lineage (CD31, CD34, FLI-1), which were uniformly positive in HSVN. Immunohistochemical stains (p53, c-Myc, GLUT-1, and Ki-67) for possible malignant potential are suggestive of a benign/low-grade tumor. Capture-based next-generation sequencing (using an assay that targets the coding regions of more than 500 cancer genes) identified an activating hotspot GNAQ mutation in 2 of 3 (67%) tested samples, and one of these cases also had a hotspot mutation in PIK3CA. When compared with hepatic AS (n=10) and cavernous hemangioma (n=6), the Ki-67 proliferative index is the most helpful tool in excluding AS, which demonstrated a tumor cell proliferative index greater than 10% in all cases. Strong p53 and diffuse c-Myc staining was also significantly associated with AS but not with HSVN or cavernous hemangioma. There have been no cases with rupture/hemorrhage, disseminated intravascular coagulation, or Kasabach-Merritt syndrome. Thus far, there has been no metastasis or recurrence of HSVN, but complete resection and close clinical follow-up are recommended because the outcome remains unknown.

Abstract LB-B18: Epithelial to mesenchymal transition in human tumor biopsies: Quantitative, histopathological proof of the existence of EMT in vivo by immunofluorescence microscopy

Epithelial-mesenchymal transition (EMT) is a dynamic process whereby epithelial cells acquire mesenchymal properties. Despite the clinical significance of the acquired mesenchymal properties for metastasis and drug resistance, histopathological evidence of transitional cells in patient samples is lacking and EMT remains an unproven clinical hypothesis. We previously developed and validated a multiplex immunofluorescence assay (IFA) that quantifies the levels of EMT biomarkers (E-Cadherin, Vimentin, β-catenin) in snap-frozen, formalin-fixed, paraffin-embedded (FFPE) tumor tissue (Navas et al, AACR 2013). Building upon that method, we now report a precise, quantitative and unbiased IFA method of tissue analysis (EMT-IFA) using Definiens® software to quantify co-expression of the epithelial marker E-cadherin (E) and mesenchymal marker Vimentin (V) at the cellular level in FFPE clinical biopsies. FFPE human tumor xenografts and cell lines serve as calibrators and reference materials for establishing initial image acquisition parameters for segmented tumor regions of interest. Flanking H&E sections of the clinical biopsies are initially annotated by an anatomic pathologist to identify regions of tumor tissue, non-tumor related areas (including normal or stromal tissues), inflammatory and/or necrotic regions, and freeze artifacts. Adjacent sections are used for the EMT-IFA, and further tumor segmentation from stroma is applied to extracted regions of interests (fields) using the β-catenin layer. Within segmented tumor regions, E-cadherin (E) and Vimentin (V) sub-cellular pixel areas are measured using predetermined thresholds for each biomarker and reported as Log10 (V:E). High resolution images confirmed the co-localization of plasma membrane E-cadherin and cytoplasmic Vimentin to individual transitional tumor cells, and the co-localization of E and V within individual tumor cells of the segmented regions of interest was key for distinguishing EMT from tumor heterogeneity in which adjacent tumor cells can be exclusively E+ or V+. Quantitative analysis of a clinical biopsy series of various histologies revealed all possible phenotypes: epithelial (E+V- colorectal carcinoma), mesenchymal (E-V+ sarcomas), heterogeneous mixtures of E+V- and E-V+ subpopulations, and EMT. Importantly, using the EMT-IFA, we discovered that pharmacological targeting of VEGFR/FGFR/PDGFR signaling with the multi-kinase inhibitor pazopanib stimulated EMT in a preclinical xenograft model of gastric carcinoma (MKN45), as revealed by the significant increase in the V:E ratio (P = 0.0023) coupled with an increase in the EMT phenotype (co-localized V+E+ at the individual cell level) (P = 0.0070) in biopsy specimens. Thus, the EMT-IFA has potential value for investigating EMT in the clinic and its ramifications for drug response and other clinical endpoints. Funded by NCI Contract No. HHSN261200800001E.

Citation Format: Tony Navas, Robert J. Kinders, Scott M. Lawrence, Katherine Ferry-Galow, Thomas D. Pfister, Apurva K. Srivastava, Sergio Y. Alcoser, Melinda G. Hollingshead, Lindsay M. Dutko, Brad A. Gouker, Donna O. Butcher, Hala Makhlouf, Rodrigo Chuaqui, Donald P. Bottaro, Shivaani Kummar, Alice Chen, James H. Doroshow, Ralph E. Parchment. Epithelial to mesenchymal transition in human tumor biopsies: Quantitative, histopathological proof of the existence of EMT in vivo by immunofluorescence microscopy. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr LB-B18.

Robustness of Next Generation Sequencing on Older Formalin-Fixed Paraffin-Embedded Tissue

Next Generation Sequencing (NGS) technologies are used to detect somatic mutations in tumors and study germ line variation. Most NGS studies use DNA isolated from whole blood or fresh frozen tissue. However, formalin-fixed paraffin-embedded (FFPE) tissues are one of the most widely available clinical specimens. Their potential utility as a source of DNA for NGS would greatly enhance population-based cancer studies. While preliminary studies suggest FFPE tissue may be used for NGS, the feasibility of using archived FFPE specimens in population based studies and the effect of storage time on these specimens needs to be determined. We conducted a study to determine whether DNA in archived FFPE high-grade ovarian serous adenocarcinomas from Surveillance, Epidemiology and End Results (SEER) registries Residual Tissue Repositories (RTR) was present in sufficient quantity and quality for NGS assays. Fifty-nine FFPE tissues, stored from 3 to 32 years, were obtained from three SEER RTR sites. DNA was extracted, quantified, quality assessed, and subjected to whole exome sequencing (WES). Following DNA extraction, 58 of 59 specimens (98%) yielded DNA and moved on to the library generation step followed by WES. Specimens stored for longer periods of time had significantly lower coverage of the target region (6% lower per 10 years, 95% CI: 3-10%) and lower average read depth (40x lower per 10 years, 95% CI: 18-60), although sufficient quality and quantity of WES data was obtained for data mining. Overall, 90% (53/59) of specimens provided usable NGS data regardless of storage time. This feasibility study demonstrates FFPE specimens acquired from SEER registries after varying lengths of storage time and under varying storage conditions are a promising source of DNA for NGS.

Predictors of all-cause mortality and liver-related mortality in patients with non-alcoholic fatty liver disease (NAFLD)

AIM

Non-alcoholic steatohepatitis (NASH) patients are at increased risk for progression to cirrhosis. The aim of this study was to assess all-cause and liver-specific mortality in a cohort of non-alcoholic fatty liver disease (NAFLD) patients.

METHODS

Biopsy-proven NAFLD patients with and without NASH from two historic databases were included. Clinico-demographic information from the time of biopsy was available. Mortality data were obtained from National Death Index-Plus and used for estimating overall and cause-specific mortality. The non-parametric Kaplan-Meier method with log-rank test and multivariate analyses with Cox proportional hazard model were used to compare cohorts.

RESULTS

Two hundred eighty-nine NAFLD patients were included (50.3 ± 14.5 years old, 39.4 % male, 78.6 % Caucasian, 46.0 % obese, 26.0 % diabetic, 5.9 % with family history of liver diseases). Of these, 59.2 % had NASH whereas 40.8 % had non-NASH NAFLD. NASH patients were predominantly female, had higher aspartate aminotranserase, alanine aminotransferase and fasting serum glucose. During follow-up (median 150 months, maximum 342 months), patients with NASH had higher probability of mortality from liver-related causes than non-NASH NAFLD patients (p value = 0.0026). In the entire NAFLD cohort, older age [aHR = 1.07 (95 % CI = 1.05-1.10)] and presence of type II diabetes [aHR = 2.09 (1.39-3.14)] were independent predictors of overall mortality. However, in addition to age [aHR = 1.06 (1.02-1.10)] having histologic NASH [aHR = 9.16 (2.10-9.88)] was found to be an independent predictor of liver-related mortality. Additionally, presence of type II diabetes was associated with liver-related mortality [aHR = 2.19 (1.00-4.81)].

CONCLUSIONS

This long-term follow-up of NAFLD patients confirms that NASH patients have higher risk of liver-related mortality than non-NASH. Additionally, patients with NAFLD and type II diabetes are at highest risk for overall and liver-related mortality.

Pathologic criteria for nonalcoholic steatohepatitis: interprotocol agreement and ability to predict liver-related mortality

Since the initial description of nonalcoholic steatohepatitis (NASH), several sets of pathologic criteria for its diagnosis have been proposed. However, their interprotocol agreement and ability to predict long-term liver-related mortality (LRM) have not been demonstrated. In this study, we examined patients with biopsy-proven nonalcoholic fatty liver disease (NAFLD) for whom liver biopsy slides and clinical and mortality data were available. Liver biopsy samples were evaluated for a number of pathologic features and were classified according to the presence or absence of NASH by (1) the original criteria for NAFLD subtypes, (2) the nonalcoholic fatty liver disease activity score (NAS), (3) the Brunt criteria, and (4) the current study's criteria. All NASH diagnostic criteria and individual pathologic features were tested for agreement and for their independent associations with LRM, which were determined with a Cox proportional hazards model. Two hundred fifty-seven NAFLD patients with complete data were included. The diagnoses of NASH by the original NAFLD subtypes and by the current study's definition of NASH were in almost perfect agreement (κ = 0.896). However, their agreement was moderate with NAS (κ = 0.470 and κ = 0.511, respectively) and only fair to moderate with the Brunt criteria (κ = 0.365 and κ = 0.441, respectively). Furthermore, the agreement of the Brunt criteria with NAS was relatively poor (κ = 0.178). During the follow-up (median = 146 months), 31% of the patients died (9% were LRM). After we controlled for confounders, a diagnosis of NASH by the original criteria for NAFLD subtypes [adjusted hazard ratio = 9.94 (95% confidence interval = 1.28-77.08)] demonstrated the best independent association with LRM. Among the individual pathologic features, advanced fibrosis showed the best independent association with LRM [adjusted hazard ratio = 5.68 (95% confidence interval = 1.50-21.45)].

CONCLUSION

The original criteria for NAFLD subtypes and the current study's criteria for NASH were in almost perfect agreement, but their level of agreement with the NAS and Brunt criteria was lower. A diagnosis of NASH by the original criteria for NAFLD subtypes demonstrated the best predictability for LRM in NAFLD patients.

Farglitazar lacks antifibrotic activity in patients with chronic hepatitis C infection

BACKGROUND & AIMS

Farglitazar (GI262570), an insulin-sensitizing agent, selectively binds and activates peroxisome proliferator-activated receptor gamma (PPARgamma) and inhibits stellate cell activation. We evaluated its antifibrotic effect in patients with chronic hepatitis C that did not respond to standard-of-care therapy.

METHODS

Patients with fibrosis of Ishak stages 2-4 (n = 265), based on analysis of liver biopsy samples, were randomly assigned to groups given once-daily doses of 0.5 mg farglitazar, 1.0 mg farglitazar, or placebo for 52 weeks; repeat liver biopsy samples were then obtained. The primary end points were changes in levels of alpha-smooth muscle actin (SMA) expression and collagen, based on morphometry and ranked histologic assessments.

RESULTS

Two hundred nine patients had paired biopsy specimens adequate for analysis (81.5% with pretreatment Ishak scores of stage 2 or 3). There was no overall difference in SMA (P = .58) or collagen (P = .99) levels at week 52. SMA levels increased by a median of 49% in samples from patients given placebo, 58% in patients given 0.5 mg farglitizar and 52% in patients given 1.0 mg farglitizar, respectively. Collagen increased by 27% in placebo samples and 31% in samples from patients given either dose of farglitizar. There were no significant differences between treatment groups in the ranked assessment of paired biopsy specimens or in the proportion of patients with a change in fibrosis score > or = Ishak stage.

CONCLUSIONS

In patients with chronic hepatitis C and moderate fibrosis, 52 weeks of treatment with farglitazar does not affect stellate cell activation or fibrosis (measured by morphometry or comparison of paired biopsy specimens).

Gastrointestinal stromal tumors of the jejunum and ileum: a clinicopathologic, immunohistochemical, and molecular genetic study of 906 cases before imatinib with long-term follow-up

Gastrointestinal (GI) stromal tumors (GISTs), the specific KIT- or PDFGRA-signaling driven mesenchymal tumors, are the most common mesenchymal tumors of the GI tract. This study analyzed 1091 tumors originally classified as smooth muscle tumors of the small intestine (including jejunum or ileum and excluding duodenum), and found that 906 (83%) of these were GISTs. The GIST patients had 55:45 male-to-female ratio with a median age of 59 years (range, 13-94 years). Only 0.6% of tumors occurred before the age of 21 years and 13.6% before the age of 40 years. The tumors varied from 0.3 to 40 cm (median, 7.0 cm) and most commonly presented with GI bleeding or acute abdomen; 18% were incidentally detected. Histologically, the tumors were relatively monotypic with spindle cell (86%), epithelioid (5%), or mixed patterns (9%). Skeinoid fibers were present in 44% of cases, and their presence was associated with a favorable course. Most epithelioid tumors were malignant, and this morphology sometimes emerged from less cellular and less mitotically active spindle cell tumors, suggesting that it represented a transformation. KIT was immunohistochemically detected in 98%, CD34 in 40%, smooth muscle actin in 34%, desmin in 0.2%, and S-100 protein in 14% of the tumors tested. Outcome was strongly dependent on tumor size and mitotic activity, with an overall 39% tumor-related mortality, twice that for gastric GISTs. Only <3% of tumors <5 cm and < or = 5 mitoses/50 HPF metastasized, whereas 86% of tumors >10 cm and >5 mitoses/50 HPF metastasized. In stark contrast to corresponding gastric tumors, tumors >10 cm with mitotic activity < or = 5/50 HPF and those < or = 5 cm with mitoses >5/50 HPF had a high metastatic rate (>50%); tumors >5 cm < or = 10 cm with low mitotic rate had a 24% metastatic rate. The median survival times of patients with low mitotic rate tumors who died of disease decreased by increasing tumor size. KIT exon 11 mutations were detected in 90 cases, exon 9 mutation in 17 cases, and exon 17 mutation in 1 case; the presence of mutation or mutation type was not prognostically significant. There were no PDGFRA exon 12 or 8 mutations. Systematic data on prognosis of small intestinal GISTs of various size and mitotic activity categories can be helpful in management and surveillance of patients with these tumors.

Calcipotriol-betamethasone ointment versus calcipotriol ointment in the treatment of psoriasis vulgaris

Of 17 patients (10 men and 7 women) with psoriasis vulgaris, aged between 12 and 59 years, included in this study, 4 patients were excluded (3 because of a treatment follow-up irregularity and 1 due to severe irritation). Thirteen patients completed the 6-week treatment course where each patient was instructed to apply calcipotriol-betamethasone ointment on the right side and calcipotriol ointment on the left side. The treatment effect was assessed according to the psoriasis area severity index (PASI) changes, and complete blood count and serum calcium was done prior to and at the end of the treatment. Results showed that both sides had improved by 92.3%, with a marked reduction in the mean PASI (from 11.5 to 2.2); a better reduction was observed in the right side during the second and third visits. A marked improvement to complete clearance was seen in 84.6% in calcipotriol-betamethasone side and 76.9% in calcipotriol alone. Mild irritation was reported in the left side in 15.4% which was tolerated with the continuation of treatment application. No telangiectasia or atrophy was observed on the right side. In conclusion, calcipotriol-betamethasone may be recommended in the early weeks of the treatment of psoriasis vulgaris, and it is helpful in psoriasis patients with irritation to calcipotriol alone.

Binding to delta and mu opioid receptors by deltorphin I/II analogues modified at the Phe3 and Asp4/Glu4 side chains: a report of 32 new analogues and a QSAR study

The synthesis and binding affinities of 32 X3Gly4 dual-substitution analogues of the natural opioid heptapeptides deltorphin I and II are reported. A multiple regression QSAR analysis was performed using those results along with literature data for the X3Asp4 and Phe3X4 side chain analogues. Fitting to a three-term potential well model with hydrophobic and van der Waals attraction terms and a steric repulsion term indicates that the delta and mu receptor sites for binding the residue three side chain are similar, and that the binding interaction is primarily van der Waals and secondarily hydrophobic. Further analysis indicates that both sites are more constrained with respect to side chain length than width or thickness, and the mu site appears to be somewhat larger. A binding model consistent with these findings pictures the native third residues Phe ring laying on a step notched out of the receptor surface, pointing toward the back (riser) of the step, and sandwiched between the receptor and ligand. However, the binding sites for the residue four side chains are quite different on delta and mu receptors. Binding to the delta site appears to involve both electrostatic attraction (probably to a partial positive charge) and van der Waals attraction, but not necessarily hydrogen bonding, and more constraint with respect to side chain length than width or thickness. In contrast, there is no evidence for any kind of binding attraction between the side chain of residue four and the mu site, which acts more as steric repulsion site, as though the space that is a pocket on the delta receptor is filled in on the mu receptor. A regression model based only on steric repulsion by van der Waals bulk and/or the effective bulk of a hydration layer accounts for over 80% of the residue four related variation in mu affinity.