1,721,009 research outputs found
sj-docx-1-tpx-10.1177_01926233221099273 – Supplemental material for Scientific and Regulatory Policy Committee Points to Consider: Primary Digital Histopathology Evaluation and Peer Review for Good Laboratory Practice (GLP) Nonclinical Toxicology Studies
No full textSupplemental material, sj-docx-1-tpx-10.1177_01926233221099273 for Scientific and Regulatory Policy Committee Points to Consider: Primary Digital Histopathology Evaluation and Peer Review for Good Laboratory Practice (GLP) Nonclinical Toxicology Studies by Thomas Forest, Famke Aeffner, Dinesh S. Bangari, Bhupinder Bawa, Jonathan Carter, James Fikes, Wanda High, Shim-mo Hayashi, Matthew Jacobsen, LuAnn McKinney, Daniel Rudmann, Thomas Steinbach, Vanessa Schumacher, Oliver Turner, Jerrold M. Ward and Cynthia J. Willson in Toxicologic Pathology</p
Abstract 4582: Evaluating benefits of PD-L1 image analysis for the clinical setting
No full textAbstract
Tissue-based investigations can prove challenging due to complex tissue architecture and heterogeneous biomarker expression, visual and cognitive “traps” that affect interpretive precision, and subjective assessments that affect reproducibility. A major concern is that these challenges could increase the risk of failure for therapeutic/diagnostic co-development and clinical use, as the biomarker measurements continue to increase in complexity and require increasingly precise diagnostic cut-points.
Image analysis tools have been developed to overcome some of the challenges for conventional anatomic pathology practices, capitalizing on the objectivity and computational power of a digital platform. A computer, however, lacks the cognitive ability and experience of a human to interpret tissue architecture and context. Flagship Biosciences’ computational Tissue Analysis (cTA™) platform integrates the power of our tissue Image Analysis (tIA™) technology with the contextual experience of an anatomic pathologist to produce robust, precise, quantitative results that demonstrate biomarker content in the tissue context. Flagship Biosciences envisions the integration of our cTA™ technology into a computer-aided clinical pathology workflow as a method to improve the precision of scoring for even some of the most challenging tissue-based biomarker measurements.
In a proof-of-concept study, we evaluated the performance of manual versus digital scoring approaches in a cohort of non-small cell lung carcinoma (NSCLC) samples stained with the IHC protocol for the PD-L1 PharmDx 28-8 complementary diagnostic. A comparison of the 2 modalities demonstrated that in nearly all cases, the within sample standard deviation of the cTA™ digital score results was less than the manual score (median inter-pathologist %CVs were reduced from 124.9% to 7.8% and intra-pathologists from 65.4% to 7.6% for manual and digital scores, respectively). As an additional exploratory examination, the effect of heterogeneity on PD-L1 interpretation was also investigated. Pathologists evaluated the same whole tissue slides within 5 high powered fields (HPFs) using both manual and cTA™ -derived scoring. Results demonstrated that the use of cTA™ provides improves agreement between HPF and whole slide assessments (absolute difference between the manual scores from HPF to whole slide were larger than the absolute differences for the digitally derived scores, at 3.14% and 8.27%, respectively). Taken together, these studies demonstrate that the use of cTA™ can significantly reduce variability in PD-L1 scoring, as compared to a manual scoring approach.
Citation Format: Staci Kearney, Joshua Black, Famke Aeffner, Joshua Black, Luke Pratte, Joseph Krueger. Evaluating benefits of PD-L1 image analysis for the clinical setting [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4582. doi:10.1158/1538-7445.AM2017-4582</jats:p
Abstract 661: Evaluating "harmonization" of PD-L1 assays using image analysis
No full textAbstract
The current diagnostics landscape for therapeutics that target the PD1/PD-L1 pathway is highly complex. Four different companion or complementary diagnostics have been developed for pembrolizumab in NSCLC, nivolumab in NSCLC and melanoma, and atezolizumab in urothelial carcinoma. The need to reconcile diagnostics for this class of targeted therapies has been recognized by the creation of the FDA-AACR-ASCO “PD-L1 Blueprint” working group to explore means to “harmonize” PD-L1 testing in tissue based IHC assays. The results reported from this working group noted similarities, but also several important discrepancies, between the current assays. Since each test uses a specific interpretation for each assay and indication, this creates a highly complex diagnostic landscape, which is likely to continue to increase in complexity as more PD-1/PD-L1 therapeutics and potentially novel diagnostics continue to be approved in additional indications.
To address the need for adaptive, sustainable harmonization for PD-L1 diagnostics, Flagship Biosciences evaluated the utility of image analysis-based methods to harmonize multiple PD-L1 tests. We executed a proof-of-concept study utilizing a cohort of serial tissue sections from the same NSCLC patients, stained with the FDA approved Dako PD-L1 tests (28-8 and 22C3 clones), and our in-house PD-L1 assays (SP142 and E1L3N clones) for comparison. We digitized the tissue slides using a whole slide scanner, and evaluated the samples with our tissue Image Analysis (tIA™) technology. As expected, the patient samples stained with the separate PD-L1 assays yielded differences in staining and, thus, the reported scores for PD-L1 expression based on each test used, despite serial sections being derived from the same patient. To attempt to harmonize the scoring approaches for each test, we leveraged our computational Tissue Analysis (cTA™) platform to create a mathematically-derived “virtual slide score” for each sample, which enabled calibration of the various tests to deliver cross PD-L1 comparative scores. Based on the proof-of-concept demonstrated in this study, the cTA™ approaches could enable harmonization of the various PD-L1 tests through use of a digital pathology platform. The data presented provides a foundation for potential application of the cTA™ platform in the clinical laboratory setting to achieve harmonization of multiple PD-L1 tests.
Citation Format: Nathan T. Martin, Joshua C. Black, Zachary Pollack, Famke Aeffner, Joseph Krueger. Evaluating "harmonization" of PD-L1 assays using image analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 661. doi:10.1158/1538-7445.AM2017-661</jats:p
Abstract 1710: Providing confidence around computational tissue analysis using heterogeneity assessments
No full textAbstract
Background: Though the techniques to interrogate the appearance of a biomarker in tissue sections have greatly advanced, there are limitations as to how representative an analysis of a tissue section is compared to the entire diseased tissue. Depending on the heterogeneous expression level of a biomarker, tissue sampling can result in different interpretations of the biomarker’s appearance, and hence could potentially lead to a false therapeutic intervention.
Hypothesis: Digital image analysis has demonstrated tremendous value in quantifying many features related to biomarker distribution and expression in biological tissues. The information can be collected for various indications and biomarkers and a phenotypic signature can be established that describes a biomarker representation across indications. Moreover, the assessment of new samples can be compared to the established phenotypic signature and a confidence score applied in support to the determined endpoint.
Approach: For a proof of concept, 6 prostate cancer samples were processed and a single section was collected after every 100microns. A total of 7 sections per sample were stained for the lymphocyte marker CD3, and the number of positive target cells were determined in the tumor and tumor microenvironment using tissue Image Analysis (tIA™). To assess how indicative the evaluation of a single tissue section would be for the entire tumor, the heterogeneity level was determined on the section level as well as by random grid analysis on each individual section. Both criteria were utilized to define an indication and biomarker specific confidence interval and heterogeneity score.
Conclusion: The combination of IHC and tIA is a powerful tool to convert complex data into meaningful interpretations. tIA is also a capable tool to catalogue valuable information about the biomarker’s expression pattern across different disease stages and hence could be used to evaluate how representative a single biomarker evaluation is in the grand scheme. Ultimately, we demonstrated a technique that can be applied to any biomarker and would assist in guiding therapeutic decisions.
Citation Format: Carsten Schnatwinkel, Daniel Rudmann, Famke Aeffner, Jasmeet Bajwa, Natalie Hutnick, Michael Sharp, Gerry Chu, JD Alvarez. Providing confidence around computational tissue analysis using heterogeneity assessments [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1710. doi:10.1158/1538-7445.AM2017-1710</jats:p
A Primer for Oncoimmunology (Immunooncology)
No full text Oncoimmunology (or immunooncology) is a burgeoning specialty of precision (“personalized”) medicine designed to heighten the antitumor response of the immune system against molecules expressed excessively or only by tumor cells. This focus is necessary, as cancers are polyclonal tissues comprised of antigenically heterogeneous cells, the exact composition of which is shaped by the balance between antitumor immunity and tumor-promoting inflammation. Key targets include enhancing immune system (especially T cell) reactivity, inhibiting immune checkpoints, and promoting tumor cytolysis. Therapeutic modalities to address these targets include administering antibodies, cytokines, or small molecules that directly stimulate the immune system, attack tumor-associated antigens, or interfere with tumor–stroma interactions; adoptive transfer of autologous T cells following ex vivo selection/expansion/activation (typically after lymphoid-depleting regimens and in conjunction with immunostimulatory therapy); and vaccination (against tumor antigens). Pathology involvement in oncoimmunology product development is critical to assess expression of target molecules in tumor cells, stromal cells, and tumor-infiltrating leukocytes. </jats:p
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Proposed mechanism for altered airway responsiveness to methacholine in ovalbumin-sensitized mice following RSV infection.
No full text<p>In unsensitized or OVA-sensitized, uninfected mice, methacholine binds to M<sub>3</sub>-subtype muscarinic receptors (M<sub>3</sub>R), resulting in release of Gαq and downstream activation of phospholipase C (PLC). PLC then activates protein kinase C (PKC) and increases intracellular Ca<sup>++</sup> (Ca<sup>++</sup><sub>i</sub>), leading to bronchoconstriction. RSV infection of respiratory epithelial cells in OVA-sensitized mice induces release of keratinocyte cytokine (KC), which binds to epithelial CXCR2 receptors in either an autocrine or paracrine fashion. KC receptor binding can be replicated in OVA-sensitized, uninfected mice by recombinant murine KC (<u>rmKC</u>), but is blocked by a neutralizing antibody to KC (<i>anti-KC</i>). Activation of CXCR2 liberates pertussis toxin (<i>PTX</i>)-sensitive Gαi, resulting in reversal of hyperresponsiveness to methacholine. Gαi can also be directly activated by <u>melittin</u>. As in previous studies <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046660#pone.0046660-McGraw1" target="_blank">[22]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046660#pone.0046660-McGraw2" target="_blank">[29]</a>, reversal of airway hyperresponsiveness may be a consequence of inhibition of the phospholipase C (PLC)/protein kinase C (PKC) pathway by Gαi, although we did not formally demonstrate this in the current study. Experimental agonists are shown underlined. Experimental antagonists are shown in italics. Broken lines indicate postulated mechanisms that were not formally demonstrated in this study.</p
RSV infection reverses hyperresponsiveness to methacholine in OVA-sensitized mice via a pertussis toxin-sensitive pathway.
No full text<p>Bronchoconstrictive response to increasing doses of nebulized methacholine (MCH) following pretreatment with saline (100 µl i.p.; <i>n</i> = 4) or pertussis toxin (PTX, 100 µg/kg in 100 µl saline i.p.; <i>n</i> = 9). ***MCH dose-response curve differs significantly (<i>P</i><0.0005) from OVA/DAY 2 mice (OVA-sensitized mice infected with 10<sup>6</sup> pfu/mouse RSV A2 for 2 days; <i>n</i> = 16).</p
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