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Nirmal AJ, Maliga Z, Vallius T, Quattrochi B, Chen AA, Jacobson CA, Pelletier RJ, Yapp C, Arias-Camison R, Chen YA, Lian CG, Murphy GF, Santagata S, Sorger PK. The Spatial Landscape of Progression and Immunoediting in Primary Melanoma at Single-Cell Resolution. Cancer Discov 2022; 12:1518-1541. [PMID: 35404441 PMCID: PMC9167783 DOI: 10.1158/2159-8290.cd-21-1357] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/05/2022] [Accepted: 04/01/2022] [Indexed: 11/16/2022]
Abstract
Cutaneous melanoma is a highly immunogenic malignancy that is surgically curable at early stages but life-threatening when metastatic. Here we integrate high-plex imaging, 3D high-resolution microscopy, and spatially resolved microregion transcriptomics to study immune evasion and immunoediting in primary melanoma. We find that recurrent cellular neighborhoods involving tumor, immune, and stromal cells change significantly along a progression axis involving precursor states, melanoma in situ, and invasive tumor. Hallmarks of immunosuppression are already detectable in precursor regions. When tumors become locally invasive, a consolidated and spatially restricted suppressive environment forms along the tumor-stromal boundary. This environment is established by cytokine gradients that promote expression of MHC-II and IDO1, and by PD1-PDL1-mediated cell contacts involving macrophages, dendritic cells, and T cells. A few millimeters away, cytotoxic T cells synapse with melanoma cells in fields of tumor regression. Thus, invasion and immunoediting can coexist within a few millimeters of each other in a single specimen. SIGNIFICANCE The reorganization of the tumor ecosystem in primary melanoma is an excellent setting in which to study immunoediting and immune evasion. Guided by classic histopathology, spatial profiling of proteins and mRNA reveals recurrent morphologic and molecular features of tumor evolution that involve localized paracrine cytokine signaling and direct cell-cell contact. This article is highlighted in the In This Issue feature, p. 1397.
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Chen WS, Chen YA, Lee CH, Chen YJ. Recycling Vanadium and Proton-Exchange Membranes from Waste Vanadium Flow Batteries through Ion Exchange and Recast Methods. MATERIALS 2022; 15:ma15113749. [PMID: 35683047 PMCID: PMC9181544 DOI: 10.3390/ma15113749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/19/2022] [Accepted: 05/22/2022] [Indexed: 11/18/2022]
Abstract
This study aims to provide a system to recycle vanadium resources and recover membranes from waste proton-exchange membranes. This research is divided into two parts. To begin, ion exchange batch and column experiments were applied to adsorb vanadium in a membrane. In this process, the waste membrane was initially dissolved in a 50% ethanol solution, and the suspension obtained by dispersing the membrane had 74 mg/L of vanadium. Then, Dowex G26 resin was used to adsorb vanadium from the membrane dispersion in the ion-exchange process. The adsorptive behavior and optimal parameters were explored in this study. The vanadium ions were then eluted by HCl to obtain an enrichment solution, and the V2O5 was received through precipitation and calcination methods. After obtaining the vanadium-free dispersion, the recycled membrane was prepared by recasting it in the second part. The characteristics of the recycled membrane, such as the moisture, FTIR spectra, ion-exchange capacity, and ion conductivity, are discussed. The results revealed that the adsorption capacity of vanadium through Dowex G26 was 81.86 mg/g. The eluting efficiency of HCl was 97.5%, and the optimal parameters of the precipitation and calcination processes were set as pH 5, NH4Cl:V = 2:1, and 350 °C. The moisture of the recycled membrane was 25.98%, and the IEC was 0.565 meq/g. The consequences of FTIR and ion conductivity demonstrated that the vanadium in the recycled membrane was eliminated by the ion-exchange method; however, the microstructure of the recycled membrane was influenced during ion exchange and recasting.
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Smiley KT, Clay LA, Ross AD, Chen YA. Multi-scalar and multi-dimensional conceptions of social capital and mental health impacts after disaster: the case of Hurricane Harvey. DISASTERS 2022; 46:473-498. [PMID: 33432691 DOI: 10.1111/disa.12474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
While much research investigates how social capital relates to mental health after disasters, less work employs a multi-scalar, multi-dimensional social capital framework. This study applies such a construct to an analysis of novel survey data of approximately 1,000 rural and urban Texans after Hurricane Harvey struck the United States in August 2017. On the individual level, it finds that greater social support is linked to fewer mental health impacts, but that greater civic and organisational engagement is connected to greater mental health impacts. At the community level, it finds that neither a density of bridging social capital organisations nor of bonding social capital organisations is associated with poorer mental health, although a greater number of bonding organisations is related to negative mental health impacts on rural residents. The paper concludes by focusing on how individual and community social capital relationships with mental health are contingent on measurement, scale, and rural or urban location.
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Wu CH, Guo HR, Patel AK, Singhania RR, Chen YA, Kuo JM, Dong CD. Production and characterization of lucrative hypoglycemic collagen-peptide-chromium from tilapia scale. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Schapiro D, Sokolov A, Yapp C, Chen YA, Muhlich JL, Hess J, Creason AL, Nirmal AJ, Baker GJ, Nariya MK, Lin JR, Maliga Z, Jacobson CA, Hodgman MW, Ruokonen J, Farhi SL, Abbondanza D, McKinley ET, Persson D, Betts C, Sivagnanam S, Regev A, Goecks J, Coffey RJ, Coussens LM, Santagata S, Sorger PK. MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging. Nat Methods 2022; 19:311-315. [PMID: 34824477 PMCID: PMC8916956 DOI: 10.1038/s41592-021-01308-y] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 09/22/2021] [Indexed: 01/02/2023]
Abstract
Highly multiplexed tissue imaging makes detailed molecular analysis of single cells possible in a preserved spatial context. However, reproducible analysis of large multichannel images poses a substantial computational challenge. Here, we describe a modular and open-source computational pipeline, MCMICRO, for performing the sequential steps needed to transform whole-slide images into single-cell data. We demonstrate the use of MCMICRO on tissue and tumor images acquired using multiple imaging platforms, thereby providing a solid foundation for the continued development of tissue imaging software.
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Schapiro D, Yapp C, Sokolov A, Reynolds SM, Chen YA, Sudar D, Xie Y, Muhlich J, Arias-Camison R, Arena S, Taylor AJ, Nikolov M, Tyler M, Lin JR, Burlingame EA, Chang YH, Farhi SL, Thorsson V, Venkatamohan N, Drewes JL, Pe'er D, Gutman DA, Herrmann MD, Gehlenborg N, Bankhead P, Roland JT, Herndon JM, Snyder MP, Angelo M, Nolan G, Swedlow JR, Schultz N, Merrick DT, Mazzili SA, Cerami E, Rodig SJ, Santagata S, Sorger PK. MITI minimum information guidelines for highly multiplexed tissue images. Nat Methods 2022; 19:262-267. [PMID: 35277708 PMCID: PMC9009186 DOI: 10.1038/s41592-022-01415-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The imminent release of tissue atlases combining multi-channel microscopy with single cell sequencing and other omics data from normal and diseased specimens creates an urgent need for data and metadata standards that guide data deposition, curation and release. We describe a Minimum Information about highly multiplexed Tissue Imaging (MITI) standard that applies best practices developed for genomics and other microscopy data to highly multiplexed tissue images and traditional histology.
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Guerriero JL, Baker GJ, Lin JR, Chen YA, Pastorello R, Vallius T, Davis J, Yapp C, Church SE, Miller E, Färkkilä A, Vinayak S, Telli ML, Fulci G, D'Andrea A, Shapiro GI, Tolaney SM, Santagata S, Sorger PK, Mittendorf EA. Abstract P2-07-13: High-dimensional, single-cell analysis and transcriptional profiling reveal novel correlatives of response to PARP inhibition plus PD-1 blockade in triple-negative breast cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.sabcs21-p2-07-13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: TOPACIO was a phase I/II study evaluating the PARP inhibitor (PARPi) niraparib in combination with the anti-PD-1 antibody pembrolizumab in patients with locally advanced and metastatic triple-negative breast cancer (TNBC, n=55) and ovarian cancer irrespective of BRCA mutation status. In the efficacy-evaluable population (n=47) the objective response rate (ORR) was 21% and disease control rate (DCR) 49%. Although activity was greater in patients with BRCA mutations (7/15, ORR=47% and 12/15, DCR=80%), durable clinical benefit was seen in patients with wild-type BRCA tumors (3/27, ORR=11% and 9/27, DCR=33%). In a limited cohort of 20 patients with durable clinical benefit, there were 8 BRCA wildtype patients, four of whom had mutations in genes associated with the homologous recombination repair and other DNA damage repair pathways. Pre-treatment tissues were collected and evaluated for tumor PD-L1 status. Patients with PD-L1 positive tumors (28/47, 60%) had a higher response rate (9/28, ORR=32%) than those with PD-L1 negative tumors (1/13, ORR=8%; 6 tumors had unknown PD-L1 status). It remains unstudied whether the tumor’s gene expression profile or immune status in baseline biospecimens is predictive of treatment response. In this study we conducted exploratory biomarker analyses to test the hypothesis that gene expression patterns and immune status are associated with treatment response. Methods: Transcriptional profiling of baseline samples was performed using the BC360 (n=41) and PanCancer IO360 (n=42) panels (Nanostring) and multigene signatures were used to measure tumor and immune activities as well as relative immune cell abundance. Transcriptional analysis was paired with high-dimensional, single-cell cyclic immunofluorescence (CyCIF) of samples that had adequate tissue for analysis (n=19) to characterize the composition and topology of the immune microenvironment at single-cell resolution. Results: Nanostring transcriptional analysis revealed that PAM50 genes stratified tumor samples into 4 subgroups with distinct histology as determined by CyCIF. Each subgroup was capable of responding to niraparib plus pembrolizumab. Multiple genes involved in WNT signaling (WNT5B, TANKS1, TANKS2, PARP4, and NET02) were associated with favorable clinical responses. Low neuropilin and tolloid-like protein 2 (NETO2) gene expression was strongly correlated with favorable progression free survival (PFS; R=-0.61, p=0.0008, Spearman’s correlation), suggesting it may be a predictive biomarker of therapeutic response. Nanostring gene expression signatures for tumor inflammation, apoptosis, and inflammatory chemokines also distinguished responders from non-responders (p<0.05). CyCIF analysis performed on whole tissue sections accounting for 2.97 million single cells revealed 43 distinct cell-states comprising the tumor microenvironment. PD1+CD4+ T cells were significantly correlated with extended PFS (R=0.65, p=0.006, Spearman’s correlation). However, PD1+CD4+ T cells were less abundant in patients who continue to respond to the therapy (2.7-fold reduced, p=0.004), suggesting two groups of responders. Conclusion: WNT signaling, NETO2 and PD1+CD4 T cells are candidate biomarkers for predicting response to niraparib plus pembrolizumab. Further studies are underway to characterize the biological underpinnings of these correlative findings.
Citation Format: Jennifer L Guerriero, Gregory J Baker, Jia-Ren Lin, Yu-An Chen, Ricardo Pastorello, Tuulia Vallius, Janae Davis, Clarence Yapp, Sarah E Church, Eric Miller, Anniina Färkkilä, Shaveta Vinayak, Melinda L Telli, Giulia Fulci, Alan D'Andrea, Geoffrey I Shapiro, Sara M Tolaney, Sandro Santagata, Peter K Sorger, Elizabeth A Mittendorf. High-dimensional, single-cell analysis and transcriptional profiling reveal novel correlatives of response to PARP inhibition plus PD-1 blockade in triple-negative breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-07-13.
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Jessup J, Krueger R, Warchol S, Hoffer J, Muhlich J, Ritch CC, Gaglia G, Coy S, Chen YA, Lin JR, Santagata S, Sorger PK, Pfister H. Scope2Screen: Focus+Context Techniques for Pathology Tumor Assessment in Multivariate Image Data. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2022; 28:259-269. [PMID: 34606456 PMCID: PMC8805697 DOI: 10.1109/tvcg.2021.3114786] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Inspection of tissues using a light microscope is the primary method of diagnosing many diseases, notably cancer. Highly multiplexed tissue imaging builds on this foundation, enabling the collection of up to 60 channels of molecular information plus cell and tissue morphology using antibody staining. This provides unique insight into disease biology and promises to help with the design of patient-specific therapies. However, a substantial gap remains with respect to visualizing the resulting multivariate image data and effectively supporting pathology workflows in digital environments on screen. We, therefore, developed Scope2Screen, a scalable software system for focus+context exploration and annotation of whole-slide, high-plex, tissue images. Our approach scales to analyzing 100GB images of 109 or more pixels per channel, containing millions of individual cells. A multidisciplinary team of visualization experts, microscopists, and pathologists identified key image exploration and annotation tasks involving finding, magnifying, quantifying, and organizing regions of interest (ROIs) in an intuitive and cohesive manner. Building on a scope-to-screen metaphor, we present interactive lensing techniques that operate at single-cell and tissue levels. Lenses are equipped with task-specific functionality and descriptive statistics, making it possible to analyze image features, cell types, and spatial arrangements (neighborhoods) across image channels and scales. A fast sliding-window search guides users to regions similar to those under the lens; these regions can be analyzed and considered either separately or as part of a larger image collection. A novel snapshot method enables linked lens configurations and image statistics to be saved, restored, and shared with these regions. We validate our designs with domain experts and apply Scope2Screen in two case studies involving lung and colorectal cancers to discover cancer-relevant image features.
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Chang CC, Chen YJ, Chen YA, Liao YC. Acute Hepatitis Due to Agomelatine Use in Elderly Women with Depression: Case Series. CLINICAL PSYCHOPHARMACOLOGY AND NEUROSCIENCE 2021; 19:789-792. [PMID: 34690134 PMCID: PMC8553533 DOI: 10.9758/cpn.2021.19.4.789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 12/24/2022]
Abstract
Although agomelatine may be associated with an increased risk of hepatotoxicity, the incidence rate of acute hepatitis seemed divergent between clinical trials and daily practice. Whether aging or gender is a risk factor in developing hepatotoxicity due to agomelatine is not clear. We present 3 older female cases with acute hepatitis occurring due to highly probable idiosyncratic drug-induced liver injury caused by agomelatine. From these cases, regular surveillance on liver function in the older women taking antidepressants would be of benefits.
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Li CW, Lin SY, Chou HS, Chen TY, Chen YA, Liu SY, Liu YL, Chen CA, Huang YC, Chen SL, Mao YC, Abu PAR, Chiang WY, Lo WS. Detection of Dental Apical Lesions Using CNNs on Periapical Radiograph. SENSORS 2021; 21:s21217049. [PMID: 34770356 PMCID: PMC8588190 DOI: 10.3390/s21217049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 12/16/2022]
Abstract
Apical lesions, the general term for chronic infectious diseases, are very common dental diseases in modern life, and are caused by various factors. The current prevailing endodontic treatment makes use of X-ray photography taken from patients where the lesion area is marked manually, which is therefore time consuming. Additionally, for some images the significant details might not be recognizable due to the different shooting angles or doses. To make the diagnosis process shorter and efficient, repetitive tasks should be performed automatically to allow the dentists to focus more on the technical and medical diagnosis, such as treatment, tooth cleaning, or medical communication. To realize the automatic diagnosis, this article proposes and establishes a lesion area analysis model based on convolutional neural networks (CNN). For establishing a standardized database for clinical application, the Institutional Review Board (IRB) with application number 202002030B0 has been approved with the database established by dentists who provided the practical clinical data. In this study, the image data is preprocessed by a Gaussian high-pass filter. Then, an iterative thresholding is applied to slice the X-ray image into several individual tooth sample images. The collection of individual tooth images that comprises the image database are used as input into the CNN migration learning model for training. Seventy percent (70%) of the image database is used for training and validating the model while the remaining 30% is used for testing and estimating the accuracy of the model. The practical diagnosis accuracy of the proposed CNN model is 92.5%. The proposed model successfully facilitated the automatic diagnosis of the apical lesion.
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Sun SH, Chang CH, Zhan ZW, Chang WH, Chen YA, Dong YH. Risk of COPD Exacerbations Associated with Statins versus Fibrates: A New User, Active Comparison, and High-Dimensional Propensity Score Matched Cohort Study. Int J Chron Obstruct Pulmon Dis 2021; 16:2721-2733. [PMID: 34621122 PMCID: PMC8491865 DOI: 10.2147/copd.s323391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/03/2021] [Indexed: 11/23/2022] Open
Abstract
Background Several observational studies have found that statins may materially decrease the risk of chronic obstructive pulmonary disease (COPD) exacerbations. However, most of these studies used a prevalent user, non-user comparison approach, which may lead to overestimation of the clinical benefits of statins. We aimed to explore the risk of COPD exacerbations associated with statins with a new user, active comparison approach to address potential methodological concerns. We selected fibrates, another class of lipid-lowering agents, as the reference group because no evidence suggests that fibrates have an effect on COPD exacerbations. Methods We identified patients with COPD who initiated statins or fibrates from a nationwide Taiwanese database. Patients were followed from cohort entry to the earliest of the following: hospitalization for COPD exacerbations, death, end of the data, or 180 days after cohort entry. Stratified Cox regression models were used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) of COPD exacerbations comparing statins with fibrates after variable-ratio propensity score (PS) matching and high-dimensional PS (hd-PS) matching, respectively. Results We identified a total of 134,909 eligible patients (110,726 initiated statins; 24,183 initiated fibrates); 1979 experienced COPD exacerbations during follow-up. The HRs were 1.10 (95% CI, 0.96 to 1.26) after PS matching and 1.08 (95% CI, 0.94 to 1.24) after hd-PS matching. The results did not differ materially by type of statins and patient characteristic and did not change with longer follow-up durations. Conclusion This large-scale, population-based cohort study did not show that use of statins was associated with a reduced risk of acute exacerbations in patients with COPD using state-of-the-art pharmacoepidemiologic approaches. The findings emphasize the importance of applying appropriate methodology in exploring statin effectiveness in real-world settings.
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Lo UG, Chen YA, Khamis ZI, Kao WH, Hsieh JT, Sang QXA. Studies of hormonal regulation, phenotype plasticity, bone metastasis, and experimental therapeutics in androgen-repressed human prostate cancer (ARCaP) model. AMERICAN JOURNAL OF CLINICAL AND EXPERIMENTAL UROLOGY 2021; 9:277-286. [PMID: 34541026 PMCID: PMC8446760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
First established by Dr. Leland W. K. Chung's lab, the androgen-repressed prostate cancer cell (ARCaP) line is derived from the ascitic fluid of a prostate cancer (PCa) patient with widely metastatic disease. Based on its unique characteristic of growth suppression in the presence of androgen, ARCaP cell line has contributed to the research of PCa disease progression toward therapy- and castration-resistant PCa (t-CRPC). It has been widely applied in studies exploring experimental therapeutic reagents including Genistein, Vorinostat and Silibinin. ARCaP cells have showed increased metastatic potential to the bone and soft tissues. In addition, accumulating studies using ARCaP model have demonstrated the epithelial-to-mesenchymal transitional plasticity of PCa using epithelial-like ARCaPE line treated in vitro with growth factors derived from bone microenvironment. The resulting mesenchymal-like ARCaPM sub-clone derived from bone-metastasized tumor has high expression of several factors correlated with cancer metastasis, such as N-Cadherin, Vimentin, MCM3, Granzyme B, β2-microglobulin and RANKL. In particular, the increased secretion of RANKL in ARCaPM further facilitates its capacity of inducing osteoclastogenesis at the bone microenvironment, leading to bone resorption and tumor colonization. Meanwhile, sphingosine kinase 1 (SphK1) acts as a key molecule driver in the neuroendocrine differentiation (NED) of ARCaP sublines, suggesting the unique facet of ARCaP cells for insightful studies in more malignant neuroendocrine prostate cancer (NEPC). Overall, the establishment of ARCaP line has provided a valuable model to explore the mechanisms underlying PCa progression toward metastatic t-CRPC. In this review, we will focus on the contribution of ARCaP model in PCa research covering hormone receptor activity, skeletal metastasis, plasticity of epithelial-to-mesenchymal transition (EMT) and application of therapeutic strategies.
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Chen YA, Li Y, Lee JC, Chen JW. Staged surgery for advanced cardiac intimal sarcoma involving the right atrium and the inferior vena cava. J Card Surg 2021; 36:3973-3975. [PMID: 34331777 DOI: 10.1111/jocs.15885] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/18/2021] [Accepted: 07/20/2021] [Indexed: 11/27/2022]
Abstract
Intimal sarcomas simultaneously involving the right atrium and the inferior vena cava (IVC) are rare. We report an advanced cardiac intimal sarcoma in the right atrium of a 19-year-old man that was complicated by tumor-related IVC thrombosis. We initially performed partial tumor resection and vena cava thrombectomy to resolve the circulatory obstruction, because complete resection was difficult due to the invading malignancy and an unclear margin. The patient received adjuvant chemo- and radiotherapy along with anticoagulant therapy. After 3 months, the border of the residual sarcoma was clear, and the patient underwent a secondary complete sarcoma excision (including that of the right atrium) and a suprahepatic vena cava reconstruction. At the 2-year follow-up, there was no tumor recurrence. We conclude that aggressive treatment and a staged complete resection can lead to improved outcomes for advanced cardiac intimal sarcoma with poor prognosis.
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Hwang JD, Hwang YE, Chen YA. Base-width modulation effects on the optoelectronic characteristics of n-ITO/p-NiO/n-ZnO heterojunction bipolar phototransistors. NANOTECHNOLOGY 2021; 32:405501. [PMID: 33887705 DOI: 10.1088/1361-6528/abfabd] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
ITO/NiO/ZnO npn heterojunction bipolar phototransistors (HBPTs) with various base widths are fabricated using a radio-frequency sputtering system. The effects of base-width modulation on the optoelectronic characteristics of the prepared HBPTs are studied. The dark current of HBPTs decreases with increasing base width because the injected electrons from the emitter are recombined in the wide base region. The photocurrent increases with decreasing base width, which is attributed to higher emitter-base injection efficiency. The responsivity increases with the collector-emitter voltage (VCE) in the HBPTs with a 100 nm base width, whereas the responsivity sharply decreases atVCE> 4 V for the HBPTs with a thinner base width (80 nm) due to the punch-through effect. In contrast, the responsivity approaches saturation at largeVCEfor HBPTs with a thicker base width (120 nm). The responsivity and detectivity decrease with increasing incident light intensity, which is caused by an increase in the base recombination loss. The HBPTs with a base width of 100 nm exhibits the largest responsivity and detectivity; their detectivity is higher than that of HBPTs with base widths of 80 and 120 nm by approximately two and three orders, respectively.
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Chang CC, Wang WF, Li YY, Chen YA, Chen YJ, Liao YC, Jhang KM, Wu HH. Using the Apriori Algorithm to Explore Caregivers' Depression by the Combination of the Patients with Dementia and Their Caregivers. Risk Manag Healthc Policy 2021; 14:2953-2963. [PMID: 34285609 PMCID: PMC8286245 DOI: 10.2147/rmhp.s316361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/16/2021] [Indexed: 11/23/2022] Open
Abstract
Purpose The purpose of this study was to identify the caring scenarios that result in severe depression in caregivers caring for dementia patients. Patients and Methods A cross-sectional study with 1111 dementia patients and their caregivers in Taiwan from October 2015 to January 2020 was conducted. Gender, age, type of dementia, clinical dementia rating, walking ability, mood symptoms, behavioral symptoms, and psychological symptoms were the variables from the dementia patients. Age, relation to the patient, employment, type of primary care, frequency of care, mood symptoms, and the score from the Center for Epidemiologic Studies Depression Scale were the variables from the caregivers. A comprehensive viewpoint of both dementia patients and their caregivers was evaluated by the Apriori algorithm to find the attributes resulting in different caregiving depressions. Results Forty-seven rules were found with 18 rules of mild depressive symptomatology, 17 rules of moderate depressive symptomatology, and 12 rules of severe depressive symptomatology. A total of 7 general rules were summarized to be the severe depressive symptomatology. The results showed that an unemployed or retired caregiver with the mood symptoms such as helplessness, anger, emotional liability, or anxiety who took care of AD patients or AD patients with a moderate severity would have severe depression. Increased care frequencies (≥6 days per week) and multiple mood problems from caregivers result in severe depression. The composition of adult children, patients' aggression, and caregivers' helplessness as well as the combinations of male patients aged 75-84 years with the caregiver's mood of helplessness or nervousness and hopelessness were highly associated with severe depression. Conclusion For those caring for AD patients, severe depression was associated with the combination of different parameters to constitute each of these seven scenarios. Unlike previous studies which often evaluated one or two variables related to caregiver's depression, this study provided a more comprehensive viewpoint that enabled the collaborative team to efficiently identify and manage different scenarios by summarizing the rules of caregivers with severe depression from a systematic viewpoint.
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Lin JR, Campton DE, Cooper J, Chen YA, McCarty EF, Ligon KL, Kaldjian EP, Teplitz K, Reese S, Santagata S, Sorger PK. Abstract 482: Rapid highly multiplexed immunoprofiling of human fixed tissues by Orion imaging. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The dramatic impact of immune checkpoint inhibitors (ICIs) has focused interest in investigating immune-tumor cell interactions to understand mechanisms of ICI sensitivity and resistance, to identify patients that are responsive to specific treatments, and to develop new therapies. Multiplexed tissue imaging is a highly promising approach to immunoprofile tumors; it can assess many cell types and states within the context of preserved tumor architecture. However, the promise of highly multiplexed tissue imaging remains largely unfulfilled by current methods which are not compatible with pathology workflows. Here we present the development and implementation of Orion™ technology that permits whole-slide rapid single-pass imaging of up to 21 markers from formalin fixed paraffin embedded (FFPE) tissues. This method measures spectra for specific fluorophores to optimally sample the emitted light spectrum and distinguish multiple fluorescence excitation and emission channels across the spectral range of optical microscopes (~400-900 nm). To establish the utility of the Orion™ platform for immuno-phenotyping and immune checkpoint protein detection, we created an immunoprofiling panel of 21 qualified antibodies and labelled with fluorophores to subdivide the available emission spectrum in the 438-893 nm range. The panel includes markers that define subsets of T cells and macrophages. FFPE sections of human tonsil and matched primary and brain metastatic lung adenocarcinoma were stained and imaged in a single pass demonstrating staining patterns consistent with known micro-anatomic compartments and cell types in tonsil and identifying immune cell subtypes and heterogeneous checkpoint protein expression in tumor samples. An unexpected benefit of imaging with the Orion platform is the reduction of autofluorescence which is highly advantageous for the detection of proteins, like PD-L1, that function at very low levels. Orion imaging promises to accelerate discovery of predictive and prognostic biomarkers, enable pharmacodynamics study of immuno-oncology drugs undergoing clinical trials and ultimately provide clinically actionable diagnostic tests.
Citation Format: Jia-Ren Lin, Daniel E. Campton, Jeremy Cooper, Yu-An Chen, Erin F. McCarty, Keith L. Ligon, Eric P. Kaldjian, Kyla Teplitz, Steve Reese, Sandro Santagata, Peter K. Sorger. Rapid highly multiplexed immunoprofiling of human fixed tissues by Orion imaging [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 482.
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Liu D, Lin JR, Robitschek EJ, Kasumova GG, Heyde A, Shi A, Kraya A, Zhang G, Moll T, Frederick DT, Chen YA, Wang S, Schapiro D, Ho LL, Bi K, Sahu A, Mei S, Miao B, Sharova T, Alvarez-Breckenridge C, Stocking JH, Kim T, Fadden R, Lawrence D, Hoang MP, Cahill DP, Malehmir M, Nowak MA, Brastianos PK, Lian CG, Ruppin E, Izar B, Herlyn M, Van Allen EM, Nathanson K, Flaherty KT, Sullivan RJ, Kellis M, Sorger PK, Boland GM. Evolution of delayed resistance to immunotherapy in a melanoma responder. Nat Med 2021; 27:985-992. [PMID: 33941922 PMCID: PMC8474080 DOI: 10.1038/s41591-021-01331-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/24/2021] [Indexed: 02/02/2023]
Abstract
Despite initial responses1-3, most melanoma patients develop resistance4 to immune checkpoint blockade (ICB). To understand the evolution of resistance, we studied 37 tumor samples over 9 years from a patient with metastatic melanoma with complete clinical response to ICB followed by delayed recurrence and death. Phylogenetic analysis revealed co-evolution of seven lineages with multiple convergent, but independent resistance-associated alterations. All recurrent tumors emerged from a lineage characterized by loss of chromosome 15q, with post-treatment clones acquiring additional genomic driver events. Deconvolution of bulk RNA sequencing and highly multiplexed immunofluorescence (t-CyCIF) revealed differences in immune composition among different lineages. Imaging revealed a vasculogenic mimicry phenotype in NGFRhi tumor cells with high PD-L1 expression in close proximity to immune cells. Rapid autopsy demonstrated two distinct NGFR spatial patterns with high polarity and proximity to immune cells in subcutaneous tumors versus a diffuse spatial pattern in lung tumors, suggesting different roles of this neural-crest-like program in different tumor microenvironments. Broadly, this study establishes a high-resolution map of the evolutionary dynamics of resistance to ICB, characterizes a de-differentiated neural-crest tumor population in melanoma immunotherapy resistance and describes site-specific differences in tumor-immune interactions via longitudinal analysis of a patient with melanoma with an unusual clinical course.
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MESH Headings
- B7-H1 Antigen/antagonists & inhibitors
- B7-H1 Antigen/genetics
- B7-H1 Antigen/immunology
- Chromosomes, Human, Pair 15/genetics
- Drug Resistance, Neoplasm/drug effects
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Immune Checkpoint Inhibitors/adverse effects
- Immune Checkpoint Inhibitors/therapeutic use
- Immunotherapy/adverse effects
- Male
- Melanoma/genetics
- Melanoma/immunology
- Melanoma/pathology
- Melanoma/therapy
- Neoplasm Metastasis
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/immunology
- Neoplasm Recurrence, Local/pathology
- Neoplasm Recurrence, Local/therapy
- Nerve Tissue Proteins/genetics
- Nerve Tissue Proteins/immunology
- Phylogeny
- Receptors, Nerve Growth Factor/genetics
- Receptors, Nerve Growth Factor/immunology
- Tumor Microenvironment/drug effects
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Chen YA, Chang CC, Wang WF, Lin YS, Jhang KM, Lo TY, Wu HH. Association Between Caregivers' Burden and Neuropsychiatric Symptoms in Female Patients with Alzheimer's Disease with Varying Dementia Severity. J Multidiscip Healthc 2021; 14:929-940. [PMID: 33953562 PMCID: PMC8090980 DOI: 10.2147/jmdh.s298196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/11/2021] [Indexed: 01/14/2023] Open
Abstract
Purpose This study examined the attributes causing higher burdens for caregivers caring for female patients with Alzheimer’s disease by analyzing a combination of various variables, including demographic data, dementia severity, and neuropsychiatric symptoms. Patients and Methods This study included 99 female patients with Alzheimer’s disease who were cared for by the dementia collaborative care team at Changhua Christian Hospital, Taiwan. Neuropsychiatric symptoms used in this study included affections (9 types), behavior symptoms (9 symptoms), and psychological symptoms (3 symptoms). The Apriori algorithm was employed to identify association rules that reveal the relationships among demographic data, dementia severity, neuropsychiatric symptoms, and caregivers’ burden. Results A total of 185 rules were determined, including 51 rules with little or no burden, 108 rules with mild to moderate burden, and 26 rules with moderate to severe burden. The major findings are as follows. Neuropsychiatric symptoms were associated with varying degrees of caregivers’ burden among female patients aged 75 to 84 years with mild dementia. Crying spells and aggression were specifically associated with a moderate to severe burden. Delusion was associated with a mild to moderate and moderate to severe burden. Dysthymia and depression were associated with little or no burden to moderate to severe burden. Conclusion Clinicians can provide early interventions to reduce the burden of caregivers caring for female patients with Alzheimer’s disease and can refer caregivers for timely assistance to reduce their burden.
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Ou KL, Wen CC, Lan CY, Chen YA, Wang CH, Wang YW. The Optimal Application of Medium Potency Topical Corticosteroids in Preventing Laser-Induced Inflammatory Responses-An Animal Study. Life (Basel) 2021; 11:life11040350. [PMID: 33920511 PMCID: PMC8073345 DOI: 10.3390/life11040350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 01/07/2023] Open
Abstract
Background: During ablative fractional resurfacing (AFR) laser therapy, thermal damage to the skin is inevitable, resulting in inflammatory responses and small wounds. Corticosteroids are known for their anti-inflammatory effect. However, inappropriate application of corticosteroids carries the risk of delayed wound healing. Therefore, we aimed to find the optimal administration route, timing, and duration of medium potency corticosteroid treatment to prevent AFR laser-induced inflammatory responses and to minimize the risk of delayed wound healing. Methods: We determined the anti-inflammatory efficacy of corticosteroids by skin erythema and tissue biopsies on C57BL/6 mice. Wound healing was evaluated by crust area and epithelial gap. Finally, Masson’s trichrome stain and α-SMA immunohistochemistry stain were used to analyze scar contracture. Results: Our results demonstrated that one dose of medium-potency topical corticosteroid applied immediately after AFR laser treatment could prevent erythema effectively with minimal disruption to wound healing. Notably, when more than one dose was administered, wound healing was delayed and scar contracture was aggravated by the application of medium-potency topical corticosteroids in a dosage-dependent manner. Conclusion: Our findings suggested that single-dose medium-potency topical corticosteroids could potentially improve AFR laser-induced acute inflammatory responses in clinical applications.
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Chen YA, Lai YR, Wu HY, Lo YJ, Chang YF, Hung CL, Lin CJ, Lo UG, Lin H, Hsieh JT, Chiu CH, Lin YH, Lai CH. Bacterial Genotoxin-Coated Nanoparticles for Radiotherapy Sensitization in Prostate Cancer. Biomedicines 2021; 9:biomedicines9020151. [PMID: 33557143 PMCID: PMC7913852 DOI: 10.3390/biomedicines9020151] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/17/2021] [Accepted: 01/20/2021] [Indexed: 12/25/2022] Open
Abstract
Prostate cancer (PCa) is one of the most commonly diagnosed cancers in men and usually becomes refractory because of recurrence and metastasis. CD44, a transmembrane glycoprotein, serves as a receptor for hyaluronic acid (HA). It has been found to be abundantly expressed in cancer stem cells (CSCs) that often exhibit a radioresistant phenotype. Cytolethal distending toxin (CDT), produced by Campylobacter jejuni, is a tripartite genotoxin composed of CdtA, CdtB, and CdtC subunits. Among the three, CdtB acts as a type I deoxyribonuclease (DNase I), which creates DNA double-strand breaks (DSBs). Nanoparticles loaded with antitumor drugs and specific ligands that recognize cancerous cell receptors are promising methods to overcome the therapeutic challenges. In this study, HA-decorated nanoparticle-encapsulated CdtB (HA-CdtB-NPs) were prepared and their targeted therapeutic activity in radioresistant PCa cells was evaluated. Our results showed that HA-CdtB-NPs sensitized radioresistant PCa cells by enhancing DSB and causing G2/M cell-cycle arrest, without affecting the normal prostate epithelial cells. HA-CdtB-NPs possess maximum target specificity and delivery efficiency of CdtB into the nucleus and enhance the effect of radiation in radioresistant PCa cells. These findings demonstrate that HA-CdtB-NPs exert target specificity accompanied with radiomimetic activity and can be developed as an effective strategy against radioresistant PCa.
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Du B, Chong Y, Jiang X, Yu M, Lo UG, Dang A, Chen YA, Li S, Hernandez E, Lin JC, Hsieh JT, Zheng J. Hyperfluorescence Imaging of Kidney Cancer Enabled by Renal Secretion Pathway Dependent Efflux Transport. Angew Chem Int Ed Engl 2021; 60:351-359. [PMID: 32876994 PMCID: PMC8635778 DOI: 10.1002/anie.202010187] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Indexed: 12/14/2022]
Abstract
Renal tubular secretion is an active efflux pathway for the kidneys to remove molecules but has yet to be used to enhance kidney cancer targeting. We report indocyanine green (ICG) conjugated with a 2100 Da PEG molecule (ICG-PEG45) as a renal-tubule-secreted near-infrared-emitting fluorophore for hyperfluorescence imaging of kidney cancers, which cannot be achieved with hepatobiliary- and glomerular-clearable ICG. This pathway-dependent targeting of kidney cancer arises from the fact that the secretion pathway enables ICG-PEG45 to be effectively effluxed out of normal proximal tubules through P-glycoprotein transporter while being retained in cancerous kidney tissues with low P-glycoprotein expression. Tuning elimination pathways and utilizing different efflux kinetics of medical agents in normal and diseased tissues could be a new strategy for tackling challenges in disease diagnosis and treatments that cannot be addressed with passive and ligand-receptor-mediated active targeting.
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Kung PY, Hung CI, Wu KH, Tzeng WC, Yang PL, Chen YA, Wang YW. The clinical english communication situations and the requirement of nursing staff on improving their clinical english communication abilities. JOURNAL OF MEDICAL SCIENCES 2021. [DOI: 10.4103/jmedsci.jmedsci_68_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Pai PY, Chou WC, Chan SH, Wu SY, Chen HI, Li CW, Hsieh PL, Chu PM, Chen YA, Ou HC, Tsai KL. Epigallocatechin Gallate Reduces Homocysteine-Caused Oxidative Damages through Modulation SIRT1/AMPK Pathway in Endothelial Cells. THE AMERICAN JOURNAL OF CHINESE MEDICINE 2020; 49:113-129. [PMID: 33371812 DOI: 10.1142/s0192415x21500063] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Elevated plasma concentration of total homocysteine is a pathological condition that causes vascular endothelial injury and subsequently leads to the progression of endothelial apoptosis in atherosclerosis. Epigallocatechin gallate (EGCG), a well-known anti-oxidant in green tea, has been reported with benefits on metabolic and cardiovascular diseases. This study aimed to explore that EGCG ameliorates homocysteine-induced endothelial cell apoptosis through enhancing the sirtuin 1 (SIRT1)/AMP-activated protein kinase (AMPK) survival signaling pathway. Human umbilical endothelial cells were treated with homocysteine in the presence or absence of EGCG. We found that EGCG significantly increased the activities of SIRT1 and AMPK. EGCG diminished homocysteine-mediated nicotinamide adenine dinucleotide phosphate (NADPH) oxidase activation by inhibiting protein kinase C activation as well as reactive oxygen species (ROS) generation and recovered the activity of the endogenous antioxidant enzyme, superoxidase dismutase (SOD). Besides, EGCG also restores homocysteine-mediated dephosphorylation of Akt and decreases endothelial NO synthase (eNOS) expression. Furthermore, EGCG ameliorates homocysteine-activated pro-apoptotic events. The present study shows that EGCG prevents homocysteine-induced endothelial cell apoptosis via enhancing SIRT1/AMPK as well as Akt/eNOS signaling pathways. Results from this study indicated that EGCG might have some benefits for hyperhomocysteinemia.
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Wang J, Zhang J, Nguyen NTD, Chen YA, Hsieh JT, Dong X. Quantitative measurements of IR780 in formulations and tissues. J Pharm Biomed Anal 2020; 194:113780. [PMID: 33280993 DOI: 10.1016/j.jpba.2020.113780] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/21/2020] [Accepted: 11/16/2020] [Indexed: 12/15/2022]
Abstract
PURPOSE IR780 iodide, a promising near-infrared dye, is widely used to prepare nanoparticles as a theranostic agent for tumor imaging and therapy. However, there are no validated (bio)analytical methods to measure IR780 in nanoparticles and tissues in literature. The aim of this study is to develop and validate a new HPLC method to measure IR780 concentration in IR780 formulations as well as a new LC-MS/MS method to measure IR780 concentration in tissue samples, particularly in liver and lung. MATERIALS AND METHODS IR780 granules that produced IR780 in situ self-assembled nanoparticles upon contact with water were prepared at two drug loadings (0.2 % and 0.37 %). An HPLC method was developed and validated to measure IR780 concentrations in IR780 granules and nanoparticles. Furthermore, a validated LC-MS/MS method was developed to measure IR780 in mouse liver and lung. Both HPLC method and LC-MS/MS method were validated in terms of specificity, stability, linearity, limit of detection, limit of quantification, accuracy and precision. RESULTS Both HPLC method and LC-MS/MS method achieved the criteria for method validation. The HPLC method was accurate in the concentration range of 0.5-25 μg/mL. The measured drug loadings were 95 % of the theoretical drug loadings. The validated LC-MS/MS method can quantitatively measure the concentrations of IR780 in liver and lung. The linear range of the LC-MS/MS method was 1-1000 ng/mL for both liver and lung samples. IR780 granules showed the lung selectivity compared to IR780 solution at 2 h after oral administration. CONCLUSION A validated HPLC method was developed to measure IR780 concentration in pharmaceutical formulations and a validated LC-MS/MS method was developed to measure IR780 concentration in tissues. These quantitative methods provide reliable measurements of IR780 in pharmaceutic formulations and biological samples, which will significantly facilitate the research of IR780 as a theranostic agent for cancer therapy and imaging.
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Hoffer J, Rashid R, Muhlich JL, Chen YA, Russell DPW, Ruokonen J, Krueger R, Pfister H, Santagata S, Sorger PK. Minerva: a light-weight, narrative image browser for multiplexed tissue images. JOURNAL OF OPEN SOURCE SOFTWARE 2020; 5:2579. [PMID: 33768192 PMCID: PMC7989801 DOI: 10.21105/joss.02579] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Advances in highly multiplexed tissue imaging are transforming our understanding of human biology by enabling detection and localization of 10-100 proteins at subcellular resolution (Bodenmiller, 2016). Efforts are now underway to create public atlases of multiplexed images of normal and diseased tissues (Rozenblatt-Rosen et al., 2020). Both research and clinical applications of tissue imaging benefit from recording data from complete specimens so that data on cell state and composition can be studied in the context of overall tissue architecture. As a practical matter, specimen size is limited by the dimensions of microscopy slides (2.5 × 7.5 cm or ~2-8 cm2 of tissue depending on shape). With current microscopy technology, specimens of this size can be imaged at sub-micron resolution across ~60 spectral channels and ~106 cells, resulting in image files of terabyte size. However, the rich detail and multiscale properties of these images pose a substantial computational challenge (Rashid et al., 2020). See Rashid et al. (2020) for an comparison of existing visualization tools targeting these multiplexed tissue images.
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