Harmonizing the Generation and Pre-publication Stewardship of FAIR Image data

Together with the molecular knowledge of genes and proteins, biological images promise to significantly enhance the scientific understanding of complex cellular systems and to advance predictive and personalized therapeutic products for human health. For this potential to be realized, quality-assured image data must be shared among labs at a global scale to be compared, pooled, and reanalyzed, thus unleashing untold potential beyond the original purpose for which the data was generated. There are two broad sets of requirements to enable image data sharing in the life sciences. One set of requirements is articulated in the companion White Paper entitled "Enabling Global Image Data Sharing in the Life Sciences," which is published in parallel and addresses the need to build the cyberinfrastructure for sharing the digital array data (arXiv:2401.13023 [q-bio.OT], https://doi.org/10.48550/arXiv.2401.13023). In this White Paper, we detail a broad set of requirements, which involves collecting, managing, presenting, and propagating contextual information essential to assess the quality, understand the content, interpret the scientific implications, and reuse image data in the context of the experimental details. We start by providing an overview of the main lessons learned to date through international community activities, which have recently made considerable progress toward generating community standard practices for imaging Quality Control (QC) and metadata. We then provide a clear set of recommendations for amplifying this work. The driving goal is to address remaining challenges, and democratize access to common practices and tools for a spectrum of biomedical researchers, regardless of their expertise, access to resources, and geographical location.

Community-developed checklists for publishing images and image analyses

Images document scientific discoveries and are prevalent in modern biomedical research. Microscopy imaging in particular is currently undergoing rapid technological advancements. However, for scientists wishing to publish obtained images and image-analysis results, there are currently no unified guidelines for best practices. Consequently, microscopy images and image data in publications may be unclear or difficult to interpret. Here, we present community-developed checklists for preparing light microscopy images and describing image analyses for publications. These checklists offer authors, readers and publishers key recommendations for image formatting and annotation, color selection, data availability and reporting image-analysis workflows. The goal of our guidelines is to increase the clarity and reproducibility of image figures and thereby to heighten the quality and explanatory power of microscopy data.

Mitochondrial regulator PGC-1a in neuronal metabolism and brain aging

The brain is a high energy tissue, and the cell types of which it is comprised are distinct in function and in metabolic requirements. The transcriptional co-activator PGC-1a is a master regulator of mitochondrial function and is highly expressed in the brain; however, its cell-type specific role in regulating metabolism has not been well established. Here, we show that PGC-1a is responsive to aging and that expression of the neuron specific PGC-1a isoform allows for specialization in metabolic adaptation. Transcriptional profiles of the cortex from male mice show an impact of age on immune, inflammatory, and neuronal functional pathways and a highly integrated metabolic response that is associated with decreased expression of PGC-1a. Proteomic analysis confirms age-related changes in metabolism and further shows changes in ribosomal and RNA splicing pathways. We show that neurons express a specialized PGC-1a isoform that becomes active during differentiation from stem cells and is further induced during the maturation of isolated neurons. Neuronal but not astrocyte PGC-1a responds robustly to inhibition of the growth sensitive kinase GSK3b, where the brain specific promoter driven dominant isoform is repressed. The GSK3b inhibitor lithium broadly reprograms metabolism and growth signaling, including significantly lower expression of mitochondrial and ribosomal pathway genes and suppression of growth signaling, which are linked to changes in mitochondrial function and neuronal outgrowth. In vivo, lithium treatment significantly changes the expression of genes involved in cortical growth, endocrine, and circadian pathways. These data place the GSK3b/PGC-1a axis centrally in a growth and metabolism network that is directly relevant to brain aging.

Community-developed checklists for publishing images and image analyses

Images document scientific discoveries and are prevalent in modern biomedical research. Microscopy imaging in particular is currently undergoing rapid technological advancements. However for scientists wishing to publish the obtained images and image analyses results, there are to date no unified guidelines. Consequently, microscopy images and image data in publications may be unclear or difficult to interpret. Here we present community-developed checklists for preparing light microscopy images and image analysis for publications. These checklists offer authors, readers, and publishers key recommendations for image formatting and annotation, color selection, data availability, and for reporting image analysis workflows. The goal of our guidelines is to increase the clarity and reproducibility of image figures and thereby heighten the quality and explanatory power of microscopy data is in publications.

Abstract 2472: Tumor/normal and live/dead classification in live tumor fragments using label-free multiphoton microscopy

We have developed a live tumor fragment (LTF) platform for predicting clinical response to cancer drugs. The success of this approach depends on screening tissue fragments derived from biopsies and excisions before drug treatment to select those that have acceptable levels of viability and tumor content. To enable this screening, we are developing label-free methods for integrated assessment of LTF histology, viability, and metabolic status using intrinsic multiphoton-excited fluorescence lifetime microscopy (MP-FLIM). We cut live EMT6 tumors and mammary fat pad into rectangular fragments that were then sorted and cultured in glass-bottomed multi-well plates. To induce cancer cell death, we treated one group with a therapeutic agent, e.g., the multi-kinase inhibitor, staurosporine, or the alkylating agent, cisplatin. Before and after treatment, we imaged LTF structure and metabolic status based on the intrinsically fluorescent metabolic co-factors nicotinamide dinucleotides (NAD(P)H) and flavin adenine dinucleotides (FAD) fluorescence intensity and lifetime using dual-excitation multiphoton microscopy. As a ground truth viability reference, we then stained and re-imaged the fragments using nuclear and cell viability probes such as Hoechst, SYTOX, TMRE and/or propidium iodide (PI). We analyzed the data by fitting fluorescence decay curves with dual or triple exponents to generate images of lifetime parameters, including the mean and individual component lifetimes and amplitudes. Finally, we co-registered the extrinsically labeled and autofluorescent lifetime images for 3D spatial analysis using commercial and custom software. We verified the methods using monolayer cell cultures and ATP luminescence and flow cytometry viability assays. Image spatial heterogeneity was quantified utilizing entropy metrics. Intrinsic contrast from multiphoton imaging revealed cellular and tissue structures. The median entropy was higher and its distribution negatively skewed for EMT6 (p<0.01), allowing us to distinguish tumor from its corresponding normal tissue of origin. In viable cells, nuclei were distinguishable from the cytoplasm via higher cytoplasmic NADH signal. Upon loss of cell viability, nuclear NADH signals increased, with characteristically short lifetimes, and the overall NADH intensity decreased, reducing the contrast between nuclei and their surrounding cytoplasm. We detected an increase in the whole fragment mean lifetime (τm p<0.002) and concomitant decrease in the short lifetime component (α1 p< 0.002) within 24 hours of staurosporine exposure. We have demonstrated that MP-FLIM can distinguish tumor from normal and live from dead in LTFs without labels. This approach will facilitate selection of fragments with acceptable viability and tumor content for subsequent drug treatment as part of a platform built for personalizing cancer therapy.

Citation Format: Jonathan Ouellette, John Rafter, Kelsey Tweed, Leung Kau Tang, Christina Scribano, Pichet Adstamongkonkul, Mikaela Schultz, Justine Coburn, Maged Aldeeb, Neil Anthony, Christin Johnson, Kevin Eliceiri, Jonathan Oliner, Tomasz Zal. Tumor/normal and live/dead classification in live tumor fragments using label-free multiphoton microscopy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2472.

Abstract 2779: A live tumor fragment (LTF) platform with real-time imaging for immune response assays

Immuno-Oncology (IO) therapies provide remarkable clinical benefits. However, too few patients respond, and there are no diagnostic tools that predict IO response with high accuracy. Moreover, as more IO drugs and combinations are approved, selecting the best IO-based regimen for each patient will become more complex. To facilitate this selection, we are developing an ex vivo live tumor fragment (LTF) screening platform that retains representation of a patient’s tumor microenvironment (TME) including immune cells, enabling development of deep neural networks to predict IO response and thereby individualize therapy. Here we present preliminary data from our proof-of-concept platform that performs tissue fragmentation/sorting, liquid handling, drug treatment, high-resolution dynamic imaging, and multiplex immuno-assays. Human tumor excisions were obtained from the Univ. of Wisconsin (IRB approved), and CT26 tumors were grown in mice subcutaneously. Live tumors were cut into 300 x 300 µm fragments of 100 - 300 µm thickness, sorted into multi-well plates, and cultured for 48 or 72 h in the presence or absence of anti-PD1 (nivolumab or mouse equivalent), anti-PD1 plus anti-CTLA4 (ipilimumab or mouse equivalent), or concanavalin A (ConA) as a positive control. Cell viability was measured by ATP luminescence assay or flow cytometry. Motility of CD8+ cells was tracked in human LTF using camelid VHH anti-hCD8a-AF594 and 3D multiphoton microscopy for 30 min. Supernatant cytokines were measured using bead immunoassay and T cell markers by flow cytometry. T cells were retained within LTFs, and the proportion of lymphocytes in LTFs was independent of fragment thickness (1.6%/2.1% for 300 µm, 1.4%/2.3% for 200 µm and 1.4%/2.8% for 100 µm thickness, for CD4+ and CD8+ T cells, respectively). Total cell viability and T cell viability exceeded 80% at 48h, and 3D LTF structure remained intact for at least 48 h. We treated LTFs with anti-PD1, anti-PD1 plus anti-CTLA4, or ConA and confirmed the presence of IFN-γ and 10 (mouse) or 16 (human) other cytokines associated with immune activation in both the ConA and anti-PD1 treated samples, but not the control. In human LTFs, cytokine panel upregulation was observed for anti-PD1 vs. control (p=1.1e-5) and anti-PD1 plus anti-CTLA4 vs. anti-PD1 (p=3.7e-9). Using multiphoton microscopy and CD8-binding nanobodies, we observed vigorous CD8+ T cell motility in human LTFs, with a speed of 10 µm/min, which is comparable to that reported in vivo. Our LTF platform has an immuno-competent TME in which we can detect cellular and secreted immune response markers, compare alternative treatments, and track the surveillance activity of infiltrating T cells. Future work will further advance the platform, enabling clinical trials for training and validating deep neural networks to predict response to checkpoint inhibitors and other IO drugs.

Citation Format: Tomasz Zal, Leung Kau Tang, Laura Hrycyniak, Anura Shrestha, Dinesh Joshi, Pichet Adstamongkonkul, Kelsey Tweed, Wesley A. Cox-Muranami, Sean Caenepeel, Hinco J. Gierman, Kevin Eliceiri, Kristina A. Matkowskyj, Sam J. Lubner, John Rafter, Mike Szulczewski, Maneesh Arora, Jonathan Oliner. A live tumor fragment (LTF) platform with real-time imaging for immune response assays [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2779.

Abstract P351: Grayscale Texture Feature Angular Second Moment Correlates With Collagen Alignment in Carotid Artery Plaques

Introduction: Grayscale (GS) texture features that examine homogeneity and echogenicity have been used to identify vulnerable plaques with in vivo ultrasound imaging have been shown to correlate with plaque tissue composition. However, the relationship of collagen fiber organization to GS texture features extracted from in vivo images is a novel idea to provide additional information about plaque structure. We hypothesize that collagen fiber alignment is clinically relevant to identify vulnerable plaques. The objective of this feasibility study was to use multiscale imaging (in vivo ultrasound and high resolution optical microscopy) to determine how GS texture features are related to plaque collagen structure.

Methods: Participants (n=6) scheduled for clinically indicated carotid endarterectomy underwent in vivo carotid ultrasound imaging with texture feature extraction (spatial gray level dependence matrices method for calculating angular second moment [SGLDM-ASM] and grayscale median value [GSM]). Plaque specimens were sent to histopathology and stained with H&E. The collagen fibers in the fibrous cap of the plaque histopathology slides were imaged with liquid crystal based polarization microscopy and quantified using an established software tool (CurveAlign). Correlations between collagen alignment coefficient (range 0-1, 1 represents perfectly aligned fibers) and the texture feature SGLDM-ASM (a measure of homogeneity, higher values are more homogenous) and GSM (a measure of echogenicity higher values are more echogenic) were examined.

Results: Participants were mean (SD) 72.5 (6.1) years of age, had 71.67 (8.16) percent stenosis. The mean SGLDM-ASM was 0.0017 (0.0023), the mean SD GSM was 73.13 (30.98). SGLDM-ASM was significantly correlated to collagen alignment (r=0.83; p=0.028). There was no significant correlation detected between GSM and collagen alignment (r=-0.43;p=0.38).

Conclusion: Results of this study indicate the potential role for using high resolution optical microscopy with ultrasound to characterize collagen fiber alignment in plaques with measures of homogeneity. Future studies are needed to see how multiscale imaging can be used to inform in vivo imaging for identification of vulnerable plaque features.

Introduction to the Biophotonics Congress 2020 feature issue

The guest editors introduce a feature issue containing papers based on research presented at the OSA Biophotonics Congress (the former BIOMED) 20-23 April 2020, in the first all virtual, web conference format undertaken by OSA.

Transglutaminase-2 Mediates the Biomechanical Properties of the Colorectal Cancer Tissue Microenvironment that Contribute to Disease Progression

Colorectal cancer is the third most common cancer worldwide, and the fourth leading cause of malignancy-related mortality. This highlights the need to understand the processes driving this disease in order to develop new treatments and improve patient outcomes. A potential therapeutic target is the increased stiffness of the tumour microenvironment, which is linked to aggressive cancer cell behaviour by enhancing biomechanical signalling. In this study, we used an siRNA-based approach to investigate the contribution of the protein cross-linking enzyme transglutaminase-2 (TG2) to matrix remodelling and biomechanical properties of the tumour microenvironment. TG2 inhibited cancer cell growth in organotypic 3D fibroblast/SW480 co-culture models, and biomechanical analysis demonstrated that colorectal cancer cells induced fibroblast-mediated stiffness which was inhibited by silencing TG2. These biomechanical changes were associated with observed alterations to collagen fibre structure, notably fibre thickness. Our in vitro findings of collagen composition changes were also seen with imaging biopsied tissues from patients with colorectal cancer, with TG2 correlating positively with thicker collagen fibres, and associating with poor outcome as determined by disease recurrence post-surgery and overall survival. In conclusion, this study demonstrates a role for TG2 in the stromal response to invading tumour, leading to tissue stiffening and poor outcome in patients.

Impact of tissue preservation on collagen fiber architecture

Microarchitectural features of collagen-rich extracellular matrices provide the mechanical foundation for tissue function and exhibit topographical cues that influence cellular behavior including proliferation, migration and protein expression. Preservation of tissue microarchitecture is required for accurate evaluation of tissue characteristics and pathology. It is unclear whether common tissue preservation methods possess equal ability to preserve microarchitecture. We investigated collagen microarchitecture in samples that had been flash frozen, fixed in formalin or preserved in RNAlater®, and which contained both collagen-rich and collagen-sparse regions. Fibrillar collagen organization was characterized using picrosirius red staining and second harmonic generation (SHG) microscopy. Maintenance of collagen fiber characteristics compared to the gold standard of flash freezing depended on both the method of preservation and the local collagen content of the tissue. Both formalin fixation and RNAlater® preserved collagen fiber characteristics similar to flash freezing in collagen-rich areas of the tissue, but not in collagen-sparse regions. Analysis using picrosirius red staining indicated preservation-dependent changes in overall tissue architecture and suprafibrillar organization. Together with considerations of cost, ease of use, storage conditions and ability to use the preserved tissue for RNA or protein analysis, our quantitative characterization of the effects of preservation method on collagen microarchitecture may help investigators select the most appropriate preservation approach for their needs.

Syndecan-1 induction in lung microenvironment supports the establishment of breast tumor metastases

Background

Syndecan-1 (Sdc1), a cell surface heparan sulfate proteoglycan normally expressed primarily by epithelia and plasma cells, is aberrantly induced in stromal fibroblasts of breast carcinomas. Stromal fibroblast-derived Sdc1 participates in paracrine growth stimulation of breast carcinoma cells and orchestrates stromal extracellular matrix fiber alignment, thereby creating a migration and invasion-permissive microenvironment. Here, we specifically tested the role of stromal Sdc1 in metastasis.

Methods

The metastatic potential of the aggressive mouse mammary carcinoma cell lines, 4T1 and E0776, was tested in wild-type and genetically Sdc1-deficient host animals. Metastatic lesions were characterized by immunohistochemical analysis.

Results

After orthotopic inoculation, the lung metastatic burden was reduced in Sdc1−/− animals by 97% and more than 99%, in BALB/cJ and C57BL/6 animals, respectively. The difference in metastatic efficiency was maintained when the tumor cells were injected into the tail vein, suggesting that host Sdc1 exerts its effect during later stages of the metastatic cascade. Co-localization studies identified Sdc1 expression in stromal fibroblasts within the metastatic microenvironment and in normal airway epithelial cells but not in other cells (endothelial cells, α-smooth muscle actin positive cells, leucocytes, macrophages). The Ki67 proliferation index and the rate of apoptosis of the metastatic tumor cells were diminished in Sdc1−/− vs. Sdc1+/+ animals, and leucocyte density was indistinguishable. Sdc1-mediated metastatic efficiency was abolished when the animals were housed at a thermoneutral ambient temperature of 31 °C, suggesting that the host Sdc1 effect on metastasis requires mild cold stress.

Conclusions

In summary, Sdc1 is induced in the lung microenvironment after mammary carcinoma cell dissemination and promotes outgrowth of metastases in a temperature-dependent manner.

Electronic supplementary material

The online version of this article (10.1186/s13058-018-0995-x) contains supplementary material, which is available to authorized users.

Abstract 2641: The presence of Cyclooxygenase 2, tumor-associated macrophages, and collagen features as prognostic markers for invasive breast carcinoma patients

Inflammation and the organization of collagen in the breast tumor microenvironment is an important mediator of tumor progression. The objective of this study was to assess whether the tissue localization of COX-2 and tumor-associated macrophages were associated with clinicopathological features of invasive carcinoma, including collagen deposition and patient survival outcome. A tumor microarray (TMA) of 371 biopsy specimens from patients with invasive breast carcinoma was analyzed for expression levels of COX-2, the macrophage marker CD68 and activated macrophage marker CD163 in either the tumor nest (TN) or the tumor-associated stroma (TS). The TMA cohort included females; age 18 to 80, with a median follow up of 8.4 years. Biomarkers were correlated against clinicopathological and collagen features. Additionally, survival curves were calculated according to the Kaplan-Meier method. We found that high expression of COX-2 was associated with tumor size (P = 0.006), grade (P < 0.0001), proliferation (P < 0.0001), ER+ (P = 0.001), collagen deposition (P < 0.0001) and density (P = 0.001). One possible mechanism for this, is COX-2 dependent recruitment of macrophages to the tumor microenvironment. This is supported by our finding of high infiltration of both macrophage markers that were associated with tumor size and proliferation; however, only high levels of stromal CD163 were associated with collagen deposition. In order to better analyze patient survival data, samples were divided into quartiles based on their levels of COX-2 expression and/or macrophage infiltration. COX-2 localization in the TN (P = 0.016, HR = 1.71), perpendicular alignment of collagen to the tumor boundary (TACS-3) (P = 0.049, HR = 1.65) and macrophage recruitment were predictors of poor overall survival (OS). Furthermore, patient survival was worsened if patients had a high CD163 macrophage infiltration (TN: P < 0.0001, HR = 2.86; TS: P = 0.002, HR = 2.54). This notion is further established by the finding of our multivariate analysis that high numbers of CD163+ macrophages in the TS as an independent prognostic factor (P = 0.001, HR = 2.90). These results suggest that in invasive carcinoma the localization of inflammatory markers within the tumor are biomarkers for patient survival outcome. Therefore, we propose that these patients may benefit from a selective COX-2 inhibitor and/or immune modulation therapies.

Citation Format: Karla Esbona, Yanyao Yi, Menggang Yu, Rachel Van Doorn, Matthew Conklin, Douglas Graham, Kari Wisinski, Suzanne Ponik, Kevin Eliceiri, Lee Wilke, Patricia Keely. The presence of Cyclooxygenase 2, tumor-associated macrophages, and collagen features as prognostic markers for invasive breast carcinoma patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2641.

3D second harmonic generation imaging tomography by multi-view excitation

Biological tissues have complex 3D collagen fiber architecture that cannot be fully visualized by conventional second harmonic generation (SHG) microscopy due to electric dipole considerations. We have developed a multi-view SHG imaging platform that successfully visualizes all orientations of collagen fibers. This is achieved by rotating tissues relative to the excitation laser plane of incidence, where the complete fibrillar structure is then visualized following registration and reconstruction. We evaluated high frequency and Gaussian weighted fusion reconstruction algorithms, and found the former approach performs better in terms of the resulting resolution. The new approach is a first step toward SHG tomography.

Abstract TMEM-015: QUANTITATIVE ASSESSMENT OF THE ROLE OF COLLAGEN ALTERATIONS IN OVARIAN CANCER

A profound remodeling of the extracellular matrix (ECM) occurs in human ovarian cancer but it unknown how this affects tumor growth, where this understanding could lead to better diagnostics and therapeutic approaches. To this end, we utilized collagen-specific Second Harmonic Generation (SHG) imaging microscopy and optical scattering measurements to probe structural differences in the extracellular matrix of normal stroma, benign tumors, endometrioid tumors, and low and high-grade serous (LGS and HGS) tumors. The SHG and scattering metrics are sensitive to the organization of collagen on the sub-micron size. We found these sub-resolution determinations are consistent with the dualistic classification of type I and II serous tumors. However, type I endometrioid tumors have strongly differing ECM architecture than the serous malignancies. Moreover, our analyses are further consistent with LGS and benign tumors having similar etiology. Further, the SHG metrics and optical scattering measurements were then used to form a linear discriminant model to classify the tissues, and we obtained high accuracy (~90%) between the tissue types, and this delineation is superior to current clinical performance. To also quantify these alterations we implemented a new form of 3D texture analysis to classify the collagen morphologies in these tissues. We developed a tailored set of 3D filters which extract textural features in each tissue class and we achieved 83-91% accuracies for the six classes. This classification based on ECM structural changes will complement conventional classification based on genetic profiles and can serve as an additional biomarker.

We further investigate the role of these ECM alterations by using multiphoton excited (MPE) polymerization to fabricate biomimetic models to investigate operative cell-matrix interactions in invasion/metastasis. This process is akin to 3D printing except is performed at much higher resolution and with the proteins that comprise the native ECM. We specifically use this technique to create collagen scaffolds with complex, 3D submicron morphology as ovarian stromal models. The scaffold designs are derived directly from “blueprints” based on the SHG images of normal, high risk, benign tumors, and malignant ovarian tissues. The models are seeded with different cancer cell lines and this allows decoupling of the roles of cell characteristics (metastatic potential) and ECM structure and composition (normal vs cancer) on adhesion/migration dynamics. We found the malignant stroma structure promoted enhanced migration persistence and cell proliferation and also cytoskeletal alignment. Moreover, the method allows varying fiber properties such as fiber diameters and characteristic frequency as well as overall alignment. While alignment has been well studied, we found that the migration dynamics are highly dependent upon the morphological properties of the fibers themselves. These models cannot be synthesized by other conventional fabrication methods and we suggest the MPE image-based fabrication method will enable a variety of studies in cancer biology. This work is currently by a new grant from NCI R01 CA206561-01.

Citation Format: Visar Ajeti, Manish Patankar, Kevin Eliceiri, and Paul J. Campagnola. QUANTITATIVE ASSESSMENT OF THE ROLE OF COLLAGEN ALTERATIONS IN OVARIAN CANCER [abstract]. In: Proceedings of the 11th Biennial Ovarian Cancer Research Symposium; Sep 12-13, 2016; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(11 Suppl):Abstract nr TMEM-015.

Non-line-of-sight imaging using a time-gated single photon avalanche diode

By using time-of-flight information encoded in multiply scattered light, it is possible to reconstruct images of objects hidden from the camera's direct line of sight. Here, we present a non-line-of-sight imaging system that uses a single-pixel, single-photon avalanche diode (SPAD) to collect time-of-flight information. Compared to earlier systems, this modification provides significant improvements in terms of power requirements, form factor, cost, and reconstruction time, while maintaining a comparable time resolution. The potential for further size and cost reduction of this technology make this system a good base for developing a practical system that can be used in real world applications.

Abstract 332: Extracellular matrix stiffness regulates metabolic state in metastatic, but not quiescent, breast carcinoma cells

Increased breast density is associated with a 4-6 fold increased risk of developing breast cancer, and is associated with an increase in deposition of extracellular matrix (ECM) proteins, most abundantly collagen I. Collagen, like other ECM proteins, plays a structural role fundamental to tissue organization. High levels of collagen deposition correspond with a stiffer ECM, which is emerging as an important regulator of cell proliferation and tumor progression. Our previously reported microarray implicated changes in mammary epithelial cell metabolism in response to increased matrix stiffness, consistent with the expanding role of the ECM in tumor cell signaling. Here we report that increased matrix stiffness regulates the expression of pyruvate dehydrogenase kinase 1, a key regulator between lactic acid production and pyruvate entry into the mitochondria, in highly metastatic 4T1 breast carcinoma cells. Interestingly, we do not observe this same metabolic regulation in quiescent (dormant) 4T07 tumor cells of the same lineage. These alterations in protein expression correlated to changes in cellular NADH metabolism observed by several independent approaches, including metabolic flux analysis and quantitative imaging fluorescence lifetime microscopy. Thus, we find that alterations in collagen stiffness cause metabolic shifts between oxidative phosphorylation and aerobic glycolysis in highly metastatic cells, but not in quiescent cells. These findings identify stiffness of the ECM as an important regulator of metabolic state, and further identify quiescence as a dominant trait that is not overcome by ECM stiffness.

Citation Format: Brett A. Morris, Brian Burkel, Suzanne Ponik, Kevin Eliceiri, Julio Aguirre-Ghiso, John Condeelis, James Castracane, Patricia J. Keely. Extracellular matrix stiffness regulates metabolic state in metastatic, but not quiescent, breast carcinoma cells. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 332. doi:10.1158/1538-7445.AM2015-332

Abstract B02: Matrix stiffness regulates local metabolism of breast carcinoma cells

Dense breast tissue is one of the single largest risk factors for the development of breast cancer, and one of the primary proteins responsible for increased breast density is the core extracellular matrix (ECM) component, collagen. Similar to other ECM proteins, collagen plays a structural role underlying tissue organization and increased collagen deposition correlates to a stiffer ECM and cellular microenvironment. Interestingly, changes to the stiffness of the ECM or microenvironment have profound and poorly-understood effects on cell migration, cell proliferation, and cancer progression. Consistent with an expanding role of ECM stiffness in cell signaling, we report that increased matrix stiffness also affects cellular metabolism and respiration. Using specific pharmacological inhibitors and quantitative imaging modalities like fluorescence lifetime microscopy, we are able to show that changes in collagen stiffness can cause a metabolic shift towards a more glycolytic, Warburg-like equilibrium in breast carcinoma cells. Matrix stiffness regulates the expression of several metabolic enzymes, including PDHK-1, which is poised to regulate this shift.

Note: This abstract was not presented at the conference.

Citation Format: Brian Burkel, Suzanne Ponik, Brett Morris, Kevin Eliceiri, Patricia Keely. Matrix stiffness regulates local metabolism of breast carcinoma cells. [abstract]. In: Abstracts: AACR Special Conference on Cellular Heterogeneity in the Tumor Microenvironment; 2014 Feb 26-Mar 1; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(1 Suppl):Abstract nr B02. doi:10.1158/1538-7445.CHTME14-B02

Abstract 1116: Response to cyclooxygenase-2 inhibition is regulated by collagen dense stroma

Increased mammographic density correlates with over four-fold increase risk for breast cancer, making it one of the greatest risk factors known for this disease. High breast density is correlated to increased collagen in the breast tissue, and we have found that increased collagen in the Col1a1tm1jae mouse model promotes mammary tumor formation and progression. Increased collagen density in vitro elevates expression of PTGS2 (prostaglandin-endoperoxide synthase 2), the gene for cyclooxygenase-2 (COX-2), by over four fold. Because COX-2 over-expression is observed in 40% of invasive breast carcinoma cases and correlates with poor prognosis, we hypothesized that inhibition of COX-2 may be an effective therapeutic in the context of mammary tumors arising in dense tissue. Celecoxib is a selective non-steroidal anti-inflammatory drug (NSAID) that specifically inhibits COX-2. To understand how COX-2 affects response to collagen matrix density, we made use of our previously characterized mouse model of MMTV-PyVT tumors in a wild type (wt) or Col1a1tm1jae background (HD). Col1a1tm1jae /+ or wild-type (+/+) littermates were randomly assigned at 11 weeks of age to treatment with vehicle or celecoxib at 0.2mg per mouse per day. Oral treatment was given daily for 21 days. We found a link between matrix density and the role of COX-2. Tumors that arose on the dense Col1a1tm1jae background (HD) were larger and more invasive (p < .0001) and expressed higher levels of COX-2 and PGE2. COX-2 (wt = p = 0.0025, HD = p < 0.0001) and PGE2 (wt = p < 0.0196, HD = p = 0.0002) levels were both decreased in animals treated with celecoxib. Notably, cell proliferation as determined by Ki-67 staining decreased only in HD mice, and not in wt littermates, that received treatment with celecoxib (p = 0.0003, p = 0.0007, respectively). Additionally, the cancer associated fibroblast (CAF) population was diminished by celecoxib only in HD mice and not wt littermates (p = 0.0002). Celecoxib treatment altered collagen structure and the expression of the stromal protein, syndecan, only in Col1a1tm1jae/+ animals. Other features were affected by celecoxib in a non-density manner, as the total number of macrophages (wt = p = 0.0052, HD = p < 0.0001) and normal fibroblasts (wt = p = 0.0133, HD = p = 0.0003) were diminished in animals treated with celecoxib in both Col1a1tm1jae /+ and +/+ animals. Ongoing studies are aimed at identifying different macrophage populations, and which stromal cell populations are expressing COX-2 and PGE2. These findings suggest that COX-2 has a direct role in modulating tumor progression in dense matrices, which in turn promote more aggressive tumors. As dense breast tissue is a common occurrence, these findings suggest that COX-2 may be an effective therapeutic target for women with dense breast tissue.

Citation Format: Karla Esbona, David Inman, Sandeep Saha, Kevin Eliceiri, Lee G. Wilke, Patricia J. Keely. Response to cyclooxygenase-2 inhibition is regulated by collagen dense stroma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1116. doi:10.1158/1538-7445.AM2014-1116

SORCS1 is necessary for normal insulin secretory granule biogenesis in metabolically stressed β cells

We previously positionally cloned Sorcs1 as a diabetes quantitative trait locus. Sorcs1 belongs to the Vacuolar protein sorting-10 (Vps10) gene family. In yeast, Vps10 transports enzymes from the trans-Golgi network (TGN) to the vacuole. Whole-body Sorcs1 KO mice, when made obese with the leptin(ob) mutation (ob/ob), developed diabetes. β Cells from these mice had a severe deficiency of secretory granules (SGs) and insulin. Interestingly, a single secretagogue challenge failed to consistently elicit an insulin secretory dysfunction. However, multiple challenges of the Sorcs1 KO ob/ob islets consistently revealed an insulin secretion defect. The luminal domain of SORCS1 (Lum-Sorcs1), when expressed in a β cell line, acted as a dominant-negative, leading to SG and insulin deficiency. Using syncollin-dsRed5TIMER adenovirus, we found that the loss of Sorcs1 function greatly impairs the rapid replenishment of SGs following secretagogue challenge. Chronic exposure of islets from lean Sorcs1 KO mice to high glucose and palmitate depleted insulin content and evoked an insulin secretion defect. Thus, in metabolically stressed mice, Sorcs1 is important for SG replenishment, and under chronic challenge by insulin secretagogues, loss of Sorcs1 leads to diabetes. Overexpression of full-length SORCS1 led to a 2-fold increase in SG content, suggesting that SORCS1 is sufficient to promote SG biogenesis.

Extraction of optical properties and prediction of light distribution in rat brain tissue

Predicting the distribution of light inside any turbid media, such as biological tissue, requires detailed information about the optical properties of the medium, including the absorption and scattering coefficients and the anisotropy factor. Particularly, in biophotonic applications where photons directly interact with the tissue, this information translates to system design optimization, precision in light delivery, and minimization of unintended consequences, such as phototoxicity or photobleaching. In recent years, optogenetics has opened up a new area in deep brain stimulation with light and the method is widely adapted by researchers for the study of the brain circuitries and the dynamics of neurological disorders. A key factor for a successful optogenetic stimulation is delivering an adequate amount of light to the targeted brain objects. The adequate amount of light needed to stimulate each brain object is identified by the tissue optical properties as well as the type of opsin expressed in the tissue, wavelength of the light, and the physical dimensions of the targeted area. Therefore, to implement a precise light delivery system for optogenetics, detailed information about the optical properties of the brain tissue and a mathematical model that incorporates all determining factors is needed to find a good estimation of light distribution in the brain. In general, three measurements are required to obtain the optical properties of any tissue, namely diffuse transmitted light, diffuse reflected light, and transmitted ballistic beam. In this report, these parameters were measured in vitro using intact rat brain slices of 500 μm thickness via a two-integrating spheres optical setup. Then, an inverse adding doubling method was used to extract the optical properties of the tissue from the collected data. These experiments were repeated to cover the whole brain tissue with high spatial resolution for the three different cuts (transverse, sagittal, and coronal) and three different wavelengths (405, 532, and 635 nm) in the visible range of the spectrum. A three-dimensional atlas of the rat brain optical properties was constructed based on the experimental measurements. This database was linked to a Monte Carlo toolbox to simulate light distribution in the tissue for different light source configurations.

Abstract P1-06-02: Inflammatory stromal cell response induced by collagen dense stroma is regulated by cyclooxygenase-2 in a mouse breast cancer model

Breast cancer is the most common invasive cancer in women, causing 40,000 deaths yearly in the United States. Increased mammographic density correlates with over four-fold increase risk for breast cancer, making it one of the greatest risk factors known for this disease. High breast density is mainly attributable to elevated collagen matrix deposition in the breast tissue, and we have found that increased collagen in the Col1a1tm1jae mouse model promotes mammary tumor formation and progression. Increased collagen density in vitro increases expression of PTGS2 (prostaglandin-endoperoxide synthase 2), the gene for cyclooxygenase-2 (COX-2), by over four fold. COX-2 over-expression is observed in 40% of invasive breast carcinoma cases and correlates with poor prognosis. Based on these findings, we hypothesized that inhibition of COX-2 may be an effective therapeutic in the context of mammary tumors arising in dense tissue. Celecoxib is a selective non-steroidal anti-inflammatory drug (NSAID) that specifically inhibits COX-2. To understand how COX-2 affects response to collagen matrix density, we utilized our previously characterized mouse model of MMTV-PyVT tumors in a wild type (wt) or Col1a1tm1jae background (HD, High Density). Col1a1tm1jae heterozygote or wt littermates were randomly assigned at 11 weeks of age to treatment with vehicle or celecoxib at 0.2mg per mouse per day. Oral treatment was given daily for 21 days. We found that MMTV-PyVT tumors responded to celecoxib in a manner that is regulated by matrix density. Tumors that arose on the dense Col1a1tm1jae background (HD) were larger and more invasive (p < .0001) and expressed higher levels of COX-2 and PGE2 than their wt littermates. Both COX-2 (wt: p = 0.0025, HD: p < 0.0001) and PGE2 (wt: p = 0.0196, HD: p = 0.0002) levels were decreased in animals treated with celecoxib. However, Ki-67 and syndecan 1 levels decreased only in HD mice that received treatment with celecoxib (p = 0.0003, p = 0.0007, respectively). In addition, total number of macrophages (wt: p = 0.0052, HD: p < 0.0001) and fibroblasts (wt: p = 0.0133, HD: p = 0.0003) were diminished in animals treated with celecoxib independently of collagen density. On the other hand, cancer associated fibroblast (CAF) population was diminished only in HD mice treated with celecoxib (p = 0.0002) which, along with the synedan-1 result suggests that celecoxib selectively abrogates the inflammatory response from reactive stroma only. Consequently, we find that celecoxib treatment remodels collagen fiber organization, such that it more closely resembles wt assembly. Ongoing studies will identify different macrophage populations, and which stromal cell populations express COX-2 and PGE2. These findings suggest that COX-2 has a direct role in modulating tumor progression in dense matrices which promote invasion. Moreover, these findings suggest that COX-2 may be an effective therapeutic target for women with dense breast tissue.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P1-06-02.

Abstract A35: Aligned collagen is a prognostic signature for survival in human breast carcinoma

Evidence for the potent influence of stromal organization and function on invasion and metastasis of breast tumors is ever growing. Here we have performed a rigorous examination of the relationship of a tumor-associated collagen signature (TACS-3), to the long term survival rate of human patients diagnosed with invasive breast cancer. TACS-3 is characterized by bundles of straightened and aligned collagen fibers that are oriented perpendicular to the tumor boundary. An evaluation of TACS-3 was performed in biopsied tissue sections from 196 patients by second harmonic generation (SHG) imaging of the backscattered signal generated by collagen. Univariate analysis of a Cox proportional hazard model demonstrated that the presence of TACS-3 was associated with poor disease-specific and disease free survival, resulting in hazard ratios between 3.0-3.9. Furthermore, TACS-3 was confirmed to be an independent prognostic indicator regardless of tumor grade and size, ER or PR status, HER-2 status, node status, and tumor subtype. Interestingly, TACS-3 was positively correlated to expression of stromal syndecan-1, a receptor for several extracellular matrix proteins including collagens. Ongoing research is currently investigating both the biochemical signaling pathways that give rise to the TACS-3 phenotype as well as the extent of the influence the mechanical properties of an aligned matrix have on invasion. Because of the strong statistical evidence for poor survival in patients with TACS, and since the assessment can be performed in routine histopathologic samples imaged via SHG or using picrosirius, we propose that quantifying collagen alignment is a viable, novel paradigm for the prediction of human breast cancer survival.

Citation Format: Matthew W. Conklin, Jens Eickhoff, Kristin Riching, Carolyn Pehlke, Kevin Eliceiri, Paolo Provenzano, Andreas Friedl, Patricia J. Keely. Aligned collagen is a prognostic signature for survival in human breast carcinoma. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Invasion and Metastasis; Jan 20-23, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;73(3 Suppl):Abstract nr A35.

Fiji: an open-source platform for biological-image analysis

Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.

Fiji: an open-source platform for biological-image analysis

Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.

Fiji: an open-source platform for biological-image analysis

Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.

Three-dimensional surface profiling and optical characterization of liquid microlens using a Shack-Hartmann wave front sensor

We demonstrate three-dimensional (3D) surface profiling of the water-oil interface in a tunable liquid microlens using a Shack-Hartmann wave front sensor. The principles and the optical setup for achieving 3D surface measurements are presented and a hydrogel-actuated liquid lens was measured at different focal lengths. The 3D surface profiles are then used to study the optical properties of the liquid lens. Our method of 3D surface profiling could foster the improvement of liquid lens design and fabrication, including surface treatment and aberration reduction.