Spectral information system for Australian spectroscopy data

Abstract presented at 2013 Fall Meeting, AGU, San Francisco, California, USA, 9-13 Dec

New markers for human ovarian cancer that link platinum resistance to the cancer stem cell phenotype and define new therapeutic combinations and diagnostic tools

BACKGROUND: Ovarian cancer is the leading cause of gynecologic cancer-related death, due in part to a late diagnosis and a high rate of recurrence. Primary and acquired platinum resistance is related to a low response probability to subsequent lines of treatment and to a poor survival. Therefore, a comprehensive understanding of the mechanisms that drive platinum resistance is urgently needed. METHODS: We used bioinformatics analysis of public databases and RT-qPCR to quantitate the relative gene expression profiles of ovarian tumors. Many of the dysregulated genes were cancer stem cell (CSC) factors, and we analyzed its relation to therapeutic resistance in human primary tumors. We also performed clustering and in vitro analyses of therapy cytotoxicity in tumorspheres. RESULTS: Using bioinformatics analysis, we identified transcriptional targets that are common endpoints of genetic alterations linked to platinum resistance in ovarian tumors. Most of these genes are grouped into 4 main clusters related to the CSC phenotype, including the DNA damage, Notch and C-KIT/MAPK/MEK pathways. The relative expression of these genes, either alone or in combination, is related to prognosis and provide a connection between platinum resistance and the CSC phenotype. However, the expression of the CSC-related markers was heterogeneous in the resistant tumors, most likely because there were different CSC pools. Furthermore, our in vitro results showed that the inhibition of the CSC-related targets lying at the intersection of the DNA damage, Notch and C-KIT/MAPK/MEK pathways sensitize CSC-enriched tumorspheres to platinum therapies, suggesting a new option for the treatment of patients with platinum-resistant ovarian cancer. CONCLUSIONS: The current study presents a new approach to target the physiology of resistant ovarian tumor cells through the identification of core biomarkers. We hypothesize that the identified mutations confer platinum resistance by converging to activate a few pathways and to induce the expression of a few common, measurable and targetable essential genes. These pathways include the DNA damage, Notch and C-KIT/MAPK/MEK pathways. Finally, the combined inhibition of one of these pathways with platinum treatment increases the sensitivity of CSC-enriched tumorspheres to low doses of platinum, suggesting a new treatment for ovarian cancerSpanish Ministry of Education FPU12/01380Spanish Ministry of Economy and Competitivity, Plan Estatal de I + D + I 2013–2016Spanish Ministry of Science, Innovation and Universities (RTI2018–097455-B-I00)CIBER de Cáncer (CD16/12/00275)Spanish Consejería de Salud of the Junta de Andalucia (PI-0397-2017

Supplementary Information: NAD pool as an antitumor target against cancer stem cells in head and neck cancer

Supplementary table 1. Analysis of CD10, CD184, CD19, CD133, CD166 and CD44 positive subpopulations by FACS in HNSCC cell lines.-- Supplementary Table 2. Differential genes common to CD10, CD184, CD19 and NAMPT subpopulations obtained from transcriptomic analysis. All the genes in color are related to tumorigenic process, acting as oncogenes (in red), tumor suppressor genes (in blue), ambiguous genes depending on the type of the tumor (in green).-- Supplementary Table 3: IC50s for NAMPT inhibitors in parental and NAMPT CRISPR clones of both cell lines.-- Supplementary figure 1: Verification of NAMPT overexpression in RPMI and Detroit HNSCC cell lines. A: Western blot showing increased NAMPT ectopic overexpression. B: increased NAD total and NAD+ pools in cells overexpressing NAMPT (in orange).-- Supplementary Figure 2. Overall survival of HNSCC patients from the TCGA database. Kaplan-Meier curves show the overall survival of HNSCC patients with high and low expression levels of CD10, CD184, CD19, CD133, CD166 and NAMPT genes from the TCGA (The Cancer Genome Atlas) database, N=520.-- Supplementary Figure 3. GO term analysis. Analysis of the genes by the terms GO biological process, molecular function and cellular component (p<0.05).-- Supplementary Figure 4. Transcriptomic analysis of differential genes common to CD10, CD184, CD19 and NAMPT subpopulations in HNSCC cell lines. Venn diagram represents the differential genes common to positive and negative CD10, CD184 and CD19 populations and NAMPT overexpression and CRISPRs in RPMI-2650 and Detroit-562 cell lines obtained by NGS sequencing.-- Supplementary Figure 5: Densitometric quantification of NAMPT expression in the WB of figure 2C.-- Supplementary Figure 6: Densitometric quantification of NAMPT and NAPRT expression in the WB of Figure 5C.-- Supplementary materials: Original images of western blots.Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous group of tumors that affect different anatomical locations. Despite this heterogeneity, HNSCC treatment depends on the anatomical location, TNM stage and resectability of the tumor. Classical chemotherapy is based on platinum-derived drugs (cisplatin, carboplatin and oxaliplatin), taxanes (docetaxel, paclitaxel) and 5-fluorouracil1. Despite advances in HNSCC treatment, the rate of tumor recurrence and patient mortality remain high. Therefore, the search for new prognostic identifiers and treatments targeting therapy-resistant tumor cells is vital. Our work demonstrates that there are different subgroups with high phenotypic plasticity within the CSC population in HNSCC. CD10, CD184, and CD166 may identify some of these CSC subpopulations with NAMPT as a common metabolic gene for the resilient cells of these subpopulations. We observed that NAMPT reduction causes a decrease in tumorigenic and stemness properties, migration capacity and CSC phenotype through NAD pool depletion. However, NAMPT-inhibited cells can acquire resistance by activating the NAPRT enzyme of the Preiss-Handler pathway. We observed that coadministration of the NAMPT inhibitor with the NAPRT inhibitor cooperated inhibiting tumor growth. The use of an NAPRT inhibitor as an adjuvant improved NAMPT inhibitor efficacy and reduced the dose and toxicity of these inhibitors. Therefore, it seems that the reduction in the NAD pool could have efficacy in tumor therapy. This was confirmed by in vitro assays supplying the cells with products of inhibited enzymes (NA, NMN or NAD) and restoring their tumorigenic and stemness properties. In conclusion, the coinhibition of NAMPT and NAPRT improved the efficacy of antitumor treatment, indicating that the reduction in the NAD pool is important to prevent tumor growth.This research was funded by Grants RTI2018-097455-B-I00 and PID2021-122629OB-I00 funded by MCIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe”, by the “European Union”. Additional grants from CIBER de Cáncer (CB16/12/00275), from Consejeria de Salud (PI-0397–2017) and Project P18-RT-2501 from 2018 competitive research projects call within the scope of PAIDI 2020—80% co-financed by the European Regional Development Fund (ERDF) from the Regional Ministry of Economic Transformation, Industry, Knowledge and Universities. Junta de Andalucía. Special thanks to the AECC (Spanish Association of Cancer Research) Founding Ref. GC16173720CARR for supporting this work. AES was funded by a grant from the Fundación AECC. EMVS was funded by a postdoctoral fellowship from Junta de Andalucía (CTEICU/PAIDI 2020). LEN, ES-M and LS-D were funded by Spanish ministry of education (FPU16/0290; FPU17/02173; FPU18/01009).Peer reviewe

Validating canopy clumping retrieval methods using hemispherical photography in a simulated Eucalypt forest

The so-called clumping factor (Ω) quantifies deviation from a random 3D distribution of material in a vegetation canopy and therefore characterises the spatial distribution of gaps within a canopy. Ω is essential to convert effective Plant or Leaf Area Index into actual LAI or PAI, which has previously been shown to have a significant impact on biophysical parameter retrieval using optical remote sensing techniques in forests, woodlands, and savannas. Here, a simulation framework was applied to assess the performance of existing in situ clumping retrieval methods in a 3D virtual forest canopy, which has a high degree of architectural realism. The virtual canopy was reconstructed using empirical data from a Box Ironbark Eucalypt forest in Eastern Australia. Hemispherical photography (HP) was assessed due to its ubiquity for indirect LAI and structure retrieval. Angular clumping retrieval method performance was evaluated using a range of structural configurations based on varying stem distribution and LAI. The CLX clumping retrieval method (Leblanc et al., 2005) with a segment size of 15° was the best performing clumping method, matching the reference values to within 0.05 Ω on average near zenith. Clumping error increased linearly with zenith angle to > 0.3 Ω (equivalent to a 30% PAI error) at 75° for all structural configurations. At larger zenith angles, PAI errors were found to be around 25–30% on average when derived from the 55–60° zenith angle. Therefore, careful consideration of zenith angle range utilised from HP is recommended. We suggest that plot or site clumping factors should be accompanied by the zenith angle used to derive them from gap size and gap size distribution methods. Furthermore, larger errors and biases were found for HPs captured within 1 m of unrepresentative large tree stems, so these situations should be avoided in practice if possible

Vegetation spectroscopy

Field spectroscopy involves the study of the interrelationships between the spectral characteristics of objects and their biophysical attributes in the field environment (Bauer et al., 1986; Milton, 1987). When applied to vegetated surfaces, the spectral characteristics are function of the status, composition and structure of the elements measured. There are more elements that add undesired effects to the overall signal as the soil background or the viewing and illumination geometry. Like every other measurement in the field, it is very important to be familiar with the instrument used and conscious of good practices that ensure the acquisition of reliable measurements. Moreover, for the comprehensive use of the data in future studies, it is very important to document the measurement protocol and a proper collection of measurement auxiliary data. This chapter compiles some basic theory about photon-vegetation interaction and some guidelines for field spectroscopy measurement

Spectral information system development for Australia

Scientific efforts to observe the state of natural systems over time, allowing the prediction of future states, have led to a burgeoning interest for organised storage of spectral field data and associated metadata, seen as being key to the successful and efficient modeling of such systems. A centralised system for such data established for the Australian remote sensing community aims to standardise storage parameters and metadata thus fostering best practice protocols and collaborative research. Supported by funding from the Australian National Data Service (ANDS), whose aim is to promote connections between data, projects, researchers and institutions, a spectral database system based on the already operational SPECCHIO system is being augmented to specifically meet the needs of the Australian remote sensing community, and is aligned with the TERN Auscover facility. In this paper we outline the envisaged dataflow and usage of the database as a case study within the context of TERN Auscover. The development of a national spectral database will not only ensure the long-term storage of data but support scientists in data analysis activities, essentially leading to improved repeatability of results, superior reprocessing capabilities, and promotion of best practice

THEMS: an automated thermal and hyperspectral proximal sensing system for canopy reflectance, radiance and temperature

Background Earth Observation 'EO' remote sensing technology development enables original insights into vegetation function and health at ever finer temporal, spectral and spatial resolution. Research sites equipped with monitoring infrastructure such as flux towers operate at a key bridging scale between satellite platform measurements and on-the-ground leaf-level processes. Results This paper presents the technical details of the design and operation of a proximal observation system 'THEMS' that generates unattended long-term high quality thermal and hyperspectral images of a forest canopy on a short (sub-daily) timescale. The primary purpose of the system is to measure canopy temperature, spectral reflectance and radiance coincident with a highly instrumented flux tower site for benchmarking purposes. Basic system capability is demonstrated through low level data product descriptions of the high-resolution multi-angular imagery and ancillary data streams. The system has been successfully operational for more than 2 years with little to no intervention. Conclusions These data can then be used to derive remotely sensed proxies of canopy and ecosystem function to study temporal forest dynamics over a wide range of wavelengths, spatial scales (individual trees to canopy), and temporal scales (minutes to multiple years). The multi-purpose system is intended to provide unprecedented spatio-temporal ecophysiological insight and to underpin upscaling of remotely sensed dynamic ecosystem water, CO2, and energy exchange processes

WOODY VEGETATION LANDSCAPE FEATURE GENERATION FROM MULTISPECTRAL AND LIDAR DATA (A CRCSI 2.07 WOODY ATTRIBUTION PAPER)

ABSTRACT There is a need for accurate estimation of Australian woody vegetation parameters. State and Commonwealth land management agencies are mandated to report about forest condition every five years. The CRCSI 2.07 &quot;Australian woody vegetation landscape feature generation from multisource airborne and space-borne imaging and ranging data&quot; aims at producing ready-to-use methods to report forest condition based on remote sensing data. The first efforts have focus on field data techniques and canopy structure characterization using LiDAR data. Results demonstrate canopy profile can be accurately estimated using Weibull probability density functions at 30x30m pixel size. Moreover different field techniques to measure vegetation fractional cover has been tested and compare finding differences up to 15%. Index Terms-Australian woody vegetation, forest extent, fractional cover, canopy vertical profile

Using discrete-return airborne laser scanning to quantify number of canopy strata across diverse forest types

The vertical arrangement of forest canopies is a key descriptor of canopy structure, a driver of ecosystem function and indicative of forest successional stage. Yet techniques to attribute for canopy vertical structure across large and potentially heterogeneously forested areas remain elusive. This study introduces a new technique to estimate the Number of Strata (NoS) that comprise a canopy profile, using discrete-return Airborne Laser Scanning (ALS) data. Vertically resolved gap probability (P-gap) aggregated over a plot is generalized with a nonparametric cubic spline regression (P-s). Subsequently a count of the positive zero-crossings of second derivative of 1 - P-s is used to estimate NoS. Comparison with inventory derived estimates at 24 plots across three diverse study areas shows a good agreement between the two techniques (RMSE=041 strata). Furthermore, this is achieved without altering model parameters, indicating the transferability of the technique across diverse forest types. NoS values ranged from 0 to 4 at a further 239 plots, emphasizing the need for a method to quantify canopy vertical structure across forested landscapes. Comparison of NoS with other commonly derived ALS descriptors of canopy structure (canopy height, canopy cover and return height coefficient of determination) returned only a moderate correlation (r(2

The impact of sensor characteristics for obtaining accurate ground-based measurements of LAI

Calibration and validation of LAI products require accurate ground-based measurements. Many indirect ground-based sensors such as digital hemispherical photography (DHP), ceptometers, and terrestrial laser scanners (TLS) are used interchangeably to estimate reference values. However these sensors have biases in regards to the true LAI value, which can never be known in the field. Results from three representative woody ecosystems in Eastern Australia are presented from real field measurements. Significant differences were found between methods at the individual measurement and plot scale. Furthermore, one of the sites in South East Australia was measured and modeled in a 3D deterministic model. In this digital environment where the truth is known, sensors can be simulated to determine their bias