Summary of Study ST002248

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001436. The data can be accessed directly via it's Project DOI: 10.21228/M83Q6B This work is supported by NIH grant, U2C- DK119886.

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This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST002248
Study TitleQuantitative multi-Omics analysis of paclitaxel-loaded Poly(lactide-co-glycolide) nanoparticles for identification of potential biomarkers for head and neck cancer
Study SummaryThe narrow therapeutic index and significant potential for toxicity of chemotherapeutic drugs are two of the factors that restrict their use. Because of the usage of nanoparticles (NPs) as carriers for chemotherapeutic agents, the therapeutic efficacy of these treatments has been significantly boosted. This was accomplished by increasing the bioavailability of the pharmaceuticals and changing the bio-distribution profile of the drugs. Untargeted metabolomics has recently risen to the forefront as a potentially useful method for better comprehending the growth of tumours and the treatment outcomes of many kinds of cancer cells. In the current study, we used LCMS/MS-based untargeted metabolomics to identify differences in the metabolic profile of head and neck squamous cell carcinomas FaDu that were treated with the anticancer drug paclitaxel (PTX) delivered as free drug versus paclitaxel-loaded poly(lactide-co-glycolide) nanoparticles (PXT-PLGA-NPs). The experimental design consisted of four groups: those treated with DMSO (serving as a control), those treated with drug-free PXT, those treated with PXT-PLGA-NPs, and those treated with PLGA-NPs that lacked PTX. MetaboScape (V4, Bruker Daltonics) was used as the platform for the data analysis, and the results were compared to the Bruker Human Metabolome Data Base (HMDB) spectrum library 2.0. We found a total of 162 metabolites with a high level of confidence ascribed to them. The principal component analysis of the metabolites showed that PTX-free drugs grouped along with PXT-PLGA-NPs, but the control and PLGA-NPs without PXT clustered apart from drug-treated cells but together with each other. In further group pairwise comparisons, it was shown that 37 metabolites were substantially dysregulated (p 0.05) between the PTX-free medication and the PXT-PLGA-NPs. Out of these, it is important to call attention to the metabolites that became more abundant as a result of treatment with PXT-PLGA-NPs. These include 5-Thymidyclic acid with a 7.8-fold change (FC) and 3,4,5-Trimethoxycinnamic acid, both of which have been linked in the past to effective anticancer drug treatment (Quinn et al. 2015; Anantharaju et al. 2017). The findings suggest a more successful anti-drug therapy that makes use of NP, and also indicate a number of metabolites that have the potential to serve as indicators for determining how well an antidrug treatment is working. Our previous findings are consistent with these findings.
Institute
University of Sharjah
DepartmentSharjah institute of medical research
LaboratoryDrug Delivery
Last NameJagal
First NameJayalakshmi
AddressSharjah
Emailjjagal@sharjh.ac.ae
Phone0552863009
Submit Date2022-07-14
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2023-07-14
Release Version1
Jayalakshmi Jagal Jayalakshmi Jagal
https://dx.doi.org/10.21228/M83Q6B
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001436
Project DOI:doi: 10.21228/M83Q6B
Project Title:Quantitative multi-Omics analysis of paclitaxel-loaded Poly(lactide-co-glycolide) nanoparticles for identification of potential biomarkers for head and neck cancer
Project Type:LC-MS/MS
Project Summary:Chemotherapeutic agents are limited by their narrow therapeutic index and high risk for toxicity. The use of nanoparticles (NPs) as carriers for chemotherapeutic agents has considerably increased the therapeutic effect of those drugs by improving their bioavailability and altering their bio-distribution profile. Untargeted metabolomics has emerged as potential approach to understand better tumor progression and treatment outcome of multiple cancer cell types. Herein, we have employed LCMS/MS based untargeted metabolomics to pinpoint differences in metabolic profile of head and neck squamous cell carcinomas FaDu, when treated with anticancer Paclitaxel (PTX) delivered as free drugversus Paclitaxel-loaded poly(lactide-co-glycolide) nanoparticle (PXT-PLGA-NPs). The experimental design include four groups treated with DMSO (control), treated with drug free PXT, PXT-PLGA-NPs and PLGA-NPs without PXT. Data was analyzed using MetaboScape (V4, Bruker Daltonics) platform and matched to Bruker Human Metabolome Data Base (HMDB) spectral library 2.0. We identified and total of 162 high confident assigned metabolites. Principle component analysis of the metabolites revealed that PTX free drug clustered together with PXT-PLGA-NPs, whereas control and PLGA-NPs without PXT clustered away from drug treated cells but apart from each other (see figure below). Further group pairwise comparisons indicated 37 metabolites significantly (p<0.05) dysregulated between PTX free drug and PXT-PLGA-NPs. Of these, it is worthy highlight metabolites that became more abundant with PXT-PLGA-NPs treatment, such as 5-Thymidyclic acid 7. 8 fold change (FC) and 3,4,5-Trimethoxycinnamic acid that have been associated previously associated with effective anticancer drug treatment (Quinn et al. 2015; Anantharaju et al. 2017). The results are in line with our pervious findings supporting a more effective antidrug treatment using NP and we indicate a number of metabolites that are potential markers for monitoring the efficacy antidrug treatment.
Institute:University of Sharjah
Department:Sharjah Institute for Medical Research
Laboratory:Drug Delivery
Last Name:Jagal
First Name:Jayalakshmi
Address:SIMR, Medical Campus, University of Sharjah, 27272, Sharjah
Email:jjagal@sharjah.ac.ae
Phone:+971552863009

Subject:

Subject ID:SU002334
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Mammals

Factors:

Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Treatment
SA216190Control 02_2_8_1_938Control
SA216191Control 01_2_7_1_936Control
SA216192Control 03_1_9_1_939Control
SA216193Control 04_1_10_1_941Control
SA216194Control 04_2_10_1_942Control
SA216195Control 01_1_7_1_935Control
SA216196Control 03_2_9_1_940Control
SA216197Control 02_1_8_1_937Control
SA216198DF nP 02_2_16_1_954Drug Free PLGA Nanoparticle
SA216199DF nP 03_1_17_1_955Drug Free PLGA Nanoparticle
SA216200DF nP 02_1_16_1_953Drug Free PLGA Nanoparticle
SA216201DF nP 01_2_15_1_952Drug Free PLGA Nanoparticle
SA216202DF nP 01_1_15_1_951Drug Free PLGA Nanoparticle
SA216203DF nP 03_2_17_1_956Drug Free PLGA Nanoparticle
SA216204DF nP 04_1_18_1_957Drug Free PLGA Nanoparticle
SA216205DF nP 04_2_18_1_958Drug Free PLGA Nanoparticle
SA216206Free Drug 02_2_12_1_946Free PTX
SA216207Free Drug 01_2_11_1_944Free PTX
SA216208Free Drug 01_1_11_1_943Free PTX
SA216209Free Drug 03_1_13_1_947Free PTX
SA216210Free Drug 03_2_13_1_948Free PTX
SA216211Free Drug 02_1_12_1_945Free PTX
SA216212Free Drug 04_2_14_1_950Free PTX
SA216213Free Drug 04_1_14_1_949Free PTX
SA216214nP 04_1_22_1_965PTX-PLGA Nanoparticle
SA216215nP 03_2_21_1_964PTX-PLGA Nanoparticle
SA216216nP 03_1_21_1_963PTX-PLGA Nanoparticle
SA216217nP 04_2_22_1_966PTX-PLGA Nanoparticle
SA216218nP 01_2_19_1_960PTX-PLGA Nanoparticle
SA216219nP 01_1_19_1_959PTX-PLGA Nanoparticle
SA216220nP 02_2_20_1_962PTX-PLGA Nanoparticle
SA216221nP 02_1_20_1_961PTX-PLGA Nanoparticle
Showing results 1 to 32 of 32

Collection:

Collection ID:CO002327
Collection Summary:The process of extracting metabolites from FaDu cells was carried out in a manner that was similar to that which was utilized for the extraction of proteins. Following the addition of PTX (40 μM), PTX-PLGA NPs (40 μM), and drug-free PLGA NPs to the culture medium, the media was changed to PBS, and the cells were scraped off the plates using cell scrapers. After that, the detached cell pellets were collected by centrifuging them at a speed of 15000 rpm for ten minutes at a temperature of 4 degrees Celsius using a Universal 320R Benchtop Centrifuge (Hettich, Beverly, Massachusetts, United States). The collected cell pellets were first treated with 0.1 % FA in methanol, which was followed by sonication using a probe ultrasonicator Q500 (Terra Universal, Inc., Fullerton, California, USA) for 30 seconds at 30 %amplitude 16. This was done in order to release a wide variety of metabolites. After that, the samples were centrifuged at 15,000 rpm for 10 minutes at 4 degrees Celsius, and the upper phase was transferred into LC vials so that it could be dried further using a Genevac evaporator (SP Industries, Warminster, PA, USA). After the reaction was halted with formic acid (FA) at a concentration of one percent, it was dried using a Genevac evaporator. In preparation for subsequent LC-MS/MS examination, the dried samples were kept at a temperature of 80 degrees Celsius. The version 4.0 of MetaboScape was used for both the processing and the statistical analysis (Bruker Daltonics). Analyte bucketing and identification were accomplished by using the software that was made available to us called T-ReX 2D/3D workflow. The settings that were used were as follows: an intensity threshold of larger than 1000 counts and a peak duration of equal to 7 spectra or higher. Quantification of features was carried out by calculating peak area and for statistical analysis, only characteristics that were present in at least three out of twelve samples for each cell type were taken into account. On import, the spectra of the analyte were averaged, and additional consideration was given to just those features that eluted between 0.3 and 25 minutes and had mz values between 50 and 1000. Using a two-tailed independent Student’s t-test, a comparison was made between each drug treatment condition and DMSO-only treated controls. It was shown that there were significantly differently abundant metabolites between the two groups. As a result of this, volcano plots were developed in order to visualize and display the significance (p-value) of dysregulation of cellular metabolites, along with the fold changes associated with each condition. Metabo analyst, which can be found at https://www.metaboanalyst.ca, was used in order to carry out functional enrichment studies. Analyte metabolite identification was carried out by making use of both MS2 spectra and retention time (RT), although the MS/MS spectra were required as a bare minimum for a valid identification to be made. We conducted annotation using Bruker's version of the Human Metabolome Database (HMDB-4.0) for the set of compounds that satisfied this requirement, either by using MS/MS alone or by utilizing MS/MS plus RT. All of the chosen compounds were then compared to this library to find a match. These putatively matching features were filtered by considering for those each feature with the highest annotation quality score (AQ score) among other putative matches for the same metabolite, i.e., those features exhibiting the best fit across the greatest number of factors such as retention time, MS/MS, m/z values, analyte list, and spectral library matching were ranked first for the associated identifier.
Sample Type:Head and neck Cancer cell line

Treatment:

Treatment ID:TR002346
Treatment Summary:The extraction of metabolites from FaDu cells was carried out following a similar procedure used in protein extraction. After treatment with PTX (40μM), PTX-PLGA NPs (40 μM), drug-free PLGA NPs and culture media, PBS replaced media and the cells were collected from the dishes using cell scrapers. The detached cell pellets were then collected by centrifugation at 15000 rpm for 10 min at 4oC using Universal 320R Benchtop Centrifuge (Hettich, Beverly, MA, USA) to remove excess PBS. To release a broad range of metabolites, the collected cell pellets were first treated with 0.1% FA in methanol followed by sonication using probe ultrasonicator Q500 (Terra Universal, Inc, Fullerton, CA, USA)for 30 sec at 30% amplitude 16. The samples were then centrifuged at 15,000 rpm for 10 minutes at 4oC, and the upper phase was transferred into LC vials for further drying using a Genevac evaporator (SP Industries, Warminster, PA, USA). The reaction was stopped with 1% formic acid (FA) followed by drying using a Genevac evaporator. Dried samples were stored at −80 °C for further LC-MS/MS analysis.

Sample Preparation:

Sampleprep ID:SP002340
Sampleprep Summary:After treatment with PTX (40μM), PTX-PLGA NPs (40 μM), drug-free PLGA NPs and culture media , PBS replaced media and the cells were collected from the dishes using cell scrapers. The detached cell pellets were then collected by centrifugation at 15000 rpm for 10 min at 4oC using Universal 320R Benchtop Centrifuge (Hettich, Beverly, MA, USA) to remove excess PBS. To release a broad range of metabolites, the collected cell pellets were first treated with 0.1% FA in methanol followed by sonication using probe ultrasonicator Q500 (Terra Universal, Inc, Fullerton, CA, USA)for 30 sec at 30% amplitude 16. The samples were then centrifuged at 15,000 rpm for 10 minutes at 4oC, and the upper phase was transferred into LC vials for further drying using a Genevac evaporator (SP Industries, Warminster, PA, USA). The reaction was stopped with 1% formic acid (FA) followed by drying using a Genevac evaporator. Dried samples were stored at −80 °C for further LC-MS/MS analysis.

Combined analysis:

Analysis ID AN003674
Analysis type MS
Chromatography type Reversed phase
Chromatography system Bruker Elute
Column Hamilton Intensity Solo 2 C18
MS Type ESI
MS instrument type QTOF
MS instrument name Bruker timsTOF
Ion Mode POSITIVE
Units AU

Chromatography:

Chromatography ID:CH002724
Instrument Name:Bruker Elute
Column Name:Hamilton Intensity Solo 2 C18
Column Temperature:35
Flow Gradient:1%B to 99%B in 15 min
Flow Rate:250 uL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS003425
Analysis ID:AN003674
Instrument Name:Bruker timsTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Processing and statistical analysis were performed using MetaboScape® 4.0 (Bruker Daltonics). Analyte bucketing and identification were done using the software provided available T-ReX 2D/3D workflow with the following parameters: intensity threshold greater than 1000 counts and peak length equal to 7 spectra or greater. Feature quantitation was, performed using peak area and , for features present in at least 3 (of 12) samples (per cell type) were considered for statistical analysis. Analyte MS2 spectra were averaged on import and only features eluting between 0.3 and 25 min with mz between 50 and 1000 were considered further.
Ion Mode:POSITIVE
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