Characterization of cell-free breast cancer patient-derived scaffolds using liquid chromatography-mass spectrometry/mass spectrometry data and RNA sequencing data

Landberg, Göran; Jonasson, Emma; Gustafsson, Anna; Fitzpatrick, Paul; Isakson, Pauline; Karlsson, Jan Ch; Larsson, Erik; Svanström, Andreas; Rafnsdóttir, Svanheiður; Persson, Emma; Andersson, Daniel; Rosendahl, Jennifer; Petronis, Šarūnas; Ranji, Parmida; Gregersson, Pernilla; Magnusson, Yvonne; Håkansson, Joakim; Ståhlberg, Anders

doi:10.1016/j.dib.2020.105860

Cited by 8 publications

(7 citation statements)

References 9 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In this context, our recently developed PDS model offers the advantage of transferring the clinical variability of the tumor microenvironment into a simple in vitro cell culture model. Published data also supports that the cellfree scaffold obtained in the PDS model system includes an imprint of important events in cancer progression including cues from different cell types and does not consist of only regular ECM proteins [13]. The possibility to decode this imprinted information via an adapter cell line that sense and adjust to the patient specific environment and then treat the "out-of-patient" model system with cancer drugs, will create a valuable surrogate system for modelling drug resistance and treatment prediction.…”

Section: Discussionsupporting

confidence: 57%

“…We have recently developed an experimental patientderived scaffold (PDS) model system and described how this 3D culture approach based on in vivo tumor material can recapitulate important patient specific clinical characteristics as relapse and cancer specific survival [11,12]. The PDS model system consists of decellularized tumor samples including an imprint of important cancer progressing properties and events [13] that can be decoded by monitoring gene expression changes in an adapting standard cancer cell line [11,12]. We have also demonstrated the advantage of the PDS model approach compared to 2D culture as a drug testing platform to monitor cellular responses to breast cancer chemotherapies and endocrine treatments in relation to the breast tumor microenvironment [14,15].…”

mentioning

confidence: 99%

See 1 more Smart Citation

5-fluorouracil treatment of patient-derived scaffolds from colorectal cancer reveal clinically critical information

et al. 2022

Self Cite

View full text Add to dashboard Cite

Background Colorectal cancer is a commonly diagnosed cancer worldwide. Unfortunately, many patients do not respond to standard chemotherapy treatments and develop disease relapse and metastases. Besides cancer cell specific genetic changes, heterogeneity in the tumor microenvironment contribute to the clinical presentation of the disease and can potentially also influence drug resistance. By using a recently developed patient-derived scaffold method monitoring how a standardized reporter cancer cell line adapts to various microenvironments treated with chemotherapy, we wanted to clarify how individual patient specific microenvironments influence the chemotherapy response in colorectal cancer. Methods Surgically resected colorectal cancer specimens from 89 patients were decellularized to produce patient-derived scaffold, which were seeded with HT29 cells, cultured for 3 weeks, and treated with 5-fluorouracil. Gene expression changes of adapted and treated HT29 cells were monitored by qPCR and compared with clinical parameters including disease-free survival. Results The effects of 5-fluorouracil treatment varied between different patient-derived scaffold, but generally induced a reduced expression of proliferation genes and increased expression of pluripotency and epithelial-to-mesenchymal transition genes. Interestingly, patient-derived scaffold cultures obtained from patients with disease recurrences showed a significantly less pronounced anti-proliferative effect of 5-fluorouracil and more pronounced increase of pluripotency, with MKI67 and POU5F1 being among the most significant genes linked to disease relapse in colorectal cancer. Conclusions Colorectal patient-derived scaffold can decode clinically relevant tumor microenvironmental influence of 5-fluorouracil treatment effects opening up for optimized precision medicine in colorectal cancer treatment.

show abstract

Section: Discussionsupporting

confidence: 57%

mentioning

confidence: 99%

5-fluorouracil treatment of patient-derived scaffolds from colorectal cancer reveal clinically critical information

et al. 2022

Self Cite

View full text Add to dashboard Cite

show abstract

“…In fact, several proteomic studies have been conducted using these dECMs, which have profoundly clarified the composition and pathological alterations of the ECM in tumor and metastatic niches (Table 3). These investigations on healthy tissue and BC tumor tissue ECMs have been used to identify the role in tumor ECM generation by stromal and/or tumor cells [75][76][77][78] , describe the differences between different healthy and tumor ECMs 75,[78][79][80] , to elucidate new functions of tumor ECM 77,81 , to find protein-level differences between low and highly metastatic carcinomas 75 , and to identify new potential prognostic and diagnostic biomarkers 75,79,81,82 . The diversity and heterogeneity found in the composition of healthy, tumor, or premetastatic ECM emphasize the importance of recapitulating the whole set of BC ECM components to study tumor behavior, rather than individual ECM proteins.…”

Section: Decellularized Extracellular Matrix (Decm) As a New Approach To Clarify The Role Of The Bc Ecm Microenvironmentmentioning

confidence: 99%

The biomimetic extracellular matrix: a therapeutic tool for breast cancer research

Tamayo-Angorrilla

Andrés

Jiménez

et al. 2022

Translational Research

View full text Add to dashboard Cite

This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

show abstract

“…Although its application is fundamentally related to microbiological identification (39) applications combined with other bioinformatic analysis platforms have recently emerged (40,41) . In line with the above, the use of artificial intelligence has disruptively entered the field of health, thus becoming a new tool to be considered for the diagnosis of different pathologies (42–44) . The first attempts to discriminate Streptococcus from the viridans group, using mass spectrometry, were encouraging according to the published results which were based on a small number of isolates or creating a specific database for this group of microorganisms ( 45,46) .…”

Section: Discussionmentioning

confidence: 93%

À la carte,Streptococcus pneumoniaecapsular typing: using MALDI-TOF mass spectrometry and machine learning algorithms as complementary tools for the determination of PCV13 serotypes and the most prevalent NON PCV13 serotypes according to Argentina’s epidemiology

Zintgraff

Rocca

Eluchans

et al. 2022

Preprint

View full text Add to dashboard Cite

Laboratory surveillance of Streptococcus pneumoniae serotypes is crucial for the successful implementation of vaccines to prevent invasive pneumococcal diseases. The reference method of serotyping is the Quellung reaction, which is labor-intensive and expensive. In the last few years, the introduction of MALDI-TOF MS into the microbiology laboratory has been revolutionary. In brief, this new technology compares protein profiles by generating spectra based on the mass to charge ratio (m/z). We evaluated the performance of MALDI-TOF MS for typing serotypes of S. pneumoniae isolates included in the PCV13 vaccine using a machine learning approach. We challenged our classification algorithms in real time with a total of new 100 isolates of S. pneumoniae from Argentinian nationwide surveillance. Our best approach could correctly identify the isolates with a sensitivity of 58.33 % ([95%IC 40.7-71.7]); specificity of 81.48 % ([95%IC 53.6-79.7]); accuracy of 63.0% ([95%IC 61.9-93.7]); PPV of 80.77% ([95%IC 64.5-90.6]) and NPV of 59.46% ([95%IC 48.9-69.2]). In this work, it was possible to demonstrate that the combination of MALDI-TOF mass spectrometry and multivariate analysis allows the development of new strategies for the identification and characterization of Spn isolates of clinical importance; and we consider that by using AI, as more data becomes available the models will get better and more precise.

show abstract

Characterization of cell-free breast cancer patient-derived scaffolds using liquid chromatography-mass spectrometry/mass spectrometry data and RNA sequencing data

Cited by 8 publications

References 9 publications

5-fluorouracil treatment of patient-derived scaffolds from colorectal cancer reveal clinically critical information

5-fluorouracil treatment of patient-derived scaffolds from colorectal cancer reveal clinically critical information

The biomimetic extracellular matrix: a therapeutic tool for breast cancer research

À la carte,Streptococcus pneumoniaecapsular typing: using MALDI-TOF mass spectrometry and machine learning algorithms as complementary tools for the determination of PCV13 serotypes and the most prevalent NON PCV13 serotypes according to Argentina’s epidemiology

Contact Info

Product

Resources

About