Potential use of absorbance scanning in differentiating tumor microenvironment compositions from endoscopic biopsy of colorectal cancer patients.

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Abstract

Background: The microtumor environment is an area where tumor cells are surrounded by several cells such as immune cells, stromal cells and endothelial cells as well as blood and lymphatic vessels. It is known that various cytokines and growth factors are released by various cells surrounding the tumor and affect the growth of tumor cells. Differences in chemical composition in the microtumor environment can be detected using spectrometry. The aim of this study was to examine the potential of scanning absorbance spectrometry in differentiating cells based on the chemical composition of endoscopic biopsies of colorectal cancer patients. Methods: : An endoscopic biopsy of the patient from Cipto Mangunkusumo Hospital, Jakarta was collected and homogenized in phosphate buffer saline using TissueLyser. Scanning absorbance was performed using a UV-VIS spectrophotometer. The results of scanning absorbance were then processed using principal component analysis (PCA) in Orange Data-Mining version 3.28.0 software and the results were represented in a scatter plot diagram. Results: : Based on the results of the analysis using PCA, three patients were identified in different quadrant regions, crc006 and crc011 obtained from patients with the differentiation status located close together while crc009 and undifferentiated were located far apart. Conclusion: This indicates the potential of scanning absorbance in differentiating the chemical composition of the tumor microenvironment from patient biopsies.
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Noor" } ], "publisher": { "@type": "Organization", "name": "F1000Research", "logo": { "@type": "ImageObject", "url": "https://f1000research.com/img/AMP/F1000Research_image.png", "height": 480, "width": 60 } }, "image": { "@type": "ImageObject", "url": "https://f1000research.com/img/AMP/F1000Research_image.png", "height": 1200, "width": 150 }, "description": "Background: The microtumor environment is an area where tumor cells are surrounded by several cells such as immune cells, stromal cells and endothelial cells as well as blood and lymphatic vessels. It is known that various cytokines and growth factors are released by various cells surrounding the tumor and affect the growth of tumor cells. Differences in chemical composition in the microtumor environment can be detected using spectrometry. The aim of this study was to examine the potential of scanning absorbance spectrometry in differentiating cells based on the chemical composition of endoscopic biopsies of colorectal cancer patients. Methods: An endoscopic biopsy of the patient from Cipto Mangunkusumo Hospital, Jakarta was collected and homogenized in phosphate buffer saline using TissueLyser. Scanning absorbance was performed using a UV-VIS spectrophotometer. The results of scanning absorbance were then processed using principal component analysis (PCA) in Orange Data-Mining version 3.28.0 software and the results were represented in a scatter plot diagram. Results: Based on the results of the analysis using PCA, three patients were identified in different quadrant regions, crc006 and crc011 obtained from patients with the differentiation status located close together while crc009 and undifferentiated were located far apart. Conclusion: This indicates the potential of scanning absorbance in differentiating the chemical composition of the tumor microenvironment from patient biopsies." } { "@context": "http://schema.org", "@type": "BreadcrumbList", "itemListElement": [ { "@type": "ListItem", "position": "1", "item": { "@id": "https://f1000research.com/", "name": "Home" } }, { "@type": "ListItem", "position": "2", "item": { "@id": "https://f1000research.com/browse/articles", "name": "Browse" } }, { "@type": "ListItem", "position": "3", "item": { "@id": "https://f1000research.com/articles/10-1300/v1", "name": "Potential use of absorbance scanning in differentiating tumor microenvironment..." } } ] } Home Browse Potential use of absorbance scanning in differentiating tumor microenvironment... ALL Metrics - Views Downloads Get PDF Get XML Cite How to cite this article Abdullah M, Pitarini Utari A, Aziza Nursyirwan S and Noor DR. Potential use of absorbance scanning in differentiating tumor microenvironment compositions from endoscopic biopsy of colorectal cancer patients. [version 1; peer review: 1 not approved] . F1000Research 2021, 10 :1300 ( https://doi.org/10.12688/f1000research.74480.1 ) NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article. Close Copy Citation Details Export Export Citation Sciwheel EndNote Ref. Manager Bibtex ProCite Sente EXPORT Select a format first Track Share ▬ ✚ Brief Report Potential use of absorbance scanning in differentiating tumor microenvironment compositions from endoscopic biopsy of colorectal cancer patients. [version 1; peer review: 1 not approved] Murdani Abdullah https://orcid.org/0000-0002-8801-0283 1,2 , Amanda Pitarini Utari 1 , Saskia Aziza Nursyirwan https://orcid.org/0000-0003-0166-7651 1 , Dimas R. Noor 2 Murdani Abdullah https://orcid.org/0000-0002-8801-0283 1,2 , Amanda Pitarini Utari 1 , Saskia Aziza Nursyirwan https://orcid.org/0000-0003-0166-7651 1 , Dimas R. Noor 2 PUBLISHED 21 Dec 2021 Author details Author details 1 Department of Internal Medicine, Faculty of Medicine, Faculty of Medicine Universitas Indonesia, GH Building, Jalan Diponegoro No. 71, Kenari, Senen, Jakarta, 10430, Indonesia 2 Human Cancer Research Center, Indonesia Medical Education and Research Institute, Faculty of Medicine Universitas Indonesia,, Jalan Salemba Raya No.6, RW.5, Kenari, Senen, Jakarta, 10430, Indonesia Murdani Abdullah Roles: Conceptualization, Funding Acquisition, Supervision, Writing – Original Draft Preparation, Writing – Review & Editing Amanda Pitarini Utari Roles: Funding Acquisition, Resources, Writing – Original Draft Preparation, Writing – Review & Editing Saskia Aziza Nursyirwan Roles: Funding Acquisition, Resources, Writing – Original Draft Preparation, Writing – Review & Editing Dimas R. Noor Roles: Methodology, Writing – Original Draft Preparation OPEN PEER REVIEW DETAILS REVIEWER STATUS This article is included in the Oncology gateway. Abstract Background: The microtumor environment is an area where tumor cells are surrounded by several cells such as immune cells, stromal cells and endothelial cells as well as blood and lymphatic vessels. It is known that various cytokines and growth factors are released by various cells surrounding the tumor and affect the growth of tumor cells. Differences in chemical composition in the microtumor environment can be detected using spectrometry. The aim of this study was to examine the potential of scanning absorbance spectrometry in differentiating cells based on the chemical composition of endoscopic biopsies of colorectal cancer patients. Methods: An endoscopic biopsy of the patient from Cipto Mangunkusumo Hospital, Jakarta was collected and homogenized in phosphate buffer saline using TissueLyser. Scanning absorbance was performed using a UV-VIS spectrophotometer. The results of scanning absorbance were then processed using principal component analysis (PCA) in Orange Data-Mining version 3.28.0 software and the results were represented in a scatter plot diagram. Results: Based on the results of the analysis using PCA, three patients were identified in different quadrant regions, crc006 and crc011 obtained from patients with the differentiation status located close together while crc009 and undifferentiated were located far apart. Conclusion: This indicates the potential of scanning absorbance in differentiating the chemical composition of the tumor microenvironment from patient biopsies. READ ALL READ LESS Keywords absorbance scanning, tumor microenvironment, compositions, endoscopic biopsy, colorectal cancer Corresponding Author(s) Murdani Abdullah ( [email protected] ) Close Corresponding author: Murdani Abdullah Competing interests: No competing interests were disclosed. Grant information: We thank HIBAH PUTI Q2 Universitas Indonesia (NKB-1540/UN2.RST/HKP.05.00/2020) for funding our study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Copyright: © 2021 Abdullah M et al . This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. How to cite: Abdullah M, Pitarini Utari A, Aziza Nursyirwan S and Noor DR. Potential use of absorbance scanning in differentiating tumor microenvironment compositions from endoscopic biopsy of colorectal cancer patients. [version 1; peer review: 1 not approved] . F1000Research 2021, 10 :1300 ( https://doi.org/10.12688/f1000research.74480.1 ) First published: 21 Dec 2021, 10 :1300 ( https://doi.org/10.12688/f1000research.74480.1 ) Latest published: 21 Dec 2021, 10 :1300 ( https://doi.org/10.12688/f1000research.74480.1 ) Introduction The tumor microenvironment is an area surrounding a tumor consisting of various cells including stromal cells ( Wang et al ., 2017 ), immune cells ( Winkler et al ., 2020 ), endothelial cells, blood, and lymph vessels ( Wei et al ., 2020 ). The intra-tumoral composition of the tumor microenvironment can influence the tumor progression ( Whiteside, 2008 ) and the clinical outcome of patients. To be able to determine the intra-tumoural composition, one common method is histopathological evaluation of the patient's biopsy ( Schillaci et al ., 2019 ). However, the biochemical composition of the biopsy such as metabolites and cytokines requires further tests such as immunohistochemistry of cell markers. ( Oudijk et al ., 2015 ) On the other hand, tumor progression may be influenced by chemical compositions within the tumor microenvironment such as cytokines and growth factors ( Landskron et al ., 2014 ; Yuan et al ., 2016 ). One of the simple methods that can be used to distinguish chemical compositions is spectrometry and potential differences of chemical compositions in malignancy such as changes in amino acid concentrations ( Balan et al ., 2019 ). Previously, Nogueira et al ., (2021) showed that a tumor can be detected using diffuse reflectance spectroscopy in colorectal cancer diagnosis. Another study by Yang et al ., (2016) showed the potentiality of visible-absorption spectroscopy as a biomarker to predict treatment and prognosis of esophageal cancer. In this study, we report absorbance scanning to distinguish three biopsies from three different patients. The absorbance scanning was carried out at a wavelength of 400–1000 nm using a spectrophotometer followed by Principal Component Analysis Orange Data Mining. Methods Patients and sample collection All subjects gave their written informed consent for inclusion before participating in the study. The study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Ethical Committee of the Faculty of Medicine, Universitas Indonesia (Protocol ID: 20-04-0643, version 02, June 29th, 2020). The tissue samples taken from an endoscopic biopsy from patients from Cipto Mangunkusumo Hospital, Jakarta were confirmed as cancer by an anatomic pathologist in the Department of Pathological Anatomy, Faculty of Medicine, Universitas Indonesia. They were then put into transport media in phosphate buffer saline (PBS) and transferred to the laboratory of the Indonesia Medical Education and Research Institute, Faculty of Medicine, Universitas Indonesia in less than two hours. Tissue extractions The samples were minced into smaller tissue fragments, transferred to 1.5 ml centrifuge tubes, and homogenized by TissueLyser II (Qiagen, Germany) for 10 minutes. The suspensions were diluted in PBS to 1 mL. Absorption spectrum profiles of the biopsy The samples underwent wavelength scanning at λ = 400–1000 nm using the Agilent Cary 60 UV-Vis spectrophotometer (Agilent, Unites States). The absorption spectrum of the lysate cell was examined and feature selection was carried out using principal component analysis (PCA) to simplify the wavelength dimensions into principal component (PC) features that were not correlated ( Abdullah et al ., 2021 ). The resulting PC features were then used to classify the cancer patient samples into a scatterplot. The absorption/absorption spectrum pre-processing and PCA analysis were performed using Orange Data-Mining version 3.28.0 (Orange Data Mining, RRID: SCR_019811) ( Demšar et al ., 2013 ). Results In this study, we recruited three different patients namely CRC006, CRC009, and CRC011. In the samples collected from patients, CRC006 and CRC011 similar clinical characteristics such as histopathology results were observed. Welldifferentiated rectal adenocarcinoma with metastatic sites were found in both patients. The sample collected from patient CRC009 had different clinical characteristics compared to CRC006 and CRC011, and CRC009 was found to have undifferentiated adenocarcinoma without metastasis. Sample data are shown in Table 1 . ( Abdullah et al ., 2021 ) Table 1. Patient clinical and histopathology profiles. Sample ID Histopathology results Metastasis CRC006 Well differentiated rectal adenocarcinoma Yes CRC009 Undifferentiated adenocarcinoma No CRC011 Well differentiated adenocarcinoma Yes Figure 1 shows that each cell produces an absorption spectrum fingerprint in the wavelength range of 400–1000 nm. Just by observing the form of the absorption/absorption spectrum, it can be seen at first glance that fingerprints were only contributed to by the concentration of the molecule. To investigate the characteristic features of the spectrum, a principal component analysis (PCA) was carried out, which resulted in PC1 as the main feature ( Abdullah et al ., 2021 ). The results of the scatterplot with PC1 and PC2 showed that the sample CRC011 was well grouped in quadrant 1, CRC006 in quadrant 4, while CRC009 was spread between quadrants 2 and 3. From Figure 1 it can also be seen that each type of sample group appears to experience separation/classification when compared to other groups. Figure 1. Absorbance spectrum of the lysate cells scanned using nanospectrophotometers from 400–1000 nm. CRC: sample number. Discussion The light absorption spectrum is known as a “molecular fingerprint” which allows the analysis of molecular types and their amounts/concentrations. In Table 1 , we show three representative colorectal cancer biopsies collected endoscopically from patients: CRC006 was a patient with welldifferentiated rectal adenocarcinoma with metastasis, CRC009 was from a patient with undifferentiated adenocarcinoma, CRC011 was from a patient with welldifferentiated adenocarcinoma with metastasis. Interestingly, based on the PCA analysis of the absorption spectrum of the lysate sample (shown in Figure 2 ), the CRC006 quadrant was closer to CRC011, which has similar clinical features of welldifferentiated adenocarcinoma and metastasis. On the other hand, CRC009 with undifferentiated and located far from CRC006 and CRC011 respectively, which indicated their closer chemical composition. Such existence of grouping indicates that there were differences in cellular composition between the three samples; although further studies with a larger number of samples are needed to further confirm the clustering that occurs. Figure 2. Scatterplot of cell suspensions from samples taken from patients CRC006, CRC009, and CRC011 (n = 3) based on PC1 and PC2 values. In biological tissue samples, several molecules contribute to the absorption spectrum in the ultraviolet (UV) to nearinfrared (NIR) regions. Protein and DNA absorb in the UV region, whereas tryptophan, NAD + (nicotinamide adenine dinucleotide), collagen, elastin, NADH, and FAD (flavin adenine dinucleotide) are important endogenous chromophores in biological tissue ( Yang et al ., 2016 ). FAD, tryptophan, and NADPH (nicotinamide adenine dinucleotide phosphate) have been used as a measuring tool to see the mitochondrial metabolic response before and after therapy such as in prostate cancer ( Alam et al ., 2017 ). In cell lysate samples such as in this study, further molecular analysis is needed to determine the differences in the composition of compounds in the absorption/absorption spectrum between lysates from cancer patients. Conclusions The combinations of principal component analysis (PCA) and absorbance scanning were able to group patients with similar histopathology and metastasis based on their chemical compositions. Although further investigation is needed, molecular fingerprinting using absorbance scanning to predict intratumoral similarity and difference is exciting. Data availability Underlying data Open Science Framework: Underlying data for ‘Potential use of absorbance scanning in differentiating tumor microenvironment compositions from endoscopic biopsy of colorectal cancer patients available at https://doi.org/10.17605/OSF.IO/QV7H5 ( Abdullah et al ., 2021 ). This project contains the following underlying data: • Absorbance – Orange data.docx • UV-Vis Spectrum data.xlsx Data are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0). Consent Written informed consent for publication of the patients’ details was obtained from the patients. Grant information We thank HIBAH PUTI Q2 Universitas Indonesia (NKB4127/UN2.RST/HKP.05.00/2020) for funding our study. Acknowledgements We thank Dr Aryo Tedjo from the Department of Medical Chemistry and Drug Development Cluster for supporting the absorbance scanning and Orange mining data analysis. References Abdullah M, Utari AP, Nursyirwan S, et al. : Potential Use of Absorbance Scanning in Differentiating Tumor Microenvironment Compositions from Endoscopic Biopsy of Colorectal Cancer Patients.2021. Publisher Full Text Alam SR, Wallrabe H, Svindrych Z, et al. : Investigation of Mitochondrial Metabolic Response to Doxorubicin in Prostate Cancer Cells: An NADH, FAD and Tryptophan FLIM Assay. Sci. Rep. 2017; 7 : 10451. PubMed Abstract | Publisher Full Text Balan V, Mihai C-T, Cojocaru F-D, et al. : Vibrational Spectroscopy Fingerprinting in Medicine: from Molecular to Clinical Practice. Materials. 2019; 12 . PubMed Abstract | Publisher Full Text Demšar J, Curk T, Erjavec A, et al. : Orange: Data Mining Toolbox in Python. J. Mach. Learn. Res. 2013; 14 : 2349–2353. Landskron G, De la Fuente M, Thuwajit P, et al. : Chronic inflammation and cytokines in the tumor microenvironment. J. Immunol. Res. 2014; 2014 : 149185–149185. Publisher Full Text Nogueira MS, Maryam S, Amissah M, et al. : Evaluation of wavelength ranges and tissue depth probed by diffuse reflectance spectroscopy for colorectal cancer detection. Sci. Rep. 2021; 11 : 798. PubMed Abstract | Publisher Full Text Oudijk L, Neuhofer CM, Lichtenauer UD, et al. : Immunohistochemical expression of stem cell markers in pheochromocytomas/paragangliomas is associated with SDHx mutations. Eur. J. Endocrinol. 2015; 173 : 43–52. PubMed Abstract | Publisher Full Text Schillaci O, Scimeca M, Toschi N, et al. : Combining Diagnostic Imaging and Pathology for Improving Diagnosis and Prognosis of Cancer. Contrast Media Mol. Imaging. 2019; 2019 : 1–10. PubMed Abstract | Publisher Full Text Wang M, Zhao J, Zhang L, et al. : Role of tumor microenvironment in tumorigenesis. J. Cancer. 2017; 8 : 761–773. 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PubMed Abstract | Publisher Full Text Yuan Y, Jiang Y-C, Sun C-K, et al. : Role of the tumor microenvironment in tumor progression and the clinical applications (Review). Oncol. Rep. 2016; 35 : 2499–2515. Publisher Full Text Comments on this article Comments (0) Version 1 VERSION 1 PUBLISHED 21 Dec 2021 ADD YOUR COMMENT Comment Author details Author details 1 Department of Internal Medicine, Faculty of Medicine, Faculty of Medicine Universitas Indonesia, GH Building, Jalan Diponegoro No. 71, Kenari, Senen, Jakarta, 10430, Indonesia 2 Human Cancer Research Center, Indonesia Medical Education and Research Institute, Faculty of Medicine Universitas Indonesia,, Jalan Salemba Raya No.6, RW.5, Kenari, Senen, Jakarta, 10430, Indonesia Murdani Abdullah Roles: Conceptualization, Funding Acquisition, Supervision, Writing – Original Draft Preparation, Writing – Review & Editing Amanda Pitarini Utari Roles: Funding Acquisition, Resources, Writing – Original Draft Preparation, Writing – Review & Editing Saskia Aziza Nursyirwan Roles: Funding Acquisition, Resources, Writing – Original Draft Preparation, Writing – Review & Editing Dimas R. Noor Roles: Methodology, Writing – Original Draft Preparation Competing interests No competing interests were disclosed. Grant information We thank HIBAH PUTI Q2 Universitas Indonesia (NKB-1540/UN2.RST/HKP.05.00/2020) for funding our study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Article Versions (1) version 1 Published: 21 Dec 2021, 10:1300 https://doi.org/10.12688/f1000research.74480.1 Copyright © 2021 Abdullah M et al . This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Download Export To Sciwheel Bibtex EndNote ProCite Ref. Manager (RIS) Sente metrics Views Downloads F1000Research - - PubMed Central info_outline Data from PMC are received and updated monthly. - - Citations open_in_new 0 open_in_new 0 open_in_new SEE MORE DETAILS CITE how to cite this article Abdullah M, Pitarini Utari A, Aziza Nursyirwan S and Noor DR. Potential use of absorbance scanning in differentiating tumor microenvironment compositions from endoscopic biopsy of colorectal cancer patients. [version 1; peer review: 1 not approved] . F1000Research 2021, 10 :1300 ( https://doi.org/10.12688/f1000research.74480.1 ) NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS track receive updates on this article Track an article to receive email alerts on any updates to this article. TRACK THIS ARTICLE Share Open Peer Review Current Reviewer Status: ? Key to Reviewer Statuses VIEW HIDE Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions Version 1 VERSION 1 PUBLISHED 21 Dec 2021 Views 0 Cite How to cite this report: Sier CF. Reviewer Report For: Potential use of absorbance scanning in differentiating tumor microenvironment compositions from endoscopic biopsy of colorectal cancer patients. [version 1; peer review: 1 not approved] . F1000Research 2021, 10 :1300 ( https://doi.org/10.5256/f1000research.78241.r126731 ) The direct URL for this report is: https://f1000research.com/articles/10-1300/v1#referee-response-126731 NOTE: it is important to ensure the information in square brackets after the title is included in this citation. Close Copy Citation Details Reviewer Report 28 Mar 2022 Cornelis FM Sier , Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands Not Approved VIEWS 0 https://doi.org/10.5256/f1000research.78241.r126731 The brief report by Murdani Abdullah and co-authors reports rather preliminary looking results of PBS- homogenates from biopsy material from 3 colorectal cancer patients which were scanned in a UV-Vis spectrophotometer from 400-1000 nm. Although the introduction focuses slightly on ... Continue reading READ ALL The brief report by Murdani Abdullah and co-authors reports rather preliminary looking results of PBS- homogenates from biopsy material from 3 colorectal cancer patients which were scanned in a UV-Vis spectrophotometer from 400-1000 nm. Although the introduction focuses slightly on the tumor microenvironment there is no actual research question formulated. The cohort of samples (n=3) is definitely not enough to draw conclusions about the applicability of the method. In conclusion, this version of the manuscript does not contribute to the scientific literature. Minor remarks: The word potential in the title seems rather opportunistic Next to a larger and more defined cohort, tissue biopsies are often rather superficial and might not represent the whole tumor. The authors could/should consider including normal tissue adjacent to the tumor to establish the difference with the tumor within single patients. Homogenates and lysates are not synonyms, the latter usually contains a detergent. PCA analysis should be better explained. The table needs to be extended, legends of figures need revision. Is the work clearly and accurately presented and does it cite the current literature? No Is the study design appropriate and is the work technically sound? No Are sufficient details of methods and analysis provided to allow replication by others? No If applicable, is the statistical analysis and its interpretation appropriate? Not applicable Are all the source data underlying the results available to ensure full reproducibility? Yes Are the conclusions drawn adequately supported by the results? No Competing Interests: No competing interests were disclosed. Reviewer Expertise: biomarkers in oncology, including colorectal cancer I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above. Close READ LESS CITE CITE HOW TO CITE THIS REPORT Sier CF. Reviewer Report For: Potential use of absorbance scanning in differentiating tumor microenvironment compositions from endoscopic biopsy of colorectal cancer patients. [version 1; peer review: 1 not approved] . F1000Research 2021, 10 :1300 ( https://doi.org/10.5256/f1000research.78241.r126731 ) The direct URL for this report is: https://f1000research.com/articles/10-1300/v1#referee-response-126731 NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS Report a concern Respond or Comment COMMENT ON THIS REPORT Comments on this article Comments (0) Version 1 VERSION 1 PUBLISHED 21 Dec 2021 ADD YOUR COMMENT Comment keyboard_arrow_left keyboard_arrow_right Open Peer Review Reviewer Status info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions Reviewer Reports Invited Reviewers 1 Version 1 21 Dec 21 read Cornelis FM Sier , Leiden University Medical Center, Leiden, The Netherlands Comments on this article All Comments (0) Add a comment Sign up for content alerts Sign Up You are now signed up to receive this alert Browse by related subjects keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2022 Sier C. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 28 Mar 2022 | for Version 1 Cornelis FM Sier , Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands 0 Views copyright © 2022 Sier C. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. format_quote Cite this report speaker_notes Responses (0) Not Approved info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions The brief report by Murdani Abdullah and co-authors reports rather preliminary looking results of PBS- homogenates from biopsy material from 3 colorectal cancer patients which were scanned in a UV-Vis spectrophotometer from 400-1000 nm. Although the introduction focuses slightly on the tumor microenvironment there is no actual research question formulated. The cohort of samples (n=3) is definitely not enough to draw conclusions about the applicability of the method. In conclusion, this version of the manuscript does not contribute to the scientific literature. Minor remarks: The word potential in the title seems rather opportunistic Next to a larger and more defined cohort, tissue biopsies are often rather superficial and might not represent the whole tumor. The authors could/should consider including normal tissue adjacent to the tumor to establish the difference with the tumor within single patients. Homogenates and lysates are not synonyms, the latter usually contains a detergent. PCA analysis should be better explained. The table needs to be extended, legends of figures need revision. Is the work clearly and accurately presented and does it cite the current literature? No Is the study design appropriate and is the work technically sound? No Are sufficient details of methods and analysis provided to allow replication by others? No If applicable, is the statistical analysis and its interpretation appropriate? Not applicable Are all the source data underlying the results available to ensure full reproducibility? Yes Are the conclusions drawn adequately supported by the results? No Competing Interests No competing interests were disclosed. Reviewer Expertise biomarkers in oncology, including colorectal cancer I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above. reply Respond to this report Responses (0) Sier CF. Peer Review Report For: Potential use of absorbance scanning in differentiating tumor microenvironment compositions from endoscopic biopsy of colorectal cancer patients. [version 1; peer review: 1 not approved] . F1000Research 2021, 10 :1300 ( https://doi.org/10.5256/f1000research.78241.r126731) NOTE: it is important to ensure the information in square brackets after the title is included in this citation. The direct URL for this report is: https://f1000research.com/articles/10-1300/v1#referee-response-126731 Alongside their report, reviewers assign a status to the article: Approved - the paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations - A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved - fundamental flaws in the paper seriously undermine the findings and conclusions Adjust parameters to alter display View on desktop for interactive features Includes Interactive Elements View on desktop for interactive features Competing Interests Policy Provide sufficient details of any financial or non-financial competing interests to enable users to assess whether your comments might lead a reasonable person to question your impartiality. 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Text is read by the "Ask this paper" AI Q&A widget below. Extraction quality varies by source — PMC NXML preserves structure cleanly, OA-HTML may include some navigation residue, and OA-PDF can have broken hyphenation. The publisher copy (via DOI) is the canonical version.

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Ask this paper AI returns verbatim quotes from the full text · source: preprint-html

Answers must be backed by verbatim quotes from this paper's full text. Hallucinated quotes are dropped automatically; if no verbatim passage answers the question, we say so. How this works

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We don't have any in-corpus citations linked to this paper yet. The paper's references may be in our DB but unresolved to ``paper_id`` (resolution happens at ingest when the cited DOI matches a row we already have). Run the cross-source citation reconcile pass to retry.

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europepmc
last seen: 2026-05-19T01:45:01.086888+00:00
unpaywall
last seen: 2026-05-24T02:00:01.246996+00:00
License: CC-BY-4.0