Potential applications of gene expression profiles obtained from circulating extracellular vesicles in breast cancer
Background: Liquid biopsy-based biomarkers offer several advantages since they are minimally invasive, can be useful in longitudinal monitoring of the disease and have higher patient compliance. We describe a protocol using minimal volumes of archival and prospective serum/plasma samples to define t...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-03-01
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| Series: | The Journal of Liquid Biopsy |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2950195425000037 |
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| author | Aritra Gupta Siddharth Bhardwaj Sayan Ghorai Rosina Ahmed Sanjit Agarwal Geetashree Mukherjee Kartiki V. Desai |
| author_facet | Aritra Gupta Siddharth Bhardwaj Sayan Ghorai Rosina Ahmed Sanjit Agarwal Geetashree Mukherjee Kartiki V. Desai |
| author_sort | Aritra Gupta |
| collection | DOAJ |
| description | Background: Liquid biopsy-based biomarkers offer several advantages since they are minimally invasive, can be useful in longitudinal monitoring of the disease and have higher patient compliance. We describe a protocol using minimal volumes of archival and prospective serum/plasma samples to define the RNA contents of EVs and discuss its benefits and limitations. Methods: RNA-seq analysis of matched tumor biopsy, circulating EVs from breast cancer patients (EV-C, n = 26) and healthy donors (EV-H, n = 4) was performed and differentially expressed genes were validated by RT-PCR in a separate series of samples (EV-C, n = 32 and EV-H, n = 22). A total of 84 samples were studied. Results: RNA-seq data from 500 μl serum samples yielded more than 17000 genes, of which 320 were DEGs (adjusted p value ≤ 0.05) between EV-C and EV-H samples. Pathways for Myc V1, reactive oxygen species, angiogenesis, allograft rejection and Interferon regulated genes were over-represented in EV-C samples. Computational deconvolution algorithms for cell signatures identified immune cells such as Th1 and memory T-cells, endothelial cells, and osteoblasts from the stromal compartment as significant. Top 6 genes were validated by qRT-PCR in all samples (n = 84) and they consistently and correctly classified cancer and healthy groups. An independent set of 374 and 640 DEGs could segregate ER positive/ER negative and non-metastatic versus metastatic samples, respectively. EVs from metastatic samples had higher variability in gene expression patterns whereas those from non-metastatic samples showed a better correlation. Conclusion: By using low serum amounts successfully for EV transcriptomics, we demonstrate that a minimally invasive technique could be converted to a microinvasive format. These data lay the foundation for EV RNA based biomarker discovery for segregating breast cancers. |
| format | Article |
| id | doaj-art-e3c4a8f2a0ae4ab39505df0435a5cbbc |
| institution | Kabale University |
| issn | 2950-1954 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | The Journal of Liquid Biopsy |
| spelling | doaj-art-e3c4a8f2a0ae4ab39505df0435a5cbbc2025-08-20T03:44:28ZengElsevierThe Journal of Liquid Biopsy2950-19542025-03-01710028710.1016/j.jlb.2025.100287Potential applications of gene expression profiles obtained from circulating extracellular vesicles in breast cancerAritra Gupta0Siddharth Bhardwaj1Sayan Ghorai2Rosina Ahmed3Sanjit Agarwal4Geetashree Mukherjee5Kartiki V. Desai6Biotechnology Research Innovation Council-National Institute of Biomedical Genomics (BRIC-NIBMG), Kalyani, India; Regional Centre for Biotechnology, PhD Program, IndiaBiotechnology Research Innovation Council-National Institute of Biomedical Genomics (BRIC-NIBMG), Kalyani, IndiaBiotechnology Research Innovation Council-National Institute of Biomedical Genomics (BRIC-NIBMG), Kalyani, India; Regional Centre for Biotechnology, PhD Program, IndiaTata Medical Centre, 14 MAR (DH Block), New Town, Rajarhat, Kolkata, 700160, IndiaTata Medical Centre, 14 MAR (DH Block), New Town, Rajarhat, Kolkata, 700160, IndiaTata Medical Centre, 14 MAR (DH Block), New Town, Rajarhat, Kolkata, 700160, IndiaBiotechnology Research Innovation Council-National Institute of Biomedical Genomics (BRIC-NIBMG), Kalyani, India; Corresponding author. BRIC-National Institute of Biomedical Genomics P.O. N.S.S, Kalyani, 741251, India.Background: Liquid biopsy-based biomarkers offer several advantages since they are minimally invasive, can be useful in longitudinal monitoring of the disease and have higher patient compliance. We describe a protocol using minimal volumes of archival and prospective serum/plasma samples to define the RNA contents of EVs and discuss its benefits and limitations. Methods: RNA-seq analysis of matched tumor biopsy, circulating EVs from breast cancer patients (EV-C, n = 26) and healthy donors (EV-H, n = 4) was performed and differentially expressed genes were validated by RT-PCR in a separate series of samples (EV-C, n = 32 and EV-H, n = 22). A total of 84 samples were studied. Results: RNA-seq data from 500 μl serum samples yielded more than 17000 genes, of which 320 were DEGs (adjusted p value ≤ 0.05) between EV-C and EV-H samples. Pathways for Myc V1, reactive oxygen species, angiogenesis, allograft rejection and Interferon regulated genes were over-represented in EV-C samples. Computational deconvolution algorithms for cell signatures identified immune cells such as Th1 and memory T-cells, endothelial cells, and osteoblasts from the stromal compartment as significant. Top 6 genes were validated by qRT-PCR in all samples (n = 84) and they consistently and correctly classified cancer and healthy groups. An independent set of 374 and 640 DEGs could segregate ER positive/ER negative and non-metastatic versus metastatic samples, respectively. EVs from metastatic samples had higher variability in gene expression patterns whereas those from non-metastatic samples showed a better correlation. Conclusion: By using low serum amounts successfully for EV transcriptomics, we demonstrate that a minimally invasive technique could be converted to a microinvasive format. These data lay the foundation for EV RNA based biomarker discovery for segregating breast cancers.http://www.sciencedirect.com/science/article/pii/S2950195425000037Liquid biopsyDiagnosisTranscriptomics |
| spellingShingle | Aritra Gupta Siddharth Bhardwaj Sayan Ghorai Rosina Ahmed Sanjit Agarwal Geetashree Mukherjee Kartiki V. Desai Potential applications of gene expression profiles obtained from circulating extracellular vesicles in breast cancer The Journal of Liquid Biopsy Liquid biopsy Diagnosis Transcriptomics |
| title | Potential applications of gene expression profiles obtained from circulating extracellular vesicles in breast cancer |
| title_full | Potential applications of gene expression profiles obtained from circulating extracellular vesicles in breast cancer |
| title_fullStr | Potential applications of gene expression profiles obtained from circulating extracellular vesicles in breast cancer |
| title_full_unstemmed | Potential applications of gene expression profiles obtained from circulating extracellular vesicles in breast cancer |
| title_short | Potential applications of gene expression profiles obtained from circulating extracellular vesicles in breast cancer |
| title_sort | potential applications of gene expression profiles obtained from circulating extracellular vesicles in breast cancer |
| topic | Liquid biopsy Diagnosis Transcriptomics |
| url | http://www.sciencedirect.com/science/article/pii/S2950195425000037 |
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