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Zayakin P, Sadovska L, Eglītis K, Romanchikova N, Radoviča-Spalviņa I, Endzeliņš E, Liepniece-Karele I, Eglītis J, Linē A. Extracellular Vesicles-A Source of RNA Biomarkers for the Detection of Breast Cancer in Liquid Biopsies. Cancers (Basel) 2023; 15:4329. [PMID: 37686605 PMCID: PMC10487078 DOI: 10.3390/cancers15174329] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 08/19/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
Over the past decade, extracellular vesicles (EVs) have emerged as a promising source of cancer-derived RNAs for liquid biopsies. However, blood contains a pool of heterogeneous EVs released by a variety of cell types, making the identification of cancer RNA biomarkers challenging. Here, we performed deep sequencing of plasma EV RNA cargo in 32 patients with locally advanced breast cancer (BC) at diagnosis and 7 days after breast surgery and in 30 cancer-free healthy controls (HCs). To identify BC-derived RNA biomarkers, we searched for RNAs that had higher levels in BC EVs at the time of diagnosis compared with HCs and decreased after surgery. Data analysis showed that the fractions of miRNAs, snRNAs, snoRNAs, and tRFs were increased, but the fraction of lncRNAs was decreased in BC EVs as compared to HCs. BC-derived biomarker candidates were identified across various RNA biotypes. Considered individually, they had very high specificity but moderate sensitivity for the detection of BC, whereas a biomarker model composed of eight RNAs: SNORD3H, SNORD1C, SNORA74D, miR-224-5p, piR-32949, lnc-IFT-122-2, lnc-C9orf50-4, and lnc-FAM122C-3 was able to distinguish BC from HC EVs with an AUC of 0.902 (95% CI = 0.872-0.931, p = 3.4 × 10-9) in leave-one-out cross-validation. Furthermore, a number of RNA biomarkers were correlated with the ER and HER2 expression and additional biomarker models were created to predict hormone receptor and HER2 status. Overall, this study demonstrated that the RNA composition of plasma EVs is altered in BC patients and that they contain cancer-derived RNA biomarkers that can be used for BC detection and monitoring using liquid biopsies.
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Affiliation(s)
- Pawel Zayakin
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k-1, LV-1067 Riga, Latvia; (P.Z.); (L.S.); (N.R.); (E.E.)
| | - Lilite Sadovska
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k-1, LV-1067 Riga, Latvia; (P.Z.); (L.S.); (N.R.); (E.E.)
| | - Kristaps Eglītis
- Latvian Oncology Center, Riga Eastern Clinical University Hospital, LV-1038 Riga, Latvia; (K.E.)
| | - Nadezhda Romanchikova
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k-1, LV-1067 Riga, Latvia; (P.Z.); (L.S.); (N.R.); (E.E.)
| | | | - Edgars Endzeliņš
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k-1, LV-1067 Riga, Latvia; (P.Z.); (L.S.); (N.R.); (E.E.)
| | | | - Jānis Eglītis
- Latvian Oncology Center, Riga Eastern Clinical University Hospital, LV-1038 Riga, Latvia; (K.E.)
| | - Aija Linē
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k-1, LV-1067 Riga, Latvia; (P.Z.); (L.S.); (N.R.); (E.E.)
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Bajo-Santos C, Brokāne A, Zayakin P, Endzeliņš E, Soboļevska K, Belovs A, Jansons J, Sperga M, Llorente A, Radoviča-Spalviņa I, Lietuvietis V, Linē A. Plasma and urinary extracellular vesicles as a source of RNA biomarkers for prostate cancer in liquid biopsies. Front Mol Biosci 2023; 10:980433. [PMID: 36818049 PMCID: PMC9935579 DOI: 10.3389/fmolb.2023.980433] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 01/20/2023] [Indexed: 02/05/2023] Open
Abstract
Introduction: Extracellular vesicles (EVs) have emerged as a very attractive source of cancer- derived RNA biomarkers for the early detection, prognosis and monitoring of various cancers, including prostate cancer (PC). However, biofluids contain a mixture of EVs released from a variety of tissues and the fraction of total EVs that are derived from PC tissue is not known. Moreover, the optimal biofluid-plasma or urine-that is more suitable for the detection of EV- enclosed RNA biomarkers is not yet clear. Methodology: In the current study, we performed RNA sequencing analysis of plasma and urinary EVs collected before and after radical prostatectomy, and matched tumor and normal prostate tissues of 10 patients with prostate cancer. Results and Discussion: The most abundant RNA biotypes in EVs were miRNA, piRNA, tRNA, lncRNA, rRNA and mRNA. To identify putative cancer-derived RNA biomarkers, we searched for RNAs that were overexpressed in tumor as compared to normal tissues, present in the pre-operation EVs and decreased in the post-operation EVs in each RNA biotype. The levels of 63 mRNAs, 3 lncRNAs, 2 miRNAs and 1 piRNA were significantly increased in the tumors and decreased in the post-operation urinary EVs, thus suggesting that these RNAs mainly originate from PC tissue. No such RNA biomarkers were identified in plasma EVs. This suggests that the fraction of PC-derived EVs in urine is larger than in plasma and allows the detection and tracking of PC-derived RNAs.
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Affiliation(s)
| | - Agnese Brokāne
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Pawel Zayakin
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | | | | | | | | | - Alicia Llorente
- Department Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway,Department for Mechanical, Electronics and Chemical Engineering, Oslo Metropolitan University, Oslo, Norway
| | | | | | - Aija Linē
- Latvian Biomedical Research and Study Centre, Riga, Latvia,*Correspondence: Aija Linē,
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Sadovska L, Zayakin P, Eglītis K, Endzeliņš E, Radoviča-Spalviņa I, Avotiņa E, Auders J, Keiša L, Liepniece-Karele I, Leja M, Eglītis J, Linē A. Comprehensive characterization of RNA cargo of extracellular vesicles in breast cancer patients undergoing neoadjuvant chemotherapy. Front Oncol 2022; 12:1005812. [PMID: 36387168 PMCID: PMC9644097 DOI: 10.3389/fonc.2022.1005812] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/10/2022] [Indexed: 08/30/2023] Open
Abstract
Extracellular vesicles (EVs) are g7aining increased attention as carriers of cancer-derived molecules for liquid biopsies. Here, we studied the dynamics of EV levels in the plasma of breast cancer (BC) patients undergoing neoadjuvant chemotherapy (NAC) and explored the relevance of their RNA cargo for the prediction of patients' response to the therapy. EVs were isolated from serial blood samples collected at the time of diagnosis, at the end of NAC, and 7 days, 6, and 12 months after the surgery from 32 patients with locally advanced BC, and 30 cancer-free healthy controls (HCs) and quantified by nanoparticle tracking analysis. The pre-treatment levels of EVs in BC patients were higher than in HCs, significantly increased during the NAC and surgery, and decreased to the levels found in HCs 6 months after surgery, thus showing that a substantial fraction of plasma EVs in BC patients are produced due to the disease processes and treatment. RNA sequencing analysis revealed that the changes in the EV levels were associated with the alterations in the proportions of various RNA biotypes in EVs. To search for RNA biomarkers that predict response to the NAC, patients were dichotomized as responders and non-responders based on Miller-Payne grades and differential expression analyses were carried out between responders and non-responders, and HCs. This resulted in the identification of 6 miRNAs, 4 lncRNAs, and 1 snoRNA that had significantly higher levels in EVs from non-responders than responders at the time of diagnosis and throughout the NAC, and significantly lower levels in HCs, thus representing biomarkers for the prediction of response to NAC at the time of diagnosis. In addition, we found 14 RNAs representing piRNA, miRNA, lncRNA, snoRNA, and snRNA biotypes that were induced by NAC in non-responders and 2 snoRNAs and 1 piRNA that were induced by NAC in patients with early disease progression, thus warranting further functional studies on their role in chemoresistance and metastasis.
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Affiliation(s)
- Lilite Sadovska
- Cancer Biomarker group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Pawel Zayakin
- Cancer Biomarker group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Kristaps Eglītis
- Latvian Oncology Center, Riga Eastern Clinical University Hospital, Riga, Latvia
| | - Edgars Endzeliņš
- Cancer Biomarker group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | - Elīza Avotiņa
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
| | - Jānis Auders
- Cancer Biomarker group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Laura Keiša
- Cancer Biomarker group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Inta Liepniece-Karele
- Latvian Oncology Center, Riga Eastern Clinical University Hospital, Riga, Latvia
- Department of Pathology, Riga Stradins University, Riga, Latvia
| | - Mārcis Leja
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
| | - Jānis Eglītis
- Latvian Oncology Center, Riga Eastern Clinical University Hospital, Riga, Latvia
- University of Latvia, Faculty of Medicine, University of Latvia, Riga, Latvia
| | - Aija Linē
- Cancer Biomarker group, Latvian Biomedical Research and Study Centre, Riga, Latvia
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