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Peng H, Pan M, Zhou Z, Chen C, Xing X, Cheng S, Zhang S, Zheng H, Qian K. The impact of preanalytical variables on the analysis of cell-free DNA from blood and urine samples. Front Cell Dev Biol 2024; 12:1385041. [PMID: 38784382 PMCID: PMC11111958 DOI: 10.3389/fcell.2024.1385041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Cell-free DNA (cfDNA), a burgeoning class of molecular biomarkers, has been extensively studied across a variety of biomedical fields. As a key component of liquid biopsy, cfDNA testing is gaining prominence in disease detection and management due to the convenience of sample collection and the abundant wealth of genetic information it provides. However, the broader clinical application of cfDNA is currently impeded by a lack of standardization in the preanalytical procedures for cfDNA analysis. A number of fundamental challenges, including the selection of appropriate preanalytical procedures, prevention of short cfDNA fragment loss, and the validation of various cfDNA measurement methods, remain unaddressed. These existing hurdles lead to difficulties in comparing results and ensuring repeatability, thereby undermining the reliability of cfDNA analysis in clinical settings. This review discusses the crucial preanalytical factors that influence cfDNA analysis outcomes, including sample collection, transportation, temporary storage, processing, extraction, quality control, and long-term storage. The review provides clarification on achievable consensus and offers an analysis of the current issues with the goal of standardizing preanalytical procedures for cfDNA analysis.
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Affiliation(s)
- Hongwei Peng
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ming Pan
- Taihe Skills Training Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Zongning Zhou
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Congbo Chen
- Department of Urology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Xing Xing
- Department of Urology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Shaoping Cheng
- Department of Urology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Shanshan Zhang
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hang Zheng
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kaiyu Qian
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
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Diez-Feijóo R, Andrade-Campos M, Gibert J, Sánchez-González B, Fernández-Ibarrondo L, Fernández-Rodríguez C, Garcia-Gisbert N, Camacho L, Lafuente M, Vázquez I, Colomo L, Salar A, Bellosillo B. Cell-Free DNA as a Biomarker at Diagnosis and Follow-Up in 256 B and T-Cell Lymphomas. Cancers (Basel) 2024; 16:321. [PMID: 38254810 PMCID: PMC10813584 DOI: 10.3390/cancers16020321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Cell-free DNA (cfDNA) analysis has become a promising tool for the diagnosis, prognosis, and monitoring of lymphoma cases. Until now, research in this area has mainly focused on aggressive lymphomas, with scanty information from other lymphoma subtypes. METHODS We selected 256 patients diagnosed with lymphomas, including a large variety of B-cell and T-cell non-Hodgkin and Hodgkin lymphomas, and quantified cfDNA from plasma at the time of diagnosis. We further selected 49 large B-cell lymphomas (LBCL) and analyzed cfDNA levels at diagnosis (pre-therapy) and after therapy. In addition, we performed NGS on cfDNA and tissue in this cohort of LBCL. RESULTS Lymphoma patients showed a statistically significant higher cfDNA concentration than healthy controls (mean 53.0 ng/mL vs. 5.6 ng/mL, p < 0.001). The cfDNA concentration was correlated with lymphoma subtype, lactate dehydrogenase, the International Prognostic Index (IPI) score, Ann Arbor (AA), and B-symptoms. In 49 LBCL cases, the cfDNA concentration decreased after therapy in cases who achieved complete response (CR) and increased in non-responders. The median cfDNA at diagnosis of patients who achieved CR and later relapsed was higher (81.5 ng/mL) compared with levels of those who did not (38.6 ng/mL). A concordance of 84% was observed between NGS results in tumor and cfDNA samples. Higher VAF in cfDNA is correlated with advanced stage and bulky disease. CONCLUSIONS cfDNA analysis can be easily performed in almost all lymphoma cases. The cfDNA concentration correlated with the characteristics of the aggressiveness of the lymphomas and, in LBCL, with the response achieved after therapy. These results support the utility of cfDNA analysis as a complementary tool in the management of lymphoma patients.
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Affiliation(s)
- Ramón Diez-Feijóo
- Department of Hematology, Hospital del Mar, 08003 Barcelona, Spain; (R.D.-F.); (M.A.-C.); (B.S.-G.)
- Cancer Research Program, Hospital del Mar Research Institute, 08003 Barcelona, Spain; (J.G.); (L.F.-I.); (C.F.-R.); (N.G.-G.); (L.C.); (M.L.); (L.C.); (B.B.)
| | - Marcio Andrade-Campos
- Department of Hematology, Hospital del Mar, 08003 Barcelona, Spain; (R.D.-F.); (M.A.-C.); (B.S.-G.)
- Cancer Research Program, Hospital del Mar Research Institute, 08003 Barcelona, Spain; (J.G.); (L.F.-I.); (C.F.-R.); (N.G.-G.); (L.C.); (M.L.); (L.C.); (B.B.)
| | - Joan Gibert
- Cancer Research Program, Hospital del Mar Research Institute, 08003 Barcelona, Spain; (J.G.); (L.F.-I.); (C.F.-R.); (N.G.-G.); (L.C.); (M.L.); (L.C.); (B.B.)
| | - Blanca Sánchez-González
- Department of Hematology, Hospital del Mar, 08003 Barcelona, Spain; (R.D.-F.); (M.A.-C.); (B.S.-G.)
- Cancer Research Program, Hospital del Mar Research Institute, 08003 Barcelona, Spain; (J.G.); (L.F.-I.); (C.F.-R.); (N.G.-G.); (L.C.); (M.L.); (L.C.); (B.B.)
| | - Lierni Fernández-Ibarrondo
- Cancer Research Program, Hospital del Mar Research Institute, 08003 Barcelona, Spain; (J.G.); (L.F.-I.); (C.F.-R.); (N.G.-G.); (L.C.); (M.L.); (L.C.); (B.B.)
| | - Concepción Fernández-Rodríguez
- Cancer Research Program, Hospital del Mar Research Institute, 08003 Barcelona, Spain; (J.G.); (L.F.-I.); (C.F.-R.); (N.G.-G.); (L.C.); (M.L.); (L.C.); (B.B.)
- Department of Pathology, Hospital del Mar, Hospital del Mar Research Institute, 08003 Barcelona, Spain;
| | - Nieves Garcia-Gisbert
- Cancer Research Program, Hospital del Mar Research Institute, 08003 Barcelona, Spain; (J.G.); (L.F.-I.); (C.F.-R.); (N.G.-G.); (L.C.); (M.L.); (L.C.); (B.B.)
- Department of Pathology, Hospital del Mar, Hospital del Mar Research Institute, 08003 Barcelona, Spain;
| | - Laura Camacho
- Cancer Research Program, Hospital del Mar Research Institute, 08003 Barcelona, Spain; (J.G.); (L.F.-I.); (C.F.-R.); (N.G.-G.); (L.C.); (M.L.); (L.C.); (B.B.)
- Department of Pathology, Hospital del Mar, Hospital del Mar Research Institute, 08003 Barcelona, Spain;
| | - Marta Lafuente
- Cancer Research Program, Hospital del Mar Research Institute, 08003 Barcelona, Spain; (J.G.); (L.F.-I.); (C.F.-R.); (N.G.-G.); (L.C.); (M.L.); (L.C.); (B.B.)
| | - Ivonne Vázquez
- Department of Pathology, Hospital del Mar, Hospital del Mar Research Institute, 08003 Barcelona, Spain;
| | - Luis Colomo
- Cancer Research Program, Hospital del Mar Research Institute, 08003 Barcelona, Spain; (J.G.); (L.F.-I.); (C.F.-R.); (N.G.-G.); (L.C.); (M.L.); (L.C.); (B.B.)
- Department of Pathology, Hospital del Mar, Hospital del Mar Research Institute, 08003 Barcelona, Spain;
| | - Antonio Salar
- Department of Hematology, Hospital del Mar, 08003 Barcelona, Spain; (R.D.-F.); (M.A.-C.); (B.S.-G.)
- Cancer Research Program, Hospital del Mar Research Institute, 08003 Barcelona, Spain; (J.G.); (L.F.-I.); (C.F.-R.); (N.G.-G.); (L.C.); (M.L.); (L.C.); (B.B.)
| | - Beatriz Bellosillo
- Cancer Research Program, Hospital del Mar Research Institute, 08003 Barcelona, Spain; (J.G.); (L.F.-I.); (C.F.-R.); (N.G.-G.); (L.C.); (M.L.); (L.C.); (B.B.)
- Department of Pathology, Hospital del Mar, Hospital del Mar Research Institute, 08003 Barcelona, Spain;
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Fernández-Miranda I, Pedrosa L, Llanos M, Franco FF, Gómez S, Martín-Acosta P, García-Arroyo FR, Gumá J, Horcajo B, Ballesteros AK, Gálvez L, Martínez N, Marín M, Sequero S, Navarro M, Yanguas-Casás N, Calvo V, Rueda-Domínguez A, Provencio M, Sánchez-Beato M. Monitoring of Circulating Tumor DNA Predicts Response to Treatment and Early Progression in Follicular Lymphoma: Results of a Prospective Pilot Study. Clin Cancer Res 2023; 29:209-220. [PMID: 36269794 PMCID: PMC9811164 DOI: 10.1158/1078-0432.ccr-22-1654] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/26/2022] [Accepted: 10/19/2022] [Indexed: 02/07/2023]
Abstract
PURPOSE Follicular lymphoma (FL) is the most frequent indolent non-Hodgkin lymphoma. Around 20% of patients suffer early disease progression within 24 months (POD24) of diagnosis. This study examined the significance of circulating tumor DNA (ctDNA) in predicting response to therapy and POD24 in patients with FL. EXPERIMENTAL DESIGN We collected 100 plasma samples, before and during the treatment, from 36 patients with FL prospectively enrolled in 8 Spanish hospitals. They were treated with a chemotherapy-rituximab regimen and followed up for a median of 3.43 years. We performed targeted deep sequencing in cell-free DNA (cfDNA) and tumor genomic DNA from 31 diagnostic biopsy samples. RESULTS Of the alterations detected in the diagnostic tissue samples, 73% (300/411) were also identified in basal cfDNA. The mean numbers of alterations per basal cfDNA sample in patients who suffered progression of disease within 24 months (POD24-pos) or did not achieve complete response (non-CR) were significantly higher than in POD24-neg or CR patients (unpaired samples t test, P = 0.0001 and 0.001, respectively). Pretreatment ctDNA levels, as haploid genome equivalents per milliliter of plasma, were higher in patients without CR (P = 0.02) and in POD24-pos patients compared with POD24-neg patients (P < 0.001). Dynamic analysis showed that ctDNA levels decreased dramatically after treatment, although the reduction was more significant in patients with CR and POD24-neg patients. CONCLUSIONS Basal ctDNA levels are associated with the risk of early progression and response to treatment in FL. cfDNA monitoring and genotyping during treatment and follow-up predict response to treatment and early progression.
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Affiliation(s)
- Ismael Fernández-Miranda
- Department of Medical Oncology, Lymphoma Research Group, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain.,PhD Program in Molecular Biosciences, Doctoral School, Universidad Autónoma de Madrid, Madrid, Spain
| | - Lucía Pedrosa
- Department of Medical Oncology, Lymphoma Research Group, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain.,PhD Program in Molecular Biosciences, Doctoral School, Universidad Autónoma de Madrid, Madrid, Spain
| | - Marta Llanos
- Department of Medical Oncology, Hospital Universitario de Canarias, Tenerife, Spain.,Grupo Oncológico para el Tratamiento y Estudio de los Linfomas (GOTEL), Madrid, Spain
| | - Fernando F. Franco
- Department of Medical Oncology, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Sagrario Gómez
- Department of Medical Oncology, Lymphoma Research Group, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain
| | - Paloma Martín-Acosta
- Department of Pathology, Cancer Molecular Pathology Group, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, CIBERONC, Madrid, Spain
| | - Francisco R. García-Arroyo
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas (GOTEL), Madrid, Spain.,Department of Medical Oncology, Complejo Hospitalario de Pontevedra, Spain
| | - Josep Gumá
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas (GOTEL), Madrid, Spain.,Department of Medical Oncology, IISPV-URV, Hospital Universitari Sant Joan de Reus, Reus, Spain
| | - Beatriz Horcajo
- Department of Medical Oncology, Lymphoma Research Group, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain
| | - Ana K. Ballesteros
- Department of Medical Oncology, Lymphoma Research Group, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain
| | - Laura Gálvez
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas (GOTEL), Madrid, Spain.,Department of Medical Oncology, Hospitales Universitarios Regional y Virgen de la Victoria de Málaga, Spain
| | - Natividad Martínez
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas (GOTEL), Madrid, Spain.,Department of Medical Oncology, Dr. Balmis General University Hospital, Alicante Institute for Health and Biomedical Research (ISABIAL), Alicante, Spain
| | - Miguel Marín
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas (GOTEL), Madrid, Spain.,Department of Medical Oncology, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
| | - Silvia Sequero
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas (GOTEL), Madrid, Spain.,Department of Medical Oncology, Hospital Universitario San Cecilio, Granada, Spain
| | - Marta Navarro
- Department of Medical Oncology, Lymphoma Research Group, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain
| | - Natalia Yanguas-Casás
- Department of Medical Oncology, Lymphoma Research Group, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain.,Centro de Investigación Biomédica en Red Fragilidad y Envejecimiento Saludable (CIBERFES), Madrid, Spain
| | - Virginia Calvo
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas (GOTEL), Madrid, Spain.,Department of Medical Oncology, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Antonio Rueda-Domínguez
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas (GOTEL), Madrid, Spain.,Department of Medical Oncology, Hospitales Universitarios Regional y Virgen de la Victoria de Málaga, Spain
| | - Mariano Provencio
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas (GOTEL), Madrid, Spain.,Department of Medical Oncology, Hospital Universitario Puerta de Hierro-Majadahonda, Facultad de Medicina, Universidad Autónoma de Madrid, IDIPHISA, Madrid, Spain
| | - Margarita Sánchez-Beato
- Department of Medical Oncology, Lymphoma Research Group, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Corresponding Author: Margarita Sánchez-Beato, Joaquín Rodrigo 2, Majadahonda, Madrid 28222, Spain. Phone: 349-1191-6095; E-mail:
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Whole Transcriptome Sequencing Reveals Cancer-Related, Prognostically Significant Transcripts and Tumor-Infiltrating Immunocytes in Mantle Cell Lymphoma. Cells 2022; 11:cells11213394. [PMID: 36359790 PMCID: PMC9654955 DOI: 10.3390/cells11213394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 11/29/2022] Open
Abstract
Mantle cell lymphoma (MCL) is an aggressive B-cell non-Hodgkin lymphoma (NHL) subtype characterized by overexpression of CCND1 and SOX11 genes. It is generally associated with clinically poor outcomes despite recent improvements in therapeutic approaches. The genes associated with the development and prognosis of MCL are still largely unknown. Through whole transcriptome sequencing (WTS), we identified mRNAs, lncRNAs, and alternative transcripts differentially expressed in MCL cases compared with reactive tonsil B-cell subsets. CCND1, VCAM1, and VWF mRNAs, as well as MIR100HG and ROR1-AS1 lncRNAs, were among the top 10 most significantly overexpressed, oncogenesis-related transcripts. Survival analyses with each of the top upregulated transcripts showed that MCL cases with high expression of VWF mRNA and low expression of FTX lncRNA were associated with poor overall survival. Similarly, high expression of MSTRG.153013.3, an overexpressed alternative transcript, was associated with shortened MCL survival. Known tumor suppressor candidates (e.g., PI3KIP1, UBXN) were significantly downregulated in MCL cases. Top differentially expressed protein-coding genes were enriched in signaling pathways related to invasion and metastasis. Survival analyses based on the abundance of tumor-infiltrating immunocytes estimated with CIBERSORTx showed that high ratios of CD8+ T-cells or resting NK cells and low ratios of eosinophils are associated with poor overall survival in diagnostic MCL cases. Integrative analysis of tumor-infiltrating CD8+ T-cell abundance and overexpressed oncogene candidates showed that MCL cases with high ratio CD8+ T-cells and low expression of FTX or PCA3 can potentially predict high-risk MCL patients. WTS results were cross-validated with qRT-PCR of selected transcripts as well as linear correlation analyses. In conclusion, expression levels of oncogenesis-associated transcripts and/or the ratios of microenvironmental immunocytes in MCL tumors may be used to improve prognostication, thereby leading to better patient management and outcomes.
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