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Housini M, Dariya B, Ahmed N, Stevens A, Fiadjoe H, Nagaraju GP, Basha R. Colorectal cancer: Genetic alterations, novel biomarkers, current therapeutic strategies and clinical trials. Gene 2024; 892:147857. [PMID: 37783294 DOI: 10.1016/j.gene.2023.147857] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/04/2023]
Abstract
Colorectal cancer (CRC) is the third most commonly detected cancer with a serious global health issue. The rates for incidence and mortality for CRC are alarming, especially since the prognosis is abysmal when the CRC is diagnosed at an advanced or metastatic stage. Both type of (modifiable/ non-modifiable) types of risk factors are established for CRC. Despite the advances in recent technology and sophisticated research, the survival rate is still meager due to delays in diagnosis. Therefore, there is urgently required to identify critical biomarkers aiming at early diagnosis and improving effective therapeutic strategies. Additionally, a complete understanding of the dysregulated pathways like PI3K/Akt, Notch, and Wnt associated with CRC progression and metastasis is very beneficial in designing a therapeutic regimen. This review article focused on the dysregulated signaling pathways, genetics and epigenetics alterations, and crucial biomarkers of CRC. This review also provided the list of clinical trials targeting signaling cascades and therapies involving small molecules. This review discusses up-to-date information on novel diagnostic and therapeutic strategies alongside specific clinical trials.
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Affiliation(s)
- Mohammad Housini
- Texas College of Osteopathic Medicine, University of North Texas Health Science Center, Fort Worth, TX 76107, United States
| | - Begum Dariya
- Center for Drug Design, University of Minnesota, Minneapolis, MN 5545, United States
| | - Nadia Ahmed
- Department of Diagnostic Radiology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Alyssa Stevens
- Missouri Southern State University, Joplin, MO 64801, United States
| | - Hope Fiadjoe
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, United States
| | - Ganji Purnachandra Nagaraju
- Division of Hematology & Oncology, The University of Alabama at Birmingham, Birmingham, AL 35233, United States.
| | - Riyaz Basha
- Texas College of Osteopathic Medicine, University of North Texas Health Science Center, Fort Worth, TX 76107, United States; Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, United States.
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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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Hadipour M, Darani HY, Talebzadeh H, Eslamian M, Aboutalebian S, Harandi MF, Mirhendi H. Sensitive detection of specific cell-free DNA in serum samples from sheep with cystic echinococcosis. PLoS Negl Trop Dis 2023; 17:e0011715. [PMID: 37856565 PMCID: PMC10617735 DOI: 10.1371/journal.pntd.0011715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 10/31/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Developing more sensitive methods for the diagnosis of echinococcosis is essential. In this study PCR assay for sensitive detection of specific cell-free DNA (cfDNA) of Echinococcus granulosus sensu lato in the sera of the sheep naturally infected with echinococcosis was investigated. METHODS To extract cfDNA from 35 infected sheep, the modified phenol-chloroform method was used for two different volumes (0.5 and 2 ml) of serum samples. From each extracted sample, two DNA volumes (5 and 10 μl) were amplified using both standard PCR and semi-nested PCR targeting NADH dehydrogenase subunit I. RESULTS Standard and semi-nested PCR on 0.5 ml of serum samples detected Echinococcus DNA in 8 and 12 out of 35 sheep, respectively; however, using 2 ml of serum samples, they detected 24 and 27 samples. By increasing the volume of template DNA, the PCRs could detect 29 and 33 out of 35 samples. The results were confirmed by sequencing of randomly selected PCR amplicons and comparing them with GenBank databases. CONCLUSIONS Larger volumes of serum for DNA extraction, greater volumes of DNA template for PCR, and employing a semi-nested PCR protocol, increased the sensitivity of PCR to 95%. This approach can also be applied to the diagnosis of echinococcosis in humans.
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Affiliation(s)
- Mahboubeh Hadipour
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hossein Yousofi Darani
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hamid Talebzadeh
- Department of Surgery, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Eslamian
- Department of Surgery, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shima Aboutalebian
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Majid Fasihi Harandi
- Research Center for Hydatid Disease in Iran; Dept. of Parasitology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Hossein Mirhendi
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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Ning W, Zhang C, Tian Z, Wu M, Luo Z, Hu S, Pan H, Li Y. Ω-shaped fiber optic LSPR biosensor based on mismatched hybridization chain reaction and gold nanoparticles for detection of circulating cell-free DNA. Biosens Bioelectron 2023; 228:115175. [PMID: 36871422 DOI: 10.1016/j.bios.2023.115175] [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: 10/19/2022] [Revised: 01/10/2023] [Accepted: 02/20/2023] [Indexed: 02/23/2023]
Abstract
Circulating cell-free DNA (cfDNA) is a promising biomarker of liquid biopsy, but it still faces some difficulties in achieving sensitive and convenient detection. Herein, an Ω-shaped fiber optic localized surface plasmon resonance (FO-LSPR) biosensor based on hybridization chain reaction (HCR) coupled with gold nanoparticles (AuNPs) was developed, and applied in simple and sensitive detection of cfDNA. Specifically, one-base mismatch was designed in HCR hairpins (H1 and H2) to obtain high reaction efficiency, and AuNPs was introduced onto H1 through poly-adenine to construct HCR coupled with AuNPs strategy. Meanwhile, target cfDNA was designed into two domains: one could trigger HCR to generate dsDNA concatemer carrying numerous AuNPs, and the other could hybridize with capture DNA on the surface of Ω-shaped fiber optic (FO) probes. Thus, the presence of target cfDNA would initiate HCR, and bring the formed dsDNA concatemer and AuNPs to approach the probe surface, resulting in dramatically amplified LSPR signal. Besides, HCR required simple isothermal and enzyme-free condition, and Ω-shaped FO probe with high refractive index sensitivity just needed to be immersed into HCR solution directly for signal monitoring. Benefiting from the synergetic amplification of mismatched HCR and AuNPs, the proposed biosensor exhibited high sensitivity with a limit of detection of 14.0 pM, and therefore could provide a potential strategy for biomedical analysis and disease diagnosis.
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Affiliation(s)
- Wei Ning
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Chuyan Zhang
- Medical Equipment Innovation Research Center, Precision Medicine Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ziyi Tian
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Mengfan Wu
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu, 610065, China
| | - Zewei Luo
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu, 610065, China
| | - Shunming Hu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Hongzhi Pan
- The Affiliated Zhoupu Hospital, Shanghai University of Medicine & Health Sciences, Shanghai, 201318, China.
| | - Yongxin Li
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China.
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Linke C, Hunger R, Reinwald M, Deckert M, Mantke R. Quantification of mitochondrial cfDNA reveals new perspectives for early diagnosis of colorectal cancer. BMC Cancer 2023; 23:291. [PMID: 36997875 PMCID: PMC10064655 DOI: 10.1186/s12885-023-10748-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 03/16/2023] [Indexed: 04/01/2023] Open
Abstract
BACKGROUND To unravel how the integrity of nuclear and mitochondrial circulating cell-free DNA (cfDNA) contributes to its plasma quantity in colorectal cancer (CRC) patients. METHODS CfDNA from plasma samples of 80 CRC patients stratified by tumour stage and 50 healthy individuals were extracted. Total cfDNA concentration was determined and equal template concentrations (ETC) were analyzed by quantitative real-time PCR (qPCR) resulting in small and long fragments of KRAS, Alu and MTCO3. The obtained data was also examined relative to the total cfDNA concentration (NTC) and diagnostic accuracy was estimated using receiver operating characteristics. RESULTS Total cfDNA levels were significantly higher in CRC group compared to healthy control and increased with tumour stage. Long nuclear fragment levels were significantly lower in CRC patients in ETC but not NTC condition. The integrity indices of nuclear cfDNA decreased from controls to patients with highly malignant tumor. Mitochondrial cfDNA fragment quantities were strongly reduced in early and late stages of tumor patients and prognostic value was higher in ETC. Predictive models based on either ETC or NTC predictor set showed comparable classification performance. CONCLUSION Increased blood cfDNA concentration in late UICC stages inversely correlate with nuclear cfDNA integrity index and suggest that necrotic degradation is not a major cause for higher total cfDNA quantity. The diagnostic and prognostic value of MTCO3 is highly significant in early stages of CRC and can be evaluated more comprehensively, using ETC for qPCR analysis. TRIAL REGISTRATION The study was registered retrospectively on DRKS, the german register for clinical trials (DRKS00030257, 29/09/2022).
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Affiliation(s)
- Christian Linke
- Department of General and Gastrointestinal Surgery, University Hospital Brandenburg, Brandenburg Medical School Theodor Fontane, Brandenburg, Germany.
- Department of Hematology, Oncology and Palliative Medicine, University Hospital Brandenburg, Brandenburg Medical School Theodor Fontane, Brandenburg, Germany.
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany.
| | - Richard Hunger
- Department of General and Gastrointestinal Surgery, University Hospital Brandenburg, Brandenburg Medical School Theodor Fontane, Brandenburg, Germany
| | - Mark Reinwald
- Department of Hematology, Oncology and Palliative Medicine, University Hospital Brandenburg, Brandenburg Medical School Theodor Fontane, Brandenburg, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
| | - Markus Deckert
- Department of Hematology, Oncology and Palliative Medicine, University Hospital Brandenburg, Brandenburg Medical School Theodor Fontane, Brandenburg, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
| | - René Mantke
- Department of General and Gastrointestinal Surgery, University Hospital Brandenburg, Brandenburg Medical School Theodor Fontane, Brandenburg, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
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Papadimitriou MA, Levis P, Kotronopoulos G, Stravodimos K, Avgeris M, Scorilas A. Preoperative Cell-Free DNA (cfDNA) in Muscle-Invasive Bladder Cancer Treatment Outcome. Clin Chem 2023; 69:399-410. [PMID: 36738246 DOI: 10.1093/clinchem/hvac218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/22/2022] [Indexed: 02/05/2023]
Abstract
BACKGROUND Tumor heterogeneity and lack of personalized prognosis leads to bladder cancer (BlCa) patients' lifelong surveillance with invasive interventions, highlighting the need for modern minimally invasive tools for disease management. Herein, we have evaluated the clinical utility of preoperative serum cell-free DNA (cfDNA) in ameliorating patients' risk-stratification and prognosis. METHODS cfDNA was purified from 190 preoperative BlCa patients and 26 healthy individuals' serum samples and quantified by 2 assays: an in-house quantitative real-time PCR (qPCR) assay using LEP as reference control and a direct fluorometric assay using Qubit HS dsDNA. Capillary electrophoresis was performed in 31 samples for cfDNA fragment profiling. Tumor relapse/progression and metastasis/death were used as clinical endpoints for non-muscle-invasive bladder cancer and muscle-invasive bladder cancer (MIBC), respectively. RESULTS cfDNA profiling by capillary electrophoresis highlighted that total and fragment-related cfDNA levels were significantly increased in BlCa and associated with advance disease stages. Evaluation of cfDNA levels by both Qubit/qPCR displayed highly consistent results (rs = 0.960; P < 0.001). Higher cfDNA was correlated with MIBC and stronger risk for early metastasis (Qubit:hazard ratio [HR] = 3.016, P = 0.009; qPCR:HR = 2.918, P = 0.004) and poor survival (Qubit:HR = 1.898, P = 0.042; qPCR:HR = 1.888, P = 0.026) of MIBC patients. Multivariate cfDNA-fitted models led to superior risk stratification and net benefit for MIBC prognosis compared to disease established markers. CONCLUSIONS Elevated preoperative cfDNA levels are strongly associated with higher risk for short-term metastasis and poor outcome of MIBC, supporting modern noninvasive disease prognosis and management.
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Affiliation(s)
- Maria-Alexandra Papadimitriou
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiotis Levis
- First Department of Urology, "Laiko" General Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios Kotronopoulos
- First Department of Urology, "Laiko" General Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantinos Stravodimos
- First Department of Urology, "Laiko" General Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Margaritis Avgeris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece.,Laboratory of Clinical Biochemistry - Molecular Diagnostics, Second Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, "P. & A. Kyriakou" Children's Hospital, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
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El Hejjioui B, Bouguenouch L, Melhouf MA, El Mouhi H, Bennis S. Clinical Evidence of Circulating Tumor DNA Application in Aggressive Breast Cancer. Diagnostics (Basel) 2023; 13:470. [PMID: 36766575 PMCID: PMC9914403 DOI: 10.3390/diagnostics13030470] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/28/2022] [Accepted: 01/01/2023] [Indexed: 01/31/2023] Open
Abstract
Breast cancer is clinically and biologically heterogeneous and is classified into different subtypes according to the molecular landscape of the tumor. Triple-negative breast cancer is a subtype associated with higher tumor aggressiveness, poor prognosis, and poor response to treatment. In metastatic breast cancer, approximately 6% to 10% of new breast cancer cases are initially staged IV (de novo metastatic disease). The number of metastatic recurrences is estimated to be 20-30% of all existing breast tumor cases, whereby the need to develop specific genetic markers to improve the prognosis of patients suffering from these deadly forms of breast cancer. As an alternative, liquid biopsy methods can minutely identify the molecular architecture of breast cancer, including aggressive forms, which provides new perspectives for more precise diagnosis and more effective therapeutics. This review aimed to summarize the current clinical evidence for the application of circulating tumor DNA in managing breast cancer by detailing the increased usefulness of this biomarker as a diagnostic, prognostic, monitoring, and surveillance marker for breast cancer.
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Affiliation(s)
- Brahim El Hejjioui
- Biomedical and Translational Research Laboratory, Faculty of Medicine and Pharmacy, Sidi Mohamed Ben Abdellah University, Fez 30050, Morocco
- Department of Medical Genetics and Oncogenetics, HASSAN II University Hospital, Fez 30050, Morocco
| | - Laila Bouguenouch
- Department of Medical Genetics and Oncogenetics, HASSAN II University Hospital, Fez 30050, Morocco
| | | | - Hind El Mouhi
- Department of Medical Genetics and Oncogenetics, HASSAN II University Hospital, Fez 30050, Morocco
| | - Sanae Bennis
- Biomedical and Translational Research Laboratory, Faculty of Medicine and Pharmacy, Sidi Mohamed Ben Abdellah University, Fez 30050, Morocco
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Martínez-Laperche C, Sanz-Villanueva L, Díaz Crespo FJ, Muñiz P, Martín Rojas R, Carbonell D, Chicano M, Suárez-González J, Menárguez J, Kwon M, Diez Martín JL, Buño I, Bastos Oreiro M. EZH2 mutations at diagnosis in follicular lymphoma: a promising biomarker to guide frontline treatment. BMC Cancer 2022; 22:982. [PMID: 36104682 PMCID: PMC9476261 DOI: 10.1186/s12885-022-10070-z] [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: 02/27/2022] [Accepted: 08/05/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractEZH2 is mutated in nearly 25% of follicular lymphoma (FL) cases. Little is known about how EZH2 affects patients’ response to therapy. In this context, the aim of this study was to retrospectively analyze the frequency of mutations in EZH2 at diagnosis in tissue and ctDNA in patients with FL and to assess the patients’ outcomes after receiving immunochemotherapy, depending on the EZH2 mutation status. Among the 154 patients included in the study, 27% had mutated EZH2 (46% with high-grade and 26% with low-grade FL). Of the mutated tissue samples, the mutation in ctDNA was identified in 44% of cases. EZH2 mutation in ctDNA was not identified in any patient unmutated in the tissue.Unmutated patients who received R-CHOP had significantly more relapses than patients who received R-Bendamustine (16/49 vs. 2/23, p = 0.040). Furthermore, our results show that patients with mutated EZH2 treated with R-CHOP vs. those treated with R-Bendamustine present a lower incidence of relapse (10% vs. 42% p = 0.09 at 4 years), a higher PFS (92% vs. 40% p = 0.039 at 4 years), and higher OS (100% vs. 78% p = 0.039 at 4 years). Based on these data, RCHOP could be a more suitable regimen for mutated patients, and R-bendamustine for unmutated patients. These findings could mean the first-time identification of a useful biomarker to guide upfront therapy in FL.
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Vodickova L, Horak J, Vodicka P. Genetic Susceptibility in Understanding of Pancreatic Ductal Adenocarcinoma Risk: A Decade-Long Effort of the PANDORA Consortium. Cancer Epidemiol Biomarkers Prev 2022; 31:942-948. [PMID: 35506247 PMCID: PMC9306286 DOI: 10.1158/1055-9965.epi-21-1340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 02/08/2022] [Accepted: 03/02/2022] [Indexed: 01/07/2023] Open
Abstract
Pancreatic cancer, a complex disease, emerges as a severe health problem worldwide and it exhibits a poor prognosis and high mortality. Risk factors associated with sporadic pancreatic cancer remain poorly understood, even less is known about disease prognosis due to its rapid progression. The PANcreatic Disease ReseArch (PANDoRA) consortium, of which the authors are members, was established to coordinate the efforts of different research groups to uncover new genetic factors for pancreatic cancer risk, response to treatment, and patient survival. PANDoRA consortium has contributed to the identification of several low-penetrance risk loci for the disease both by candidate variants approach and genome-wide association studies, including those in cell-cycle and DNA damage response, telomere homeostasis, SCL and ABC transporters, ABO locus variability, mitochondrial metabolism and it participated on collaborative genome-wide association study approach and implementation of a search for functional-based pancreatic cancer risk loci and long noncoding RNAs. Complex studies covering genetic, environmental and microenvironmental factors in the pancreatic cancer onset, progression and its prognosis are warranted.
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Affiliation(s)
- Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, 1 Faculty of Medicine Charles University, Prague, Czech Republic
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Josef Horak
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, 1 Faculty of Medicine Charles University, Prague, Czech Republic
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
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Designing highly multiplex PCR primer sets with Simulated Annealing Design using Dimer Likelihood Estimation (SADDLE). Nat Commun 2022; 13:1881. [PMID: 35410464 PMCID: PMC9001684 DOI: 10.1038/s41467-022-29500-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 03/18/2022] [Indexed: 11/09/2022] Open
Abstract
One major challenge in the design of highly multiplexed PCR primer sets is the large number of potential primer dimer species that grows quadratically with the number of primers to be designed. Simultaneously, there are exponentially many choices for multiplex primer sequence selection, resulting in systematic evaluation approaches being computationally intractable. Here, we present and experimentally validate Simulated Annealing Design using Dimer Likelihood Estimation (SADDLE), a stochastic algorithm for design of multiplex PCR primer sets that minimize primer dimer formation. In a 96-plex PCR primer set (192 primers), the fraction of primer dimers decreases from 90.7% in a naively designed primer set to 4.9% in our optimized primer set. Even when scaling to 384-plex (768 primers), the optimized primer set maintains low dimer fraction. In addition to NGS, SADDLE-designed primer sets can also be used in qPCR settings to allow highly multiplexed detection of gene fusions in cDNA, with a single-tube assay comprising 60 primers detecting 56 distinct gene fusions recurrently observed in lung cancer. The design of highly multiplex PCR primers to amplify and enrich many different DNA sequences is increasing in biomedical importance as new mutations and pathogens are identified. The authors present and experimentally validate Simulated Annealing Design using Dimer Likelihood Estimation (SADDLE), a stochastic algorithm for design of highly multiplex PCR primer sets that minimize primer dimer formation.
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Purification and Phosphoproteomic Analysis of Plasma-Derived Extracellular Vesicles. Methods Mol Biol 2022; 2504:147-156. [PMID: 35467285 PMCID: PMC9437911 DOI: 10.1007/978-1-0716-2341-1_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A successful phosphoproteomics analysis of extracellular vesicles (EVs) requires a unique approach, fine-tuned to address the challenges that have plagued plasma-based biomarker discovery. Here, I detail a procedure, which combines EVtrap-based high-recovery EV isolation, phase-transfer surfactant method for protein extraction, and PolyMAC-based enrichment of phosphopeptides. The combination of these methods provides a highly effective strategy for EV-based phosphoproteome analysis and leads to the discovery of novel phospho-markers previously undetectable.
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12
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Ye Y, Tong F, Wang S, Jiang J, Gao J, Liu L, Liu K, Wang F, Wang Z, Ou J, Chen B, Wilson DA, Tu Y, Peng F. Apoptotic Tumor DNA Activated Nanomotor Chemotaxis. NANO LETTERS 2021; 21:8086-8094. [PMID: 34559543 DOI: 10.1021/acs.nanolett.1c02441] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Inspired by the tactic organisms in Nature that can self-direct their movement following environmental stimulus gradient, we proposed a DNase functionalized Janus nanoparticle (JNP) nanomotor system for the first time, which can be powered by ultralow nM to μM levels of DNA. The system exhibited interesting chemotactic behavior toward a DNA richer area, which is physiologically related with many diseases including tumors. In the presence of the subtle DNA gradient generated by apoptotic tumor cells, the cargo loaded nanomotors were able to sense the DNA signal released by the cells and demonstrate directional motion toward tumor cells. For our system, the subtle DNA gradient by a small amount (10 μL) of tumor cells is sufficient to induce the chemotaxis behavior of self-navigating and self-targeting ability of our nanomotor system, which promises to shed new light for tumor diagnosis and therapy.
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Affiliation(s)
- Yicheng Ye
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
- School of Materials Science and Engineering, Sun Yat-Sen University, Guangzhou 510275, China
| | - Fei Tong
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Shuanghu Wang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Jiamiao Jiang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Junbin Gao
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Lu Liu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Kun Liu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Fei Wang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Zhen Wang
- School of Materials Science and Engineering, Sun Yat-Sen University, Guangzhou 510275, China
| | - Juanfeng Ou
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Bin Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Daniela A Wilson
- Institute for Molecules and Materials, Radboud University, Nijmegen, 6525 AJ, The Netherlands
| | - Yingfeng Tu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Fei Peng
- School of Materials Science and Engineering, Sun Yat-Sen University, Guangzhou 510275, China
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13
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de Miranda FS, Barauna VG, dos Santos L, Costa G, Vassallo PF, Campos LCG. Properties and Application of Cell-Free DNA as a Clinical Biomarker. Int J Mol Sci 2021; 22:9110. [PMID: 34502023 PMCID: PMC8431421 DOI: 10.3390/ijms22179110] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/18/2021] [Accepted: 04/20/2021] [Indexed: 12/17/2022] Open
Abstract
Biomarkers are valuable tools in clinical practice. In 2001, the National Institutes of Health (NIH) standardized the definition of a biomarker as a characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacological responses to a therapeutic intervention. A biomarker has clinical relevance when it presents precision, standardization and reproducibility, suitability to the patient, straightforward interpretation by clinicians, and high sensitivity and/or specificity by the parameter it proposes to identify. Thus, serum biomarkers should have advantages related to the simplicity of the procedures and to the fact that venous blood collection is commonplace in clinical practice. We described the potentiality of cfDNA as a general clinical biomarker and focused on endothelial dysfunction. Circulating cell-free DNA (cfDNA) refers to extracellular DNA present in body fluid that may be derived from both normal and diseased cells. An increasing number of studies demonstrate the potential use of cfDNA as a noninvasive biomarker to determine physiologic and pathologic conditions. However, although still scarce, increasing evidence has been reported regarding using cfDNA in cardiovascular diseases. Here, we have reviewed the history of cfDNA, its source, molecular features, and release mechanism. We also show recent studies that have investigated cfDNA as a possible marker of endothelial damage in clinical settings. In the cardiovascular system, the studies are quite new, and although interesting, stronger evidence is still needed. However, some drawbacks in cfDNA methodologies should be overcome before its recommendation as a biomarker in the clinical setting.
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Affiliation(s)
- Felipe Silva de Miranda
- Post Graduation Program in Biology and Biotechnology of Microorganisms, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil;
- Department of Biological Science, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
- Laboratory of Applied Pathology and Genetics, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
| | - Valério Garrone Barauna
- Post Graduation Program in Health Sciences, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil;
- Molecular Physiology Laboratory of Exercise Science, Federal University of Espírito Santo, Vitória 29075-910, Espírito Santo, Brazil
- Post Graduation Program in Physiological Sciences, Federal University of Espírito Santo, Vitória 29075-910, Espírito Santo, Brazil; (G.C.); (P.F.V.)
| | - Leandro dos Santos
- Academic Unit of Serra Talhada, Rural Federal University of Pernambuco, Serra Talhada 56909-535, Pernambuco, Brazil;
| | - Gustavo Costa
- Post Graduation Program in Physiological Sciences, Federal University of Espírito Santo, Vitória 29075-910, Espírito Santo, Brazil; (G.C.); (P.F.V.)
| | - Paula Frizera Vassallo
- Post Graduation Program in Physiological Sciences, Federal University of Espírito Santo, Vitória 29075-910, Espírito Santo, Brazil; (G.C.); (P.F.V.)
- Clinical Hospital, Federal University of Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil
| | - Luciene Cristina Gastalho Campos
- Post Graduation Program in Biology and Biotechnology of Microorganisms, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil;
- Department of Biological Science, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
- Laboratory of Applied Pathology and Genetics, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
- Post Graduation Program in Health Sciences, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil;
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Cervena K, Pardini B, Urbanova M, Vodenkova S, Eva P, Veskrnova V, Levy M, Buchler T, Mokrejs M, Naccarati A, Vodicka P, Vymetalkova V. Mutational landscape of plasma cell-free DNA identifies molecular features associated with therapeutic response in patients with colon cancer. A pilot study. Mutagenesis 2021; 36:358-368. [PMID: 34214148 DOI: 10.1093/mutage/geab024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/30/2021] [Indexed: 12/29/2022] Open
Abstract
Cell-free DNA (cfDNA) has recently been used as a non-invasive diagnostic tool for detecting tumor-specific mutations. cfDNA may also be used for monitoring disease progression and treatment response, but so far researchers focused on one or few genes only. A genomic profile may provide better information on patient prognosis compared to single specific mutations. In this hypothesis-generating study, we profiled by whole exome sequencing serial plasma samples from 10 colon cancer (CC) patients collected before and after 5-fluorouracil-based therapy, and one year after diagnosis to determine alterations associated with treatment response. In parallel, genome profiling was also performed in patients' corresponding tumor tissue to ascertain the molecular landscape of resistant tumors. The mutation concordance between cfDNA and tumor tissue DNA was higher in more advanced tumor stages than in the early stages of the disease. In non-responders, a specific mutation profile was observed in tumor tissues (TPSD1 p.Ala92Thr, CPAMD8 p.Arg341Gln, OBP2A p.ArgTyr123CysHis). A pathogenic APC mutation (p.Ser1315Ter) was detected only in cfDNA of one poor responder one year after the diagnosis and after therapy termination. Another poor responder presented a likely pathogenic TP53 mutation (p.Arg110Pro) in cfDNA of all plasma samplings and in tumor tissue. In conclusion, cfDNA could be used for genetic characterization of CC patients and might be clinically useful for non-invasive therapy response monitoring.
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Affiliation(s)
- Klara Cervena
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 142 20 Prague, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic
| | - Barbara Pardini
- IIGM Italian Institute for Genomic Medicine, Sp142 Km3.95, 10060 Candiolo, Turin, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Sp142 Km3.95, 10060 Candiolo,Turin, Italy
| | - Marketa Urbanova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic
| | - Sona Vodenkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 142 20 Prague, Czech Republic.,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, AlejSvobody 76, 323 00 Pilsen, Czech Republic
| | - Pazourkova Eva
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic.,Department of Nephrology, First Faculty of Medicine, Charles University and General Faculty Hospital in Prague, Czech Republic
| | - Veronika Veskrnova
- Department of Oncology, First Faculty of Medicine, Charles University and Thomayer Hospital, Videnska 800, 140 59, Prague, Czech Republic
| | - Miroslav Levy
- Department of Surgery, Thomayer University Hospital, Videnska 800, 140 59, Prague, Czech Republic
| | - Tomas Buchler
- Department of Oncology, First Faculty of Medicine, Charles University and Thomayer Hospital, Videnska 800, 140 59, Prague, Czech Republic
| | - Martin Mokrejs
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 142 20 Prague, Czech Republic.,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, AlejSvobody 76, 323 00 Pilsen, Czech Republic
| | - Alessio Naccarati
- IIGM Italian Institute for Genomic Medicine, Sp142 Km3.95, 10060 Candiolo, Turin, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Sp142 Km3.95, 10060 Candiolo,Turin, Italy
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 142 20 Prague, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic.,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, AlejSvobody 76, 323 00 Pilsen, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 142 20 Prague, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic.,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, AlejSvobody 76, 323 00 Pilsen, Czech Republic
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15
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The Feasibility of Patient-Specific Circulating Tumor DNA Monitoring throughout Multi-Modality Therapy for Locally Advanced Esophageal and Rectal Cancer: A Potential Biomarker for Early Detection of Subclinical Disease. Diagnostics (Basel) 2021; 11:diagnostics11010073. [PMID: 33466369 PMCID: PMC7824834 DOI: 10.3390/diagnostics11010073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/21/2020] [Accepted: 12/30/2020] [Indexed: 12/12/2022] Open
Abstract
As non-operative management (NOM) of esophageal and rectal cancer is becoming more prevalent, blood-biomarkers such as circulating tumor DNA (ctDNA) may provide clinical information in addition to endoscopy and imaging to aid in treatment decisions following chemotherapy and radiation therapy. In this feasibility study, we prospectively collected plasma samples from locally advanced esophageal (n = 3) and rectal cancer (n = 2) patients undergoing multimodal neoadjuvant therapy to assess the feasibility of serial ctDNA monitoring throughout neoadjuvant therapy. Using the Dual-Index Degenerate Adaptor-Sequencing (DIDA-Seq) error-correction method, we serially interrogated plasma cell-free DNA at 28-41 tumor-specific genomic loci throughout therapy and in surveillance with an average limit of detection of 0.016% mutant allele frequency. In both rectal cancer patients, ctDNA levels were persistently elevated following total neoadjuvant therapy with eventual detection of clinical recurrence prior to salvage surgery. Among the esophageal cancer patients, ctDNA levels closely correlated with tumor burden throughout and following neoadjuvant therapy, which was associated with a pathologic complete response in one patient. In this feasibility study, patient- and tumor-specific ctDNA levels correlated with clinical outcomes throughout multi-modality therapy suggesting that serial monitoring of patient ctDNA has the potential to serve as a highly sensitive and specific biomarker to risk-stratify esophageal and rectal cancer patients eligible for NOM. Further prospective investigation is warranted.
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16
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Thakral D, Gupta R, Sahoo RK, Verma P, Kumar I, Vashishtha S. Real-Time Molecular Monitoring in Acute Myeloid Leukemia With Circulating Tumor DNA. Front Cell Dev Biol 2020; 8:604391. [PMID: 33363162 PMCID: PMC7759522 DOI: 10.3389/fcell.2020.604391] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/21/2020] [Indexed: 02/06/2023] Open
Abstract
The clonal evolution of acute myeloid leukemia (AML), an oligoclonal hematological malignancy, is driven by a plethora of cytogenetic abnormalities, gene mutations, abnormal epigenetic patterns, and aberrant gene expressions. These alterations in the leukemic blasts promote clinically diverse manifestations with common characteristics of high relapse and drug resistance. Defining and real-time monitoring of a personalized panel of these predictive genetic biomarkers is rapidly being adapted in clinical setting for diagnostic, prognostic, and therapeutic decision-making in AML. A major challenge remains the frequency of invasive biopsy procedures that can be routinely performed for monitoring of AML disease progression. Moreover, a single-site biopsy is not representative of the tumor heterogeneity as it is spatially and temporally constrained and necessitates the understanding of longitudinal and spatial subclonal dynamics in AML. Hematopoietic cells are a major contributor to plasma cell-free DNA, which also contain leukemia-specific aberrations as the circulating tumor-derived DNA (ctDNA) fraction. Plasma cell-free DNA analysis holds immense potential as a minimally invasive tool for genomic profiling at diagnosis as well as clonal evolution during AML disease progression. With the technological advances and increasing sensitivity for detection of ctDNA, both genetic and epigenetic aberrations can be qualitatively and quantitatively evaluated. However, challenges remain in validating the utility of liquid biopsy tools in clinics, and universal recommendations are still awaited towards reliable diagnostics and prognostics. Here, we provide an overview on the scope of ctDNA analyses for prognosis, assessment of response to treatment and measurable residual disease, prediction of disease relapse, development of acquired resistance and beyond in AML.
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Affiliation(s)
- Deepshi Thakral
- Laboratory Oncology Unit, Dr. BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Ritu Gupta
- Laboratory Oncology Unit, Dr. BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Ranjit Kumar Sahoo
- Department of Medical Oncology, Dr. BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Pramod Verma
- Laboratory Oncology Unit, Dr. BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Indresh Kumar
- Laboratory Oncology Unit, Dr. BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Sangeeta Vashishtha
- Laboratory Oncology Unit, Dr. BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
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Abstract
Dr Francesca Ciccarelli (The Francis Crick Institute, UK) and Dr James De Gregori (University of Colorado, USA) interview 3 top scientists in clinical (Dr Charles Swanton, The Francis Crick Institute, UK), molecular (Dr Kornelia Polyak, Dana-Farber Cancer Institute, USA), and evolutionary cancer research (Dr Carlo Maley, Arizona State University, USA) to discuss the current status of knowledge, the challenges, and the opportunities to move the field forward.
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Affiliation(s)
- Francesca D. Ciccarelli
- Cancer Systems Biology Laboratory, the Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE11UL, UK
| | - James DeGregori
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, U S A
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18
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Ying H, Fengying S, Feng H, Yanhong W, Xianru X, Xiaolei T. Diagnostic value of quantification of circulating free DNA for gall bladder cancer using a chemiluminescence DNA biosensor system based on DNA G-quadruplex/ hemin enzyme. Transl Oncol 2020; 14:100928. [PMID: 33212417 PMCID: PMC7679247 DOI: 10.1016/j.tranon.2020.100928] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/07/2020] [Accepted: 10/23/2020] [Indexed: 12/24/2022] Open
Abstract
In this study, we designed a novel detection system to detect DNA based on DNA G-quadruplex/hemin enzyme. It consisted of DNA probes with hemin that can form a special structure via self-assembly after paring with target DNA. The special structure containing hemin showed enzyme activity catalyzing substrates for coloration or luminescence. Based on this chemiluminescence DNA biosensor system using DNA G-quadruplex/hemin enzyme, we designed a pair of DNA probes targeting β-actin DNA to detect circulating free DNA (cfDNA) in human serum from patients with gall bladder cancer (GBC), patients with cholecystitis, and healthy donors and calculated concentrations of cfDNA according to a standard curve. In the serum of patients with GBC, the level of cfDNA was higher than those in the serum of patients with cholecystitis and healthy donors. This is a convenient, economic, and promising approach to aid the diagnosis of patients with GBC via detecting serum cfDNA.
Gall bladder cancer (GBC) is an insidious but rapidly progressed disease with a poor prognosis and high mortality rate. To explore a novel method for GBC diagnosis, we quantified circulating free DNA (cfDNA) in serum samples from 228 participants, including 83 patients with GBC, 75 patients with cholecystitis, and 70 healthy donors, using a chemiluminescence DNA biosensor system based on DNA G-quadruplex/hemin enzyme. We measured β-actin gene expression to evaluate serum cfDNA levels representing as chemiluminescence intensity with the addition of sufficient probes. We analyzed associations of cfDNA quantities in serum samples and corresponding pathological stages and found that the concentration of cfDNA was significantly higher in GBC group than in the healthy control and cholecystitis groups. The levels of cfDNA were significantly associated with TNM stage, lymph node involvement, metastasis, and jaundice. The ROC curves showed that the diagnostic value of chemiluminescence DNA biosensor system was nearly equivalent to that of qPCR. Our method can distinguish patients with GBC from healthy donors and patients with cholecystitis clearly; however, this method was not available to distinguish patients with cholecystitis from the healthy controls. In summary, cfDNA maybe serve as a new diagnostic and noninvasive marker for the diagnosis of GBC using chemiluminescence DNA biosensor system based on DNA G-quadruplex/hemin enzyme.
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Affiliation(s)
- Hua Ying
- Vascular disease research center, Basic Medical Laboratory, the Second affiliated Hospital of Wannan Medical College, Kangfu Road 10# of Jinghu District, Wuhu 241000, China; School of Nursing, Wannan Medical College, Wuhu 241000, China
| | - Sun Fengying
- Department of Clinical Laboratory, The second people's hospital of Wuhu city, Wuhu 241000, China
| | - Hu Feng
- Department of blood transfusion, Yijishan Hospital of Wannan Medical College, Wuhu 241000, China
| | - Wu Yanhong
- Department of immunology and microbiology, Wannan Medical College, Wuhu 241000, China
| | - Xia Xianru
- Department of Clinical Laboratory, Affiliated Taihe hospital of Hubei Univiersity of Medicine, Renminnan Road 32# of Maojian District, Shiyan 442008, China
| | - Tang Xiaolei
- Vascular disease research center, Basic Medical Laboratory, the Second affiliated Hospital of Wannan Medical College, Kangfu Road 10# of Jinghu District, Wuhu 241000, China.
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19
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Ponti G, Maccaferri M, Percesepe A, Tomasi A, Ozben T. Liquid biopsy with cell free DNA: new horizons for prostate cancer. Crit Rev Clin Lab Sci 2020; 58:60-76. [PMID: 32805148 DOI: 10.1080/10408363.2020.1803789] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Although prostate cancer (PCa) is one of the most common tumors in European males, the only minimally invasive diagnostic tool in PCa setup is the determination of PSA in serum. Cell-free DNA (cfDNA) has been demonstrated to be helpful for PCa diagnosis but has not yet been integrated into the clinical setting. This review aims to provide a systematic update of cfDNA and its fragmentation patterns in PCa reported in literature published over the last twenty years. Due to the high variability of the scientific methods adopted and a lack of standardized median cfDNA levels, results fluctuate across different studies. These differences may be due to the cfDNA source, the quantification method, or the fragmentation pattern. Blood plasma is the most frequently analyzed biological fluid, but seminal plasma has been reported to contain higher cfDNA concentration due to its vicinity to the tumor origin. CfDNA has been shown to be composed of single-stranded (ssDNA) and double-stranded DNA (dsDNA), so the total cfDNA concentration should be preferred as it corresponds best to the tumor mass. Fluorometry and capillary electrophoresis (CE) may be quick and cost-effective tools for cfDNA assessment in a clinical setting. The greatest future challenge is the elaboration of common guidelines and standardized procedures for diagnostic laboratories performing cfDNA analysis. A multiparametric approach combining the analysis of total cfDNA (both ssDNA and dsDNA), cfDNA fragment length, and specific genetic mutations (ctDNA assessment) is required for optimal future applications of liquid biopsy.
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Affiliation(s)
- Giovanni Ponti
- Division of Clinical Pathology, Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncological and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Monia Maccaferri
- Dermatology Unit, Azienda Ospedaliero-Universitaria of Modena, Modena, Italy
| | - Antonio Percesepe
- Medical Genetics Unit, Azienda Ospedaliero-Universitaria of Parma, Parma, Italy
| | - Aldo Tomasi
- Division of Clinical Pathology, Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncological and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Tomris Ozben
- Faculty of Medicine, Department of Clinical Biochemistry, Akdeniz University, Antalya, Turkey
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Filip S, Vymetalkova V, Petera J, Vodickova L, Kubecek O, John S, Cecka F, Krupova M, Manethova M, Cervena K, Vodicka P. Distant Metastasis in Colorectal Cancer Patients-Do We Have New Predicting Clinicopathological and Molecular Biomarkers? A Comprehensive Review. Int J Mol Sci 2020; 21:E5255. [PMID: 32722130 PMCID: PMC7432613 DOI: 10.3390/ijms21155255] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) remains a serious health problem worldwide. Approximately half of patients will develop distant metastasis after CRC resection, usually with very poor prognosis afterwards. Because patient performance after distant metastasis surgery remains very heterogeneous, ranging from death within 2 years to a long-term cure, there is a clinical need for a precise risk stratification of patients to aid pre- and post-operative decisions. Furthermore, around 20% of identified CRC cases are at IV stage disease, known as a metastatic CRC (mCRC). In this review, we overview possible molecular and clinicopathological biomarkers that may provide prognostic and predictive information for patients with distant metastasis. These may comprise sidedness of the tumor, molecular profile and epigenetic characteristics of the primary tumor and arising metastatic CRC, and early markers reflecting cancer cell resistance in mCRC and biomarkers identified from transcriptome. This review discusses current stage in employment of these biomarkers in clinical practice as well as summarizes current experience in identifying predictive biomarkers in mCRC treatment.
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Affiliation(s)
- Stanislav Filip
- Department of Oncology and Radiotherapy, Charles University, Faculty of Medicine in Hradec Kralove, Šimkova 870, 50001 Hradec Králové, Czech Republic; (J.P.); (O.K.); (S.J.)
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic; (V.V.); (L.V.); (K.C.)
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655, 32300 Pilsen, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 12800 Prague, Czech Republic
| | - Jiri Petera
- Department of Oncology and Radiotherapy, Charles University, Faculty of Medicine in Hradec Kralove, Šimkova 870, 50001 Hradec Králové, Czech Republic; (J.P.); (O.K.); (S.J.)
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic; (V.V.); (L.V.); (K.C.)
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655, 32300 Pilsen, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 12800 Prague, Czech Republic
| | - Ondrej Kubecek
- Department of Oncology and Radiotherapy, Charles University, Faculty of Medicine in Hradec Kralove, Šimkova 870, 50001 Hradec Králové, Czech Republic; (J.P.); (O.K.); (S.J.)
| | - Stanislav John
- Department of Oncology and Radiotherapy, Charles University, Faculty of Medicine in Hradec Kralove, Šimkova 870, 50001 Hradec Králové, Czech Republic; (J.P.); (O.K.); (S.J.)
| | - Filip Cecka
- Department of Surgery, University Hospital in Hradec Kralove, Sokolská 581, 50005 Hradec Králové, Czech Republic;
| | - Marketa Krupova
- The Fingerland Department of Pathology, University Hospital in Hradec Kralove, Sokolská 581, 50005 Hradec Králové, Czech Republic; (M.K.); (M.M.)
| | - Monika Manethova
- The Fingerland Department of Pathology, University Hospital in Hradec Kralove, Sokolská 581, 50005 Hradec Králové, Czech Republic; (M.K.); (M.M.)
| | - Klara Cervena
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic; (V.V.); (L.V.); (K.C.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 12800 Prague, Czech Republic
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic; (V.V.); (L.V.); (K.C.)
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655, 32300 Pilsen, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 12800 Prague, Czech Republic
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21
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Iliuk A, Wu X, Li L, Sun J, Hadisurya M, Boris RS, Tao WA. Plasma-Derived Extracellular Vesicle Phosphoproteomics through Chemical Affinity Purification. J Proteome Res 2020; 19:2563-2574. [PMID: 32396726 DOI: 10.1021/acs.jproteome.0c00151] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The invasive nature and the pain caused to patients inhibit the routine use of tissue biopsy-based procedures for cancer diagnosis and surveillance. The analysis of extracellular vesicles (EVs) from biofluids has recently gained significant traction in the liquid biopsy field. EVs offer an essential "snapshot" of their precursor cells in real time and contain an information-rich collection of nucleic acids, proteins, lipids, and so on. The analysis of protein phosphorylation, as a direct marker of cellular signaling and disease progression could be an important stepping stone to successful liquid biopsy applications. Here we introduce a rapid EV isolation method based on chemical affinity called EVtrap (extracellular vesicle total recovery and purification) for the EV phosphoproteomics analysis of human plasma. By incorporating EVtrap with high-performance mass spectrometry (MS), we were able to identify over 16 000 unique peptides representing 2238 unique EV proteins from just 5 μL of plasma sample, including most known EV markers, with substantially higher recovery levels compared with ultracentrifugation. Most importantly, more than 5500 unique phosphopeptides representing almost 1600 phosphoproteins in EVs were identified using only 1 mL of plasma. Finally, we carried out a quantitative EV phosphoproteomics analysis of plasma samples from patients diagnosed with chronic kidney disease or kidney cancer, identifying dozens of phosphoproteins capable of distinguishing disease states from healthy controls. The study demonstrates the potential feasibility of our robust analytical pipeline for cancer signaling monitoring by tracking plasma EV phosphorylation.
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Affiliation(s)
- Anton Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Tymora Analytical Operations, West Lafayette, Indiana 47906, United States
| | - Xiaofeng Wu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Li Li
- Tymora Analytical Operations, West Lafayette, Indiana 47906, United States
| | - Jie Sun
- College of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Marco Hadisurya
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ronald S Boris
- Department of Urology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Tymora Analytical Operations, West Lafayette, Indiana 47906, United States.,Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.,College of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.,Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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22
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Siskova A, Cervena K, Kral J, Hucl T, Vodicka P, Vymetalkova V. Colorectal Adenomas-Genetics and Searching for New Molecular Screening Biomarkers. Int J Mol Sci 2020; 21:ijms21093260. [PMID: 32380676 PMCID: PMC7247353 DOI: 10.3390/ijms21093260] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 05/01/2020] [Accepted: 05/02/2020] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is a malignant disease with an incidence of over 1.8 million new cases per year worldwide. CRC outcome is closely related to the respective stage of CRC and is more favorable at less advanced stages. Detection of early colorectal adenomas is the key to survival. In spite of implemented screening programs showing efficiency in the detection of early precancerous lesions and CRC in asymptomatic patients, a significant number of patients are still diagnosed in advanced stages. Research on CRC accomplished during the last decade has improved our understanding of the etiology and development of colorectal adenomas and revealed weaknesses in the general approach to their detection and elimination. Recent studies seek to find a reliable non-invasive biomarker detectable even in the blood. New candidate biomarkers could be selected on the basis of so-called liquid biopsy, such as long non-coding RNA, microRNA, circulating cell-free DNA, circulating tumor cells, and inflammatory factors released from the adenoma into circulation. In this work, we focused on both genetic and epigenetic changes associated with the development of colorectal adenomas into colorectal carcinoma and we also discuss new possible biomarkers that are detectable even in adenomas prior to cancer development.
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Affiliation(s)
- Anna Siskova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 14200 Prague, Czech Republic; (K.C.); (J.K.); (V.V.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 12800 Prague, Czech Republic
- Correspondence: (A.S.); (P.V.); Tel.: +420-241062251 (A.S.); +420-241062694 (P.V.)
| | - Klara Cervena
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 14200 Prague, Czech Republic; (K.C.); (J.K.); (V.V.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 12800 Prague, Czech Republic
| | - Jan Kral
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 14200 Prague, Czech Republic; (K.C.); (J.K.); (V.V.)
- Institute for Clinical and Experimental Medicine, Videnska 1958/9, 14021 Prague, Czech Republic;
| | - Tomas Hucl
- Institute for Clinical and Experimental Medicine, Videnska 1958/9, 14021 Prague, Czech Republic;
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 14200 Prague, Czech Republic; (K.C.); (J.K.); (V.V.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 12800 Prague, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300 Pilsen, Czech Republic
- Correspondence: (A.S.); (P.V.); Tel.: +420-241062251 (A.S.); +420-241062694 (P.V.)
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 14200 Prague, Czech Republic; (K.C.); (J.K.); (V.V.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 12800 Prague, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300 Pilsen, Czech Republic
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