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Połeć A, Ekstrøm PO, Fougner C, Sørlie T, Norum JH. Rapid assessment of 3-dimensional intra-tumor heterogeneity through cycling temperature capillary electrophoresis. BMC Res Notes 2023; 16:167. [PMID: 37568187 PMCID: PMC10416412 DOI: 10.1186/s13104-023-06437-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 07/20/2023] [Indexed: 08/13/2023] Open
Abstract
OBJECTIVE Tumors are heterogeneous three-dimensional masses populated by numerous cell types, including distinct sub-clones of cancerous cells. Various sub-clones within the same tumor mass may respond differently to cancer treatment, and intra-tumor heterogeneity contributes to acquired therapeutic resistance. Thus, one tissue biopsy will in most cases not be representative of the entire genetic landscape of a tumor mass. In this study, we aimed to establish an easily accessible, low cost method to address intra-tumor heterogeneity in three dimensions, for a limited number of DNA alterations. RESULTS This study includes analyses of the three-dimensional (3D) distribution of DNA mutations in human colon cancer and mouse mammary gland tumor tissue samples. We used laser capture microdissection for the unbiased collection of tissue in several XY-planes throughout the tumor masses. Cycling temperature capillary electrophoresis was used to determine mutant allele frequency. High-resolution distribution maps of KRAS and Trp53 mutations were generated for each XY-plane in human and mouse tumor samples, respectively. To provide a holistic interpretation of the mutation distribution, we generated interactive 3D heatmaps giving an easily interpretable understanding of the spatial distribution of the analyzed mutations. The method described herein provides an accessible way of describing intra-tumor heterogeneity for a limited number of mutations.
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Affiliation(s)
- Anna Połeć
- Department of Cancer Genetics, Institute for Cancer Research, Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Per Olaf Ekstrøm
- Department of Tumor Biology, Institute for Cancer Research, Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Christian Fougner
- Department of Cancer Genetics, Institute for Cancer Research, Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Therese Sørlie
- Department of Cancer Genetics, Institute for Cancer Research, Radium Hospital, Oslo University Hospital, Oslo, Norway
- Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Jens Henrik Norum
- Department of Cancer Genetics, Institute for Cancer Research, Radium Hospital, Oslo University Hospital, Oslo, Norway.
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Applications of Probiotic-Based Multi-Components to Human, Animal and Ecosystem Health: Concepts, Methodologies, and Action Mechanisms. Microorganisms 2022; 10:microorganisms10091700. [PMID: 36144301 PMCID: PMC9502345 DOI: 10.3390/microorganisms10091700] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/12/2022] [Accepted: 08/20/2022] [Indexed: 02/05/2023] Open
Abstract
Probiotics and related preparations, including synbiotics and postbiotics, are living and non-living microbial-based multi-components, which are now among the most popular bioactive agents. Such interests mainly arise from the wide range and numerous beneficial effects of their use for various hosts. The current minireview article attempts to provide an overview and discuss in a holistic way the concepts, methodologies, action mechanisms, and applications of probiotic-based multi-components in human, animal, plant, soil, and environment health. Probiotic-based multi-component preparations refer to a mixture of bioactive agents, containing probiotics or postbiotics as main functional ingredients, and prebiotics, protectants, stabilizers, encapsulating agents, and other compounds as additional constituents. Analyzing, characterizing, and monitoring over time the traceability, performance, and stability of such multi-component ingredients require relevant and sensitive analytical tools and methodologies. Two innovative profiling and monitoring methods, the thermophysical fingerprinting thermogravimetry-differential scanning calorimetry technique (TGA-DSC) of the whole multi-component powder preparations, and the Advanced Testing for Genetic Composition (ATGC) strain analysis up to the subspecies level, are presented, illustrated, and discussed in this review to respond to those requirements. Finally, the paper deals with some selected applications of probiotic-based multi-components to human, animal, plant, soil and environment health, while mentioning their possible action mechanisms.
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Refinetti P, Morgenthaler S, Thilly WG, Arstad C, Ekstrøm PO. Tracing of Human Tumor Cell Lineages by Mitochondrial Mutations. Front Oncol 2020; 10:523860. [PMID: 33344219 PMCID: PMC7745703 DOI: 10.3389/fonc.2020.523860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 10/28/2020] [Indexed: 11/21/2022] Open
Abstract
Background Previous studies have shown the value in studying lineage tracing in slices of human tumors. However, a tumor is not a two-dimensional structure and to better understand how a tumor, and its corresponding metastasis grow, a three-dimensional (3-D) view is necessary. Results Using somatic mitochondrial mutations as a marker for lineage tracing, it is possible to identify and follow tumor specific cell lineages. Using cycling temperature capillary electrophoresis (CTCE) a total of 8 tissues from 5 patients (4 primary tumors and 4 metastasis) containing clear mitochondrial markers of tumor lineages were selected. From these 8 tissues over 9,500 laser capture microdisection (LCM) samples were taken and analyzed, in a way that allows 3-D rendering of the observations. Conclusion Using CTCE combined with LCM makes it possible to study the 3-D patterns formed by tumors and metastasis as they grow. These results clearly show that the majority of the volume occupied by a tumor is not composed of tumor derived cells. These cells are most likely recruited from the neighboring tissue.
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Affiliation(s)
- Paulo Refinetti
- Chair of Applied Statistics, Mathematics Section, School of Basic Sciences, École Polytechnique Fédéral de Lausanne (EPFL), Lausanne, Switzerland
| | - Stephan Morgenthaler
- Chair of Applied Statistics, Mathematics Section, School of Basic Sciences, École Polytechnique Fédéral de Lausanne (EPFL), Lausanne, Switzerland
| | - William G Thilly
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Christian Arstad
- Department of Tumor Biology, Norwegian Radium Hospital, Oslo, Norway
| | - Per O Ekstrøm
- Department of Tumor Biology, Norwegian Radium Hospital, Oslo, Norway
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Somatic Mitochondrial DNA Point Mutations Used as Biomarkers to Demonstrate Genomic Heterogeneity in Primary Prostate Cancer. Prostate Cancer 2020; 2020:7673684. [PMID: 32908706 PMCID: PMC7474793 DOI: 10.1155/2020/7673684] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/03/2020] [Accepted: 08/13/2020] [Indexed: 12/23/2022] Open
Abstract
Primary prostate tumor heterogeneity is poorly understood, leaving research efforts with challenges regarding the initiation and advancement of the disease. The growth of tumor cells is accompanied by mutations in nuclear and in mitochondrial genomes. Thus, mitochondrial DNA mutations may be used as tumor cell markers. By the use of laser capture microdissection coupled with assays for mitochondrial point mutation detection, mtDNA mutations were used to trace mutated cells at a histological level. Point mutations in mtDNA were determined in 12 primary prostate cancers. The tumors represent different pathology-prognostic grade groups. Known mutational hotspots of the mtDNA were scanned for heteroplasmy. All specimens with mtDNA heteroplasmy were subsequently subsampled by laser capture microdissection. From a total number of 1728 microsamples, mitochondrial DNA target sequences were amplified and base substitutions detected by cycling temperature capillary electrophoresis. Real-time PCR was used as a quantitative assay to determine the relative mtDNA copy number of 12 tumors studied, represented by two samples from each (N = 24); a high degree (75%) demonstrated tumor specimen heterogeneity. A grid of 96 spots isolated by laser capture microdissection demonstrated interfocal sample heterogeneity and increased the limit of detection. The spots demonstrated a wide range of mutant fractions from 0 to 100% mutant copies. The mitochondrial DNA copy number in the samples was determined by real-time PCR. No correlation between copy number and pathology-prognostic grade groups was observed. Somatic mitochondrial DNA point mutations represent traceable biomarkers demonstrating heterogeneity in primary prostate cancer. Mutations can be detected in areas before changes in tissue histopathology are evident to the pathologist.
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Liu Y, Wang W, Jia M, Liu R, Liu Q, Xiao H, Li J, Xue Y, Wang Y, Yan C. Recent advances in microscale separation. Electrophoresis 2017; 39:8-33. [DOI: 10.1002/elps.201700271] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 08/03/2017] [Accepted: 08/04/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Yuanyuan Liu
- School of Pharmacy; Shanghai Jiao Tong University; Shanghai P. R. China
| | - Weiwei Wang
- School of Pharmacy; Shanghai Jiao Tong University; Shanghai P. R. China
| | - Mengqi Jia
- School of Pharmacy; Shanghai Jiao Tong University; Shanghai P. R. China
| | - Rangdong Liu
- School of Pharmacy; Shanghai Jiao Tong University; Shanghai P. R. China
| | - Qing Liu
- School of Pharmacy; Shanghai Jiao Tong University; Shanghai P. R. China
| | - Han Xiao
- School of Pharmacy; Shanghai Jiao Tong University; Shanghai P. R. China
| | - Jing Li
- Unimicro (shanghai) Technologies Co., Ltd.; Shanghai P. R. China
| | - Yun Xue
- School of Pharmacy; Shanghai Jiao Tong University; Shanghai P. R. China
| | - Yan Wang
- School of Pharmacy; Shanghai Jiao Tong University; Shanghai P. R. China
| | - Chao Yan
- School of Pharmacy; Shanghai Jiao Tong University; Shanghai P. R. China
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Arstad C, Refinetti P, Kristensen AT, Giercksky KE, Ekstrøm PO. Is detection of intraperitoneal exfoliated tumor cells after surgical resection of rectal cancer a prognostic factor of survival? BMC Cancer 2017; 17:406. [PMID: 28592327 PMCID: PMC5461707 DOI: 10.1186/s12885-017-3365-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 05/17/2017] [Indexed: 01/30/2023] Open
Abstract
Background The prognostic significance of free cancer cells detected in peritoneal fluid at the time of rectal surgery remains unclear. A substantial number of patients will develop metastatic disease even with successful local treatment. This prospective non-randomized study investigated the prognostic value of intraperitoneal free cancer cells harvested in peritoneal lavage after surgery for rectal cancer. Mutational hotspots in mitochondrial DNA were examined as potential molecular signatures to detect circulating intraperitoneal free cancer cells when present in primary tumor and in lavage. Methods Point mutations in mitochondrial DNA amplifications were determined in primary tumors and corresponding exfoliated intraperitoneal free cancer cells in lavage from 191 patients with locally advanced rectal cancer scheduled for radical treatment. Mitochondrial DNA target sequences were amplified by polymerase chain reaction and base substitutions were detected by denaturant, cycling temperature capillary electrophoresis. Detection of intraperitoneal free cancer cells was correlated to survival. Results Of 191patients analyzed, 138 (72%) were identified with somatic mitochondrial point mutations in rectal cancer tumors. From this fraction, 45 patients (33%) had positive lavage fluid with corresponding somatic mtDNA point mutations in lavage representing circulating intraperitoneal free cancer cells. There was no significant survival difference between patients identified with or without somatic mitochondrial DNA point mutations in the corresponding lavage. Conclusion Somatic mitochondrial DNA point mutations identified in primary rectal tumors enable detection of circulating intraperitoneal free cancer cells in lavage fluid. Intraperitoneal free cancer cells harvested from lavage immediately after surgery for rectal cancer does not represent an independent prognostic factor on survival.
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Affiliation(s)
- Christian Arstad
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo, Norway.
| | - Paulo Refinetti
- Chaire de Statistique Appliques, Section de Mathematiques, EPFL, Lausanne, Switzerland
| | | | - Karl-Erik Giercksky
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo, Norway
| | - Per Olaf Ekstrøm
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo, Norway
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Refinetti P, Arstad C, Thilly WG, Morgenthaler S, Ekstrøm PO. Mapping mitochondrial heteroplasmy in a Leydig tumor by laser capture micro-dissection and cycling temperature capillary electrophoresis. BMC Clin Pathol 2017; 17:6. [PMID: 28405177 PMCID: PMC5385042 DOI: 10.1186/s12907-017-0042-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 03/27/2017] [Indexed: 12/13/2022] Open
Abstract
Background The growth of tumor cells is accompanied by mutations in nuclear and mitochondrial genomes creating marked genetic heterogeneity. Tumors also contain non-tumor cells of various origins. An observed somatic mitochondrial mutation would have occurred in a founding cell and spread through cell division. Micro-anatomical dissection of a tumor coupled with assays for mitochondrial point mutations permits new insights into this growth process. More generally, the ability to detect and trace, at a histological level, somatic mitochondrial mutations in human tissues and tumors, makes these mutations into markers for lineage tracing. Method A tumor was first sampled by a large punch biopsy and scanned for any significant degree of heteroplasmy in a set of sequences containing known mutational hotspots of the mitochondrial genome. A heteroplasmic tumor was sliced at a 12 μm thickness and placed on membranes. Laser capture micro-dissection was used to take 25000 μm2 subsamples or spots. After DNA amplification, cycling temperature capillary electrophoresis (CTCE) was used on the laser captured samples to quantify mitochondrial mutant fractions. Results Of six testicular tumors studied, one, a Leydig tumor, was discovered to carry a detectable degree of heteroplasmy for two separate point mutations: a C → T mutation at bp 64 and a T → C mutation found at bp 152. From this tumor, 381 spots were sampled with laser capture micro-dissection. The ordered distribution of spots exhibited a wide range of fractions of the mutant sequences from 0 to 100% mutant copies. The two mutations co-distributed in the growing tumor indicating they were present on the same genome copies in the founding cell. Conclusion Laser capture microdissection of sliced tumor samples coupled with CTCE-based point mutation assays provides an effective and practical means to obtain maps of mitochondrial mutational heteroplasmy within human tumors.
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Affiliation(s)
- Paulo Refinetti
- Chair of Applied Statistics, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Christian Arstad
- Institute for Cancer Research, The Norwegian Radium Hospital, Oslo, Norway
| | - William G Thilly
- Laboratory in Metakaryotic Biology, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Stephan Morgenthaler
- Chair of Applied Statistics, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Per Olaf Ekstrøm
- Institute for Cancer Research, The Norwegian Radium Hospital, Oslo, Norway
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Arstad C, Refinetti P, Warren D, Giercksky KE, Ekstrøm PO. Scanning the mitochondrial genome for mutations by cycling temperature capillary electrophoresis. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 29:19-30. [PMID: 27728990 DOI: 10.1080/24701394.2016.1233532] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
To bypass possible nuclear contamination and to exclusively amplify DNA from the mitochondrion, a set of 23 primers was selected. On the mitochondrial DNA selection fragments, a second set of fragments was used to amplify and identify mutant fractions with a detection limit of 1% . This mutation scanning method analyzed 76% of the mitochondrial genome and was used to examine 94 tumours from different tissues of origin. In all, 87 tumours had one or more mutations, leaving seven samples without observed mutations. Sanger sequencing verified samples carrying mutations with a mutant fraction exceeding 30%. The generated data validate that several regions of the mitochondrial DNA have more mutations than others.
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Affiliation(s)
- Christian Arstad
- a Department of Tumor Biology , Institute for Cancer Research, The Norwegian Radium Hospital , Oslo , Norway
| | - Paulo Refinetti
- b Chaire de Statistique Appliques , Section de Mathematiques, EPFL , Lausanne , Switzerland
| | - David Warren
- c Department Medical Biochemistry , Institute for Cancer Research, The Norwegian Radium Hospital , Oslo , Norway
| | - Karl-Erik Giercksky
- a Department of Tumor Biology , Institute for Cancer Research, The Norwegian Radium Hospital , Oslo , Norway
| | - Per Olaf Ekstrøm
- a Department of Tumor Biology , Institute for Cancer Research, The Norwegian Radium Hospital , Oslo , Norway
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