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Lake KE, Colonnetta MM, Smith CA, Saunders K, Martinez-Algarin K, Mohta S, Pena J, McArthur HL, Reddy SM, Roussos Torres ET, Chen EH, Chan IS. Digital droplet PCR analysis of organoids generated from mouse mammary tumors demonstrates proof-of-concept capture of tumor heterogeneity. Front Cell Dev Biol 2024; 12:1358583. [PMID: 38827528 PMCID: PMC11140600 DOI: 10.3389/fcell.2024.1358583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/19/2024] [Indexed: 06/04/2024] Open
Abstract
Breast cancer metastases exhibit many different genetic alterations, including copy number amplifications (CNA). CNA are genetic alterations that are increasingly becoming relevant to breast oncology clinical practice. Here we identify CNA in metastatic breast tumor samples using publicly available datasets and characterize their expression and function using a metastatic mouse model of breast cancer. Our findings demonstrate that our organoid generation can be implemented to study clinically relevant features that reflect the genetic heterogeneity of individual tumors.
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Affiliation(s)
- Katherine E. Lake
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern, Dallas, TX, United States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Megan M. Colonnetta
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
- Department of Molecular Biology, University of Texas Southwestern, Dallas, TX, United States
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Clayton A. Smith
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern, Dallas, TX, United States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Kaitlyn Saunders
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern, Dallas, TX, United States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Kenneth Martinez-Algarin
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern, Dallas, TX, United States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Sakshi Mohta
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern, Dallas, TX, United States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Jacob Pena
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern, Dallas, TX, United States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Heather L. McArthur
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern, Dallas, TX, United States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Sangeetha M. Reddy
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern, Dallas, TX, United States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Evanthia T. Roussos Torres
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Elizabeth H. Chen
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
- Department of Molecular Biology, University of Texas Southwestern, Dallas, TX, United States
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Isaac S. Chan
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern, Dallas, TX, United States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
- Department of Molecular Biology, University of Texas Southwestern, Dallas, TX, United States
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States
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Tamura T, Imaizumi T, Shimojima Yamamoto K, Yamamoto T. Genomic Copy Number Analysis Using Droplet Digital PCR: A Simple Method with EvaGreen Single-Color Fluorescent Design. Methods Mol Biol 2024; 2794:293-304. [PMID: 38630238 DOI: 10.1007/978-1-0716-3810-1_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Droplet digital PCR (ddPCR) is an emerging method for the absolute quantification of PCR products, and it can detect DNA copy numbers accurately. It analyzes the end-point absolute fluorescence signals of the PCR-positive droplets and calculates the target concentration. EvaGreen is a nonspecific double-stranded DNA-binding fluorescent dye, and the ddPCR system also supports assays using this cost-effective hydrolysis probe. Here, we describe a simple method of quantification for DNA copy numbers using the EvaGreen single-color fluorescent design.
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Affiliation(s)
- Takeaki Tamura
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
- Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan
| | - Taichi Imaizumi
- Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Keiko Shimojima Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan
| | - Toshiyuki Yamamoto
- Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan.
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan.
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Wu J, Yu S, Wang Y, Zhu J, Zhang Z. New insights into the role of ribonuclease P protein subunit p30 from tumor to internal reference. Front Oncol 2022; 12:1018279. [PMID: 36313673 PMCID: PMC9606464 DOI: 10.3389/fonc.2022.1018279] [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: 08/17/2022] [Accepted: 09/28/2022] [Indexed: 11/13/2022] Open
Abstract
Ribonuclease P protein subunit p30 (RPP30) is a highly conserved housekeeping gene that exists in many species and tissues throughout the three life kingdoms (archaea, bacteria, and eukaryotes). RPP30 is closely related to a few types of tumors in human diseases but has a very stable transcription level in most cases. Based on this feature, increasing number of studies have used RPP30 as an internal reference gene. Here, the structure and basic functions of RPP30 are summarized and the likely relationship between RPP30 and various diseases in plants and human is outlined. Finally, the current application of RPP30 as an internal reference gene and its advantages over traditional internal reference genes are reviewed. RPP30 characteristics suggest that it has a good prospect of being selected as an internal reference; more work is needed to develop this research avenue.
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Affiliation(s)
- Junchao Wu
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China,Department of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Sijie Yu
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China,Department of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Yalan Wang
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China,Department of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Jie Zhu
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China
| | - Zhenhua Zhang
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China,*Correspondence: Zhenhua Zhang,
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Wu J, Tang B, Qiu Y, Tan R, Liu J, Xia J, Zhang J, Huang J, Qu J, Sun J, Wang X, Qu H. Clinical validation of a multiplex droplet digital PCR for diagnosing suspected bloodstream infections in ICU practice: a promising diagnostic tool. Crit Care 2022; 26:243. [PMID: 35941654 PMCID: PMC9358819 DOI: 10.1186/s13054-022-04116-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/31/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Droplet digital PCR (ddPCR) has emerged as a promising tool of pathogen detection in bloodstream infections (BSIs) in critical care medicine. However, different ddPCR platforms have variable sensitivity and specificity for diverse microorganisms at various infection sites. There is still a lack of prospective clinical studies aimed at validating and interpreting the discrepant ddPCR results for diagnosing BSI in intensive care unit (ICU) practice.
Methods
A prospective diagnostic study of multiplex ddPCR panels was conducted in a general ICU from May 21, 2021, to December 22, 2021. Paired blood cultures (BCs) and ddPCRs (2.5 h) were obtained synchronously to detect the 12 most common BSI pathogens and three antimicrobial resistance (AMR) genes. Firstly, ddPCR performance was compared to definite BSI. Secondly, clinical validation of ddPCR was compared to composite clinical diagnosis. Sensitivity, specificity, and positive and negative predictive values were calculated. Thirdly, the positive rate of AMR genes and related analysis was presented.
Results
A total of 438 episodes of suspected BSIs occurring in 150 critical patients were enrolled. BC and ddPCR were positive for targeted bacteria in 40 (9.1%) and 180 (41.1%) cases, respectively. There were 280 concordant and 158 discordant. In comparison with BCs, the sensitivity of ddPCR ranged from 58.8 to 86.7% with an aggregate of 72.5% in different species, with corresponding specificity ranging from 73.5 to 92.2% with an aggregate of 63.1%. Furthermore, the rate of ddPCR+/BC− results was 33.6% (147/438) with 87.1% (128 of 147) cases was associated with probable (n = 108) or possible (n = 20) BSIs. When clinically diagnosed BSI was used as true positive, the final sensitivity and specificity of ddPCR increased to 84.9% and 92.5%, respectively. In addition, 40 blaKPC, 3blaNDM, and 38 mecA genes were detected, among which 90.5% were definitely positive for blaKPC. Further, 65.8% specimens were predicted to be mecA-positive in Staphylococcus sp. according to all microbiological analysis.
Conclusions
The multiplexed ddPCR is a flexible and universal platform, which can be used as an add-on complementary to conventional BC. When combined with clinical infection evidence, ddPCR shows potential advantages for rapidly diagnosing suspected BSIs and AMR genes in ICU practice.
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Xue H, Yu A, Chen X, Lin N, Lin M, Huang H, Xu L. Prenatal diagnosis of PLP1 duplication by single nucleotide polymorphism array in a family with Pelizaeus-Merzbacher disease. Aging (Albany NY) 2021; 13:1488-1497. [PMID: 33429367 PMCID: PMC7835049 DOI: 10.18632/aging.202477] [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: 07/30/2020] [Accepted: 11/10/2020] [Indexed: 11/25/2022]
Abstract
A family with a history of Pelizaeus-Merzbacher disease (PMD) received prenatal diagnosis of PLP1 gene duplication in a fetus using a single nucleotide polymorphism (SNP) array. A 27-year-old pregnant woman was referred for genetic counseling due to her four-year-old son being diagnosed with a suspected classic type of PMD. Amniocentesis was performed at 18 and 3/7 weeks of gestation, and the SNP array was carried out on DNA from the mother, her affected son, and fetus, then further confirmed by multiplex ligation-dependent probe amplification (MLPA). Cytogenetic analysis of the fetus showed 46,XY. SNP array analysis revealed that the male fetus did not carry PLP1 gene duplication but the affected boy did, and the mother was a carrier for the duplication of the PLP1 gene. All SNP array results were further confirmed by MLPA. SNP array and MLPA analyses of peripheral blood verified the nonduplication of the PLP1 gene in the infant after birth. At present, the child (without PLP1 duplication) is developing normally. This study preliminarily suggests that SNP array is a sensitive and accurate technology for identifying PLP1 duplication and is feasible for reliable diagnosis, including for the prenatal diagnosis of PMD resulting from PLP1 duplication.
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Affiliation(s)
- Huili Xue
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Gulou, Fuzhou 350001, Fujian Province, China
| | - Aili Yu
- Reproductive Medicine Center, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Gulou, Fuzhou 350001, Fujian Province, China
| | - Xuemei Chen
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Gulou, Fuzhou 350001, Fujian Province, China
| | - Na Lin
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Gulou, Fuzhou 350001, Fujian Province, China
| | - Min Lin
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Gulou, Fuzhou 350001, Fujian Province, China
| | - Hailong Huang
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Gulou, Fuzhou 350001, Fujian Province, China
| | - Liangpu Xu
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Gulou, Fuzhou 350001, Fujian Province, China
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