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Andersson D, Kebede FT, Escobar M, Österlund T, Ståhlberg A. Principles of digital sequencing using unique molecular identifiers. Mol Aspects Med 2024; 96:101253. [PMID: 38367531 DOI: 10.1016/j.mam.2024.101253] [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] [Received: 11/16/2023] [Revised: 01/26/2024] [Accepted: 02/03/2024] [Indexed: 02/19/2024]
Abstract
Massively parallel sequencing technologies have long been used in both basic research and clinical routine. The recent introduction of digital sequencing has made previously challenging applications possible by significantly improving sensitivity and specificity to now allow detection of rare sequence variants, even at single molecule level. Digital sequencing utilizes unique molecular identifiers (UMIs) to minimize sequencing-induced errors and quantification biases. Here, we discuss the principles of UMIs and how they are used in digital sequencing. We outline the properties of different UMI types and the consequences of various UMI approaches in relation to experimental protocols and bioinformatics. Finally, we describe how digital sequencing can be applied in specific research fields, focusing on cancer management where it can be used in screening of asymptomatic individuals, diagnosis, treatment prediction, prognostication, monitoring treatment efficacy and early detection of treatment resistance as well as relapse.
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Affiliation(s)
- Daniel Andersson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
| | - Firaol Tamiru Kebede
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
| | - Mandy Escobar
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
| | - Tobias Österlund
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 413 90, Gothenburg, Sweden; Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 413 90, Gothenburg, Sweden; Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden.
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Imura T, Mitsuhara T, Horie N. Characteristics of MicroRNA Expression Depending on the Presence or Absence of Meningioma in Patients with Neurofibromatosis Type 2: A Secondary Analysis. Neurol Med Chir (Tokyo) 2024; 64:116-122. [PMID: 38267057 PMCID: PMC10992986 DOI: 10.2176/jns-nmc.2023-0200] [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] [Received: 09/05/2023] [Accepted: 11/24/2023] [Indexed: 01/26/2024] Open
Abstract
Meningioma is the second most frequent tumor in patients with neurofibromatosis type 2 (NF2). The presence of meningioma is believed to be a negative prognostic marker in these patients. However, the molecular mechanisms involved in the tumorigenesis of NF2-associated meningioma are not well characterized. Epigenetic regulation, including microRNAs (miRNAs), may be involved in the development of different tumor types in patients with NF2. The objective of this study is to explore the different characteristics of serum miRNA expression depending on the presence or absence of meningioma in patients with NF2. Nine patients with NF2 who were treated at the Department of Neurosurgery, Hiroshima University Hospital, were included. Total RNA (including small RNAs) was extracted from serum samples for the preparation of a small RNA library for next-generation sequencing analysis. Differentially expressed miRNAs (DEMs) were analyzed using the DESeq2 package to compare the characteristic miRNA expression profiles of patients with and without meningioma. In small RNA sequencing analysis, out of a total of 1,879 miRNAs registered in the database, the expressions of 657 miRNAs were observed. In DEM analysis, the expressions of four miRNAs, namely, hsa-miR-664b, hsa-miR-7706, hsa-miR-590, and hsa-miR-6513, were downregulated in patients with NF2 with meningioma compared with patients with NF2 without meningioma. Hsa-miR-193a was identified as the only upregulated miRNA in patients with NF2 with meningioma. In conclusion, we identified different circulating miRNA expression characteristics depending on the presence or absence of meningioma in patients with NF2.
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Affiliation(s)
- Takeshi Imura
- Department of Rehabilitation, Faculty of Health Sciences, Hiroshima Cosmopolitan University
| | - Takafumi Mitsuhara
- Department of Neurosurgery, Graduate School of Biomedical and Health Sciences, Hiroshima University
| | - Nobutaka Horie
- Department of Neurosurgery, Graduate School of Biomedical and Health Sciences, Hiroshima University
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Sura GH, Tran K, Fu C, Du L, Marczyk M, Gould RE, Chen E, Tasto AM, Tinnirello AA, Symmans WF. Pre-analytical effects on whole transcriptome and targeted RNA sequencing analysis in cytology: The effects of prolonged time in storage of effusion specimens prior to preservation. Cytopathology 2023; 34:551-561. [PMID: 37712171 PMCID: PMC10592006 DOI: 10.1111/cyt.13304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/16/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023]
Abstract
OBJECTIVES To investigate the pre-analytics of the molecular testing of cytology specimens, we studied the effects of time in refrigerator storage (4°C) of malignant effusions on RNA sequencing (RNAseq) results. METHODS Ten effusion specimens were stored in a refrigerator (4°C) for different durations (day 0, 1, 4, and 7). All specimens were prepared as cytospins fixed in either Carnoy's solution or 95% ethanol (EtOH) and in an RNA preservative for a fresh frozen (FF) high-quality reference. Whole transcriptome (wt) and targeted (t)RNAseq of two multigene expression signatures were performed. We then compared transcript expression levels (including mutant allele fraction) according to pre-analytical variables using a concordance correlation coefficient (CCC) and a mixed effect model. RESULTS Sequencing results were mostly stable over increasing time in storage. Cytospins fixed in Carnoy's solution were more concordant with FF samples than cytospins fixed in 95% EtOH at all timepoints. This finding was consistent for both wtRNAseq (averages: day 0 CCC = 0.98 vs 0.91; day 7 CCC = 0.88 vs 0.78) and tRNAseq methods (averages: day 0 CCC = 0.98 vs 0.81; day 7 CCC = 0.98 vs 0.90). Cytospins fixed in Carnoy's solution did not show significant changes in expression over timepoints or between expression signatures, whereas 95% EtOH did. CONCLUSION RNAseq can be accurately performed on effusion specimens after prolonged refrigerator storage. RNA extracted from scraped cytospin slides fixed in Carnoy's solution was marginally superior to 95% EtOH fixation, but either method had comparable analytic performance to high-quality FF RNA samples.
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Affiliation(s)
- Gloria H. Sura
- Department of Pathology and Genomic Medicine, Houston Methodist, Houston, Texas, USA
| | - Kevin Tran
- Department of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Chunxiao Fu
- Department of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lili Du
- Department of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michał Marczyk
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
- Yale Cancer Center, Yale University, New Haven, Connecticut, USA
| | - Rebekah E. Gould
- Department of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Eveline Chen
- Department of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Amy M. Tasto
- Department of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Agata A. Tinnirello
- Department of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - W. Fraser Symmans
- Department of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Echeverria GV, Cai S, Tu Y, Shao J, Powell E, Redwood AB, Jiang Y, McCoy A, Rinkenbaugh AL, Lau R, Trevarton AJ, Fu C, Gould R, Ravenberg EE, Huo L, Candelaria R, Santiago L, Adrada BE, Lane DL, Rauch GM, Yang WT, White JB, Chang JT, Moulder SL, Symmans WF, Hilsenbeck SG, Piwnica-Worms H. Predictors of success in establishing orthotopic patient-derived xenograft models of triple negative breast cancer. NPJ Breast Cancer 2023; 9:2. [PMID: 36627285 PMCID: PMC9831981 DOI: 10.1038/s41523-022-00502-1] [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: 05/18/2022] [Accepted: 12/13/2022] [Indexed: 01/12/2023] Open
Abstract
Patient-derived xenograft (PDX) models of breast cancer are an effective discovery platform and tool for preclinical pharmacologic testing and biomarker identification. We established orthotopic PDX models of triple negative breast cancer (TNBC) from the primary breast tumors of patients prior to and following neoadjuvant chemotherapy (NACT) while they were enrolled in the ARTEMIS trial (NCT02276443). Serial biopsies were obtained from patients prior to treatment (pre-NACT), from poorly responsive disease after four cycles of Adriamycin and cyclophosphamide (AC, mid-NACT), and in cases of AC-resistance, after a 3-month course of different experimental therapies and/or additional chemotherapy (post-NACT). Our study cohort includes a total of 269 fine needle aspirates (FNAs) from 217 women, generating a total of 62 PDX models (overall success-rate = 23%). Success of PDX engraftment was generally higher from those cancers that proved to be treatment-resistant, whether poorly responsive to AC as determined by ultrasound measurements mid-NACT (p = 0.063), RCB II/III status after NACT (p = 0.046), or metastatic relapse within 2 years of surgery (p = 0.008). TNBC molecular subtype determined from gene expression microarrays of pre-NACT tumors revealed no significant association with PDX engraftment rate (p = 0.877). Finally, we developed a statistical model predictive of PDX engraftment using percent Ki67 positive cells in the patient's diagnostic biopsy, positive lymph node status at diagnosis, and low volumetric reduction of the patient's tumor following AC treatment. This novel bank of 62 PDX models of TNBC provides a valuable resource for biomarker discovery and preclinical therapeutic trials aimed at improving neoadjuvant response rates for patients with TNBC.
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Affiliation(s)
- Gloria V Echeverria
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Lester and Sue Smith Breast Cancer Center and Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Shirong Cai
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yizheng Tu
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jiansu Shao
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Emily Powell
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Abena B Redwood
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yan Jiang
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Aaron McCoy
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Amanda L Rinkenbaugh
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Rosanna Lau
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Alexander J Trevarton
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Chunxiao Fu
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Rebekah Gould
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Elizabeth E Ravenberg
- Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Lei Huo
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Rosalind Candelaria
- Department of Breast Imaging, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Lumarie Santiago
- Department of Breast Imaging, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Beatriz E Adrada
- Department of Breast Imaging, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Deanna L Lane
- Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Gaiane M Rauch
- Department of Abdominal Imaging, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Wei T Yang
- Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jason B White
- Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jeffrey T Chang
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, TX, 77030, USA
| | - Stacy L Moulder
- Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - W Fraser Symmans
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Susan G Hilsenbeck
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Helen Piwnica-Worms
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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Sura GH, Tran K, Fu C, Du L, Marczyk M, Martinez Y, Tinnirello AA, Gould RE, Lau R, Symmans WF. Molecular testing opportunities on cytology effusion specimens: the pre-analytic effects of various body fluid cytology preparation methods on RNA extraction quality and targeted sequencing. J Am Soc Cytopathol 2023; 12:10-19. [PMID: 36270909 PMCID: PMC10644714 DOI: 10.1016/j.jasc.2022.09.003] [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: 08/03/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
INTRODUCTION RNA sequencing (RNAseq) analysis is emerging as a clinical research or diagnostic approach for cytologic samples, but there is need for formal comparison of different sample preparation methods in the cytology laboratory to identify which pre-analytic methods could provide alternatives to formalin-fixed paraffin-embedded (FFPE) sections. MATERIALS AND METHODS We prepared 13 malignant effusions (metastatic estrogen receptor-positive breast cancer) in the cytology laboratory using 6 routine cytologic methods: FFPE cell block, Carnoy's solution, 95% ethanol (EtOH), air-dried and Diff-Quik, ThinPrep, and SurePath preparations. Measurements of RNA quality, expression of 2 multigene expression signatures, molecular subtype, and 4 common activating mutation sites in each preparation were compared with fresh frozen (FF) cell pellet in RNA preservative using distribution of fragment length and concordance correlation coefficient (CCC). RESULTS The fraction of RNA fragments measuring 200 bases or more (DV200) were 24% higher from cytospins fixed in Carnoy's solution or 95% EtOH than DV200 from FFPE cell blocks. SurePath samples failed RNAseq quality control. There was high concordance of gene expression measurements with FF samples using cytospins fixed in Carnoy's solution, 95% EtOH, Diff-Quik (CCC = 0.829, 0.812, 0.760, respectively), or ThinPrep (CCC = 0.736), but lower using FFPE cell block (CCC = 0.564). The proportion of mutant transcripts was concordant between FF and any cytologic preparation methods. CONCLUSIONS Cytospin preparations fixed with Carnoy's or 95% ETOH then Papanicolaou stained produced RNAseq results that were equivalent to FF samples and superior to FFPE cell block sections.
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Affiliation(s)
- Gloria H Sura
- Department of Pathology and Genomic Medicine, Houston Methodist, Houston, Texas
| | - Kevin Tran
- Departments of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chunxiao Fu
- Departments of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lili Du
- Departments of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michał Marczyk
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland; Yale Cancer Center, Yale University, New Haven, Connecticut
| | - Yadira Martinez
- Departments of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Agata A Tinnirello
- Departments of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rebekah E Gould
- Departments of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rosanna Lau
- Departments of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - W Fraser Symmans
- Departments of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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