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Hsu FM, Chang YL, Chen CY, Lin SR, Cheng JCH. Hybridization Protection Reaction for Sensitive and Robust Gene Expression Profiling of Clinical Formalin-Fixed Paraffin-Embedded Samples. Clin Chem 2023; 69:1385-1395. [PMID: 37964418 DOI: 10.1093/clinchem/hvad170] [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: 11/23/2022] [Accepted: 10/03/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND RNA profiling of formalin-fixed paraffin-embedded (FFPE) tumor tissues for the molecular diagnostics of disease prognosis or treatment response is often irreproducible and limited to a handful of biomarkers. This has led to an unmet need for robust multiplexed assays that can profile several RNA biomarkers of interest using a limited amount of specimen. Here, we describe hybridization protection reaction (HPR), which is a novel RNA profiling approach with high reproducibility. METHODS HPR assays were designed for multiple genes, including 10 radiosensitivity-associated genes, and compared with TaqMan assays. Performance was tested with synthetic RNA fragments, and the ability to analyze RNA was investigated in FPPE samples from 20 normal lung tissues, 40 lung cancer, and 30 esophageal cancer biopsies. RESULTS Experiments performed on 3 synthetic RNA fragments demonstrated a linear dynamic range of over 1000-fold with a replicate correlation coefficient of 0.99 and high analytical sensitivity between 3.2 to 10 000 pM. Comparison of HPR with standard quantitative reverse transcription polymerase chain reaction on FFPE specimens shows nonsignificant differences with > 99% confidence interval between 2 assays in transcript profiling of 91.7% of test transcripts. In addition, HPR was effectively applied to quantify transcript levels of 10 radiosensitivity-associated genes. CONCLUSIONS Overall, HPR is an alternative approach for RNA profiling with high sensitivity, reproducibility, robustness, and capability for molecular diagnostics in FFPE tumor biopsy specimens of lung and esophageal cancer.
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Affiliation(s)
- Feng-Ming Hsu
- Division of Radiation Oncology, Department of Oncology, National Taiwan University Hospital, Taipei 100225, Taiwan
- Graduate Institute of Oncology and Cancer Research Center, National Taiwan University College of Medicine, Taipei 100025, Taiwan
| | - Yih-Leong Chang
- Department of Pathology, National Taiwan University Hospital, Taipei 100225, Taiwan
| | - Chung-Yung Chen
- Department of Bioscience Technology, Chung Yuan Christian University, Chungli District, Taoyuan 320314, Taiwan
- Center for Nanotechnology and Center for Biomedical Technology, Chung Yuan Christian University, Taoyuan 320314, Taiwan
| | - Shu-Rung Lin
- Department of Bioscience Technology, Chung Yuan Christian University, Chungli District, Taoyuan 320314, Taiwan
- Center for Nanotechnology and Center for Biomedical Technology, Chung Yuan Christian University, Taoyuan 320314, Taiwan
| | - Jason Chia-Hsien Cheng
- Division of Radiation Oncology, Department of Oncology, National Taiwan University Hospital, Taipei 100225, Taiwan
- Graduate Institute of Oncology and Cancer Research Center, National Taiwan University College of Medicine, Taipei 100025, Taiwan
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2
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Kumar K, Hallikeri K, Oli A, Goni M, Jain A, Poyya J, Shilpasree AS, Javaregowda PK. Quantitative analysis of lncRNA in formalin-fixed paraffin-embedded tissues of oral squamous cell carcinoma. Biotechniques 2023; 75:133-142. [PMID: 37589188 DOI: 10.2144/btn-2023-0033] [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: 08/18/2023] Open
Abstract
The study evaluated expression profiles of few regulatory lncRNAs in oral squamous cell carcinoma and normal mucosa adjacent to oral cancer using paired fresh frozen and formalin-fixed paraffin-embedded (FFPE) tissues stored at a different duration of time (1-5 years) using real-time quantitative PCR. The quantity and quality of total RNA isolated from FFPE tissues was less compared with that of fresh frozen tissues, which resulted in a noncorrelation of quantification cycle values. Following normalization, the expression of lncRNAs in the paired tissues did not differ significantly. The differential expression of the lncRNAs in the study was consistent with The Cancer Genome Atlas head and neck squamous cell carcinoma database. The study findings demonstrate the possibility of performing accurate quantitative analysis of lncRNAs using short amplicons and standardized real-time quantitative PCR assays in oral squamous cell carcinoma FFPE samples.
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Affiliation(s)
- Kiran Kumar
- Department of Oral and Maxillofacial Pathology and Oral Microbiology, SDM College of Dental Sciences and Hospital (a constituent unit of Shri Dharmasthala Manjunatheshwara University), Dharwad, Karnataka State, 580009, India
| | - Kaveri Hallikeri
- Department of Oral and Maxillofacial Pathology and Oral Microbiology, SDM College of Dental Sciences and Hospital (a constituent unit of Shri Dharmasthala Manjunatheshwara University), Dharwad, Karnataka State, 580009, India
| | - Ajaykumar Oli
- Department of Biomedical Science, SDM Research Institute for Biomedical Sciences (a constituent unit of Shri Dharmasthala Manjunatheshwara University), Dharwad, Karnataka State, 580009, India
| | - Mallikarjun Goni
- Department of Biomedical Science, SDM Research Institute for Biomedical Sciences (a constituent unit of Shri Dharmasthala Manjunatheshwara University), Dharwad, Karnataka State, 580009, India
| | - Apoorva Jain
- Department of Biomedical Science, SDM Research Institute for Biomedical Sciences (a constituent unit of Shri Dharmasthala Manjunatheshwara University), Dharwad, Karnataka State, 580009, India
| | - Jagadeesha Poyya
- Department of Biomedical Science, SDM Research Institute for Biomedical Sciences (a constituent unit of Shri Dharmasthala Manjunatheshwara University), Dharwad, Karnataka State, 580009, India
| | - Alagilavada S Shilpasree
- Department of Biochemistry, SDM College of Medical Sciences and Hospital (a constituent unit of Shri Dharmasthala Manjunatheshwara University), Dharwad, Karnataka State, 580009, India
| | - Palaksha Kanive Javaregowda
- Department of Biomedical Science, SDM Research Institute for Biomedical Sciences (a constituent unit of Shri Dharmasthala Manjunatheshwara University), Dharwad, Karnataka State, 580009, India
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3
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Nevone A, Lattarulo F, Russo M, Panno G, Milani P, Basset M, Avanzini MA, Merlini G, Palladini G, Nuvolone M. A Strategy for the Selection of RT-qPCR Reference Genes Based on Publicly Available Transcriptomic Datasets. Biomedicines 2023; 11:biomedicines11041079. [PMID: 37189697 DOI: 10.3390/biomedicines11041079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 04/05/2023] Open
Abstract
In the next-generation sequencing era, RT-qPCR is still widely employed to quantify levels of nucleic acids of interest due to its popularity, versatility, and limited costs. The measurement of transcriptional levels through RT-qPCR critically depends on reference genes used for normalization. Here, we devised a strategy to select appropriate reference genes for a specific clinical/experimental setting based on publicly available transcriptomic datasets and a pipeline for RT-qPCR assay design and validation. As a proof-of-principle, we applied this strategy to identify and validate reference genes for transcriptional studies of bone-marrow plasma cells from patients with AL amyloidosis. We performed a systematic review of published literature to compile a list of 163 candidate reference genes for RT-qPCR experiments employing human samples. Next, we interrogated the Gene Expression Omnibus to assess expression levels of these genes in published transcriptomic studies on bone-marrow plasma cells from patients with different plasma cell dyscrasias and identified the most stably expressed genes as candidate normalizing genes. Experimental validation on bone-marrow plasma cells showed the superiority of candidate reference genes identified through this strategy over commonly employed “housekeeping” genes. The strategy presented here may apply to other clinical and experimental settings for which publicly available transcriptomic datasets are available.
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Affiliation(s)
- Alice Nevone
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Francesca Lattarulo
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Monica Russo
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giada Panno
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Paolo Milani
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Marco Basset
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Maria Antonietta Avanzini
- Pediatric Hematology Oncology, Cell Factory, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giampaolo Merlini
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giovanni Palladini
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Mario Nuvolone
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
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4
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Connecting multiple microenvironment proteomes uncovers the biology in head and neck cancer. Nat Commun 2022; 13:6725. [PMID: 36344512 PMCID: PMC9640649 DOI: 10.1038/s41467-022-34407-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 10/25/2022] [Indexed: 11/09/2022] Open
Abstract
The poor prognosis of head and neck cancer (HNC) is associated with metastasis within the lymph nodes (LNs). Herein, the proteome of 140 multisite samples from a 59-HNC patient cohort, including primary and matched LN-negative or -positive tissues, saliva, and blood cells, reveals insights into the biology and potential metastasis biomarkers that may assist in clinical decision-making. Protein profiles are strictly associated with immune modulation across datasets, and this provides the basis for investigating immune markers associated with metastasis. The proteome of LN metastatic cells recapitulates the proteome of the primary tumor sites. Conversely, the LN microenvironment proteome highlights the candidate prognostic markers. By integrating prioritized peptide, protein, and transcript levels with machine learning models, we identify nodal metastasis signatures in blood and saliva. We present a proteomic characterization wiring multiple sites in HNC, thus providing a promising basis for understanding tumoral biology and identifying metastasis-associated signatures.
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5
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Lv Y, Li S, Li Z, Tao R, Shao Y, Chen Y. Quantitative analysis of noncoding RNA from paired fresh and formalin-fixed paraffin-embedded brain tissues. Int J Legal Med 2019; 134:873-884. [PMID: 31788707 DOI: 10.1007/s00414-019-02210-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 11/13/2019] [Indexed: 12/30/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are commonly used both clinically and in forensic pathology. Recently, noncoding RNA (ncRNA) has attracted interest among molecular medical researchers. However, it remains unclear whether newly identified ncRNAs, such as long noncoding RNA (lncRNA) and circular RNA (circRNA), remain stable for downstream molecular analysis in FFPE tissues. Here, we assessed the feasibility of using autoptic FFPE brain tissues from eight individuals to perform quantitative molecular analyses. Selected RNA targets (9 mRNAs and 15 ncRNAs) with different amplicon lengths were studied by RT-qPCR in paired fresh and FFPE specimens. For RNA quality assessment, RNA purity and yield were comparable between the two sample cohorts; however, the RNA integrity number decreased significantly during FFPE sampling. Amplification efficiency also displayed certain variability related with amplicon length and RNA species. We found molecular evidence that short amplicons of mRNA, lncRNA, and circRNA were amplified more efficiently than long amplicons. With the assistance of RefFinder, 5S, SNORD48, miR-103a, and miR-125b were selected as reference genes given their high stability. After normalization, we found that short amplicon markers (e.g., ACTB mRNA and MALAT1 lncRNA) exhibited high consistency of quantification in paired fresh/FFPE samples. In particular, circRNAs (XPO1, HIPK3, and TMEM56) presented relatively consistent and stable expression profiles in FFPE tissues compared with their corresponding linear transcripts. Additionally, we evaluated the influence of prolonged storage time on the amplification of gene transcripts and found that short amplicons still work effectively in archived FFPE biospecimens. In conclusion, our findings demonstrate the possibility of performing accurate quantitative analysis of ncRNAs using short amplicons and standardized RT-qPCR assays in autopsy-derived FFPE samples.
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Affiliation(s)
- Yehui Lv
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610065, China. .,Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China. .,School of basic medical sciences, Shanghai University of Medicine & Health Science, Shanghai, 201318, China.
| | - Shiying Li
- Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China
| | - Zhihong Li
- School of basic medical sciences, Shanghai University of Medicine & Health Science, Shanghai, 201318, China
| | - Ruiyang Tao
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610065, China.,Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China
| | - Yu Shao
- Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China
| | - Yijiu Chen
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610065, China. .,Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China.
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6
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Green TM, Jensen AK, Holst R, Falgreen S, Bøgsted M, de Stricker K, Plesner T, Mourits-Andersen T, Frederiksen M, Johnsen HE, Pedersen LM, Møller MB. Multiplex polymerase chain reaction-based prognostic models in diffuse large B-cell lymphoma patients treated with R-CHOP. Br J Haematol 2016; 174:876-86. [PMID: 27196819 DOI: 10.1111/bjh.14138] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 03/02/2016] [Indexed: 11/30/2022]
Abstract
We present a multiplex analysis for genes known to have prognostic value in an attempt to design a clinically useful classification model in patients with diffuse large B-cell lymphoma (DLBCL). Real-time polymerase chain reaction was used to measure transcript levels of 28 relevant genes in 194 de novo DLBCL patients treated with R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine, prednisone). Including International Prognostic Index (IPI) as a variable in a penalized Cox regression, we investigated the association with disease progression for single genes or gene combinations in four models. The best model was validated in data from an online available R-CHOP treated cohort. With progression-free survival (PFS) as primary endpoint, the best performing IPI independent model incorporated the LMO2 and HLADQA1 as well as gene interactions for GCSAMxMIB1, GCSAMxCTGF and FOXP1xPDE4B. This model assigned 33% of patients (n = 60) to poor outcome with an estimated 3-year PFS of 40% vs. 87% for low risk (n = 61) and intermediate (n = 60) risk groups (P < 0·001). However, a simpler, IPI independent model incorporated LMO2 and BCL2 and assigned 33% of the patients with a 3-year PFS of 35% vs. 82% for low risk group (P < 0·001). We have documented the impact of a few single genes added to IPI for assignment in new drug trials.
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Affiliation(s)
- Tina M Green
- Department of Pathology, Odense University Hospital, Odense, Denmark.,Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Andreas K Jensen
- Section of Biostatistics, University of Copenhagen, Copenhagen, Denmark
| | - René Holst
- Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Steffen Falgreen
- Department of Haematology, Clinical Cancer Research Centre, Aalborg University Hospital, Aalborg, Denmark
| | - Martin Bøgsted
- Department of Haematology, Clinical Cancer Research Centre, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Karin de Stricker
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Torben Plesner
- Department of Haematology, Vejle Hospital, Vejle, Denmark
| | | | - Mikael Frederiksen
- Department of Haematology, Hospital of Southern Denmark, Aabenraa, Denmark
| | - Hans E Johnsen
- Department of Haematology, Clinical Cancer Research Centre, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Lars M Pedersen
- Department of Haematology, Roskilde Hospital, Roskilde, Denmark
| | - Michael B Møller
- Department of Pathology, Odense University Hospital, Odense, Denmark.,Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
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7
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Kristensen L, Kristensen T, Abildgaard N, Royo C, Frederiksen M, Mourits-Andersen T, Campo E, Møller MB. LPL gene expression is associated with poor prognosis in CLL and closely related to NOTCH1 mutations. Eur J Haematol 2015; 97:175-82. [PMID: 26558352 DOI: 10.1111/ejh.12700] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2015] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Chronic lymphocytic leukemia is a heterogeneous yet incurable disease. Whole-genome and whole-exome sequencing studies have revealed recurrently occurring somatic mutations in some genes. Several other prognostic markers have previously been tested for their prognostic value in CLL. LPL is among these markers. AIM To evaluate LPL gene expression together with the well-established prognostic markers of CLL and investigate correlations with more recently identified prognostic markers, NOTCH1 and TP53 mutations. METHODS On 149 patients, LPL gene expression was analyzed by real-time RT-PCR. Exon 34 of NOTCH1 was PCR-amplified and directly sequenced. RESULTS LPL gene expression could be measured as a categorical variable (LPL+/LPL-) and was associated with time to treatment (P < 0.001) and overall survival (P = 0.007). In patients otherwise classified as having a good prognosis according to established and new prognostic markers, 3 of 4 patients, who received treatment within 24 months after diagnosis, were LPL+ (P = 0.03). There was a strong correlation between NOTCH1 mutation and LPL+ (P = 0.005). The unfavorable prognosis of LPL+ was maintained in CLL with wild-type NOTCH1. CONCLUSIONS NOTCH1 mutations are tightly associated with LPL gene expression. LPL expression is independently associated with poor outcome in CLL and can be measured as a categorical variable.
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Affiliation(s)
- Louise Kristensen
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Thomas Kristensen
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Niels Abildgaard
- Department of Hematology, Odense University Hospital, Odense, Denmark
| | - Cristina Royo
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Mikael Frederiksen
- Department of Hematology, Hospital of Southern Jutland, Aabenraa, Denmark
| | | | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clinic, University of Barcelona, Barcelona, Spain
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8
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Greytak SR, Engel KB, Bass BP, Moore HM. Accuracy of Molecular Data Generated with FFPE Biospecimens: Lessons from the Literature. Cancer Res 2015; 75:1541-7. [PMID: 25836717 DOI: 10.1158/0008-5472.can-14-2378] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 12/22/2014] [Indexed: 12/15/2022]
Abstract
Formalin-fixed and paraffin-embedded (FFPE) tissue biospecimens are a valuable resource for molecular cancer research. Although much can be gained from their use, it remains unclear whether the genomic and expression profiles obtained from FFPE biospecimens accurately reflect the physiologic condition of the patient from which they were procured, or if such profiles are confounded by biologic effects from formalin fixation and processing. To assess the physiologic accuracy of genomic and expression data generated with FFPE specimens, we surveyed the literature for articles investigating genomic and expression endpoints in case-matched FFPE and fresh or frozen human biospecimens using the National Cancer Institute's Biospecimen Research Database (http://biospecimens.cancer.gov/brd). Results of the survey revealed that the level of concordance between differentially preserved biospecimens varied among analytical parameters and platforms but also among reports, genes/transcripts of interest, and tumor status. The identified analytical techniques and parameters that resulted in strong correlations between FFPE and frozen biospecimens may provide guidance when optimizing molecular protocols for FFPE use; however, discrepancies reported for similar assays also illustrate the importance of validating protocols optimized for use with FFPE specimens with a case-matched fresh or frozen cohort for each platform, gene or transcript, and FFPE processing regime. On the basis of evidence published to date, validation of analytical parameters with a properly handled frozen cohort is necessary to ensure a high degree of concordance and confidence in the results obtained with FFPE biospecimens.
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Affiliation(s)
| | | | | | - Helen M Moore
- Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland.
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9
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Kristensen L, Kristensen T, Abildgaard N, Thomassen M, Frederiksen M, Mourits-Andersen T, Møller MB. High expression of PI3K core complex genes is associated with poor prognosis in chronic lymphocytic leukemia. Leuk Res 2015; 39:555-60. [PMID: 25840748 DOI: 10.1016/j.leukres.2015.02.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 02/13/2015] [Accepted: 02/18/2015] [Indexed: 11/16/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is the most common leukemia among adults in the Western world. Autophagy is a highly conserved process in eukaryotic cells. In CLL autophagy is involved in mediating the effect of chemotherapy but the role of autophagy in CLL pathogenesis remains unknown. In the present study, we used real-time RT-PCR to analyze expression of the PIK3C3, PIK3R4, and BECN1 genes. These genes encode the components of the PI3K core complex, which is central to initiation of autophagy. A consecutive series of 149 well-characterized CLL cases from Region of Southern Denmark were included in the study. All three genes were observed to be independent markers of prognosis in CLL with high expression being associated with more aggressive disease. With this clear association with outcome in CLL, these genes thereby represent promising candidates for future functional studies on the role of autophagy in CLL, and they may further represent targets of treatment.
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Affiliation(s)
- Louise Kristensen
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Thomas Kristensen
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Niels Abildgaard
- Department of Hematology, Odense University Hospital, Odense, Denmark
| | - Mads Thomassen
- Department of Genetics, Odense University Hospital, Odense, Denmark
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10
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Christophi GP, Caza T, Curtiss C, Gumber D, Massa PT, Landas SK. Gene expression profiles in granuloma tissue reveal novel diagnostic markers in sarcoidosis. Exp Mol Pathol 2014; 96:393-9. [PMID: 24768588 DOI: 10.1016/j.yexmp.2014.04.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 04/10/2014] [Indexed: 01/16/2023]
Abstract
Sarcoidosis is an immune-mediated multisystem disease characterized by the formation of non-caseating granulomas. The pathogenesis of sarcoidosis is unclear, with proposed infectious or environmental antigens triggering an aberrant immune response in susceptible hosts. Multiple pro-inflammatory signaling pathways have been implicated in mediating macrophage activation and granuloma formation in sarcoidosis, including IFN-γ/STAT-1, IL-6/STAT-3, and NF-κB. It is difficult to distinguish sarcoidosis from other granulomatous diseases or assess disease severity and treatment response with histopathology alone. Therefore, development of improved diagnostic tools is imperative. Herein, we describe an efficient and reliable technique to classify granulomatous disease through selected gene expression and identify novel genes and cytokine pathways contributing to the pathogenesis of sarcoidosis. We quantified the expression of twenty selected mRNAs extracted from formalin-fixed paraffin embedded (FFPE) tissue (n = 38) of normal lung, suture granulomas, sarcoid granulomas, and fungal granulomas. Utilizing quantitative real-time RT-PCR we analyzed the expression of several genes, including IL-6, COX-2, MCP-1, IFN-γ, T-bet, IRF-1, Nox2, IL-33, and eotaxin-1 and revealed differential regulation between suture, sarcoidosis, and fungal granulomas. This is the first study demonstrating that quantification of target gene expression in FFPE tissue biopsies is a potentially effective diagnostic and research tool in sarcoidosis.
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Affiliation(s)
- George P Christophi
- Department of Gastroenterology, Washington University School of Medicine, St. Louis, MO, United States.
| | - Tiffany Caza
- Department of Pathology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Christopher Curtiss
- Department of Pathology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Divya Gumber
- Department of Internal Medicine, Cleveland Clinic, Cleveland, OH, United States
| | - Paul T Massa
- Department of Microbiology & Immunology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Steve K Landas
- Department of Pathology, SUNY Upstate Medical University, Syracuse, NY, United States
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11
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Christophi GP, Rong R, Holtzapple PG, Massa PT, Landas SK. Immune markers and differential signaling networks in ulcerative colitis and Crohn's disease. Inflamm Bowel Dis 2012; 18:2342-56. [PMID: 22467146 PMCID: PMC3407828 DOI: 10.1002/ibd.22957] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2012] [Accepted: 02/27/2012] [Indexed: 12/14/2022]
Abstract
BACKGROUND Cytokine signaling pathways play a central role in the pathogenesis of inflammatory bowel disease (IBD). Ulcerative colitis (UC) and Crohn's disease (CD) have unique as well as overlapping phenotypes, susceptibility genes, and gene expression profiles. This study aimed to delineate patterns within cytokine signaling pathways in colonic mucosa of UC and CD patients, explore molecular diagnostic markers, and identify novel immune mediators in IBD pathogenesis. METHODS We quantified 70 selected immune genes that are important in IBD signaling from formalin-fixed, paraffin-embedded (FFPE) colon biopsy samples from normal control subjects and UC and CD patients having either severe colitis or quiescent disease (n = 98 subjects). We utilized and validated a new modified real-time reverse-transcription polymerase chain reaction (RT-PCR) technique for gene quantification. RESULTS Expression levels of signaling molecules including IL-6/10/12/13/17/23/33, STAT1/3/6, T-bet, GATA3, Foxp3, SOCS1/3, and downstream inflammatory mediators such as chemokines CCL-2/11/17/20, oxidative stress inducers, proteases, and mucosal genes were differentially regulated between UC and CD and between active and quiescent disease. We also document the possible role of novel genes in IBD, including SHP-1, IRF-1,TARC, Eotaxin, NOX2, arginase I, and ADAM 8. CONCLUSIONS This comprehensive approach to quantifying gene expression provides insights into the pathogenesis of IBD by elucidating distinct immune signaling networks in CD and UC. Furthermore, this is the first study demonstrating that gene expression profiling in FFPE colon biopsies might be a practical and effective tool in the diagnosis and prognosis of IBD and may help identify molecular markers that can predict and monitor response to individualized therapeutic treatments.
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Affiliation(s)
- George P. Christophi
- Department of Microbiology & Immunology, SUNY Upstate Medical University, Syracuse NY
,Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
,Corresponding Author: Mailing Address: Washington University School of Medicine Department of Internal Medicine, 660 S. Euclid Ave., Box 8121, St. Louis, MO 63110, , Tel: 314-956-9640
| | - Rong Rong
- Department of Pathology, SUNY Upstate Medical University, Syracuse NY
| | | | - Paul T. Massa
- Department of Microbiology & Immunology, SUNY Upstate Medical University, Syracuse NY
| | - Steve K. Landas
- Department of Pathology, SUNY Upstate Medical University, Syracuse NY
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Green TM, Nielsen O, de Stricker K, Xu-Monette ZY, Young KH, Møller MB. High Levels of Nuclear MYC Protein Predict the Presence of MYC Rearrangement in Diffuse Large B-cell Lymphoma. Am J Surg Pathol 2012; 36:612-9. [PMID: 22314191 DOI: 10.1097/pas.0b013e318244e2ba] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Abstract
For the past 20 years most malignant lymphomas have been classified as clinicopathological entities, each with its own combination of clinical, morphological, immunophenotypic and molecular genetic characteristics. Molecular and cytogenetic abnormalities can be detected by a wide range of techniques, ranging from conventional karyotyping to single nucleotide polymorphism analysis. In this review, we consider the common genetic abnormalities found in lymphoma and discuss the advantages and disadvantages of individual techniques used in their detection. Finally, we discuss briefly possible novel developments in the field of lymphoma diagnostics.
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Affiliation(s)
- Philip Kluin
- Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands.
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