1
|
Bhamidimarri PM, Salameh L, Mahdami A, Abdullah HW, Mahboub B, Hamoudi R. LINCATRA: Two-cycle method to amplify RNA for transcriptome analysis from formalin-fixed paraffin-embedded tissue. Heliyon 2024; 10:e32896. [PMID: 38988576 PMCID: PMC11234047 DOI: 10.1016/j.heliyon.2024.e32896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/21/2024] [Accepted: 06/11/2024] [Indexed: 07/12/2024] Open
Abstract
Whole transcriptome analysis (WTA) using RNA extracted from Formalin Fixed Paraffin Embedded (FFPE) tissue is an invaluable tool to understand the molecular pathology of disease. RNA extracted from FFPE tissue is either degraded and/or in very low quantities hampering gene expression analysis. Earlier studies described protocols applied for cellular RNA using poly-A primer-based linear amplification. The current study describes a method, LINCATRA (LINear amplifiCAtion of RNA for whole TRAnscriptome analysis). It employs random nonamer primer based method which can amplify short, fragmented RNA with high fidelity from as low as 5 ng to obtain enough material for WTA. The two-cycle method significantly amplified RNA at ∼1000 folds (p < 0.0001) improving the mean read lengths (p < 0.05) in WTA. Overall, increased mean read length positively correlated with on-target reads (Pearson's r = 0.71, p < 0.0001) in both amplified and unamplified RNA-seq analysis. Gene expression analysis compared between unamplified and amplified group displayed substantial overlap of the differentially expressed genes (DEGs) (log2 fold change cut-off < -2 and >2, p < 0.05) identified between lung cancer and asthma cohorts validating the method developed. This method is applicable in clinical molecular pathology field for both diagnostics and elucidation of disease mechanisms.
Collapse
Affiliation(s)
- Poorna Manasa Bhamidimarri
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Laila Salameh
- Rashid Hospital, Dubai Health, Dubai, 4545, United Arab Emirates
| | - Amena Mahdami
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Hanan Wael Abdullah
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Bassam Mahboub
- Rashid Hospital, Dubai Health, Dubai, 4545, United Arab Emirates
- Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Rifat Hamoudi
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Division of Surgery and Interventional Sciences, University College London, London, United Kingdom
- BIMAI-Lab, Biomedically Informed Artificial Inelligence Laboratory, University of Sharjah, Sharjah, 27272, United Arab Emirates
- Centre of Excelence for Precision Medicine, Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
| |
Collapse
|
2
|
Wang C, Zhai J, Chen Y. Novel KCNQ2 missense variant expands the genotype spectrum of DEE7. Neurol Sci 2024:10.1007/s10072-024-07655-w. [PMID: 38880853 DOI: 10.1007/s10072-024-07655-w] [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: 04/05/2024] [Accepted: 06/05/2024] [Indexed: 06/18/2024]
Abstract
BACKGROUND KCNQ is a voltage-gated K + channel that controls neuronal excitability and is mutated in epilepsy and autism spectrum disorder (ASD). We focus on the KV7.2 voltage-gated potassium channel gene (KCNQ2), which is known for its association with developmental delay and various seizures (including self-limited benign familial neonatal epilepsy and epileptic encephalopathy). But the pathogenicity of many variants remains unproven, potentially leading to misinterpretation of their functional consequences. METHODS In this study, we studied a patient who visited Nanhua Hospital. Targeted next-generation sequencing and Sanger sequencing were used to identify the pathogenic variants. Meanwhile, computational models, including hydrogen bonding and docking analyses, suggest that variants cause functional impairment. In addition, functional validation was performed in the drosophila to further evaluate the missense variant in the KCNQ2 gene as the cause of this patient. RESULTS A new missense variant in the KCNQ2 gene was identified: NM_172107.4:c.1007C > A(p.ALa336Glu), which resulted in the change from alanine to glutamate at amino acid position 336 in the KCNQ2 gene. After computational modeling, including hydrogen bond analysis and docking analysis, it is indicated that the variants cause functional impairment. Furthermore, RNAi-mediated KCNQ knockout in flies led to the onset of epileptic behavior, lifespan and climbing capacity were affected, expression of the normal human KCNQ2 rescues the in flies RNAi-mediated KCNQ knockout behavioral abnormalities. CONCLUSION Our findings expands the genetic profile of KCNQ2 and enhances the genotype - phenotype link.
Collapse
Affiliation(s)
- Chao Wang
- Department of Neurology, the Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - JinXia Zhai
- Department of Neurology, the Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - YongJun Chen
- Department of Neurology, the Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang, China.
| |
Collapse
|
3
|
Okojie J, O’Neal N, Burr M, Worley P, Packer I, Anderson D, Davis J, Kearns B, Fatema K, Dixon K, Barrott JJ. DNA Quantity and Quality Comparisons between Cryopreserved and FFPE Tumors from Matched Pan-Cancer Samples. Curr Oncol 2024; 31:2441-2452. [PMID: 38785464 PMCID: PMC11119490 DOI: 10.3390/curroncol31050183] [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: 03/18/2024] [Revised: 04/25/2024] [Accepted: 04/27/2024] [Indexed: 05/25/2024] Open
Abstract
Personalized cancer care requires molecular characterization of neoplasms. While the research community accepts frozen tissues as the gold standard analyte for molecular assays, the source of tissue for testing in clinical cancer care comes almost universally from formalin-fixed, paraffin-embedded tissue (FFPE). As newer technologies emerge for DNA characterization that requires higher molecular weight DNA, it was necessary to compare the quality of DNA in terms of DNA length between FFPE and cryopreserved samples. We hypothesized that cryopreserved samples would yield higher quantity and superior quality DNA compared to FFPE samples. We analyzed DNA metrics by performing a head-to-head comparison between FFPE and cryopreserved samples from 38 human tumors representing various cancer types. DNA quantity and purity were measured by UV spectrophotometry, and DNA from cryopreserved tissue demonstrated a 4.2-fold increase in DNA yield per mg of tissue (p-value < 0.001). DNA quality was measured on a fragment microelectrophoresis analyzer, and again, DNA from cryopreserved tissue demonstrated a 223% increase in the DNA quality number and a 9-fold increase in DNA fragments > 40,000 bp (p-value < 0.0001). DNA from the cryopreserved tissues was superior to the DNA from FFPE samples in terms of DNA yield and quality.
Collapse
Affiliation(s)
- Jeffrey Okojie
- Department of Cell Biology & Physiology, Brigham Young University, Provo, UT 84602, USA; (J.O.); (M.B.); (P.W.); (I.P.); (D.A.); (J.D.); (B.K.)
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, Pocatello, ID 83209, USA; (N.O.); (K.F.)
| | - Nikole O’Neal
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, Pocatello, ID 83209, USA; (N.O.); (K.F.)
| | - Mackenzie Burr
- Department of Cell Biology & Physiology, Brigham Young University, Provo, UT 84602, USA; (J.O.); (M.B.); (P.W.); (I.P.); (D.A.); (J.D.); (B.K.)
| | - Peyton Worley
- Department of Cell Biology & Physiology, Brigham Young University, Provo, UT 84602, USA; (J.O.); (M.B.); (P.W.); (I.P.); (D.A.); (J.D.); (B.K.)
| | - Isaac Packer
- Department of Cell Biology & Physiology, Brigham Young University, Provo, UT 84602, USA; (J.O.); (M.B.); (P.W.); (I.P.); (D.A.); (J.D.); (B.K.)
| | - DeLaney Anderson
- Department of Cell Biology & Physiology, Brigham Young University, Provo, UT 84602, USA; (J.O.); (M.B.); (P.W.); (I.P.); (D.A.); (J.D.); (B.K.)
| | - Jack Davis
- Department of Cell Biology & Physiology, Brigham Young University, Provo, UT 84602, USA; (J.O.); (M.B.); (P.W.); (I.P.); (D.A.); (J.D.); (B.K.)
| | - Bridger Kearns
- Department of Cell Biology & Physiology, Brigham Young University, Provo, UT 84602, USA; (J.O.); (M.B.); (P.W.); (I.P.); (D.A.); (J.D.); (B.K.)
| | - Kaniz Fatema
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, Pocatello, ID 83209, USA; (N.O.); (K.F.)
| | - Ken Dixon
- Specicare, 690 Medical Park Ln, Gainesville, GA 30501, USA
| | - Jared J. Barrott
- Department of Cell Biology & Physiology, Brigham Young University, Provo, UT 84602, USA; (J.O.); (M.B.); (P.W.); (I.P.); (D.A.); (J.D.); (B.K.)
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, Pocatello, ID 83209, USA; (N.O.); (K.F.)
- Specicare, 690 Medical Park Ln, Gainesville, GA 30501, USA
- Simmons Center for Cancer Research, Brigham Young University, Provo, UT 84602, USA
| |
Collapse
|
4
|
Song K, Elboudwarej E, Zhao X, Zhuo L, Pan D, Liu J, Brachmann C, Patterson SD, Yoon OK, Zavodovskaya M. RNA-seq RNAaccess identified as the preferred method for gene expression analysis of low quality FFPE samples. PLoS One 2023; 18:e0293400. [PMID: 37883360 PMCID: PMC10602291 DOI: 10.1371/journal.pone.0293400] [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: 06/02/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023] Open
Abstract
Clinical tumor tissues that are preserved as formalin-fixed paraffin-embedded (FFPE) samples result in extensive cross-linking, fragmentation, and chemical modification of RNA, posing significant challenges for RNA-seq-based gene expression profiling. This study sought to define an optimal RNA-seq protocol for FFPE samples. We employed a common RNA extraction method and then compared RNA-seq library preparation protocols including RNAaccess, RiboZero and PolyA in terms of sequencing quality and concordance of gene expression using FFPE and case-matched fresh-frozen (FF) triple-negative breast cancer (TNBC) tissues. We found that RNAaccess, a method based on exome capture, produced the most concordant results. Applying RNAaccess to FFPE gastric cancer tissues, we established a minimum RNA DV200 requirement of 10% and a RNA input amount of 10ng that generated highly reproducible gene expression data. Lastly, we demonstrated that RNAaccess and NanoString platforms produced highly concordant expression profiles from FFPE samples for shared genes; however, RNA-seq may be preferred for clinical biomarker discovery work because of the broader coverage of the transcriptome. Taken together, these results support the selection of RNA-seq RNAaccess method for gene expression profiling of FFPE samples. The minimum requirements for RNA quality and input established here may allow for inclusion of clinical FFPE samples of sub-optimal quality in gene expression analyses and ultimately increasing the statistical power of such analyses.
Collapse
Affiliation(s)
- Kai Song
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Emon Elboudwarej
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Xi Zhao
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Luting Zhuo
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - David Pan
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Jinfeng Liu
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Carrie Brachmann
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Scott D. Patterson
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Oh Kyu Yoon
- Gilead Sciences, Inc., Foster City, California, United States of America
| | | |
Collapse
|
5
|
Ng E, Dobrica MO, Harris JM, Wu Y, Tsukuda S, Wing PAC, Piazza P, Balfe P, Matthews PC, Ansari MA, McKeating JA. An enrichment protocol and analysis pipeline for long read sequencing of the hepatitis B virus transcriptome. J Gen Virol 2023; 104:001856. [PMID: 37196057 PMCID: PMC10845048 DOI: 10.1099/jgv.0.001856] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/21/2023] [Indexed: 05/19/2023] Open
Abstract
Hepatitis B virus (HBV) is one of the smallest human DNA viruses and its 3.2 Kb genome encodes multiple overlapping open reading frames, making its viral transcriptome challenging to dissect. Previous studies have combined quantitative PCR and Next Generation Sequencing to identify viral transcripts and splice junctions, however the fragmentation and selective amplification used in short read sequencing precludes the resolution of full length RNAs. Our study coupled an oligonucleotide enrichment protocol with state-of-the-art long read sequencing (PacBio) to identify the repertoire of HBV RNAs. This methodology provides sequencing libraries where up to 25 % of reads are of viral origin and enable the identification of canonical (unspliced), non-canonical (spliced) and chimeric viral-human transcripts. Sequencing RNA isolated from de novo HBV infected cells or those transfected with 1.3 × overlength HBV genomes allowed us to assess the viral transcriptome and to annotate 5' truncations and polyadenylation profiles. The two HBV model systems showed an excellent agreement in the pattern of major viral RNAs, however differences were noted in the abundance of spliced transcripts. Viral-host chimeric transcripts were identified and more commonly found in the transfected cells. Enrichment capture and PacBio sequencing allows the assignment of canonical and non-canonical HBV RNAs using an open-source analysis pipeline that enables the accurate mapping of the HBV transcriptome.
Collapse
Affiliation(s)
- Esther Ng
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mihaela-Olivia Dobrica
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Present address: Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - James M. Harris
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Yanxia Wu
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Senko Tsukuda
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Peter A. C. Wing
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Paolo Piazza
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Peter Balfe
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Philippa C. Matthews
- The Francis Crick Institute, London, UK
- Division of Infection and Immunity, University College London, London, UK
| | - M. Azim Ansari
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jane A. McKeating
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| |
Collapse
|
6
|
Oreper D, Klaeger S, Jhunjhunwala S, Delamarre L. The peptide woods are lovely, dark and deep: Hunting for novel cancer antigens. Semin Immunol 2023; 67:101758. [PMID: 37027981 DOI: 10.1016/j.smim.2023.101758] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 04/08/2023]
Abstract
Harnessing the patient's immune system to control a tumor is a proven avenue for cancer therapy. T cell therapies as well as therapeutic vaccines, which target specific antigens of interest, are being explored as treatments in conjunction with immune checkpoint blockade. For these therapies, selecting the best suited antigens is crucial. Most of the focus has thus far been on neoantigens that arise from tumor-specific somatic mutations. Although there is clear evidence that T-cell responses against mutated neoantigens are protective, the large majority of these mutations are not immunogenic. In addition, most somatic mutations are unique to each individual patient and their targeting requires the development of individualized approaches. Therefore, novel antigen types are needed to broaden the scope of such treatments. We review high throughput approaches for discovering novel tumor antigens and some of the key challenges associated with their detection, and discuss considerations when selecting tumor antigens to target in the clinic.
Collapse
Affiliation(s)
- Daniel Oreper
- Genentech, 1 DNA way, South San Francisco, 94080 CA, USA.
| | - Susan Klaeger
- Genentech, 1 DNA way, South San Francisco, 94080 CA, USA.
| | | | | |
Collapse
|
7
|
Belova V, Shmitko A, Pavlova A, Afasizhev R, Cheranev V, Tabanakova A, Ponikarovskaya N, Rebrikov D, Korostin D. Performance comparison of Agilent new SureSelect All Exon v8 probes with v7 probes for exome sequencing. BMC Genomics 2022; 23:582. [PMID: 35962321 PMCID: PMC9375261 DOI: 10.1186/s12864-022-08825-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/05/2022] [Indexed: 11/10/2022] Open
Abstract
Exome sequencing is becoming a routine in health care, because it increases the chance of pinpointing the genetic cause of an individual patient's condition and thus making an accurate diagnosis. It is important for facilities providing genetic services to keep track of changes in the technology of exome capture in order to maximize throughput while reducing cost per sample. In this study, we focused on comparing the newly released exome probe set Agilent SureSelect Human All Exon v8 and the previous probe set v7. In preparation for higher throughput of exome sequencing using the DNBSEQ-G400, we evaluated target design, coverage statistics, and variants across these two different exome capture products. Although the target size of the v8 design has not changed much compared to the v7 design (35.24 Mb vs 35.8 Mb), the v8 probe design allows you to call more of SNVs (+ 3.06%) and indels (+ 8.49%) with the same number of raw reads per sample on the common target regions (34.84 Mb). Our results suggest that the new Agilent v8 probe set for exome sequencing yields better data quality than the current Agilent v7 set.
Collapse
Affiliation(s)
- Vera Belova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation.
| | - Anna Shmitko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Anna Pavlova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Robert Afasizhev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Valery Cheranev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Anastasia Tabanakova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Natalya Ponikarovskaya
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Denis Rebrikov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Dmitriy Korostin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| |
Collapse
|
8
|
Iwahashi N, Umakoshi H, Ogata M, Fukumoto T, Kaneko H, Terada E, Katsuhara S, Uchida N, Sasaki K, Yokomoto-Umakoshi M, Matsuda Y, Sakamoto R, Ogawa Y. Whole Transcriptome Profiling of Adrenocortical Tumors Using Formalin-Fixed Paraffin-Embedded Samples. Front Endocrinol (Lausanne) 2022; 13:808331. [PMID: 35185794 PMCID: PMC8850780 DOI: 10.3389/fendo.2022.808331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/11/2022] [Indexed: 11/24/2022] Open
Abstract
Whole transcriptome profiling is a promising technique in adrenal studies; however, whole transcriptome profiling of adrenal disease using formalin-fixed paraffin-embedded (FFPE) samples has to be further explored. The aim of this study was to evaluate the utility of transcriptome data from FFPE samples of adrenocortical tumors. We performed whole transcriptome profiling of FFPE and fresh frozen samples of adrenocortical carcinoma (ACC, n = 3), aldosterone-producing adenoma (APA, n = 3), and cortisol-producing adenoma (CPA, n = 3), and examined the similarity between the transcriptome data. We further examined whether the transcriptome data of FFPE samples could be used to distinguish tumor types and detect marker genes. The number of read counts was smaller in FFPE samples than in fresh frozen samples (P < 0.01), while the number of genes detected was similar (P = 0.39). The gene expression profiles of FFPE and fresh frozen samples were highly correlated (r = 0.93, P < 0.01). Tumor types could be distinguished by consensus clustering and principal component analysis using transcriptome data from FFPE samples. In the differential expression analysis between ACC and APA-CPA, known marker genes of ACC (e.g., CCNB2, TOP2A, and MAD2L1) were detected in FFPE samples of ACC. In the differential expression analysis between APA and CPA, known marker genes of APA (e.g., CYP11B2, VSNL1, and KCNJ5) were detected in the APA of FFPE samples. The results suggest that FFPE samples may be a reliable alternative to fresh frozen samples for whole transcriptome profiling of adrenocortical tumors.
Collapse
Affiliation(s)
- Norifusa Iwahashi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hironobu Umakoshi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- *Correspondence: Hironobu Umakoshi, ; Yoshihiro Ogawa,
| | - Masatoshi Ogata
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tazuru Fukumoto
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroki Kaneko
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Eriko Terada
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shunsuke Katsuhara
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Naohiro Uchida
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Katsuhiko Sasaki
- Clinical Laboratory Department, Kyushu Pro Search Limited Liability Partnership, Fukuoka, Japan
| | - Maki Yokomoto-Umakoshi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yayoi Matsuda
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Ryuichi Sakamoto
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshihiro Ogawa
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- *Correspondence: Hironobu Umakoshi, ; Yoshihiro Ogawa,
| |
Collapse
|
9
|
Griffin CP, Paul CL, Alexander KL, Walker MM, Hondermarck H, Lynam J. Postmortem brain donations vs premortem surgical resections for glioblastoma research: viewing the matter as a whole. Neurooncol Adv 2022; 4:vdab168. [PMID: 35047819 PMCID: PMC8760897 DOI: 10.1093/noajnl/vdab168] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
There have been limited improvements in diagnosis, treatment, and outcomes of primary brain cancers, including glioblastoma, over the past 10 years. This is largely attributable to persistent deficits in understanding brain tumor biology and pathogenesis due to a lack of high-quality biological research specimens. Traditional, premortem, surgical biopsy samples do not allow full characterization of the spatial and temporal heterogeneity of glioblastoma, nor capture end-stage disease to allow full evaluation of the evolutionary and mutational processes that lead to treatment resistance and recurrence. Furthermore, the necessity of ensuring sufficient viable tissue is available for histopathological diagnosis, while minimizing surgically induced functional deficit, leaves minimal tissue for research purposes and results in formalin fixation of most surgical specimens. Postmortem brain donation programs are rapidly gaining support due to their unique ability to address the limitations associated with surgical tissue sampling. Collecting, processing, and preserving tissue samples intended solely for research provides both a spatial and temporal view of tumor heterogeneity as well as the opportunity to fully characterize end-stage disease from histological and molecular standpoints. This review explores the limitations of traditional sample collection and the opportunities afforded by postmortem brain donations for future neurobiological cancer research.
Collapse
Affiliation(s)
- Cassandra P Griffin
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Cancer Biobank: NSW Regional Biospecimen and Research Services, University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Cancer Research Alliance, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Christine L Paul
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Cancer Research Alliance, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Newcastle, New South Wales, Australia
- Priority Research Centre Cancer Research, Innovation and Translation, University of Newcastle, New South Wales, Australia
- Priority Research Centre Health Behaviour, University of Newcastle, New South Wales, Australia
| | - Kimberley L Alexander
- Neurosurgery Department, Chris O’Brien Lifehouse, Camperdown, New South Wales, Australia
- Brainstorm Brain Cancer Research, Brain and Mind Centre, The University of Sydney, New South Wales, Australia
- Neuropathology Department, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Marjorie M Walker
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Cancer Research Alliance, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Hubert Hondermarck
- Hunter Cancer Research Alliance, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Newcastle, New South Wales, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia
| | - James Lynam
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Cancer Research Alliance, University of Newcastle, Newcastle, New South Wales, Australia
- Department of Medical Oncology, Calvary Mater, Newcastle, New South Wales, Australia
| |
Collapse
|