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Choate LA, Koleilat A, Harris K, Vidal-Folch N, Guenzel A, Newman J, Peterson BJ, Peterson SE, Rice CS, Train LJ, Hasadsri L, Marcou CA, Moyer AM, Baudhuin LM. Confirmation of Insertion, Deletion, and Deletion-Insertion Variants Detected by Next-Generation Sequencing. Clin Chem 2023; 69:1155-1162. [PMID: 37566393 DOI: 10.1093/clinchem/hvad110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/03/2023] [Indexed: 08/12/2023]
Abstract
BACKGROUND Despite clinically demonstrated accuracy in next generation sequencing (NGS) data, many clinical laboratories continue to confirm variants with Sanger sequencing, which increases cost of testing and turnaround time. Several studies have assessed the accuracy of NGS in detecting single nucleotide variants; however, less has been reported about insertion, deletion, and deletion-insertion variants (indels). METHODS We performed a retrospective analysis from 2015-2022 of indel results from a subset of NGS targeted gene panel tests offered through the Mayo Clinic Genomics Laboratories. We compared results from NGS and Sanger sequencing of indels observed in clinical runs and during the intra-assay validation of the tests. RESULTS Results demonstrated 100% concordance between NGS and Sanger sequencing for over 490 indels (217 unique), ranging in size from 1 to 68 basepairs (bp). The majority of indels were deletions (77%) and 1 to 5 bp in length (90%). Variant frequencies ranged from 11.4% to 67.4% and 85.1% to 100% for heterozygous and homozygous variants, respectively, with a median depth of coverage of 2562×. A subset of indels (7%) were located in complex regions of the genome, and these were accurately detected by NGS. We also demonstrated 100% reproducibility of indel detection (n = 179) during intra-assay validation. CONCLUSIONS Together this data demonstrates that reportable indel variants up to 68 bp can be accurately assessed using NGS, even when they occur in complex regions. Depending on the complexity of the region or variant, Sanger sequence confirmation of indels is usually not necessary if the variants meet appropriate coverage and allele frequency thresholds.
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Affiliation(s)
- Lauren A Choate
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Alaa Koleilat
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Kimberley Harris
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Noemi Vidal-Folch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Adam Guenzel
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Jessica Newman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Brenda J Peterson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Sandra E Peterson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Christopher S Rice
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Laura J Train
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Linda Hasadsri
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Cherisse A Marcou
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Linnea M Baudhuin
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
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2
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Choate LA, Jiang L, Stein MI, Shen W, Baughn LB, Peterson JF. Detection of an MN1::ETV6 Gene Fusion in a Case of Acute Myeloid Leukemia with Erythroid Differentiation: A Case Report and Review of the Literature. Case Rep Hematol 2023; 2023:9771388. [PMID: 37434656 PMCID: PMC10332927 DOI: 10.1155/2023/9771388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/17/2023] [Accepted: 06/27/2023] [Indexed: 07/13/2023] Open
Abstract
The MN1::ETV6 gene fusion resulting from t(12;22)(p13;q12) has been rarely reported in myeloid neoplasms. We describe a 69-year-old male with newly diagnosed acute myeloid leukemia (AML) with erythroid differentiation and t(12;22)(p13;q12) demonstrated by conventional chromosome studies. Subsequent fluorescence in situ hybridization studies demonstrated a balanced ETV6 gene rearrangement (at 12p13). To further characterize this translocation, whole-genome sequencing was performed which confirmed t(12;22) with breakpoints involving the MN1 and ETV6 genes. Herein, we describe our case and review the literature to summarize the clinical and laboratory findings in patients with this rare but recurrent MN1::ETV6 gene fusion observed in myeloid neoplasms. Importantly, this case expands the clinical spectrum associated with the MN1::ETV6 gene fusion to include AML with erythroid differentiation. Lastly, this case demonstrates the importance of moving toward more comprehensive molecular testing to fully characterize the driver events in neoplastic genomes.
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Affiliation(s)
- Lauren A. Choate
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Liuyan Jiang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Jacksonville, Florida, USA
| | - Mariam I. Stein
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Wei Shen
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Linda B. Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jess F. Peterson
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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3
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Shen W, Sellers HL, Choate LA, Stein MI, Tandale PP, Tan J, Setlem R, Sakai Y, Fadra N, Sosa C, McClelland SP, Barnett SS, Rasmussen KJ, Runke CK, Smoley SA, Tillmans LS, Marcou CA, Rowsey RA, Thorland EC, Boczek NJ, Kearney HM. Clinical Validation of Tagmentation-Based Genome Sequencing for Germline Disorders. J Mol Diagn 2023; 25:524-531. [PMID: 37088140 DOI: 10.1016/j.jmoldx.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/09/2023] [Accepted: 04/04/2023] [Indexed: 04/25/2023] Open
Abstract
Genome sequencing (GS) is a powerful clinical tool used for the comprehensive diagnosis of germline disorders. GS library preparation typically involves mechanical DNA fragmentation, end repair, and bead-based library size selection followed by adapter ligation, which can require a large amount of input genomic DNA. Tagmentation using bead-linked transposomes can simplify the library preparation process and reduce the DNA input requirement. Here we describe the clinical validation of tagmentation-based PCR-free GS as a clinical test for rare germline disorders. Compared with the Genome-in-a-Bottle Consortium benchmark variant sets, GS had a recall >99.7% and a precision of 99.8% for single nucleotide variants and small insertion-deletions. GS also exhibited 100% sensitivity for clinically reported sequence variants and the copy number variants examined. Furthermore, GS detected mitochondrial sequence variants above 5% heteroplasmy and showed reliable detection of disease-relevant repeat expansions and SMN1 homozygous loss. Our results indicate that while lowering DNA input requirements and reducing library preparation time, GS enables uniform coverage across the genome as well as robust detection of various types of genetic alterations. With the advantage of comprehensive profiling of multiple types of genetic alterations, GS is positioned as an ideal first-tier diagnostic test for germline disorders.
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Affiliation(s)
- Wei Shen
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.
| | - Heidi L Sellers
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Lauren A Choate
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Mariam I Stein
- Division of Computational Biology, Mayo Clinic Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Pratyush P Tandale
- Division of Computational Biology, Mayo Clinic Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Jiayu Tan
- Division of Computational Biology, Mayo Clinic Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Rohit Setlem
- Division of Computational Biology, Mayo Clinic Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Yuta Sakai
- Division of Computational Biology, Mayo Clinic Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Numrah Fadra
- Division of Computational Biology, Mayo Clinic Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Carlos Sosa
- Division of Computational Biology, Mayo Clinic Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Shawn P McClelland
- Division of Computational Biology, Mayo Clinic Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Sarah S Barnett
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kristen J Rasmussen
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Cassandra K Runke
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Stephanie A Smoley
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Lori S Tillmans
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Cherisse A Marcou
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Ross A Rowsey
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Erik C Thorland
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Nicole J Boczek
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Hutton M Kearney
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.
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4
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Prokaeva T, Joshi T, Klimtchuk ES, Gibson VM, Spencer B, Siddiqi O, Nedelkov D, Hu Y, Berk JL, Cuddy SAM, Dasari S, Chiu A, Choate LA, McPhail ED, Cui H, Chen H, Burks EJ, Sanchorawala V, Connors LH. A novel substitution of proline (P32L) destabilises β2-microglobulin inducing hereditary systemic amyloidosis. Amyloid 2022; 29:255-262. [PMID: 35575118 DOI: 10.1080/13506129.2022.2072199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
BACKGROUND β2-microglobulin amyloidosis was first described in the 1980s as a protein deposition disease associated with long-term haemodialysis. More recently, two inherited forms resulting from separate point mutations in the β2-microglobulin gene have been identified. In this report, we detail a novel β2M variant, P32L, caused by a unique dinucleotide mutation that is linked to systemic hereditary β2-microglobulin amyloidosis. METHODS Three family members from a Portuguese kinship featured cardiomyopathy, requiring organ transplantation in one case, along with soft tissue involvement; other involvements included gastrointestinal, neuropathic and sicca syndrome. In vitro studies with recombinant P32L, P32G, D76N and wild-type β2-microglobulin were undertaken to compare the biophysical properties of the proteins. RESULTS The P32L variant was caused by the unique heterozygous dinucleotide mutation c.154_155delinsTT. Amyloid disease featured lowered serum β2-microglobulin levels with near equal amounts of circulating P32L and wild-type proteins; amyloid deposits were composed exclusively of P32L variant protein. In vitro studies of P32L demonstrated thermodynamic and chemical instability and enhanced susceptibility to proteolysis with rapid formation of pre-fibrillar oligomeric structures by N- and C-terminally truncated species under physiological conditions. CONCLUSIONS This work provides both clinical and experimental evidence supporting the critical role of P32 residue replacement in β2M amyloid fibrillogenesis.
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Affiliation(s)
- Tatiana Prokaeva
- Amyloidosis Center, Boston University School of Medicine, Boston, MA, USA
| | - Tracy Joshi
- Amyloidosis Center, Boston University School of Medicine, Boston, MA, USA
| | - Elena S Klimtchuk
- Amyloidosis Center, Boston University School of Medicine, Boston, MA, USA
| | - Victoria M Gibson
- Amyloidosis Center, Boston University School of Medicine, Boston, MA, USA
| | - Brian Spencer
- Amyloidosis Center, Boston University School of Medicine, Boston, MA, USA
| | - Omar Siddiqi
- Amyloidosis Center, Boston University School of Medicine, Boston, MA, USA
| | | | | | - John L Berk
- Amyloidosis Center, Boston University School of Medicine, Boston, MA, USA
| | - Sarah A M Cuddy
- Amyloidosis Program, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Surendra Dasari
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - April Chiu
- Department of Laboratory of Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Lauren A Choate
- Department of Laboratory of Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Ellen D McPhail
- Department of Laboratory of Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Haili Cui
- Amyloidosis Center, Boston University School of Medicine, Boston, MA, USA.,Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Hui Chen
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Eric J Burks
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
| | | | - Lawreen H Connors
- Amyloidosis Center, Boston University School of Medicine, Boston, MA, USA.,Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
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5
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Chou SP, Alexander AK, Rice EJ, Choate LA, Danko CG. Genetic dissection of the RNA polymerase II transcription cycle. eLife 2022; 11:78458. [PMID: 35775732 PMCID: PMC9286732 DOI: 10.7554/elife.78458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/30/2022] [Indexed: 11/20/2022] Open
Abstract
How DNA sequence affects the dynamics and position of RNA Polymerase II (Pol II) during transcription remains poorly understood. Here, we used naturally occurring genetic variation in F1 hybrid mice to explore how DNA sequence differences affect the genome-wide distribution of Pol II. We measured the position and orientation of Pol II in eight organs collected from heterozygous F1 hybrid mice using ChRO-seq. Our data revealed a strong genetic basis for the precise coordinates of transcription initiation and promoter proximal pause, allowing us to redefine molecular models of core transcriptional processes. Our results implicate DNA sequence, including both known and novel DNA sequence motifs, as key determinants of the position of Pol II initiation and pause. We report evidence that initiation site selection follows a stochastic process similar to Brownian motion along the DNA template. We found widespread differences in the position of transcription termination, which impact the primary structure and stability of mature mRNA. Finally, we report evidence that allelic changes in transcription often affect mRNA and ncRNA expression across broad genomic domains. Collectively, we reveal how DNA sequences shape core transcriptional processes at single nucleotide resolution in mammals.
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Affiliation(s)
- Shao-Pei Chou
- Baker Institute for Animal Health, Cornell University, Ithaca, United States
| | - Adriana K Alexander
- Baker Institute for Animal Health, Cornell University, Ithaca, United States
| | - Edward J Rice
- Baker Institute for Animal Health, Cornell University, Ithaca, United States
| | - Lauren A Choate
- Baker Institute for Animal Health, Cornell University, Ithaca, United States
| | - Charles G Danko
- Baker Institute for Animal Health, Cornell University, Ithaca, United States
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6
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Choate LA, Barshad G, McMahon PW, Said I, Rice EJ, Munn PR, Lewis JJ, Danko CG. Multiple stages of evolutionary change in anthrax toxin receptor expression in humans. Nat Commun 2021; 12:6590. [PMID: 34782625 PMCID: PMC8592990 DOI: 10.1038/s41467-021-26854-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 10/18/2021] [Indexed: 11/09/2022] Open
Abstract
The advent of animal husbandry and hunting increased human exposure to zoonotic pathogens. To understand how a zoonotic disease may have influenced human evolution, we study changes in human expression of anthrax toxin receptor 2 (ANTXR2), which encodes a cell surface protein necessary for Bacillus anthracis virulence toxins to cause anthrax disease. In immune cells, ANTXR2 is 8-fold down-regulated in all available human samples compared to non-human primates, indicating regulatory changes early in the evolution of modern humans. We also observe multiple genetic signatures consistent with recent positive selection driving a European-specific decrease in ANTXR2 expression in multiple tissues affected by anthrax toxins. Our observations fit a model in which humans adapted to anthrax disease following early ecological changes associated with hunting and scavenging, as well as a second period of adaptation after the rise of modern agriculture.
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Affiliation(s)
- Lauren A Choate
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Gilad Barshad
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Pierce W McMahon
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Iskander Said
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Edward J Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Paul R Munn
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - James J Lewis
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
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7
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Choate LA, Pitel BA, Smoley S, Mendoza CZ, Thompson L, Johnson SH, Smadbeck JB, Pearce K, Webley M, Koon S, Vasmatzis G, Baughn L, Boczek N, Marcou C, Rowsey R, Thorland E, Kearney H, Hoppman N. 12. Analysis of the clinical utility of mate pair sequencing to further characterize congenital chromosome abnormalities. Cancer Genet 2021. [DOI: 10.1016/j.cancergen.2021.01.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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8
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Mukai C, Choi E, Sams KL, Klampen EZ, Anguish L, Marks BA, Rice EJ, Wang Z, Choate LA, Chou SP, Kato Y, Miller AD, Danko CG, Coonrod SA. Chromatin run-on sequencing analysis finds that ECM remodeling plays an important role in canine hemangiosarcoma pathogenesis. BMC Vet Res 2020; 16:206. [PMID: 32571313 PMCID: PMC7310061 DOI: 10.1186/s12917-020-02395-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/29/2020] [Indexed: 01/20/2023] Open
Abstract
Background Canine visceral hemangiosarcoma (HSA) is a highly aggressive cancer of endothelial origin that closely resembles visceral angiosarcoma in humans, both clinically and histopathologically. Currently there is an unmet need for new diagnostics and therapies for both forms of this disease. The goal of this study was to utilize Chromatin run-on sequencing (ChRO-seq) and immunohistochemistry (IHC) to identify gene and protein expression signatures that may be important drivers of HSA progression. Results ChRO-seq was performed on tissue isolated from 17 HSA samples and 4 normal splenic samples. Computational analysis was then used to identify differentially expressed genes and these factors were subjected to gene ontology analysis. ChRO-seq analysis revealed over a thousand differentially expressed genes in HSA tissue compared with normal splenic tissue (FDR < 0.005). Interestingly, the majority of genes overexpressed in HSA tumor tissue were associated with extracellular matrix (ECM) remodeling. This observation correlated well with our histological analysis, which found that HSA tumors contain a rich and complex collagen network. Additionally, we characterized the protein expression patterns of two highly overexpressed molecules identified in ChRO-seq analysis, podoplanin (PDPN) and laminin alpha 4 (LAMA4). We found that the expression of these two ECM-associated factors appeared to be largely limited to transformed endothelial cells within the HSA lesions. Conclusion Outcomes from this study suggest that ECM remodeling plays an important role in HSA progression. Additionally, our study identified two potential novel biomarkers of HSA, PDPN and LAMA4. Interestingly, given that function-blocking anti-PDPN antibodies have shown anti-tumor effects in mouse models of canine melanoma, our studies raise the possibility that these types of therapeutic strategies could potentially be developed for treating canine HSA.
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Affiliation(s)
- Chinatsu Mukai
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
| | - Eunju Choi
- Department of Biomedical Sciences, Section of Anatomic Pathology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Kelly L Sams
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Elena Zu Klampen
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Lynne Anguish
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Brooke A Marks
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Edward J Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Zhong Wang
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Lauren A Choate
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Shao-Pei Chou
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Yukinari Kato
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Japan.,New Industry Creation Hatchery Center, Tohoku University, Sendai, Japan
| | - Andrew D Miller
- Department of Biomedical Sciences, Section of Anatomic Pathology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Scott A Coonrod
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
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9
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Abstract
Our genomes encode a wealth of transcription initiation regions (TIRs) that can be identified by their distinctive patterns of actively elongating RNA polymerase. We previously introduced dREG to identify TIRs using PRO-seq data. Here, we introduce an efficient new implementation of dREG that uses PRO-seq data to identify both uni- and bidirectionally transcribed TIRs with 70% improvement in accuracy, three- to fourfold higher resolution, and >100-fold increases in computational efficiency. Using a novel strategy to identify TIRs based on their statistical confidence reveals extensive overlap with orthogonal assays, yet also reveals thousands of additional weakly transcribed TIRs that were not identified by H3K27ac ChIP-seq or DNase-seq. Novel TIRs discovered by dREG were often associated with RNA polymerase III initiation, bound by pioneer transcription factors, or located in broad domains marked by repressive chromatin modifications. Our results suggest that transcription initiation can be a powerful tool for expanding the catalog of functional elements.
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Affiliation(s)
- Zhong Wang
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
| | - Tinyi Chu
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
- Graduate Field of Computational Biology, Cornell University, Ithaca, New York 14853, USA
| | - Lauren A Choate
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
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