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Collinge B, Ben-Neriah S, Hilton LK, Alduaij W, Tucker T, Slack GW, Farinha P, Craig JW, Boyle M, Meissner B, Villa D, Gerrie AS, Sehn LH, Savage KJ, Morin RD, Mungall AJ, Steidl C, Scott DW. Unbalanced MYC break-apart FISH patterns indicate the presence of a MYC rearrangement in HGBCL-DH-BCL2. Blood 2024; 144:1611-1616. [PMID: 39133931 DOI: 10.1182/blood.2024025603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 07/28/2024] [Indexed: 10/11/2024] Open
Abstract
ABSTRACT Fluorescence in situ hybridization (FISH) using break-apart probes is recommended for identifying high-grade B-cell lymphoma with MYC and BCL2 rearrangements (HGBCL-DH-BCL2). Unbalanced MYC break-apart patterns, in which the red or green signal is lost, are commonly reported as an equivocal result by clinical laboratories. In a cohort of 297 HGBCL-DH-BCL2, 13% of tumors had unbalanced MYC break-apart patterns with loss of red (LR; 2%) or loss of green (LG; 11%) signal. To determine the significance of these patterns, MYC rearrangements were characterized by sequencing in 130 HGBCL-DH-BCL2, including 3 LR and 14 LG tumors. A MYC rearrangement was identified for 71% of tumors with LR or LG patterns, with the majority involving immunoglobulin loci or other recurrent MYC rearrangement partners. The architecture of these rearrangements consistently preserved the rearranged MYC allele, with the MYC gene predicted to be on the derivative chromosome containing the signal that is still present in nearly all cases. MYC protein expression, MYC messenger RNA expression, and the proportion of tumors expressing the dark-zone signature was not significantly different between balanced and unbalanced groups. These results support a recommendation that unbalanced MYC break-apart FISH patterns be reported as positive for MYC rearrangement in the context of diagnosing HGBCL-DH-BCL2.
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Affiliation(s)
- Brett Collinge
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada
| | | | - Laura K Hilton
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Waleed Alduaij
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Tracy Tucker
- Cancer Genetics and Genomics Laboratory, BC Cancer, Vancouver, BC, Canada
| | - Graham W Slack
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - Pedro Farinha
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - Jeffrey W Craig
- Department of Pathology, University of Virginia, Charlottesville, VA
| | - Merrill Boyle
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | | | - Diego Villa
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Alina S Gerrie
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
- Department of Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - Laurie H Sehn
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Kerry J Savage
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
- Department of Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - Ryan D Morin
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Christian Steidl
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - David W Scott
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
- Department of Medicine, The University of British Columbia, Vancouver, BC, Canada
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2
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Liu L, Zhang J, Wood S, Newell F, Leonard C, Koufariotis LT, Nones K, Dalley AJ, Chittoory H, Bashirzadeh F, Son JH, Steinfort D, Williamson JP, Bint M, Pahoff C, Nguyen PT, Twaddell S, Arnold D, Grainge C, Simpson PT, Fielding D, Waddell N, Pearson JV. Performance of somatic structural variant calling in lung cancer using Oxford Nanopore sequencing technology. BMC Genomics 2024; 25:898. [PMID: 39350042 PMCID: PMC11441263 DOI: 10.1186/s12864-024-10792-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 09/11/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND Lung cancer is a heterogeneous disease and the primary cause of cancer-related mortality worldwide. Somatic mutations, including large structural variants, are important biomarkers in lung cancer for selecting targeted therapy. Genomic studies in lung cancer have been conducted using short-read sequencing. Emerging long-read sequencing technologies are a promising alternative to study somatic structural variants, however there is no current consensus on how to process data and call somatic events. In this study, we preformed whole genome sequencing of lung cancer and matched non-tumour samples using long and short read sequencing to comprehensively benchmark three sequence aligners and seven structural variant callers comprised of generic callers (SVIM, Sniffles2, DELLY in generic mode and cuteSV) and somatic callers (Severus, SAVANA, nanomonsv and DELLY in somatic modes). RESULTS Different combinations of aligners and variant callers influenced somatic structural variant detection. The choice of caller had a significant influence on somatic structural variant detection in terms of variant type, size, sensitivity, and accuracy. The performance of each variant caller was assessed by comparing to somatic structural variants identified by short-read sequencing. When compared to somatic structural variants detected with short-read sequencing, more events were detected with long-read sequencing. The mean recall of somatic variant events identified by long-read sequencing was higher for the somatic callers (72%) than generic callers (53%). Among the somatic callers when using the minimap2 aligner, SAVANA and Severus achieved the highest recall at 79.5% and 79.25% respectively, followed by nanomonsv with a recall of 72.5%. CONCLUSION Long-read sequencing can identify somatic structural variants in clincal samples. The longer reads have the potential to improve our understanding of cancer development and inform personalized cancer treatment.
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Affiliation(s)
- Lingchen Liu
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Jia Zhang
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Felicity Newell
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - Katia Nones
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Andrew J Dalley
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Haarika Chittoory
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Farzad Bashirzadeh
- Department of Thoracic Medicine, The Royal Brisbane & Women's Hospital, Brisbane, Australia
| | - Jung Hwa Son
- Department of Thoracic Medicine, The Royal Brisbane & Women's Hospital, Brisbane, Australia
| | - Daniel Steinfort
- Department of Thoracic Medicine, Royal Melbourne Hospital, Melbourne, Australia
| | | | - Michael Bint
- Department of Thoracic Medicine, Sunshine Coast University Hospital, Birtinya, Australia
| | - Carl Pahoff
- Department of Thoracic Medicine, Gold Coast University Hospital, Southport, Australia
| | - Phan T Nguyen
- Department of Thoracic Medicine, Royal Adelaide Hospital, Adelaide, Australia
| | - Scott Twaddell
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, Australia
| | - David Arnold
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, Australia
| | - Christopher Grainge
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, Australia
| | - Peter T Simpson
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - David Fielding
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
- Department of Thoracic Medicine, The Royal Brisbane & Women's Hospital, Brisbane, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, Australia.
- Faculty of Medicine, The University of Queensland, Brisbane, Australia.
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
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3
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Chey YCJ, Corbett MA, Arudkumar J, Piltz SG, Thomas PQ, Adikusuma F. CRISPR-mediated megabase-scale transgene de-duplication to generate a functional single-copy full-length humanized DMD mouse model. BMC Biol 2024; 22:214. [PMID: 39334101 PMCID: PMC11438084 DOI: 10.1186/s12915-024-02008-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 09/05/2024] [Indexed: 09/30/2024] Open
Abstract
BACKGROUND The development of sequence-specific precision treatments like CRISPR gene editing therapies for Duchenne muscular dystrophy (DMD) requires sequence humanized animal models to enable the direct clinical translation of tested strategies. The current available integrated transgenic mouse model containing the full-length human DMD gene, Tg(DMD)72Thoen/J (hDMDTg), has been found to have two copies of the transgene per locus in a tail-to-tail orientation, which does not accurately simulate the true (single) copy number of the DMD gene. This duplication also complicates analysis when testing CRISPR therapy editing outcomes, as large genetic alterations and rearrangements can occur between the cut sites on the two transgenes. RESULTS To address this, we performed long read nanopore sequencing on hDMDTg mice to better understand the structure of the duplicated transgenes. Following that, we performed a megabase-scale deletion of one of the transgenes by CRISPR zygotic microinjection to generate a single-copy, full-length, humanized DMD transgenic mouse model (hDMDTgSc). Functional, molecular, and histological characterisation shows that the single remaining human transgene retains its function and rescues the dystrophic phenotype caused by endogenous murine Dmd knockout. CONCLUSIONS Our unique hDMDTgSc mouse model simulates the true copy number of the DMD gene, and can potentially be used for the further generation of DMD disease models that would be better suited for the pre-clinical assessment and development of sequence specific CRISPR therapies.
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Affiliation(s)
- Yu C J Chey
- School of Biomedicine and Robinson Research Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
- Genome Editing Program, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia
| | - Mark A Corbett
- Adelaide Medical School and Robinson Research Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Jayshen Arudkumar
- School of Biomedicine and Robinson Research Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
- Genome Editing Program, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia
| | - Sandra G Piltz
- School of Biomedicine and Robinson Research Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
- Genome Editing Program, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia
- South Australian Genome Editing (SAGE) Facility, SAHMRI, Adelaide, SA, Australia
| | - Paul Q Thomas
- School of Biomedicine and Robinson Research Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia.
- Genome Editing Program, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia.
- South Australian Genome Editing (SAGE) Facility, SAHMRI, Adelaide, SA, Australia.
| | - Fatwa Adikusuma
- School of Biomedicine and Robinson Research Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia.
- Genome Editing Program, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia.
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4
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Martín R, Gaitán N, Jarlier F, Feuerbach L, de Soyres H, Arbonés M, Gutman T, Puiggròs M, Ferriz A, Gonzalez A, Estelles L, Gut I, Capella-Gutierrez S, Stein LD, Brors B, Royo R, Hupé P, Torrents D. ONCOLINER: A new solution for monitoring, improving, and harmonizing somatic variant calling across genomic oncology centers. CELL GENOMICS 2024; 4:100639. [PMID: 39216474 DOI: 10.1016/j.xgen.2024.100639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/13/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024]
Abstract
The characterization of somatic genomic variation associated with the biology of tumors is fundamental for cancer research and personalized medicine, as it guides the reliability and impact of cancer studies and genomic-based decisions in clinical oncology. However, the quality and scope of tumor genome analysis across cancer research centers and hospitals are currently highly heterogeneous, limiting the consistency of tumor diagnoses across hospitals and the possibilities of data sharing and data integration across studies. With the aim of providing users with actionable and personalized recommendations for the overall enhancement and harmonization of somatic variant identification across research and clinical environments, we have developed ONCOLINER. Using specifically designed mosaic and tumorized genomes for the analysis of recall and precision across somatic SNVs, insertions or deletions (indels), and structural variants (SVs), we demonstrate that ONCOLINER is capable of improving and harmonizing genome analysis across three state-of-the-art variant discovery pipelines in genomic oncology.
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Affiliation(s)
- Rodrigo Martín
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Nicolás Gaitán
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Frédéric Jarlier
- Institut Curie, Paris, France; U900, Paris, France; PSL Research University, Paris, France; Mines Paris Tech, Fontainebleau, France
| | - Lars Feuerbach
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Henri de Soyres
- Institut Curie, Paris, France; U900, Paris, France; PSL Research University, Paris, France; Mines Paris Tech, Fontainebleau, France
| | - Marc Arbonés
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Tom Gutman
- Institut Curie, Paris, France; U900, Paris, France; PSL Research University, Paris, France; Mines Paris Tech, Fontainebleau, France
| | - Montserrat Puiggròs
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Alvaro Ferriz
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Asier Gonzalez
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | | | - Ivo Gut
- Centro Nacional de Análisis Genómico, Barcelona, Spain
| | | | - Lincoln D Stein
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Romina Royo
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Philippe Hupé
- Institut Curie, Paris, France; U900, Paris, France; PSL Research University, Paris, France; Mines Paris Tech, Fontainebleau, France; UMR144, CNRS, Paris, France
| | - David Torrents
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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5
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Couper LI, Dodge TO, Hemker JA, Kim BY, Exposito-Alonso M, Brem RB, Mordecai EA, Bitter MC. Evolutionary adaptation under climate change: Aedes sp. demonstrates potential to adapt to warming. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.23.609454. [PMID: 39229052 PMCID: PMC11370604 DOI: 10.1101/2024.08.23.609454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Climate warming is expected to shift the distributions of mosquitoes and mosquito-borne diseases, facilitating expansions at cool range edges and contractions at warm range edges. However, whether mosquito populations could maintain their warm edges through evolutionary adaptation remains unknown. Here, we investigate the potential for thermal adaptation in Aedes sierrensis, a congener of the major disease vector species that experiences large thermal gradients in its native range, by assaying tolerance to prolonged and acute heat exposure, and its genetic basis in a diverse, field-derived population. We found pervasive evidence of heritable genetic variation in acute heat tolerance, which phenotypically trades off with tolerance to prolonged heat exposure. A simple evolutionary model based on our data shows that the estimated maximum rate of evolutionary adaptation in mosquito heat tolerance typically exceeds that of projected climate warming under idealized conditions. Our findings indicate that natural mosquito populations may have the potential to track projected warming via genetic adaptation. Prior climate-based projections may thus underestimate the range of mosquito and mosquito-borne disease distributions under future climate conditions.
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Affiliation(s)
- Lisa I Couper
- Stanford University, Department of Biology
- University of California, Berkeley, Division of Environmental Health Sciences
| | | | | | | | - Moi Exposito-Alonso
- University of California, Berkeley, Department of Integrative Biology
- Howard Hughes Medical Institute
| | - Rachel B Brem
- University of California, Berkeley, Department of Plant & Microbial Biology
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6
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Blommaert J, Sandoval-Castillo J, Beheregaray LB, Wellenreuther M. Peering into the gaps: Long-read sequencing illuminates structural variants and genomic evolution in the Australasian snapper. Genomics 2024; 116:110929. [PMID: 39216708 DOI: 10.1016/j.ygeno.2024.110929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 08/25/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Even before genome sequencing, genetic resources have supported species management and breeding programs. Current technologies, such as long-read sequencing, resolve complex genomic regions, like those rich in repeats or high in GC content. Improved genome contiguity enhances accuracy in identifying structural variants (SVs) and transposable elements (TEs). We present an improved genome assembly and SV catalogue for the Australasian snapper (Chrysophrys auratus). The new assembly is more contiguous, allowing for putative identification of 14 centromeres and transfer of 26,115 gene annotations from yellowfin seabream. Compared to the previous assembly, 35,000 additional SVs, including larger and more complex rearrangements, were annotated. SVs and TEs exhibit a distribution pattern skewed towards chromosome ends, likely influenced by recombination. Some SVs overlap with growth-related genes, underscoring their significance. This upgraded genome serves as a foundation for studying natural and artificial selection, offers a reference for related species, and sheds light on genome dynamics shaped by evolution.
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Affiliation(s)
- Julie Blommaert
- The New Zealand Institute for Plant and Food Research, Nelson, New Zealand.
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research, Nelson, New Zealand; School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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7
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Ramos-Rodríguez M, Subirana-Granés M, Norris R, Sordi V, Fernández Á, Fuentes-Páez G, Pérez-González B, Berenguer Balaguer C, Raurell-Vila H, Chowdhury M, Corripio R, Partelli S, López-Bigas N, Pellegrini S, Montanya E, Nacher M, Falconi M, Layer R, Rovira M, González-Pérez A, Piemonti L, Pasquali L. Implications of noncoding regulatory functions in the development of insulinomas. CELL GENOMICS 2024; 4:100604. [PMID: 38959898 PMCID: PMC11406191 DOI: 10.1016/j.xgen.2024.100604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/22/2024] [Accepted: 06/11/2024] [Indexed: 07/05/2024]
Abstract
Insulinomas are rare neuroendocrine tumors arising from pancreatic β cells, characterized by aberrant proliferation and altered insulin secretion, leading to glucose homeostasis failure. With the aim of uncovering the role of noncoding regulatory regions and their aberrations in the development of these tumors, we coupled epigenetic and transcriptome profiling with whole-genome sequencing. As a result, we unraveled somatic mutations associated with changes in regulatory functions. Critically, these regions impact insulin secretion, tumor development, and epigenetic modifying genes, including polycomb complex components. Chromatin remodeling is apparent in insulinoma-selective domains shared across patients, containing a specific set of regulatory sequences dominated by the SOX17 binding motif. Moreover, many of these regions are H3K27me3 repressed in β cells, suggesting that tumoral transition involves derepression of polycomb-targeted domains. Our work provides a compendium of aberrant cis-regulatory elements affecting the function and fate of β cells in their progression to insulinomas and a framework to identify coding and noncoding driver mutations.
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Affiliation(s)
- Mireia Ramos-Rodríguez
- Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Marc Subirana-Granés
- Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Richard Norris
- Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Valeria Sordi
- Diabetes Research Institute (DRI) - IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ángel Fernández
- Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Department of Physiological Science, School of Medicine, Universitat de Barcelona (UB), L'Hospitalet de Llobregat, Barcelona, Spain; Pancreas Regeneration: Pancreatic Progenitors and Their Niche Group, Regenerative Medicine Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain; Program for Advancing the Clinical Translation of Regenerative Medicine of Catalonia, P-CMR[C], L'Hospitalet de Llobregat, Barcelona, Spain
| | - Georgina Fuentes-Páez
- Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Beatriz Pérez-González
- Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Clara Berenguer Balaguer
- Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Helena Raurell-Vila
- Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Murad Chowdhury
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Raquel Corripio
- Paediatric Endocrinology Department, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Stefano Partelli
- Pancreas Translational & Research Institute, Scientific Institute San Raffaele Hospital and University Vita-Salute, Milan, Italy
| | - Núria López-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain; Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Silvia Pellegrini
- Diabetes Research Institute (DRI) - IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Eduard Montanya
- Bellvitge Hospital-IDIBELL, Barcelona, Spain; Department of Clinical Sciences, University of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Montserrat Nacher
- Bellvitge Hospital-IDIBELL, Barcelona, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Massimo Falconi
- Pancreas Translational & Research Institute, Scientific Institute San Raffaele Hospital and University Vita-Salute, Milan, Italy
| | - Ryan Layer
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA; Department of Computer Science, University of Colorado Boulder, Boulder, CO, USA
| | - Meritxell Rovira
- Department of Physiological Science, School of Medicine, Universitat de Barcelona (UB), L'Hospitalet de Llobregat, Barcelona, Spain; Pancreas Regeneration: Pancreatic Progenitors and Their Niche Group, Regenerative Medicine Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain; Program for Advancing the Clinical Translation of Regenerative Medicine of Catalonia, P-CMR[C], L'Hospitalet de Llobregat, Barcelona, Spain
| | - Abel González-Pérez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain; Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain
| | - Lorenzo Piemonti
- Diabetes Research Institute (DRI) - IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Lorenzo Pasquali
- Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
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8
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Zhu X, Farsh T, Vis D, Yu I, Li H, Liu T, Sjöström M, Shrestha R, Kneppers J, Severson T, Zhang M, Lundberg A, Moreno Rodriguez T, Weinstein AS, Foye A, Mehra N, Aggarwal RR, Bergman AM, Small EJ, Lack NA, Zwart W, Quigley DA, van der Heijden MS, Feng FY. Genomic and transcriptomic features of androgen receptor signaling inhibitor resistance in metastatic castration-resistant prostate cancer. J Clin Invest 2024; 134:e178604. [PMID: 39352383 PMCID: PMC11444163 DOI: 10.1172/jci178604] [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: 12/18/2023] [Accepted: 08/06/2024] [Indexed: 10/03/2024] Open
Abstract
BACKGROUNDAndrogen receptor signaling inhibitors (ARSIs) have improved outcomes for patients with metastatic castration-resistant prostate cancer (mCRPC), but their clinical benefit is limited by treatment resistance.METHODSTo investigate the mechanisms of ARSI resistance, we analyzed the whole-genome (n = 45) and transcriptome (n = 31) sequencing data generated from paired metastatic biopsies obtained before initiation of first-line ARSI therapy for mCRPC and after radiographic disease progression. We investigated the effects of genetic and pharmacologic modulation of SSTR1 in 22Rv1 cells, a representative mCRPC cell line.RESULTSWe confirmed the predominant role of tumor genetic alterations converging on augmenting androgen receptor (AR) signaling and the increased transcriptional heterogeneity and lineage plasticity during the emergence of ARSI resistance. We further identified amplifications involving a putative enhancer downstream of the AR and transcriptional downregulation of SSTR1, encoding somatostatin receptor 1, in ARSI-resistant tumors. We found that patients with SSTR1-low mCRPC tumors derived less benefit from subsequent ARSI therapy in a retrospective cohort. We showed that SSTR1 was antiproliferative in 22Rv1 cells and that the FDA-approved drug pasireotide suppressed 22Rv1 cell proliferation.CONCLUSIONOur findings expand the knowledge of ARSI resistance and point out actionable next steps, exemplified by potentially targeting SSTR1, to improve patient outcomes.FUNDINGNational Cancer Institute (NCI), NIH; Prostate Cancer Foundation; Conquer Cancer, American Society of Clinical Oncology Foundation; UCSF Benioff Initiative for Prostate Cancer Research; Netherlands Cancer Institute.
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MESH Headings
- Male
- Humans
- Prostatic Neoplasms, Castration-Resistant/genetics
- Prostatic Neoplasms, Castration-Resistant/pathology
- Prostatic Neoplasms, Castration-Resistant/drug therapy
- Prostatic Neoplasms, Castration-Resistant/metabolism
- Receptors, Androgen/genetics
- Receptors, Androgen/metabolism
- Drug Resistance, Neoplasm/genetics
- Drug Resistance, Neoplasm/drug effects
- Cell Line, Tumor
- Signal Transduction/drug effects
- Transcriptome
- Neoplasm Metastasis
- Receptors, Somatostatin/genetics
- Receptors, Somatostatin/metabolism
- Gene Expression Regulation, Neoplastic/drug effects
- Androgen Receptor Antagonists/pharmacology
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
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Affiliation(s)
- Xiaolin Zhu
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Tatyanah Farsh
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
| | - Daniël Vis
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Ivan Yu
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Haolong Li
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
| | - Tianyi Liu
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
| | - Martin Sjöström
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
| | - Raunak Shrestha
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
| | - Jeroen Kneppers
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Tesa Severson
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Meng Zhang
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
| | - Arian Lundberg
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
| | - Thaidy Moreno Rodriguez
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Urology, UCSF, San Francisco, California, USA
| | - Alana S. Weinstein
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Niven Mehra
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Rahul R. Aggarwal
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Andries M. Bergman
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Eric J. Small
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Nathan A. Lack
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Koç University School of Medicine, Istanbul, Turkey
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Turkey
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - David A. Quigley
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Urology, UCSF, San Francisco, California, USA
| | | | - Felix Y. Feng
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
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9
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Mortenson KL, Dawes C, Wilson ER, Patchen NE, Johnson HE, Gertz J, Bailey SD, Liu Y, Varley KE, Zhang X. 3D genomic analysis reveals novel enhancer-hijacking caused by complex structural alterations that drive oncogene overexpression. Nat Commun 2024; 15:6130. [PMID: 39033128 PMCID: PMC11271278 DOI: 10.1038/s41467-024-50387-w] [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: 01/23/2024] [Accepted: 07/05/2024] [Indexed: 07/23/2024] Open
Abstract
Cancer genomes are composed of many complex structural alterations on chromosomes and extrachromosomal DNA (ecDNA), making it difficult to identify non-coding enhancer regions that are hijacked to activate oncogene expression. Here, we describe a 3D genomics-based analysis called HAPI (Highly Active Promoter Interactions) to characterize enhancer hijacking. HAPI analysis of HiChIP data from 34 cancer cell lines identified enhancer hijacking events that activate both known and potentially novel oncogenes such as MYC, CCND1, ETV1, CRKL, and ID4. Furthermore, we found enhancer hijacking among multiple oncogenes from different chromosomes, often including MYC, on the same complex amplicons such as ecDNA. We characterized a MYC-ERBB2 chimeric ecDNA, in which ERBB2 heavily hijacks MYC's enhancers. Notably, CRISPRi of the MYC promoter led to increased interaction of ERBB2 with MYC enhancers and elevated ERBB2 expression. Our HAPI analysis tool provides a robust strategy to detect enhancer hijacking and reveals novel insights into oncogene activation.
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Affiliation(s)
- Katelyn L Mortenson
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Courtney Dawes
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Emily R Wilson
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Nathan E Patchen
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Hailey E Johnson
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, USA
| | - Jason Gertz
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Swneke D Bailey
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Surgery and Human Genetics, McGill University, Montreal, QC, Canada
| | - Yang Liu
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Katherine E Varley
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
| | - Xiaoyang Zhang
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
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10
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Çelik MH, Gagneur J, Lim RG, Wu J, Thompson LM, Xie X. Identifying dysregulated regions in amyotrophic lateral sclerosis through chromatin accessibility outliers. HGG ADVANCES 2024; 5:100318. [PMID: 38872308 PMCID: PMC11260578 DOI: 10.1016/j.xhgg.2024.100318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 06/15/2024] Open
Abstract
The high heritability of amyotrophic lateral sclerosis (ALS) contrasts with its low molecular diagnosis rate post-genetic testing, pointing to potential undiscovered genetic factors. To aid the exploration of these factors, we introduced EpiOut, an algorithm to identify chromatin accessibility outliers that are regions exhibiting divergent accessibility from the population baseline in a single or few samples. Annotation of accessible regions with histone chromatin immunoprecipitation sequencing and Hi-C indicates that outliers are concentrated in functional loci, especially among promoters interacting with active enhancers. Across different omics levels, outliers are robustly replicated, and chromatin accessibility outliers are reliable predictors of gene expression outliers and aberrant protein levels. When promoter accessibility does not align with gene expression, our results indicate that molecular aberrations are more likely to be linked to post-transcriptional regulation rather than transcriptional regulation. Our findings demonstrate that the outlier detection paradigm can uncover dysregulated regions in rare diseases. EpiOut is available at github.com/uci-cbcl/EpiOut.
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Affiliation(s)
- Muhammed Hasan Çelik
- Department of Computer Science, University of California Irvine, Irvine, CA, USA; Center for Complex Biological Systems, University of California Irvine, Irvine, CA, USA
| | - Julien Gagneur
- Department of Informatics, Technical University of Munich, Garching, Germany; Helmholtz Association - Munich School for Data Science (MUDS), Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany; Institute of Computational Biology, Helmholtz Center Munich, Neuherberg, Germany
| | - Ryan G Lim
- Institute for Memory Impairments and Neurological Disorders, University of California Irvine, Irvine, CA 92697, USA
| | - Jie Wu
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
| | - Leslie M Thompson
- Institute for Memory Impairments and Neurological Disorders, University of California Irvine, Irvine, CA 92697, USA; Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA; UCI MIND, University of California Irvine, Irvine, CA, USA; Department of Psychiatry and Human Behavior and Sue and Bill Gross Stem Cell Center, University of California Irvine, Irvine, CA, USA; Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
| | - Xiaohui Xie
- Department of Computer Science, University of California Irvine, Irvine, CA, USA.
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11
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Wiener E, Cottino L, Botha G, Nyangiri O, Noyes H, McLeod A, Jakubosky D, Adebamowo C, Awadalla P, Landouré G, Matshaba M, Matovu E, Ramsay M, Simo G, Simuunza M, Tiemessen C, Wonkam A, Sahibdeen V, Krause A, Lombard Z, Hazelhurst S. An assessment of the genomic structural variation landscape in Sub-Saharan African populations. RESEARCH SQUARE 2024:rs.3.rs-4485126. [PMID: 39041024 PMCID: PMC11261963 DOI: 10.21203/rs.3.rs-4485126/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Structural variants are responsible for a large part of genomic variation between individuals and play a role in both common and rare diseases. Databases cataloguing structural variants notably do not represent the full spectrum of global diversity, particularly missing information from most African populations. To address this representation gap, we analysed 1,091 high-coverage African genomes, 545 of which are public data sets, and 546 which have been analysed for structural variants for the first time. Variants were called using five different tools and datasets merged and jointly called using SURVIVOR. We identified 67,795 structural variants throughout the genome, with 10,421 genes having at least one variant. Using a conservative overlap in merged data, 6,414 of the structural variants (9.5%) are novel compared to the Database of Genomic Variants. This study contributes to knowledge of the landscape of structural variant diversity in Africa and presents a reliable dataset for potential applications in population genetics and health-related research.
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Affiliation(s)
- Emma Wiener
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Laura Cottino
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gerrit Botha
- Computational Biology Unit, University of Cape Town, Cape Town, South Africa
| | - Oscar Nyangiri
- College of Veterinary Medicine, Animal Resources and Biosecurity Makerere University, Kampala, Uganda
| | - Harry Noyes
- Centre for Genomic Research, University of Liverpool, Liverpool, United Kingdom
| | - Annette McLeod
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - David Jakubosky
- Department of Biomedical Informatics, University of California, San Diego, United States of America
- Institute of Genomic Medicine, University of California, San Diego, United States of America
| | - Clement Adebamowo
- Department of Epidemiology and Public Health and Greenebaum Comprehensive Cancer Center University of Maryland School of Medicine, Baltimore, United States of America
| | - Phillip Awadalla
- Ontario Institute for Cancer Research, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Guida Landouré
- Faculty of Medicine and Odontostomatology University of Sciences, Techniques and Technology of Bamako, Bamako Mali
- Neurology Department Point ”G” University Hospital, Bamako, Mali
| | - Mogomotsi Matshaba
- Botswana-Baylor Children’s Clinical Center of Excellence, Gaborone, Botswana
- Baylor College of Medicine, Houston, United States
| | - Enock Matovu
- College of Veterinary Medicine, Animal Resources and Biosecurity Makerere University, Kampala, Uganda
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Gustave Simo
- Molecular Parasitology and Entomology Unit, Department of Biochemistry University of Dschang, Dschang, Cameroon
| | - Martin Simuunza
- Department of Disease Control, School of Veterinary Medicine University of Zambia, Lusaka, Zambia
| | - Caroline Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services and Faculty of Health Sciences University of the Witwatersrand, Johannesburg, South Africa
| | - Ambroise Wonkam
- McKusick-Nathans Institute and Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States of America
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Venesa Sahibdeen
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zané Lombard
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
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12
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Mortenson KL, Dawes C, Wilson ER, Patchen NE, Johnson HE, Gertz J, Bailey SD, Liu Y, Varley KE, Zhang X. 3D genomic analysis reveals novel enhancer-hijacking caused by complex structural alterations that drive oncogene overexpression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576965. [PMID: 38328209 PMCID: PMC10849656 DOI: 10.1101/2024.01.23.576965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Cancer genomes are composed of many complex structural alterations on chromosomes and extrachromosomal DNA (ecDNA), making it difficult to identify non-coding enhancer regions that are hijacked to activate oncogene expression. Here, we describe a 3D genomics-based analysis called HAPI (Highly Active Promoter Interactions) to characterize enhancer hijacking. HAPI analysis of HiChIP data from 34 cancer cell lines identified enhancer hijacking events that activate both known and potentially novel oncogenes such as MYC, CCND1 , ETV1 , CRKL , and ID4 . Furthermore, we found enhancer hijacking among multiple oncogenes from different chromosomes, often including MYC , on the same complex amplicons such as ecDNA. We characterized a MYC - ERBB2 chimeric ecDNA, in which ERBB2 heavily hijacks MYC 's enhancers. Notably, CRISPRi of the MYC promoter led to increased interaction of ERBB2 with MYC enhancers and elevated ERBB2 expression. Our HAPI analysis tool provides a robust strategy to detect enhancer hijacking and reveals novel insights into oncogene activation.
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13
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Hayes V, Gong T, Jiang J, Bornman R, Gheybi K, Stricker P, Weischenfeldt J, Mutambirwa S. Rare pathogenic structural variants show potential to enhance prostate cancer germline testing for African men. RESEARCH SQUARE 2024:rs.3.rs-4531885. [PMID: 38947031 PMCID: PMC11213160 DOI: 10.21203/rs.3.rs-4531885/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Prostate cancer (PCa) is highly heritable, with men of African ancestry at greatest risk and associated lethality. Lack of representation in genomic data means germline testing guidelines exclude for African men. Established that structural variations (SVs) are major contributors to human disease and prostate tumourigenesis, their role is under-appreciated in familial and therapeutic testing. Utilising a clinico-methodologically matched African (n = 113) versus European (n = 57) deep-sequenced PCa resource, we interrogated 42,966 high-quality germline SVs using a best-fit pathogenicity prediction workflow. We identified 15 potentially pathogenic SVs representing 12.4% African and 7.0% European patients, of which 72% and 86% met germline testing standard-of-care recommendations, respectively. Notable African-specific loss-of-function gene candidates include DNA damage repair MLH1 and BARD1 and tumour suppressors FOXP1, WASF1 and RB1. Representing only a fraction of the vast African diaspora, this study raises considerations with respect to the contribution of kilo-to-mega-base rare variants to PCa pathogenicity and African associated disparity.
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Affiliation(s)
| | | | - Jue Jiang
- Garvan Institute of Medical Research
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14
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Zhang Y, Jin J, Wang N, Sun Q, Feng D, Zhu S, Wang Z, Li S, Ye J, Chai L, Xie Z, Deng X. Cytochrome P450 CitCYP97B modulates carotenoid accumulation diversity by hydroxylating β-cryptoxanthin in Citrus. PLANT COMMUNICATIONS 2024; 5:100847. [PMID: 38379285 PMCID: PMC11211522 DOI: 10.1016/j.xplc.2024.100847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/21/2023] [Accepted: 02/18/2024] [Indexed: 02/22/2024]
Abstract
Carotenoids in plant foods provide health benefits by functioning as provitamin A. One of the vital provitamin A carotenoids, β-cryptoxanthin, is typically plentiful in citrus fruit. However, little is known about the genetic basis of β-cryptoxanthin accumulation in citrus. Here, we performed a widely targeted metabolomic analysis of 65 major carotenoids and carotenoid derivatives to characterize carotenoid accumulation in Citrus and determine the taxonomic profile of β-cryptoxanthin. We used data from 81 newly sequenced representative accessions and 69 previously sequenced Citrus cultivars to reveal the genetic basis of β-cryptoxanthin accumulation through a genome-wide association study. We identified a causal gene, CitCYP97B, which encodes a cytochrome P450 protein whose substrate and metabolic pathways in land plants were undetermined. We subsequently demonstrated that CitCYP97B functions as a novel monooxygenase that specifically hydroxylates the β-ring of β-cryptoxanthin in a heterologous expression system. In planta experiments provided further evidence that CitCYP97B negatively regulates β-cryptoxanthin content. Using the sequenced Citrus accessions, we found that two critical structural cis-element variations contribute to increased expression of CitCYP97B, thereby altering β-cryptoxanthin accumulation in fruit. Hybridization/introgression appear to have contributed to the prevalence of two cis-element variations in different Citrus types during citrus evolution. Overall, these findings extend our understanding of the regulation and diversity of carotenoid metabolism in fruit crops and provide a genetic target for production of β-cryptoxanthin-biofortified products.
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Affiliation(s)
- Yingzi Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiajing Jin
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Nan Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Quan Sun
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Di Feng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Shenchao Zhu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zexin Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Shunxin Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Junli Ye
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Lijun Chai
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zongzhou Xie
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuxin Deng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China.
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15
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Ragnarsson C, Yang M, Moura-Castro LH, Aydın E, Gunnarsson R, Olsson-Arvidsson L, Lilljebjörn H, Fioretos T, Duployez N, Zaliova M, Zuna J, Castor A, Johansson B, Paulsson K. Constitutional and acquired genetic variants in ARID5B in pediatric B-cell precursor acute lymphoblastic leukemia. Genes Chromosomes Cancer 2024; 63:e23242. [PMID: 38738968 DOI: 10.1002/gcc.23242] [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: 02/27/2024] [Revised: 04/06/2024] [Accepted: 04/22/2024] [Indexed: 05/14/2024] Open
Abstract
Constitutional polymorphisms in ARID5B are associated with an increased risk of developing high hyperdiploid (HeH; 51-67 chromosomes) pediatric B-cell precursor acute lymphoblastic leukemia (BCP ALL). Here, we investigated constitutional and somatic ARID5B variants in 1335 BCP ALL cases from five different cohorts, with a particular focus on HeH cases. In 353 HeH ALL that were heterozygous for risk alleles and trisomic for chromosome 10, where ARID5B is located, a significantly higher proportion of risk allele duplication was seen for the SNPs rs7090445 (p = 0.009), rs7089424 (p = 0.005), rs7073837 (p = 0.03), and rs10740055 (p = 0.04). Somatic ARID5B deletions were seen in 16/1335 cases (1.2%), being more common in HeH than in other genetic subtypes (2.2% vs. 0.4%; p = 0.002). The expression of ARID5B in HeH cases with genomic deletions was reduced, consistent with a functional role in leukemogenesis. Whole-genome sequencing and RNA-sequencing in HeH revealed additional somatic events involving ARID5B, resulting in a total frequency of 3.6% of HeH cases displaying a somatic ARID5B aberration. Overall, our results show that both constitutional and somatic events in ARID5B are involved in the leukemogenesis of pediatric BCP ALL, particularly in the HeH subtype.
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Affiliation(s)
- Charlotte Ragnarsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Paediatrics, Skåne University Hospital, Lund University, Lund, Sweden
| | - Minjun Yang
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | | | - Efe Aydın
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Rebeqa Gunnarsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Linda Olsson-Arvidsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Henrik Lilljebjörn
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Thoas Fioretos
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Nicolas Duployez
- Laboratory of Haematology, Centre Hospitalier Universitaire (CHU) Lille, University of Lille, INSERM Unité 1277 Canther, Lille, France
| | - Marketa Zaliova
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University/University Hospital Motol, Prague, Czech Republic
- Childhood Leukaemia Investigation Prague (CLIP), Prague, Czech Republic
| | - Jan Zuna
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University/University Hospital Motol, Prague, Czech Republic
- Childhood Leukaemia Investigation Prague (CLIP), Prague, Czech Republic
| | - Anders Castor
- Department of Paediatrics, Skåne University Hospital, Lund University, Lund, Sweden
| | - Bertil Johansson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Kajsa Paulsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
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16
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Gunasekaran D, Ardell DH, Nobile CJ. SNP-SVant: A Computational Workflow to Predict and Annotate Genomic Variants in Organisms Lacking Benchmarked Variants. Curr Protoc 2024; 4:e1046. [PMID: 38717471 PMCID: PMC11081530 DOI: 10.1002/cpz1.1046] [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] [Indexed: 05/12/2024]
Abstract
Whole-genome sequencing is widely used to investigate population genomic variation in organisms of interest. Assorted tools have been independently developed to call variants from short-read sequencing data aligned to a reference genome, including single nucleotide polymorphisms (SNPs) and structural variations (SVs). We developed SNP-SVant, an integrated, flexible, and computationally efficient bioinformatic workflow that predicts high-confidence SNPs and SVs in organisms without benchmarked variants, which are traditionally used for distinguishing sequencing errors from real variants. In the absence of these benchmarked datasets, we leverage multiple rounds of statistical recalibration to increase the precision of variant prediction. The SNP-SVant workflow is flexible, with user options to tradeoff accuracy for sensitivity. The workflow predicts SNPs and small insertions and deletions using the Genome Analysis ToolKit (GATK) and predicts SVs using the Genome Rearrangement IDentification Software Suite (GRIDSS), and it culminates in variant annotation using custom scripts. A key utility of SNP-SVant is its scalability. Variant calling is a computationally expensive procedure, and thus, SNP-SVant uses a workflow management system with intermediary checkpoint steps to ensure efficient use of resources by minimizing redundant computations and omitting steps where dependent files are available. SNP-SVant also provides metrics to assess the quality of called variants and converts between VCF and aligned FASTA format outputs to ensure compatibility with downstream tools to calculate selection statistics, which are commonplace in population genomics studies. By accounting for both small and large structural variants, users of this workflow can obtain a wide-ranging view of genomic alterations in an organism of interest. Overall, this workflow advances our capabilities in assessing the functional consequences of different types of genomic alterations, ultimately improving our ability to associate genotypes with phenotypes. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Predicting single nucleotide polymorphisms and structural variations Support Protocol 1: Downloading publicly available sequencing data Support Protocol 2: Visualizing variant loci using Integrated Genome Viewer Support Protocol 3: Converting between VCF and aligned FASTA formats.
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Affiliation(s)
- Deepika Gunasekaran
- Quantitative and Systems Biology Graduate Program, University of California, Merced, CA, USA
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, CA, USA
| | - David H. Ardell
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, CA, USA
| | - Clarissa J. Nobile
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, CA, USA
- Health Science Research Institute, University of California, Merced, CA, USA
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17
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Joe S, Park JL, Kim J, Kim S, Park JH, Yeo MK, Lee D, Yang JO, Kim SY. Comparison of structural variant callers for massive whole-genome sequence data. BMC Genomics 2024; 25:318. [PMID: 38549092 PMCID: PMC10976732 DOI: 10.1186/s12864-024-10239-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 03/18/2024] [Indexed: 04/01/2024] Open
Abstract
BACKGROUND Detecting structural variations (SVs) at the population level using next-generation sequencing (NGS) requires substantial computational resources and processing time. Here, we compared the performances of 11 SV callers: Delly, Manta, GridSS, Wham, Sniffles, Lumpy, SvABA, Canvas, CNVnator, MELT, and INSurVeyor. These SV callers have been recently published and have been widely employed for processing massive whole-genome sequencing datasets. We evaluated the accuracy, sequence depth, running time, and memory usage of the SV callers. RESULTS Notably, several callers exhibited better calling performance for deletions than for duplications, inversions, and insertions. Among the SV callers, Manta identified deletion SVs with better performance and efficient computing resources, and both Manta and MELT demonstrated relatively good precision regarding calling insertions. We confirmed that the copy number variation callers, Canvas and CNVnator, exhibited better performance in identifying long duplications as they employ the read-depth approach. Finally, we also verified the genotypes inferred from each SV caller using a phased long-read assembly dataset, and Manta showed the highest concordance in terms of the deletions and insertions. CONCLUSIONS Our findings provide a comprehensive understanding of the accuracy and computational efficiency of SV callers, thereby facilitating integrative analysis of SV profiles in diverse large-scale genomic datasets.
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Grants
- NRF-2020M3E5D708517212, 2020M3A9I6A0103605713 Ministry of Science and ICT, South Korea
- NRF-2020M3E5D708517212, 2020M3A9I6A0103605713 Ministry of Science and ICT, South Korea
- NRF-2020M3E5D708517212, 2020M3A9I6A0103605713 Ministry of Science and ICT, South Korea
- NRF-2020M3E5D708517212, 2020M3A9I6A0103605713 Ministry of Science and ICT, South Korea
- NRF-2020M3E5D708517212, 2020M3A9I6A0103605713 Ministry of Science and ICT, South Korea
- NRF-2020M3E5D708517212, 2020M3A9I6A0103605713 Ministry of Science and ICT, South Korea
- NRF-2020M3E5D708517212, 2020M3A9I6A0103605713 Ministry of Science and ICT, South Korea
- NRF-2020M3E5D708517212, 2020M3A9I6A0103605713 Ministry of Science and ICT, South Korea
- NTIS-1711170620 KRIBB Research Initiative Program
- NTIS-1711170620 KRIBB Research Initiative Program
- NTIS-1711170620 KRIBB Research Initiative Program
- NTIS-1711170620 KRIBB Research Initiative Program
- NTIS-1711170620 KRIBB Research Initiative Program
- NTIS-1711170620 KRIBB Research Initiative Program
- NTIS-1711170620 KRIBB Research Initiative Program
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Affiliation(s)
- Soobok Joe
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Jong-Lyul Park
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Functional Genomics, University of Science and Technology (UST), 34113, Daejeon, Republic of Korea
| | - Jun Kim
- Department of Convergent Bioscience and Informatics, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Sangok Kim
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Ji-Hwan Park
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Bioscience, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Min-Kyung Yeo
- Department of Pathology, Chungnam National University School of Medicine, Daejeon, 35015, Republic of Korea
| | - Dongyoon Lee
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Jin Ok Yang
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
| | - Seon-Young Kim
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Bioscience, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
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18
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Yu H, Yau SST. Automated recognition of chromosome fusion using an alignment-free natural vector method. Front Genet 2024; 15:1364951. [PMID: 38572414 PMCID: PMC10987741 DOI: 10.3389/fgene.2024.1364951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 03/06/2024] [Indexed: 04/05/2024] Open
Abstract
Chromosomal fusion is a significant form of structural variation, but research into algorithms for its identification has been limited. Most existing methods rely on synteny analysis, which necessitates manual annotations and always involves inefficient sequence alignments. In this paper, we present a novel alignment-free algorithm for chromosomal fusion recognition. Our method transforms the problem into a series of assignment problems using natural vectors and efficiently solves them with the Kuhn-Munkres algorithm. When applied to the human/gorilla and swamp buffalo/river buffalo datasets, our algorithm successfully and efficiently identifies chromosomal fusion events. Notably, our approach offers several advantages, including higher processing speeds by eliminating time-consuming alignments and removing the need for manual annotations. By an alignment-free perspective, our algorithm initially considers entire chromosomes instead of fragments to identify chromosomal structural variations, offering substantial potential to advance research in this field.
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Affiliation(s)
- Hongyu Yu
- Department of Mathematical Sciences, Tsinghua University, Beijing, China
| | - Stephen S.-T. Yau
- Department of Mathematical Sciences, Tsinghua University, Beijing, China
- Yanqi Lake Beijing Institute of Mathematical Science and Applications (BIMSA), Beijing, China
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19
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Launonen IM, Erkan EP, Niemiec I, Junquera A, Hincapié-Otero M, Afenteva D, Liang Z, Salko M, Szabo A, Perez-Villatoro F, Falco MM, Li Y, Micoli G, Nagaraj A, Haltia UM, Kahelin E, Oikkonen J, Hynninen J, Virtanen A, Nirmal AJ, Vallius T, Hautaniemi S, Sorger P, Vähärautio A, Färkkilä A. Chemotherapy induces myeloid-driven spatial T-cell exhaustion in ovarian cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585657. [PMID: 38562799 PMCID: PMC10983974 DOI: 10.1101/2024.03.19.585657] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
To uncover the intricate, chemotherapy-induced spatiotemporal remodeling of the tumor microenvironment, we conducted integrative spatial and molecular characterization of 97 high-grade serous ovarian cancer (HGSC) samples collected before and after chemotherapy. Using single-cell and spatial analyses, we identify increasingly versatile immune cell states, which form spatiotemporally dynamic microcommunities at the tumor-stroma interface. We demonstrate that chemotherapy triggers spatial redistribution and exhaustion of CD8+ T cells due to prolonged antigen presentation by macrophages, both within interconnected myeloid networks termed "Myelonets" and at the tumor stroma interface. Single-cell and spatial transcriptomics identifies prominent TIGIT-NECTIN2 ligand-receptor interactions induced by chemotherapy. Using a functional patient-derived immuno-oncology platform, we show that CD8+T-cell activity can be boosted by combining immune checkpoint blockade with chemotherapy. Our discovery of chemotherapy-induced myeloid-driven spatial T-cell exhaustion paves the way for novel immunotherapeutic strategies to unleash CD8+ T-cell-mediated anti-tumor immunity in HGSC.
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Affiliation(s)
- Inga-Maria Launonen
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | | | - Iga Niemiec
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Ada Junquera
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | | | - Daria Afenteva
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Zhihan Liang
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Matilda Salko
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Angela Szabo
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | | | - Matias M Falco
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Yilin Li
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Giulia Micoli
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Ashwini Nagaraj
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Ulla-Maija Haltia
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
- Department of Obstetrics and Gynecology, Department of Oncology, Clinical trials unit, Comprehensive Cancer Center, Helsinki University Hospital, Helsinki, Finland
| | - Essi Kahelin
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
- Department of Pathology, University of Helsinki and HUS Diagnostic Center, Helsinki University Hospital
| | - Jaana Oikkonen
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Johanna Hynninen
- Department of Obstetrics and Gynecology, University of Turku and Turku University Hospital, Turku, Finland
| | - Anni Virtanen
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
- Department of Pathology, University of Helsinki and HUS Diagnostic Center, Helsinki University Hospital
| | - Ajit J Nirmal
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, USA
| | - Tuulia Vallius
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, USA
- Ludwig Center at Harvard
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Peter Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, USA
| | - Anna Vähärautio
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
- Foundation for the Finnish Cancer Institute, Finland
| | - Anniina Färkkilä
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
- Department of Obstetrics and Gynecology, Department of Oncology, Clinical trials unit, Comprehensive Cancer Center, Helsinki University Hospital, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
- Institute for Molecular Medicine Finland, Helsinki Institute for Life Sciences, University of Helsinki, Finland
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20
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Simpson JT. Detecting Somatic Mutations Without Matched Normal Samples Using Long Reads. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582089. [PMID: 38464143 PMCID: PMC10925087 DOI: 10.1101/2024.02.26.582089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
DNA sequencing of tumours to identify somatic mutations has become a critical tool to guide the type of treatment given to cancer patients. The gold standard for mutation calling is comparing sequencing data from the tumour to a matched normal sample to avoid mis-classifying inherited SNPs as mutations. This procedure works extremely well, but in certain situations only a tumour sample is available. While approaches have been developed to find mutations without a matched normal, they have limited accuracy or require specific types of input data (e.g. ultra-deep sequencing). Here we explore the application of single molecule long read sequencing to calling somatic mutations without matched normal samples. We develop a simple theoretical framework to show how haplotype phasing is an important source of information for determining whether a variant is a somatic mutation. We then use simulations to assess the range of experimental parameters (tumour purity, sequencing depth) where this approach is effective. These ideas are developed into a prototype somatic mutation caller, smrest, and its use is demonstrated on two highly mutated cancer cell lines. Finally, we argue that this approach has potential to measure clinically important biomarkers that are based on the genome-wide distribution of mutations: tumour mutation burden and mutation signatures.
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Affiliation(s)
- Jared T. Simpson
- Ontario Institute for Cancer Research, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
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21
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Schott CR, Koehne AL, Sayles LC, Young EP, Luck C, Yu K, Lee AG, Breese MR, Leung SG, Xu H, Shah AT, Liu HY, Spillinger A, Behroozfard IH, Marini KD, Dinh PT, Pons Ventura MV, Vanderboon EN, Hazard FK, Cho SJ, Avedian RS, Mohler DG, Zimel M, Wustrack R, Curtis C, Sirota M, Sweet-Cordero EA. Osteosarcoma PDX-Derived Cell Line Models for Preclinical Drug Evaluation Demonstrate Metastasis Inhibition by Dinaciclib through a Genome-Targeted Approach. Clin Cancer Res 2024; 30:849-864. [PMID: 37703185 PMCID: PMC10870121 DOI: 10.1158/1078-0432.ccr-23-0873] [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: 03/21/2023] [Revised: 03/26/2023] [Accepted: 08/08/2023] [Indexed: 09/15/2023]
Abstract
PURPOSE Models to study metastatic disease in rare cancers are needed to advance preclinical therapeutics and to gain insight into disease biology. Osteosarcoma is a rare cancer with a complex genomic landscape in which outcomes for patients with metastatic disease are poor. As osteosarcoma genomes are highly heterogeneous, multiple models are needed to fully elucidate key aspects of disease biology and to recapitulate clinically relevant phenotypes. EXPERIMENTAL DESIGN Matched patient samples, patient-derived xenografts (PDX), and PDX-derived cell lines were comprehensively evaluated using whole-genome sequencing and RNA sequencing. The in vivo metastatic phenotype of the PDX-derived cell lines was characterized in both an intravenous and an orthotopic murine model. As a proof-of-concept study, we tested the preclinical effectiveness of a cyclin-dependent kinase inhibitor on the growth of metastatic tumors in an orthotopic amputation model. RESULTS PDXs and PDX-derived cell lines largely maintained the expression profiles of the patient from which they were derived despite the emergence of whole-genome duplication in a subset of cell lines. The cell lines were heterogeneous in their metastatic capacity, and heterogeneous tissue tropism was observed in both intravenous and orthotopic models. Single-agent dinaciclib was effective at dramatically reducing the metastatic burden. CONCLUSIONS The variation in metastasis predilection sites between osteosarcoma PDX-derived cell lines demonstrates their ability to recapitulate the spectrum of the disease observed in patients. We describe here a panel of new osteosarcoma PDX-derived cell lines that we believe will be of wide use to the osteosarcoma research community.
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Affiliation(s)
- Courtney R. Schott
- Department of Pediatrics, University of California San Francisco, San Francisco, California
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Amanda L. Koehne
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Leanne C. Sayles
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Elizabeth P. Young
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Cuyler Luck
- Department of Pediatrics, University of California San Francisco, San Francisco, California
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California
| | - Katherine Yu
- Department of Pediatrics, University of California San Francisco, San Francisco, California
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California
| | - Alex G. Lee
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Marcus R. Breese
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Stanley G. Leung
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Hang Xu
- Departments of Genetics and Medicine, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Avanthi Tayi Shah
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Heng-Yi Liu
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Aviv Spillinger
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Inge H. Behroozfard
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Kieren D. Marini
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Phuong T. Dinh
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - María V. Pons Ventura
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Emma N. Vanderboon
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Florette K. Hazard
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Soo-Jin Cho
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Raffi S. Avedian
- Department of Orthopedic Surgery, Stanford University School of Medicine, Stanford University, Stanford, California
| | - David G. Mohler
- Department of Orthopedic Surgery, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Melissa Zimel
- Department of Orthopedic Surgery, University of California San Francisco, San Francisco, California
| | - Rosanna Wustrack
- Department of Orthopedic Surgery, University of California San Francisco, San Francisco, California
| | - Christina Curtis
- Departments of Genetics and Medicine, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Marina Sirota
- Department of Pediatrics, University of California San Francisco, San Francisco, California
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California
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22
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Ijaz J, Harry E, Raine K, Menzies A, Beal K, Quail MA, Zumalave S, Jung H, Coorens THH, Lawson ARJ, Leongamornlert D, Francies HE, Garnett MJ, Ning Z, Campbell PJ. Haplotype-specific assembly of shattered chromosomes in esophageal adenocarcinomas. CELL GENOMICS 2024; 4:100484. [PMID: 38232733 PMCID: PMC10879010 DOI: 10.1016/j.xgen.2023.100484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 10/13/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024]
Abstract
The epigenetic landscape of cancer is regulated by many factors, but primarily it derives from the underlying genome sequence. Chromothripsis is a catastrophic localized genome shattering event that drives, and often initiates, cancer evolution. We characterized five esophageal adenocarcinoma organoids with chromothripsis using long-read sequencing and transcriptome and epigenome profiling. Complex structural variation and subclonal variants meant that haplotype-aware de novo methods were required to generate contiguous cancer genome assemblies. Chromosomes were assembled separately and scaffolded using haplotype-resolved Hi-C reads, producing accurate assemblies even with up to 900 structural rearrangements. There were widespread differences between the chromothriptic and wild-type copies of chromosomes in topologically associated domains, chromatin accessibility, histone modifications, and gene expression. Differential epigenome peaks were most enriched within 10 kb of chromothriptic structural variants. Alterations in transcriptome and higher-order chromosome organization frequently occurred near differential epigenetic marks. Overall, chromothripsis reshapes gene regulation, causing coordinated changes in epigenetic landscape, transcription, and chromosome conformation.
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Affiliation(s)
- Jannat Ijaz
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK.
| | | | - Keiran Raine
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK; Health Innovation East, Unit C, Magog Court, Shelford Bottom, Cambridge CB22 3AD, UK
| | | | | | | | - Sonia Zumalave
- Mobile Genomes and Disease, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | | | - Tim H H Coorens
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Hayley E Francies
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK; GSK, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | | | - Zemin Ning
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
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23
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Dopeso H, Gazzo AM, Derakhshan F, Brown DN, Selenica P, Jalali S, Da Cruz Paula A, Marra A, da Silva EM, Basili T, Gusain L, Colon-Cartagena L, Bhaloo SI, Green H, Vanderbilt C, Oesterreich S, Grabenstetter A, Kuba MG, Ross D, Giri D, Wen HY, Zhang H, Brogi E, Weigelt B, Pareja F, Reis-Filho JS. Genomic and epigenomic basis of breast invasive lobular carcinomas lacking CDH1 genetic alterations. NPJ Precis Oncol 2024; 8:33. [PMID: 38347189 PMCID: PMC10861500 DOI: 10.1038/s41698-024-00508-x] [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: 05/10/2023] [Accepted: 12/14/2023] [Indexed: 02/15/2024] Open
Abstract
CDH1 (E-cadherin) bi-allelic inactivation is the hallmark alteration of breast invasive lobular carcinoma (ILC), resulting in its discohesive phenotype. A subset of ILCs, however, lack CDH1 genetic/epigenetic inactivation, and their genetic underpinning is unknown. Through clinical targeted sequencing data reanalysis of 364 primary ILCs, we identified 25 ILCs lacking CDH1 bi-allelic genetic alterations. CDH1 promoter methylation was frequent (63%) in these cases. Targeted sequencing reanalysis revealed 3 ILCs harboring AXIN2 deleterious fusions (n = 2) or loss-of-function mutation (n = 1). Whole-genome sequencing of 3 cases lacking bi-allelic CDH1 genetic/epigenetic inactivation confirmed the AXIN2 mutation and no other cell-cell adhesion genetic alterations but revealed a new CTNND1 (p120) deleterious fusion. AXIN2 knock-out in MCF7 cells resulted in lobular-like features, including increased cellular migration and resistance to anoikis. Taken together, ILCs lacking CDH1 genetic/epigenetic alterations are driven by inactivating alterations in other cell adhesion genes (CTNND1 or AXIN2), endorsing a convergent phenotype in ILC.
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Affiliation(s)
- Higinio Dopeso
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrea M Gazzo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fatemeh Derakhshan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - David N Brown
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pier Selenica
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sahar Jalali
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arnaud Da Cruz Paula
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Antonio Marra
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edaise M da Silva
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Thais Basili
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laxmi Gusain
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lorraine Colon-Cartagena
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shirin Issa Bhaloo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hunter Green
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chad Vanderbilt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Steffi Oesterreich
- Department of Pharmacology & Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Anne Grabenstetter
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Gabriela Kuba
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dara Ross
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dilip Giri
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hannah Y Wen
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hong Zhang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edi Brogi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fresia Pareja
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Jorge S Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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24
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Miao H, Wang L, Qu L, Liu H, Sun Y, Le M, Wang Q, Wei S, Zheng Y, Lin W, Duan Y, Cao H, Xiong S, Wang X, Wei L, Li C, Ma Q, Ju M, Zhao R, Li G, Mu C, Tian Q, Mei H, Zhang T, Gao T, Zhang H. Genomic evolution and insights into agronomic trait innovations of Sesamum species. PLANT COMMUNICATIONS 2024; 5:100729. [PMID: 37798879 PMCID: PMC10811377 DOI: 10.1016/j.xplc.2023.100729] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/17/2023] [Accepted: 10/02/2023] [Indexed: 10/07/2023]
Abstract
Sesame is an ancient oilseed crop with high oil content and quality. However, the evolutionary history and genetic mechanisms of its valuable agronomic traits remain unclear. Here, we report chromosome-scale genomes of cultivated sesame (Sesamum indicum L.) and six wild Sesamum species, representing all three karyotypes within this genus. Karyotyping and genome-based phylogenic analysis revealed the evolutionary route of Sesamum species from n = 13 to n = 16 and revealed that allotetraploidization occurred in the wild species Sesamum radiatum. Early divergence of the Sesamum genus (48.5-19.7 million years ago) during the Tertiary period and its ancient phylogenic position within eudicots were observed. Pan-genome analysis revealed 9164 core gene families in the 7 Sesamum species. These families are significantly enriched in various metabolic pathways, including fatty acid (FA) metabolism and FA biosynthesis. Structural variations in SiPT1 and SiDT1 within the phosphatidyl ethanolamine-binding protein gene family lead to the genomic evolution of plant-architecture and inflorescence-development phenotypes in Sesamum. A genome-wide association study (GWAS) of an interspecific population and genome comparisons revealed a long terminal repeat insertion and a sequence deletion in DIR genes of wild Sesamum angustifolium and cultivated sesame, respectively; both variations independently cause high susceptibility to Fusarium wilt disease. A GWAS of 560 sesame accessions combined with an overexpression study confirmed that the NAC1 and PPO genes play an important role in upregulating oil content of sesame. Our study provides high-quality genomic resources for cultivated and wild Sesamum species and insights that can improve molecular breeding strategies for sesame and other oilseed crops.
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Affiliation(s)
- Hongmei Miao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Lei Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Lingbo Qu
- College of Food Science and Technology, Henan Technology University, Zhengzhou 450001, China
| | - Hongyan Liu
- Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Yamin Sun
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Meiwang Le
- Crops Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Qiang Wang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Shuangling Wei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Yongzhan Zheng
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Wenchao Lin
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Yinghui Duan
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Hengchun Cao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Songjin Xiong
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Xuede Wang
- College of Food Science and Technology, Henan Technology University, Zhengzhou 450001, China
| | - Libin Wei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Chun Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Qin Ma
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Ming Ju
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Ruihong Zhao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Guiting Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Cong Mu
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Qiuzhen Tian
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Hongxian Mei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Tide Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Tongmei Gao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Haiyang Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China.
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Lavikka K, Oikkonen J, Li Y, Muranen T, Micoli G, Marchi G, Lahtinen A, Huhtinen K, Lehtonen R, Hietanen S, Hynninen J, Virtanen A, Hautaniemi S. Deciphering cancer genomes with GenomeSpy: a grammar-based visualization toolkit. Gigascience 2024; 13:giae040. [PMID: 39101783 PMCID: PMC11299109 DOI: 10.1093/gigascience/giae040] [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: 01/09/2024] [Revised: 05/13/2024] [Accepted: 06/19/2024] [Indexed: 08/06/2024] Open
Abstract
BACKGROUND Visualization is an indispensable facet of genomic data analysis. Despite the abundance of specialized visualization tools, there remains a distinct need for tailored solutions. However, their implementation typically requires extensive programming expertise from bioinformaticians and software developers, especially when building interactive applications. Toolkits based on visualization grammars offer a more accessible, declarative way to author new visualizations. Yet, current grammar-based solutions fall short in adequately supporting the interactive analysis of large datasets with extensive sample collections, a pivotal task often encountered in cancer research. FINDINGS We present GenomeSpy, a grammar-based toolkit for authoring tailored, interactive visualizations for genomic data analysis. By using combinatorial building blocks and a declarative language, users can implement new visualization designs easily and embed them in web pages or end-user-oriented applications. A distinctive element of GenomeSpy's architecture is its effective use of the graphics processing unit in all rendering, enabling a high frame rate and smoothly animated interactions, such as navigation within a genome. We demonstrate the utility of GenomeSpy by characterizing the genomic landscape of 753 ovarian cancer samples from patients in the DECIDER clinical trial. Our results expand the understanding of the genomic architecture in ovarian cancer, particularly the diversity of chromosomal instability. CONCLUSIONS GenomeSpy is a visualization toolkit applicable to a wide range of tasks pertinent to genome analysis. It offers high flexibility and exceptional performance in interactive analysis. The toolkit is open source with an MIT license, implemented in JavaScript, and available at https://genomespy.app/.
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Affiliation(s)
- Kari Lavikka
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Jaana Oikkonen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Yilin Li
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Taru Muranen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Giulia Micoli
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Giovanni Marchi
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Alexandra Lahtinen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Kaisa Huhtinen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
- Cancer Research Unit, Institute of Biomedicine and FICAN West Cancer Centre, University of Turku, 20521 Turku, Finland
| | - Rainer Lehtonen
- Applied Tumor Genomics Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Sakari Hietanen
- Department of Obstetrics and Gynecology, University of Turku and Turku University Hospital, 20521 Turku, Finland
| | - Johanna Hynninen
- Department of Obstetrics and Gynecology, University of Turku and Turku University Hospital, 20521 Turku, Finland
| | - Anni Virtanen
- Department of Pathology, University of Helsinki and HUS Diagnostic Center, Helsinki University Hospital, 00260 Helsinki, Finland
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
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26
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Schikora-Tamarit MÀ, Gabaldón T. Recent gene selection and drug resistance underscore clinical adaptation across Candida species. Nat Microbiol 2024; 9:284-307. [PMID: 38177305 PMCID: PMC10769879 DOI: 10.1038/s41564-023-01547-z] [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: 03/02/2023] [Accepted: 11/06/2023] [Indexed: 01/06/2024]
Abstract
Understanding how microbial pathogens adapt to treatments, humans and clinical environments is key to infer mechanisms of virulence, transmission and drug resistance. This may help improve therapies and diagnostics for infections with a poor prognosis, such as those caused by fungal pathogens, including Candida. Here we analysed genomic variants across approximately 2,000 isolates from six Candida species (C. glabrata, C. auris, C. albicans, C. tropicalis, C. parapsilosis and C. orthopsilosis) and identified genes under recent selection, suggesting a highly complex clinical adaptation. These involve species-specific and convergently affected adaptive mechanisms, such as adhesion. Using convergence-based genome-wide association studies we identified known drivers of drug resistance alongside potentially novel players. Finally, our analyses reveal an important role of structural variants and suggest an unexpected involvement of (para)sexual recombination in the spread of resistance. Our results provide insights on how opportunistic pathogens adapt to human-related environments and unearth candidate genes that deserve future attention.
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Affiliation(s)
- Miquel Àngel Schikora-Tamarit
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain.
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
- Centro Investigación Biomédica En Red de Enfermedades Infecciosas, Barcelona, Spain.
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27
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Koskela H, Li Y, Joutsiniemi T, Muranen T, Isoviita VM, Huhtinen K, Micoli G, Lavikka K, Marchi G, Hietanen S, Virtanen A, Hautaniemi S, Oikkonen J, Hynninen J. HRD related signature 3 predicts clinical outcome in advanced tubo-ovarian high-grade serous carcinoma. Gynecol Oncol 2024; 180:91-98. [PMID: 38061276 DOI: 10.1016/j.ygyno.2023.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 11/14/2023] [Accepted: 11/25/2023] [Indexed: 02/18/2024]
Abstract
OBJECTIVES We evaluated usability of single base substitution signature 3 (Sig3) as a biomarker for homologous recombination deficiency (HRD) in tubo-ovarian high-grade serous carcinoma (HGSC). MATERIALS AND METHODS This prospective observational trial includes 165 patients with advanced HGSC. Fresh tissue samples (n = 456) from multiple intra-abdominal areas at diagnosis and after neoadjuvant chemotherapy (NACT) were collected for whole-genome sequencing. Sig3 was assessed by fitting samples independently with COSMIC v3.2 reference signatures. An HR scar assay was applied for comparison. Progression-free survival (PFS) and overall survival (OS) were studied using Kaplan-Meier and Cox regression analysis. RESULTS Sig3 has a bimodal distribution, eliminating the need for an arbitrary cutoff typical in HR scar tests. Sig3 could be assessed from samples with low (10%) cancer cell proportion and was consistent between multiple samples and stable during NACT. At diagnosis, 74 (45%) patients were HRD (Sig3+), while 91 (55%) were HR proficient (HRP, Sig3-). Sig3+ patients had longer PFS and OS than Sig3- patients (22 vs. 13 months and 51 vs. 34 months respectively, both p < 0.001). Sig3 successfully distinguished the poor prognostic HRP group among BRCAwt patients (PFS 19 months for Sig3+ and 13 months for Sig3- patients, p < 0.001). However, Sig3 at diagnosis did not predict chemoresponse anymore in the first relapse. The patient-level concordance between Sig3 and HR scar assay was 87%, and patients with HRD according to both tests had the longest median PFS. CONCLUSIONS Sig3 is a prognostic marker in advanced HGSC and useful tool in patient stratification for HRD.
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Affiliation(s)
- Heidi Koskela
- Department of Obstetrics and Gynecology, University of Turku and Turku University Hospital, Turku, Finland
| | - Yilin Li
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Titta Joutsiniemi
- Department of Obstetrics and Gynecology, University of Turku and Turku University Hospital, Turku, Finland
| | - Taru Muranen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Veli-Matti Isoviita
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kaisa Huhtinen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Institute of Biomedicine and FICAN West Cancer Centre, University of Turku and Turku University Hospital, Turku, Finland
| | - Giulia Micoli
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kari Lavikka
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Giovanni Marchi
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sakari Hietanen
- Department of Obstetrics and Gynecology, University of Turku and Turku University Hospital, Turku, Finland
| | - Anni Virtanen
- Department of Pathology, University of Helsinki and HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jaana Oikkonen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Johanna Hynninen
- Department of Obstetrics and Gynecology, University of Turku and Turku University Hospital, Turku, Finland.
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28
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Tan T, Mouradov D, Lee M, Gard G, Hirokawa Y, Li S, Lin C, Li F, Luo H, Wu K, Palmieri M, Leong E, Clarke J, Sakthianandeswaren A, Brasier H, Tie J, Tebbutt NC, Jalali A, Wong R, Burgess AW, Gibbs P, Sieber OM. Unified framework for patient-derived, tumor-organoid-based predictive testing of standard-of-care therapies in metastatic colorectal cancer. Cell Rep Med 2023; 4:101335. [PMID: 38118423 PMCID: PMC10783557 DOI: 10.1016/j.xcrm.2023.101335] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/11/2023] [Accepted: 11/18/2023] [Indexed: 12/22/2023]
Abstract
Predictive drug testing of patient-derived tumor organoids (PDTOs) holds promise for personalizing treatment of metastatic colorectal cancer (mCRC), but prospective data are limited to chemotherapy regimens with conflicting results. We describe a unified framework for PDTO-based predictive testing across standard-of-care chemotherapy and biologic and targeted therapy options. In an Australian community cohort, PDTO predictions based on treatment-naive patients (n = 56) and response rates from first-line mCRC clinical trials achieve 83% accuracy for forecasting responses in patients receiving palliative treatments (18 patients, 29 treatments). Similar assay accuracy is achieved in a prospective study of third-line or later mCRC treatment, AGITG FORECAST-1 (n = 30 patients). "Resistant" predictions are associated with inferior progression-free survival; misclassification rates are similar by regimen. Liver metastases are the optimal site for sampling, with testing achievable within 7 weeks for 68.8% cases. Our findings indicate that PDTO drug panel testing can provide predictive information for multifarious standard-of-care therapies for mCRC.
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Affiliation(s)
- Tao Tan
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Dmitri Mouradov
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Margaret Lee
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Oncology, Western Health, Footscray, VIC 3011, Australia; Department of Medical Oncology, Eastern Health, Box Hill, VIC 3128, Australia; Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University, Box Hill, VIC 3128, Australia
| | - Grace Gard
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Oncology, Western Health, Footscray, VIC 3011, Australia
| | - Yumiko Hirokawa
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Shan Li
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Cong Lin
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, BGI Research, Hangzhou 310000, China; Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen 518083, China
| | - Fuqiang Li
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, BGI Research, Hangzhou 310000, China; Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen 518083, China
| | - Huijuan Luo
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, BGI Research, Hangzhou 310000, China; Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen 518083, China
| | - Kui Wu
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, BGI Research, Hangzhou 310000, China; Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen 518083, China
| | - Michelle Palmieri
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Evelyn Leong
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Jordan Clarke
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Anuratha Sakthianandeswaren
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Helen Brasier
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Jeanne Tie
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia; Department of Medical Oncology, Western Health, Footscray, VIC 3011, Australia
| | - Niall C Tebbutt
- Department of Medical Oncology, Olivia Newton-John Cancer Wellness & Research Centre, Austin Health, Heidelberg, VIC 3084, Australia
| | - Azim Jalali
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Oncology, Western Health, Footscray, VIC 3011, Australia; Department of Cancer Services, Latrobe Regional Hospital, Traralogon, VIC 3844, Australia; Department of Medical Oncology, The Northern Hospital, Epping, VIC 3076, Australia
| | - Rachel Wong
- Department of Medical Oncology, Eastern Health, Box Hill, VIC 3128, Australia; Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University, Box Hill, VIC 3128, Australia
| | - Antony W Burgess
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia; Department of Surgery, The University of Melbourne, Parkville, VIC 3050, Australia
| | - Peter Gibbs
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia; Department of Medical Oncology, Western Health, Footscray, VIC 3011, Australia
| | - Oliver M Sieber
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia; Department of Surgery, The University of Melbourne, Parkville, VIC 3050, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
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29
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Zhang W, Lazar-Stefanita L, Yamashita H, Shen MJ, Mitchell LA, Kurasawa H, Lobzaev E, Fanfani V, Haase MAB, Sun X, Jiang Q, Goldberg GW, Ichikawa DM, Lauer SL, McCulloch LH, Easo N, Lin SJ, Camellato BR, Zhu Y, Cai J, Xu Z, Zhao Y, Sacasa M, Noyes MB, Bader JS, Deutsch S, Stracquadanio G, Aizawa Y, Dai J, Boeke JD. Manipulating the 3D organization of the largest synthetic yeast chromosome. Mol Cell 2023; 83:4424-4437.e5. [PMID: 37944526 DOI: 10.1016/j.molcel.2023.10.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/11/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023]
Abstract
Whether synthetic genomes can power life has attracted broad interest in the synthetic biology field. Here, we report de novo synthesis of the largest eukaryotic chromosome thus far, synIV, a 1,454,621-bp yeast chromosome resulting from extensive genome streamlining and modification. We developed megachunk assembly combined with a hierarchical integration strategy, which significantly increased the accuracy and flexibility of synthetic chromosome construction. Besides the drastic sequence changes, we further manipulated the 3D structure of synIV to explore spatial gene regulation. Surprisingly, we found few gene expression changes, suggesting that positioning inside the yeast nucleoplasm plays a minor role in gene regulation. Lastly, we tethered synIV to the inner nuclear membrane via its hundreds of loxPsym sites and observed transcriptional repression of the entire chromosome, demonstrating chromosome-wide transcription manipulation without changing the DNA sequences. Our manipulation of the spatial structure of synIV sheds light on higher-order architectural design of the synthetic genomes.
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Affiliation(s)
- Weimin Zhang
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Luciana Lazar-Stefanita
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Hitoyoshi Yamashita
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Michael J Shen
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Leslie A Mitchell
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Hikaru Kurasawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Evgenii Lobzaev
- School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Viola Fanfani
- School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Max A B Haase
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Xiaoji Sun
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Qingwen Jiang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Gregory W Goldberg
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - David M Ichikawa
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Stephanie L Lauer
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Laura H McCulloch
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Nicole Easo
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - S Jiaming Lin
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Brendan R Camellato
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Yinan Zhu
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Jitong Cai
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Zhuwei Xu
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Yu Zhao
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Maya Sacasa
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Marcus B Noyes
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Joel S Bader
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Samuel Deutsch
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Yasunori Aizawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan; Kanagawa Institute of Industrial Science and Technology (KISTEC), Ebina, Kanagawa 243-0435, Japan.
| | - Junbiao Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA; Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, New York, NY, USA.
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30
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Ho GY, Vandenberg CJ, Lim R, Christie EL, Garsed DW, Lieschke E, Nesic K, Kondrashova O, Ratnayake G, Radke M, Penington JS, Carmagnac A, Heong V, Kyran EL, Zhang F, Traficante N, Huang R, Dobrovic A, Swisher EM, McNally O, Kee D, Wakefield MJ, Papenfuss AT, Bowtell DDL, Barker HE, Scott CL. The microtubule inhibitor eribulin demonstrates efficacy in platinum-resistant and refractory high-grade serous ovarian cancer patient-derived xenograft models. Ther Adv Med Oncol 2023; 15:17588359231208674. [PMID: 38028140 PMCID: PMC10666702 DOI: 10.1177/17588359231208674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 09/25/2023] [Indexed: 12/01/2023] Open
Abstract
Background Despite initial response to platinum-based chemotherapy and PARP inhibitor therapy (PARPi), nearly all recurrent high-grade serous ovarian cancer (HGSC) will acquire lethal drug resistance; indeed, ~15% of individuals have de novo platinum-refractory disease. Objectives To determine the potential of anti-microtubule agent (AMA) therapy (paclitaxel, vinorelbine and eribulin) in platinum-resistant or refractory (PRR) HGSC by assessing response in patient-derived xenograft (PDX) models of HGSC. Design and methods Of 13 PRR HGSC PDX, six were primary PRR, derived from chemotherapy-naïve samples (one was BRCA2 mutant) and seven were from samples obtained following chemotherapy treatment in the clinic (five were mutant for either BRCA1 or BRCA2 (BRCA1/2), four with prior PARPi exposure), recapitulating the population of individuals with aggressive treatment-resistant HGSC in the clinic. Molecular analyses and in vivo treatment studies were undertaken. Results Seven out of thirteen PRR PDX (54%) were sensitive to treatment with the AMA, eribulin (time to progressive disease (PD) ⩾100 days from the start of treatment) and 11 out of 13 PDX (85%) derived significant benefit from eribulin [time to harvest (TTH) for each PDX with p < 0.002]. In 5 out of 10 platinum-refractory HGSC PDX (50%) and one out of three platinum-resistant PDX (33%), eribulin was more efficacious than was cisplatin, with longer time to PD and significantly extended TTH (each PDX p < 0.02). Furthermore, four of these models were extremely sensitive to all three AMA tested, maintaining response until the end of the experiment (120d post-treatment start). Despite harbouring secondary BRCA2 mutations, two BRCA2-mutant PDX models derived from heavily pre-treated individuals were sensitive to AMA. PRR HGSC PDX models showing greater sensitivity to AMA had high proliferative indices and oncogene expression. Two PDX models, both with prior chemotherapy and/or PARPi exposure, were refractory to all AMA, one of which harboured the SLC25A40-ABCB1 fusion, known to upregulate drug efflux via MDR1. Conclusion The efficacy observed for eribulin in PRR HGSC PDX was similar to that observed for paclitaxel, which transformed ovarian cancer clinical practice. Eribulin is therefore worthy of further consideration in clinical trials, particularly in ovarian carcinoma with early failure of carboplatin/paclitaxel chemotherapy.
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Affiliation(s)
- Gwo Yaw Ho
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- The Royal Women’s Hospital, Parkville, VIC, Australia
- School of Clinical Sciences, Monash University, Clayton Road, Clayton, VIC 3168, Australia
| | - Cassandra J. Vandenberg
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Ratana Lim
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Elizabeth L. Christie
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Dale W. Garsed
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Elizabeth Lieschke
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Ksenija Nesic
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Olga Kondrashova
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | | | - Marc Radke
- University of Washington, Seattle, WA, USA
| | - Jocelyn S. Penington
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Amandine Carmagnac
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Valerie Heong
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Elizabeth L. Kyran
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Fan Zhang
- Department of Surgery, Austin Health, University of Melbourne, Heidelberg, VIC, Australia
| | - Nadia Traficante
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | | | | | - Alexander Dobrovic
- Department of Surgery, Austin Health, University of Melbourne, Heidelberg, VIC, Australia
| | | | - Orla McNally
- The Royal Women’s Hospital, Parkville, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, Australia
| | - Damien Kee
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
- Department of Medical Oncology, Austin Hospital, Heidelberg, VIC, Australia
| | - Matthew J. Wakefield
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, Australia
| | - Anthony T. Papenfuss
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - David D. L. Bowtell
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Holly E. Barker
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Clare L. Scott
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- The Royal Women’s Hospital, Parkville, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, Australia
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Lauer S, Luo J, Lazar-Stefanita L, Zhang W, McCulloch LH, Fanfani V, Lobzaev E, Haase MA, Easo N, Zhao Y, Yu F, Cai J, Bader JS, Stracquadanio G, Boeke JD. Context-dependent neocentromere activity in synthetic yeast chromosome VIII. CELL GENOMICS 2023; 3:100437. [PMID: 38020969 PMCID: PMC10667555 DOI: 10.1016/j.xgen.2023.100437] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 07/20/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023]
Abstract
Pioneering advances in genome engineering, and specifically in genome writing, have revolutionized the field of synthetic biology, propelling us toward the creation of synthetic genomes. The Sc2.0 project aims to build the first fully synthetic eukaryotic organism by assembling the genome of Saccharomyces cerevisiae. With the completion of synthetic chromosome VIII (synVIII) described here, this goal is within reach. In addition to writing the yeast genome, we sought to manipulate an essential functional element: the point centromere. By relocating the native centromere sequence to various positions along chromosome VIII, we discovered that the minimal 118-bp CEN8 sequence is insufficient for conferring chromosomal stability at ectopic locations. Expanding the transplanted sequence to include a small segment (∼500 bp) of the CDEIII-proximal pericentromere improved chromosome stability, demonstrating that minimal centromeres display context-dependent functionality.
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Affiliation(s)
- Stephanie Lauer
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Jingchuan Luo
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Luciana Lazar-Stefanita
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Weimin Zhang
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Laura H. McCulloch
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Viola Fanfani
- School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Evgenii Lobzaev
- School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- School of Informatics, The University of Edinburgh, Edinburgh, UK
| | - Max A.B. Haase
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Nicole Easo
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Yu Zhao
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Fangzhou Yu
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Jitong Cai
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Joel S. Bader
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | | | - Jef D. Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, USA
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32
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Rubinstein M, Makhon A, Losev Y, Valenci GZ, Gatt YE, Margalit H, Fass E, Kutikov I, Murik O, Zeevi DA, Savyon M, Tau L, Kaidar Shwartz H, Dveyrin Z, Rorman E, Nissan I. Prolonged survival of a patient with active MDR-TB HIV co-morbidity: insights from a Mycobacterium tuberculosis strain with a unique genomic deletion. Front Med (Lausanne) 2023; 10:1292665. [PMID: 38020140 PMCID: PMC10657812 DOI: 10.3389/fmed.2023.1292665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Coinfection of HIV and multidrug-resistant tuberculosis (MDR-TB) presents significant challenges in terms of the treatment and prognosis of tuberculosis, leading to complexities in managing the disease and impacting the overall outcome for TB patients. This study presents a remarkable case of a patient with MDR-TB and HIV coinfection who survived for over 8 years, despite poor treatment adherence and comorbidities. Whole genome sequencing (WGS) of the infecting Mycobacterium tuberculosis (Mtb) strain revealed a unique genomic deletion, spanning 18 genes, including key genes involved in hypoxia response, intracellular survival, immunodominant antigens, and dormancy. This deletion, that we have called "Del-X," potentially exerts a profound influence on the bacterial physiology and its virulence. Only few similar deletions were detected in other non-related Mtb genomes worldwide. In vivo evolution analysis identified drug resistance and metabolic adaptation mutations and their temporal dynamics during the patient's treatment course.
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Affiliation(s)
- Mor Rubinstein
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Andrei Makhon
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Yelena Losev
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Gal Zizelski Valenci
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Yair E. Gatt
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ephraim Fass
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Ina Kutikov
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Omer Murik
- Translational Genomics Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - David A. Zeevi
- Translational Genomics Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Michal Savyon
- Tel Aviv District Health Office, Ministry of Health, Tel Aviv, Israel
| | - Luba Tau
- Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hasia Kaidar Shwartz
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Zeev Dveyrin
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Efrat Rorman
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Israel Nissan
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
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33
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Yuzon JD, Schultzhaus Z, Wang Z. Transcriptomic and genomic effects of gamma-radiation exposure on strains of the black yeast Exophiala dermatitidis evolved to display increased ionizing radiation resistance. Microbiol Spectr 2023; 11:e0221923. [PMID: 37676019 PMCID: PMC10581076 DOI: 10.1128/spectrum.02219-23] [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: 05/25/2023] [Accepted: 07/15/2023] [Indexed: 09/08/2023] Open
Abstract
IMPORTANCE Ionizing radiation poses a significant threat to living organisms and human health, given its destructive nature and widespread use in fields such as medicine and the potential for nuclear disasters. Melanized fungi exhibit remarkable survival capabilities, enduring doses up to 1,000-fold higher than mammals. Through adaptive laboratory evolution, we validated the protective role of constitutive upregulation of DNA repair genes in the black yeast Exophiala dermatitidis, enhancing survival after radiation exposure. Surprisingly, we found that evolved strains lacking melanin still achieved high levels of radioresistance. Our study unveiled the significance of robust activation and enhancement of redox homeostasis, as evidenced by the profound transcriptional changes and increased accumulation of mutations, in substantially improving ionizing radiation resistance in the absence of melanin. These findings underscore the delicate balance between DNA repair and redox homeostasis for an organism's ability to endure and recover from radiation exposure.
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Affiliation(s)
- Jennifer D. Yuzon
- National Research Council Postdoctoral Research Associate, US Naval Research Laboratory, Washington, USA
| | - Zachary Schultzhaus
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, USA
| | - Zheng Wang
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, USA
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34
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Wang C, Niu J, Wei L, Li C, Li G, Tian Q, Ju M, Ma Q, Cao H, Duan Y, Guo H, Zhang H, Miao H. A 4.43-Kb deletion of chromosomal segment containing an ovate family protein confers long capsule in sesame (Sesamum indicum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:221. [PMID: 37819543 DOI: 10.1007/s00122-023-04465-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/14/2023] [Indexed: 10/13/2023]
Abstract
KEY MESSAGE A 4.43-Kb structural variation in the sesame genome results in the deletion of the Siofp1 gene and induces the long capsule length trait. Capsule length (CL) has a positive effect on seed weight and yield in various agronomically important species; however, the molecular mechanism underlying long capsule trait regulation in sesame remains unknown. The inheritance analysis showed that long capsule traits (CL > 4.0 cm) were dominant over normal length (average CL = 3.0 cm) and were controlled by a single gene pair. Association mapping with a RIL population and 259 natural sesame germplasm accessions indicated that the target interval was 52,830-730,961 bp of SiChr.10 in sesame. Meanwhile, the structural variation (SV) of the association mapping revealed that only SV_414325 on chromosome 10 was significantly associated with the CL trait, with a P value of 1.1135E-19. SV_414325 represents a 4430-bp deletion from 414,325 to 418,756 bp on SiChr.10, covering Sindi_2155000 (named SiOFP1). In the normal length type, Siofp1 encodes 411 amino acids of the ovate family proteins and is highly expressed in the leaf, stem, bud, and capsule tissues of sesame. In accordance with the transcriptional repressor character, Siofp1 overexpression in transgenic Arabidopsis (T0 and T1 generations) induced a 25-39% greater shortening of silique length than the wild type (P < 0.05), as well as round cauline leaves and short carpels. These results confirm that SiOFP1 plays a key role in regulating CL trait in sesame and other flowering plants. These findings provide a theoretical and material basis for sesame capsule development and high-yield breeding research.
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Affiliation(s)
- Cuiying Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Jiaojiao Niu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Libin Wei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Chun Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- The Shennong Laboratory, Zhengzhou, 450002, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Guiting Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Qiuzhen Tian
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Ming Ju
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Qin Ma
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Hengchun Cao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Yinghui Duan
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- The Shennong Laboratory, Zhengzhou, 450002, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Hui Guo
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Haiyang Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China.
- The Shennong Laboratory, Zhengzhou, 450002, Henan, China.
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China.
| | - Hongmei Miao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China.
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China.
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35
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Ariotta V, Lehtonen O, Salloum S, Micoli G, Lavikka K, Rantanen V, Hynninen J, Virtanen A, Hautaniemi S. H&E image analysis pipeline for quantifying morphological features. J Pathol Inform 2023; 14:100339. [PMID: 37915837 PMCID: PMC10616375 DOI: 10.1016/j.jpi.2023.100339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/15/2023] [Accepted: 09/30/2023] [Indexed: 11/03/2023] Open
Abstract
Detecting cell types from histopathological images is essential for various digital pathology applications. However, large number of cells in whole-slide images (WSIs) necessitates automated analysis pipelines for efficient cell type detection. Herein, we present hematoxylin and eosin (H&E) Image Processing pipeline (HEIP) for automatied analysis of scanned H&E-stained slides. HEIP is a flexible and modular open-source software that performs preprocessing, instance segmentation, and nuclei feature extraction. To evaluate the performance of HEIP, we applied it to extract cell types from ovarian high-grade serous carcinoma (HGSC) patient WSIs. HEIP showed high precision in instance segmentation, particularly for neoplastic and epithelial cells. We also show that there is a significant correlation between genomic ploidy values and morphological features, such as major axis of the nucleus.
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Affiliation(s)
- Valeria Ariotta
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Oskari Lehtonen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Shams Salloum
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
- Department of Pathology, University of Helsinki and HUS Diagnostic Center, Helsinki University Hospital, 00029 Helsinki, Finland
| | - Giulia Micoli
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Kari Lavikka
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Ville Rantanen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Johanna Hynninen
- Department of Obstetrics and Gynaecology, University of Turku and Turku University Hospital, 200521 Turku, Finland
| | - Anni Virtanen
- Department of Pathology, University of Helsinki and HUS Diagnostic Center, Helsinki University Hospital, 00029 Helsinki, Finland
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
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36
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Middelkamp S, Manders F, Peci F, van Roosmalen MJ, González DM, Bertrums EJ, van der Werf I, Derks LL, Groenen NM, Verheul M, Trabut L, Pleguezuelos-Manzano C, Brandsma AM, Antoniou E, Reinhardt D, Bierings M, Belderbos ME, van Boxtel R. Comprehensive single-cell genome analysis at nucleotide resolution using the PTA Analysis Toolbox. CELL GENOMICS 2023; 3:100389. [PMID: 37719152 PMCID: PMC10504672 DOI: 10.1016/j.xgen.2023.100389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/30/2023] [Accepted: 08/02/2023] [Indexed: 09/19/2023]
Abstract
Detection of somatic mutations in single cells has been severely hampered by technical limitations of whole-genome amplification. Novel technologies including primary template-directed amplification (PTA) significantly improved the accuracy of single-cell whole-genome sequencing (WGS) but still generate hundreds of artifacts per amplification reaction. We developed a comprehensive bioinformatic workflow, called the PTA Analysis Toolbox (PTATO), to accurately detect single base substitutions, insertions-deletions (indels), and structural variants in PTA-based WGS data. PTATO includes a machine learning approach and filtering based on recurrence to distinguish PTA artifacts from true mutations with high sensitivity (up to 90%), outperforming existing bioinformatic approaches. Using PTATO, we demonstrate that hematopoietic stem cells of patients with Fanconi anemia, which cannot be analyzed using regular WGS, have normal somatic single base substitution burdens but increased numbers of deletions. Our results show that PTATO enables studying somatic mutagenesis in the genomes of single cells with unprecedented sensitivity and accuracy.
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Affiliation(s)
- Sjors Middelkamp
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Freek Manders
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Flavia Peci
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Markus J. van Roosmalen
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Diego Montiel González
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Eline J.M. Bertrums
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
- Department of Pediatric Oncology, Erasmus Medical Center – Sophia Children’s Hospital, Rotterdam, the Netherlands
| | - Inge van der Werf
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Lucca L.M. Derks
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Niels M. Groenen
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Mark Verheul
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Laurianne Trabut
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Cayetano Pleguezuelos-Manzano
- Oncode Institute, Utrecht, the Netherlands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, the Netherlands
| | - Arianne M. Brandsma
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Evangelia Antoniou
- Department of Pediatric Hematology and Oncology, University Hospital Essen, Essen, Germany
| | - Dirk Reinhardt
- Department of Pediatric Hematology and Oncology, University Hospital Essen, Essen, Germany
| | - Marc Bierings
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | | | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
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Abdelmogod A, Papadopoulos L, Riordan S, Wong M, Weltman M, Lim R, McEvoy C, Fellowes A, Fox S, Bedő J, Penington J, Pham K, Hofmann O, Vissers JHA, Grimmond S, Ratnayake G, Christie M, Mitchell C, Murray WK, McClymont K, Luk P, Papenfuss AT, Kee D, Scott CL, Goldstein D, Barker HE. A Matched Molecular and Clinical Analysis of the Epithelioid Haemangioendothelioma Cohort in the Stafford Fox Rare Cancer Program and Contextual Literature Review. Cancers (Basel) 2023; 15:4378. [PMID: 37686662 PMCID: PMC10487006 DOI: 10.3390/cancers15174378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/21/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
BACKGROUND Epithelioid haemangioendothelioma (EHE) is an ultra-rare malignant vascular tumour with a prevalence of 1 per 1,000,000. It is typically molecularly characterised by a WWTR1::CAMTA1 gene fusion in approximately 90% of cases, or a YAP1::TFE3 gene fusion in approximately 10% of cases. EHE cases are typically refractory to therapies, and no anticancer agents are reimbursed for EHE in Australia. METHODS We report a cohort of nine EHE cases with comprehensive histologic and molecular profiling from the Walter and Eliza Hall Institute of Medical Research Stafford Fox Rare Cancer Program (WEHI-SFRCP) collated via nation-wide referral to the Australian Rare Cancer (ARC) Portal. The diagnoses of EHE were confirmed by histopathological and immunohistochemical (IHC) examination. Molecular profiling was performed using the TruSight Oncology 500 assay, the TruSight RNA fusion panel, whole genome sequencing (WGS), or whole exome sequencing (WES). RESULTS Molecular analysis of RNA, DNA or both was possible in seven of nine cases. The WWTR1::CAMTA1 fusion was identified in five cases. The YAP1::TFE3 fusion was identified in one case, demonstrating unique morphology compared to cases with the more common WWTR1::CAMTA1 fusion. All tumours expressed typical endothelial markers CD31, ERG, and CD34 and were negative for pan-cytokeratin. Cases with a WWTR1::CAMTA1 fusion displayed high expression of CAMTA1 and the single case with a YAP1::TFE3 fusion displayed high expression of TFE3. Survival was highly variable and unrelated to molecular profile. CONCLUSIONS This cohort of EHE cases provides molecular and histopathological characterisation and matching clinical information that emphasises the molecular patterns and variable clinical outcomes and adds to our knowledge of this ultra-rare cancer. Such information from multiple studies will advance our understanding, potentially improving treatment options.
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Affiliation(s)
- Arwa Abdelmogod
- Limestone Coast Local Health Network, Flinders University, Bedford Park, SA 5042, Australia;
| | - Lia Papadopoulos
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (L.P.); (R.L.); (J.B.); (J.P.); (A.T.P.); (D.K.); (C.L.S.)
- The Australian Rare Cancer Portal, BioGrid, Parkville, VIC 3051, Australia;
- Eastern Health Clinical School, Monash University, Box Hill, VIC 3128, Australia
| | - Stephen Riordan
- Prince of Wales Clinical School, University of NSW, Randwick, NSW 2031, Australia;
- Gastrointestinal and Liver Unit, Prince of Wales Hospital, Randwick, NSW 2031, Australia
| | - Melvin Wong
- Radiology Department, Prince of Wales Hospital, Randwick, NSW 2031, Australia;
| | - Martin Weltman
- Department of Gastroenterology, Nepean Hospital, Kingswood, NSW 2747, Australia;
| | - Ratana Lim
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (L.P.); (R.L.); (J.B.); (J.P.); (A.T.P.); (D.K.); (C.L.S.)
| | - Christopher McEvoy
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; (C.M.); (A.F.)
| | - Andrew Fellowes
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; (C.M.); (A.F.)
| | - Stephen Fox
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; (C.M.); (A.F.)
| | - Justin Bedő
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (L.P.); (R.L.); (J.B.); (J.P.); (A.T.P.); (D.K.); (C.L.S.)
| | - Jocelyn Penington
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (L.P.); (R.L.); (J.B.); (J.P.); (A.T.P.); (D.K.); (C.L.S.)
| | - Kym Pham
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Melbourne, VIC 3010, Australia; (K.P.); (O.H.); (J.H.A.V.); (S.G.)
| | - Oliver Hofmann
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Melbourne, VIC 3010, Australia; (K.P.); (O.H.); (J.H.A.V.); (S.G.)
| | - Joseph H. A. Vissers
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Melbourne, VIC 3010, Australia; (K.P.); (O.H.); (J.H.A.V.); (S.G.)
| | - Sean Grimmond
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Melbourne, VIC 3010, Australia; (K.P.); (O.H.); (J.H.A.V.); (S.G.)
| | | | | | - Catherine Mitchell
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; (C.M.); (W.K.M.)
| | - William K. Murray
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; (C.M.); (W.K.M.)
| | - Kelly McClymont
- Sullivan Nicolaides Pathology, Brisbane, QLD 4000, Australia;
| | - Peter Luk
- Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia;
| | - Anthony T. Papenfuss
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (L.P.); (R.L.); (J.B.); (J.P.); (A.T.P.); (D.K.); (C.L.S.)
- Department of Gastroenterology, Nepean Hospital, Kingswood, NSW 2747, Australia;
- Sir Peter MacCallum Cancer Centre, Department of Oncology, University of Melbourne, Parkville, VIC 3000, Australia
| | - Damien Kee
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (L.P.); (R.L.); (J.B.); (J.P.); (A.T.P.); (D.K.); (C.L.S.)
- The Australian Rare Cancer Portal, BioGrid, Parkville, VIC 3051, Australia;
- Sir Peter MacCallum Cancer Centre, Department of Oncology, University of Melbourne, Parkville, VIC 3000, Australia
- Austin Health, Heidelberg, VIC 3084, Australia
| | - Clare L. Scott
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (L.P.); (R.L.); (J.B.); (J.P.); (A.T.P.); (D.K.); (C.L.S.)
- The Australian Rare Cancer Portal, BioGrid, Parkville, VIC 3051, Australia;
- The Royal Womens’ Hospital, Parkville, VIC 3052, Australia;
- Sir Peter MacCallum Cancer Centre, Department of Oncology, University of Melbourne, Parkville, VIC 3000, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC 3010, Australia
| | - David Goldstein
- The Australian Rare Cancer Portal, BioGrid, Parkville, VIC 3051, Australia;
- Eastern Health Clinical School, Monash University, Box Hill, VIC 3128, Australia
- Nelune Center, Prince of Wales Hospital, Randwick, NSW 2031, Australia
| | - Holly E. Barker
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (L.P.); (R.L.); (J.B.); (J.P.); (A.T.P.); (D.K.); (C.L.S.)
- Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
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Kim J, Kim S, Yeom H, Song SW, Shin K, Bae S, Ryu HS, Kim JY, Choi A, Lee S, Ryu T, Choi Y, Kim H, Kim O, Jung Y, Kim N, Han W, Lee HB, Lee AC, Kwon S. Barcoded multiple displacement amplification for high coverage sequencing in spatial genomics. Nat Commun 2023; 14:5261. [PMID: 37644058 PMCID: PMC10465490 DOI: 10.1038/s41467-023-41019-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023] Open
Abstract
Determining mutational landscapes in a spatial context is essential for understanding genetically heterogeneous cell microniches. Current approaches, such as Multiple Displacement Amplification (MDA), offer high genome coverage but limited multiplexing, which hinders large-scale spatial genomic studies. Here, we introduce barcoded MDA (bMDA), a technique that achieves high-coverage genomic analysis of low-input DNA while enhancing the multiplexing capabilities. By incorporating cell barcodes during MDA, bMDA streamlines library preparation in one pot, thereby overcoming a key bottleneck in spatial genomics. We apply bMDA to the integrative spatial analysis of triple-negative breast cancer tissues by examining copy number alterations, single nucleotide variations, structural variations, and kataegis signatures for each spatial microniche. This enables the assessment of subclonal evolutionary relationships within a spatial context. Therefore, bMDA has emerged as a scalable technology with the potential to advance the field of spatial genomics significantly.
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Affiliation(s)
- Jinhyun Kim
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sungsik Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Huiran Yeom
- Division of Data Science, College of Information and Communication Technology, The University of Suwon, Hwaseong, 18323, Republic of Korea
| | - Seo Woo Song
- Basic Science and Engineering Initiative, Children's Heart Center, Stanford University, Stanford, CA, USA
| | - Kyoungseob Shin
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sangwook Bae
- Renal Division and Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Han Suk Ryu
- Cancer Research Institute, Seoul National University, Seoul, 03080, Republic of Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Ji Young Kim
- Biomedical Research Institute, Seoul National University Hospital, Seoul, 03080, Republic of Korea
| | - Ahyoun Choi
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sumin Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea
- Meteor Biotech, Co. Ltd., Seoul, 08826, Republic of Korea
| | - Taehoon Ryu
- ATG Lifetech Inc., Seoul, 08507, Republic of Korea
| | - Yeongjae Choi
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Hamin Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Okju Kim
- ATG Lifetech Inc., Seoul, 08507, Republic of Korea
| | - Yushin Jung
- ATG Lifetech Inc., Seoul, 08507, Republic of Korea
| | - Namphil Kim
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Wonshik Han
- Cancer Research Institute, Seoul National University, Seoul, 03080, Republic of Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul, 03080, Republic of Korea
- Department of Surgery, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Han-Byoel Lee
- Cancer Research Institute, Seoul National University, Seoul, 03080, Republic of Korea.
- Biomedical Research Institute, Seoul National University Hospital, Seoul, 03080, Republic of Korea.
- Department of Surgery, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
| | - Amos C Lee
- Bio-MAX Institute, Seoul National University, Seoul, 08826, Republic of Korea.
- Meteor Biotech, Co. Ltd., Seoul, 08826, Republic of Korea.
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea.
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea.
- Biomedical Research Institute, Seoul National University Hospital, Seoul, 03080, Republic of Korea.
- Bio-MAX Institute, Seoul National University, Seoul, 08826, Republic of Korea.
- Inter-University Semiconductor Research Center, Seoul National University, Seoul, 08826, Republic of Korea.
- Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul, 08826, Republic of Korea.
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39
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Gyüre Z, Póti Á, Németh E, Szikriszt B, Lózsa R, Krawczyk M, Richardson AL, Szüts D. Spontaneous mutagenesis in human cells is controlled by REV1-Polymerase ζ and PRIMPOL. Cell Rep 2023; 42:112887. [PMID: 37498746 DOI: 10.1016/j.celrep.2023.112887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/09/2023] [Accepted: 07/13/2023] [Indexed: 07/29/2023] Open
Abstract
Translesion DNA synthesis (TLS) facilitates replication over damaged or difficult-to-replicate templates by employing specialized DNA polymerases. We investigate the effect on spontaneous mutagenesis of three main TLS control mechanisms: REV1 and PCNA ubiquitylation that recruit TLS polymerases and PRIMPOL that creates post-replicative gaps. Using whole-genome sequencing of cultured human RPE-1 cell clones, we find that REV1 and Polymerase ζ are wholly responsible for one component of base substitution mutagenesis that resembles homologous recombination deficiency, whereas the remaining component that approximates oxidative mutagenesis is reduced in PRIMPOL-/- cells. Small deletions in short repeats appear in REV1-/-PCNAK164R/K164R double mutants, revealing an alternative TLS mechanism. Also, 500-5,000 bp deletions appear in REV1-/- and REV3L-/- mutants, and chromosomal instability is detectable in REV1-/-PRIMPOL-/- cells. Our results indicate that TLS protects the genome from deletions and large rearrangements at the expense of being responsible for the majority of spontaneous base substitutions.
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Affiliation(s)
- Zsolt Gyüre
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; Doctoral School of Molecular Medicine, Semmelweis University, 1085 Budapest, Hungary; Turbine Simulated Cell Technologies, 1027 Budapest, Hungary
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Bernadett Szikriszt
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Rita Lózsa
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Michał Krawczyk
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | | | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; National Laboratory for Drug Research and Development, 1117 Budapest, Hungary.
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40
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Abel HJ, Oetjen KA, Miller CA, Ramakrishnan SM, Day RB, Helton NM, Fronick CC, Fulton RS, Heath SE, Tarnawsky SP, Nonavinkere Srivatsan S, Duncavage EJ, Schroeder MC, Payton JE, Spencer DH, Walter MJ, Westervelt P, DiPersio JF, Ley TJ, Link DC. Genomic landscape of TP53-mutated myeloid malignancies. Blood Adv 2023; 7:4586-4598. [PMID: 37339484 PMCID: PMC10425686 DOI: 10.1182/bloodadvances.2023010156] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/19/2023] [Accepted: 06/07/2023] [Indexed: 06/22/2023] Open
Abstract
TP53-mutated myeloid malignancies are associated with complex cytogenetics and extensive structural variants, which complicates detailed genomic analysis by conventional clinical techniques. We performed whole-genome sequencing (WGS) of 42 acute myeloid leukemia (AML)/myelodysplastic syndromes (MDS) cases with paired normal tissue to better characterize the genomic landscape of TP53-mutated AML/MDS. WGS accurately determines TP53 allele status, a key prognostic factor, resulting in the reclassification of 12% of cases from monoallelic to multihit. Although aneuploidy and chromothripsis are shared with most TP53-mutated cancers, the specific chromosome abnormalities are distinct to each cancer type, suggesting a dependence on the tissue of origin. ETV6 expression is reduced in nearly all cases of TP53-mutated AML/MDS, either through gene deletion or presumed epigenetic silencing. Within the AML cohort, mutations of NF1 are highly enriched, with deletions of 1 copy of NF1 present in 45% of cases and biallelic mutations in 17%. Telomere content is increased in TP53-mutated AMLs compared with other AML subtypes, and abnormal telomeric sequences were detected in the interstitial regions of chromosomes. These data highlight the unique features of TP53-mutated myeloid malignancies, including the high frequency of chromothripsis and structural variation, the frequent involvement of unique genes (including NF1 and ETV6) as cooperating events, and evidence for altered telomere maintenance.
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Affiliation(s)
- Haley J. Abel
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Karolyn A. Oetjen
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Christopher A. Miller
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Sai M. Ramakrishnan
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Ryan B. Day
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Nichole M. Helton
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Catrina C. Fronick
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Robert S. Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Sharon E. Heath
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Stefan P. Tarnawsky
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | | | - Eric J. Duncavage
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO
| | - Molly C. Schroeder
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO
| | - Jacqueline E. Payton
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO
| | - David H. Spencer
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO
| | - Matthew J. Walter
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Peter Westervelt
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - John F. DiPersio
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Timothy J. Ley
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Daniel C. Link
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
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41
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Shiraishi Y, Koya J, Chiba K, Okada A, Arai Y, Saito Y, Shibata T, Kataoka K. Precise characterization of somatic complex structural variations from tumor/control paired long-read sequencing data with nanomonsv. Nucleic Acids Res 2023; 51:e74. [PMID: 37336583 PMCID: PMC10415145 DOI: 10.1093/nar/gkad526] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/23/2023] [Accepted: 06/07/2023] [Indexed: 06/21/2023] Open
Abstract
We present our novel software, nanomonsv, for detecting somatic structural variations (SVs) using tumor and matched control long-read sequencing data with a single-base resolution. The current version of nanomonsv includes two detection modules, Canonical SV module, and Single breakend SV module. Using tumor/control paired long-read sequencing data from three cancer and their matched lymphoblastoid lines, we demonstrate that Canonical SV module can identify somatic SVs that can be captured by short-read technologies with higher precision and recall than existing methods. In addition, we have developed a workflow to classify mobile element insertions while elucidating their in-depth properties, such as 5' truncations, internal inversions, as well as source sites for 3' transductions. Furthermore, Single breakend SV module enables the detection of complex SVs that can only be identified by long-reads, such as SVs involving highly-repetitive centromeric sequences, and LINE1- and virus-mediated rearrangements. In summary, our approaches applied to cancer long-read sequencing data can reveal various features of somatic SVs and will lead to a better understanding of mutational processes and functional consequences of somatic SVs.
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Affiliation(s)
- Yuichi Shiraishi
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Junji Koya
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Kenichi Chiba
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Ai Okada
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Yasuhito Arai
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yuki Saito
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
- Laboratory of Molecular Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Keisuke Kataoka
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Department of Hematology, Keio University School of Medicine, Tokyo, Japan
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42
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Cullen JN, Friedenberg SG. Whole Animal Genome Sequencing: user-friendly, rapid, containerized pipelines for processing, variant discovery, and annotation of short-read whole genome sequencing data. G3 (BETHESDA, MD.) 2023; 13:jkad117. [PMID: 37243692 PMCID: PMC10411559 DOI: 10.1093/g3journal/jkad117] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 02/24/2023] [Accepted: 05/20/2023] [Indexed: 05/29/2023]
Abstract
Advancements in massively parallel short-read sequencing technologies and the associated decreasing costs have led to large and diverse variant discovery efforts across species. However, processing high-throughput short-read sequencing data can be challenging with potential pitfalls and bioinformatics bottlenecks in generating reproducible results. Although a number of pipelines exist that address these challenges, these are often geared toward human or traditional model organism species and can be difficult to configure across institutions. Whole Animal Genome Sequencing (WAGS) is an open-source set of user-friendly, containerized pipelines designed to simplify the process of identifying germline short (SNP and indel) and structural variants (SVs) geared toward the veterinary community but adaptable to any species with a suitable reference genome. We present a description of the pipelines [adapted from the best practices of the Genome Analysis Toolkit (GATK)], along with benchmarking data from both the preprocessing and joint genotyping steps, consistent with a typical user workflow.
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Affiliation(s)
- Jonah N Cullen
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, 1352 Boyd Ave, Saint Paul, MN 55108, USA
| | - Steven G Friedenberg
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, 1352 Boyd Ave, Saint Paul, MN 55108, USA
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43
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Fan Y, Zou L, Zhong X, Wang Z, Wang Y, Luo C, Zheng H, Wang Y. Characteristics of DNA macro-alterations in breast cancer with liver metastasis before treatment. BMC Genomics 2023; 24:391. [PMID: 37434117 DOI: 10.1186/s12864-023-09497-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: 06/20/2022] [Accepted: 06/30/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND Whole-genome doubling (WGD) has been observed in 30% of cancers, followed by a highly complex rearranged karyotype unfavourable to breast cancer's outcome. However, the macro-alterations that characterise liver metastasis in breast cancer(BC) are poorly understood. Here, we conducted a whole-genome sequencing analysis of liver metastases to explore the status and the time frame model of these macro-alterations in pre-treatment patients with metastatic breast cancer. RESULTS Whole-genome sequencing was conducted in 11 paired primary tumours, lymph node metastasis, and liver metastasis fresh samples from four patients with late-stage breast cancer. We also chose five postoperative frozen specimens from patients with early-stage breast cancer before any treatment as control. Surprisingly, all four liver metastasis samples were classified as WGD + . However, the previous study reported that WGD happened in 30% of cancers and 2/5 in our early-stage samples. WGD was not observed in the two separate primary tumours and one lymph node metastasis of one patient with metastatic BC, but her liver metastasis showed an early burst of bi-allelic copy number gain. The phylogenetic tree proves her 4 tumour samples were the polyclonal origin and only one WGD + clone metastasis to the liver. Another 3 metastatic BC patients' primary tumour and lymph node metastasis experienced WGD as well as liver metastasis, and they all showed similar molecular time-frame of copy number(CN) gain across locations within the same patient. These patients' tumours were of monoclonal origin, and WGD happened in a founding clone before metastasis, explaining that all samples share the CN-gain time frame. After WGD, the genomes usually face instability to evolve other macro-alterations. For example, a greater quantity and variety of complex structural variations (SVs) were detected in WGD + samples. The breakpoints were enriched in the chr17: 39 Mb-40 Mb tile, which contained the HER2 gene, resulting in the formation of tyfonas, breakage-fusion-bridge cycles, and double minutes. These complex SVs may be involved in the evolutionary mechanisms of the dramatic increase of HER2 copy number. CONCLUSION Our work revealed that the WGD + clone might be a critical evolution step for liver metastasis and favoured following complex SV of breast cancer.
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Affiliation(s)
- Yu Fan
- Breast Center and Multi-Omics Laboratory of Breast Diseases, West China Hospital, Sichuan University, 5 Gongxing Street, Wuhou District, Chengdu, 610041, China
| | - Linglin Zou
- Breast Center and Multi-Omics Laboratory of Breast Diseases, West China Hospital, Sichuan University, 5 Gongxing Street, Wuhou District, Chengdu, 610041, China
| | - Xiaorong Zhong
- Breast Center and Multi-Omics Laboratory of Breast Diseases, West China Hospital, Sichuan University, 5 Gongxing Street, Wuhou District, Chengdu, 610041, China
| | - Zhu Wang
- Breast Center and Multi-Omics Laboratory of Breast Diseases, West China Hospital, Sichuan University, 5 Gongxing Street, Wuhou District, Chengdu, 610041, China
| | - Yu Wang
- Breast Center and Multi-Omics Laboratory of Breast Diseases, West China Hospital, Sichuan University, 5 Gongxing Street, Wuhou District, Chengdu, 610041, China
| | - Chuanxu Luo
- Breast Center and Multi-Omics Laboratory of Breast Diseases, West China Hospital, Sichuan University, 5 Gongxing Street, Wuhou District, Chengdu, 610041, China
| | - Hong Zheng
- Breast Center and Multi-Omics Laboratory of Breast Diseases, West China Hospital, Sichuan University, 5 Gongxing Street, Wuhou District, Chengdu, 610041, China.
| | - Yanping Wang
- Breast Center and Multi-Omics Laboratory of Breast Diseases, West China Hospital, Sichuan University, 5 Gongxing Street, Wuhou District, Chengdu, 610041, China.
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Kojima R, Nakamoto S, Kogure T, Ma Y, Ogawa K, Iwanaga T, Qiang N, Ao J, Nakagawa R, Muroyama R, Nakamura M, Chiba T, Kato J, Kato N. Re-analysis of hepatitis B virus integration sites reveals potential new loci associated with oncogenesis in hepatocellular carcinoma. World J Virol 2023; 12:209-220. [PMID: 37396703 PMCID: PMC10311580 DOI: 10.5501/wjv.v12.i3.209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/12/2023] [Accepted: 04/12/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND Hepatitis B virus (HBV) is a major cause of hepatocellular carcinoma (HCC). HBV DNA can get integrated into the hepatocyte genome to promote carcinogenesis. However, the precise mechanism by which the integrated HBV genome promotes HCC has not been elucidated. AIM To analyze the features of HBV integration in HCC using a new reference database and integration detection method. METHODS Published data, consisting of 426 Liver tumor samples and 426 paired adjacent non-tumor samples, were re-analyzed to identify the integration sites. Genome Reference Consortium Human Build 38 (GRCh38) and Telomere-to-Telomere Consortium CHM13 (T2T-CHM13 (v2.0)) were used as the human reference genomes. In contrast, human genome 19 (hg19) was used in the original study. In addition, GRIDSS VIRUSBreakend was used to detect HBV integration sites, whereas high-throughput viral integration detection (HIVID) was applied in the original study (HIVID-hg19). RESULTS A total of 5361 integration sites were detected using T2T-CHM13. In the tumor samples, integration hotspots in the cancer driver genes, such as TERT and KMT2B, were consistent with those in the original study. GRIDSS VIRUSBreakend detected integrations in more samples than by HIVID-hg19. Enrichment of integration was observed at chromosome 11q13.3, including the CCND1 pro-moter, in tumor samples. Recurrent integration sites were observed in mitochondrial genes. CONCLUSION GRIDSS VIRUSBreakend using T2T-CHM13 is accurate and sensitive in detecting HBV integration. Re-analysis provides new insights into the regions of HBV integration and their potential roles in HCC development.
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Affiliation(s)
- Ryuta Kojima
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Shingo Nakamoto
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Tadayoshi Kogure
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Yaojia Ma
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Keita Ogawa
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Terunao Iwanaga
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Na Qiang
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Junjie Ao
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Ryo Nakagawa
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Ryosuke Muroyama
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Masato Nakamura
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Tetsuhiro Chiba
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Jun Kato
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Naoya Kato
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
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Kosugi S, Kamatani Y, Harada K, Tomizuka K, Momozawa Y, Morisaki T, Terao C. Detection of trait-associated structural variations using short-read sequencing. CELL GENOMICS 2023; 3:100328. [PMID: 37388916 PMCID: PMC10300613 DOI: 10.1016/j.xgen.2023.100328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 02/17/2023] [Accepted: 04/25/2023] [Indexed: 07/01/2023]
Abstract
Genomic structural variation (SV) affects genetic and phenotypic characteristics in diverse organisms, but the lack of reliable methods to detect SV has hindered genetic analysis. We developed a computational algorithm (MOPline) that includes missing call recovery combined with high-confidence SV call selection and genotyping using short-read whole-genome sequencing (WGS) data. Using 3,672 high-coverage WGS datasets, MOPline stably detected ∼16,000 SVs per individual, which is over ∼1.7-3.3-fold higher than previous large-scale projects while exhibiting a comparable level of statistical quality metrics. We imputed SVs from 181,622 Japanese individuals for 42 diseases and 60 quantitative traits. A genome-wide association study with the imputed SVs revealed 41 top-ranked or nearly top-ranked genome-wide significant SVs, including 8 exonic SVs with 5 novel associations and enriched mobile element insertions. This study demonstrates that short-read WGS data can be used to identify rare and common SVs associated with a variety of traits.
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Affiliation(s)
- Shunichi Kosugi
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
| | - Yoichiro Kamatani
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Katsutoshi Harada
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Kohei Tomizuka
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan
| | - Takayuki Morisaki
- Division of Molecular Pathology, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan
| | | | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
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46
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Martínez-Jiménez F, Movasati A, Brunner SR, Nguyen L, Priestley P, Cuppen E, Van Hoeck A. Pan-cancer whole-genome comparison of primary and metastatic solid tumours. Nature 2023; 618:333-341. [PMID: 37165194 PMCID: PMC10247378 DOI: 10.1038/s41586-023-06054-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 04/05/2023] [Indexed: 05/12/2023]
Abstract
Metastatic cancer remains an almost inevitably lethal disease1-3. A better understanding of disease progression and response to therapies therefore remains of utmost importance. Here we characterize the genomic differences between early-stage untreated primary tumours and late-stage treated metastatic tumours using a harmonized pan-cancer analysis (or reanalysis) of two unpaired primary4 and metastatic5 cohorts of 7,108 whole-genome-sequenced tumours. Metastatic tumours in general have a lower intratumour heterogeneity and a conserved karyotype, displaying only a modest increase in mutations, although frequencies of structural variants are elevated overall. Furthermore, highly variable tumour-specific contributions of mutational footprints of endogenous (for example, SBS1 and APOBEC) and exogenous mutational processes (for example, platinum treatment) are present. The majority of cancer types had either moderate genomic differences (for example, lung adenocarcinoma) or highly consistent genomic portraits (for example, ovarian serous carcinoma) when comparing early-stage and late-stage disease. Breast, prostate, thyroid and kidney renal clear cell carcinomas and pancreatic neuroendocrine tumours are clear exceptions to the rule, displaying an extensive transformation of their genomic landscape in advanced stages. Exposure to treatment further scars the tumour genome and introduces an evolutionary bottleneck that selects for known therapy-resistant drivers in approximately half of treated patients. Our data showcase the potential of pan-cancer whole-genome analysis to identify distinctive features of late-stage tumours and provide a valuable resource to further investigate the biological basis of cancer and resistance to therapies.
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Affiliation(s)
- Francisco Martínez-Jiménez
- Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Hartwig Medical Foundation, Amsterdam, The Netherlands
| | - Ali Movasati
- Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sascha Remy Brunner
- Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Luan Nguyen
- Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
- Hartwig Medical Foundation Australia, Sydney, New South Wales, Australia
| | - Peter Priestley
- Hartwig Medical Foundation Australia, Sydney, New South Wales, Australia
| | - Edwin Cuppen
- Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands.
- Hartwig Medical Foundation, Amsterdam, The Netherlands.
| | - Arne Van Hoeck
- Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
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Lee JJK, Jung YL, Cheong TC, Espejo Valle-Inclan J, Chu C, Gulhan DC, Ljungström V, Jin H, Viswanadham VV, Watson EV, Cortés-Ciriano I, Elledge SJ, Chiarle R, Pellman D, Park PJ. ERα-associated translocations underlie oncogene amplifications in breast cancer. Nature 2023; 618:1024-1032. [PMID: 37198482 PMCID: PMC10307628 DOI: 10.1038/s41586-023-06057-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 04/05/2023] [Indexed: 05/19/2023]
Abstract
Focal copy-number amplification is an oncogenic event. Although recent studies have revealed the complex structure1-3 and the evolutionary trajectories4 of oncogene amplicons, their origin remains poorly understood. Here we show that focal amplifications in breast cancer frequently derive from a mechanism-which we term translocation-bridge amplification-involving inter-chromosomal translocations that lead to dicentric chromosome bridge formation and breakage. In 780 breast cancer genomes, we observe that focal amplifications are frequently connected to each other by inter-chromosomal translocations at their boundaries. Subsequent analysis indicates the following model: the oncogene neighbourhood is translocated in G1 creating a dicentric chromosome, the dicentric chromosome is replicated, and as dicentric sister chromosomes segregate during mitosis, a chromosome bridge is formed and then broken, with fragments often being circularized in extrachromosomal DNAs. This model explains the amplifications of key oncogenes, including ERBB2 and CCND1. Recurrent amplification boundaries and rearrangement hotspots correlate with oestrogen receptor binding in breast cancer cells. Experimentally, oestrogen treatment induces DNA double-strand breaks in the oestrogen receptor target regions that are repaired by translocations, suggesting a role of oestrogen in generating the initial translocations. A pan-cancer analysis reveals tissue-specific biases in mechanisms initiating focal amplifications, with the breakage-fusion-bridge cycle prevalent in some and the translocation-bridge amplification in others, probably owing to the different timing of DNA break repair. Our results identify a common mode of oncogene amplification and propose oestrogen as its mechanistic origin in breast cancer.
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Affiliation(s)
- Jake June-Koo Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Youngsook Lucy Jung
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Taek-Chin Cheong
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Chong Chu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Doga C Gulhan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Viktor Ljungström
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Hu Jin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Emma V Watson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Isidro Cortés-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Stephen J Elledge
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - David Pellman
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
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Jikuya R, Johnson TA, Maejima K, An J, Ju YS, Lee H, Ha K, Song W, Kim Y, Okawa Y, Sasagawa S, Kanazashi Y, Fujita M, Imoto S, Mitome T, Ohtake S, Noguchi G, Kawaura S, Iribe Y, Aomori K, Tatenuma T, Komeya M, Ito H, Ito Y, Muraoka K, Furuya M, Kato I, Fujii S, Hamanoue H, Tamura T, Baba M, Suda T, Kodama T, Makiyama K, Yao M, Shuch BM, Ricketts CJ, Schmidt LS, Linehan WM, Nakagawa H, Hasumi H. Comparative analyses define differences between BHD-associated renal tumour and sporadic chromophobe renal cell carcinoma. EBioMedicine 2023; 92:104596. [PMID: 37182269 PMCID: PMC10200853 DOI: 10.1016/j.ebiom.2023.104596] [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: 12/21/2022] [Revised: 03/21/2023] [Accepted: 04/18/2023] [Indexed: 05/16/2023] Open
Abstract
BACKGROUND Birt-Hogg-Dubé (BHD) syndrome, caused by germline alteration of folliculin (FLCN) gene, develops hybrid oncocytic/chromophobe tumour (HOCT) and chromophobe renal cell carcinoma (ChRCC), whereas sporadic ChRCC does not harbor FLCN alteration. To date, molecular characteristics of these similar histological types of tumours have been incompletely elucidated. METHODS To elucidate renal tumourigenesis of BHD-associated renal tumours and sporadic renal tumours, we conducted whole genome sequencing (WGS) and RNA-sequencing (RNA-seq) of sixteen BHD-associated renal tumours from nine unrelated BHD patients, twenty-one sporadic ChRCCs and seven sporadic oncocytomas. We then compared somatic mutation profiles with FLCN variants and RNA expression profiles between BHD-associated renal tumours and sporadic renal tumours. FINDINGS RNA-seq analysis revealed that BHD-associated renal tumours and sporadic renal tumours have totally different expression profiles. Sporadic ChRCCs were clustered into two distinct clusters characterized by L1CAM and FOXI1 expressions, molecular markers for renal tubule subclasses. Increased mitochondrial DNA (mtDNA) copy number with fewer variants was observed in BHD-associated renal tumours compared to sporadic ChRCCs. Cell-of-origin analysis using WGS data demonstrated that BHD-associated renal tumours and sporadic ChRCCs may arise from different cells of origin and second hit FLCN alterations may occur in early third decade of life in BHD patients. INTERPRETATION These data further our understanding of renal tumourigenesis of these two different types of renal tumours with similar histology. FUNDING This study was supported by JSPS KAKENHI Grants, RIKEN internal grant, and the Intramural Research Program of the National Institutes of Health (NIH), National Cancer Institute (NCI), Center for Cancer Research.
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Affiliation(s)
- Ryosuke Jikuya
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan; Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Todd A Johnson
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Jisong An
- Graduate School of Medical Science and Engineering (GSMSE), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Young-Seok Ju
- Graduate School of Medical Science and Engineering (GSMSE), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Hwajin Lee
- Biomedical Knowledge Engineering Laboratory, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kyungsik Ha
- UPPThera, Inc. BRC Laboratory 1-204 9, Songdomirae-ro, Yeonsu-gu, Incheon, Republic of Korea
| | - WooJeung Song
- UPPThera, Inc. BRC Laboratory 1-204 9, Songdomirae-ro, Yeonsu-gu, Incheon, Republic of Korea
| | - Youngwook Kim
- National Cancer Center Korea, 323 Ilsan-ro, Ilsandong-gu, Goyang-si Gyeonggi-do, Republic of Korea
| | - Yuki Okawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Shota Sasagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Yuki Kanazashi
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Masashi Fujita
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Seiya Imoto
- Human Genome Center, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan
| | - Taku Mitome
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Shinji Ohtake
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Go Noguchi
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Sachi Kawaura
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Yasuhiro Iribe
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Kota Aomori
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Tomoyuki Tatenuma
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Mitsuru Komeya
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Hiroki Ito
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Yusuke Ito
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Kentaro Muraoka
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Mitsuko Furuya
- Pathology Center, GeneticLab Co., Ltd., 28-196, N9, W15, Chuo-ku, Sapporo, 060-0009, Japan
| | - Ikuma Kato
- Department of Molecular Pathology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Satoshi Fujii
- Department of Molecular Pathology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Haruka Hamanoue
- Clinical Genetics Department, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, 236-0004, Japan
| | - Tomohiko Tamura
- Department of Immunology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan; Advanced Medical Research Center, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, 236-0004, Japan
| | - Masaya Baba
- Laboratory of Cancer Metabolism, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Toshio Suda
- Laboratory of Cancer Metabolism, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Tatsuhiko Kodama
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, 153-8904, Japan
| | - Kazuhide Makiyama
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Masahiro Yao
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Brian M Shuch
- Institute of Urologic Oncology, UCLA School of Medicine, Los Angeles, CA90095, USA
| | - Christopher J Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD20892, USA
| | - Laura S Schmidt
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD20892, USA; Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD20892, USA
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
| | - Hisashi Hasumi
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan.
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Dall G, Vandenberg CJ, Nesic K, Ratnayake G, Zhu W, Vissers JHA, Bedő J, Penington J, Wakefield MJ, Kee D, Carmagnac A, Lim R, Shield-Artin K, Milesi B, Lobley A, Kyran EL, O'Grady E, Tram J, Zhou W, Nugawela D, Stewart KP, Caldwell R, Papadopoulos L, Ng AP, Dobrovic A, Fox SB, McNally O, Power JD, Meniawy T, Tan TH, Collins IM, Klein O, Barnett S, Olesen I, Hamilton A, Hofmann O, Grimmond S, Papenfuss AT, Scott CL, Barker HE. Targeting homologous recombination deficiency in uterine leiomyosarcoma. J Exp Clin Cancer Res 2023; 42:112. [PMID: 37143137 PMCID: PMC10157936 DOI: 10.1186/s13046-023-02687-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/25/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Uterine leiomyosarcoma (uLMS) is a rare and aggressive gynaecological malignancy, with individuals with advanced uLMS having a five-year survival of < 10%. Mutations in the homologous recombination (HR) DNA repair pathway have been observed in ~ 10% of uLMS cases, with reports of some individuals benefiting from poly (ADP-ribose) polymerase (PARP) inhibitor (PARPi) therapy, which targets this DNA repair defect. In this report, we screened individuals with uLMS, accrued nationally, for mutations in the HR repair pathway and explored new approaches to therapeutic targeting. METHODS A cohort of 58 individuals with uLMS were screened for HR Deficiency (HRD) using whole genome sequencing (WGS), whole exome sequencing (WES) or NGS panel testing. Individuals identified to have HRD uLMS were offered PARPi therapy and clinical outcome details collected. Patient-derived xenografts (PDX) were generated for therapeutic targeting. RESULTS All 13 uLMS samples analysed by WGS had a dominant COSMIC mutational signature 3; 11 of these had high genome-wide loss of heterozygosity (LOH) (> 0.2) but only two samples had a CHORD score > 50%, one of which had a homozygous pathogenic alteration in an HR gene (deletion in BRCA2). A further three samples harboured homozygous HRD alterations (all deletions in BRCA2), detected by WES or panel sequencing, with 5/58 (9%) individuals having HRD uLMS. All five individuals gained access to PARPi therapy. Two of three individuals with mature clinical follow up achieved a complete response or durable partial response (PR) with the subsequent addition of platinum to PARPi upon minor progression during initial PR on PARPi. Corresponding PDX responses were most rapid, complete and sustained with the PARP1-specific PARPi, AZD5305, compared with either olaparib alone or olaparib plus cisplatin, even in a paired sample of a BRCA2-deleted PDX, derived following PARPi therapy in the patient, which had developed PARPi-resistance mutations in PRKDC, encoding DNA-PKcs. CONCLUSIONS Our work demonstrates the value of identifying HRD for therapeutic targeting by PARPi and platinum in individuals with the aggressive rare malignancy, uLMS and suggests that individuals with HRD uLMS should be included in trials of PARP1-specific PARPi.
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Affiliation(s)
- Genevieve Dall
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Cassandra J Vandenberg
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.
| | - Ksenija Nesic
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | | | - Wenying Zhu
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Joseph H A Vissers
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Justin Bedő
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- School of Computing and Information Systems, the University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jocelyn Penington
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Matthew J Wakefield
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Damien Kee
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia
- Austin Health, Heidelberg, VIC, 3084, Australia
- Australian Rare Cancer Portal, BioGrid Australia, Melbourne Health, Parkville, VIC, 3052, Australia
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
| | - Amandine Carmagnac
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Ratana Lim
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Kristy Shield-Artin
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Briony Milesi
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Royal Women's Hospital, Parkville, VIC, 3052, Australia
| | - Amanda Lobley
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Royal Women's Hospital, Parkville, VIC, 3052, Australia
| | - Elizabeth L Kyran
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Emily O'Grady
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Joshua Tram
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Warren Zhou
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Devindee Nugawela
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Kym Pham Stewart
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Reece Caldwell
- Australian Rare Cancer Portal, BioGrid Australia, Melbourne Health, Parkville, VIC, 3052, Australia
| | - Lia Papadopoulos
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Australian Rare Cancer Portal, BioGrid Australia, Melbourne Health, Parkville, VIC, 3052, Australia
| | - Ashley P Ng
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
- Royal Melbourne Hospital, Parkville, VIC, 3052, Australia
| | | | - Stephen B Fox
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
| | - Orla McNally
- Royal Women's Hospital, Parkville, VIC, 3052, Australia
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jeremy D Power
- Launceston General Hospital, Launceston, TAS, 7250, Australia
| | - Tarek Meniawy
- University of Western Australia, Perth, WA, 6009, Australia
| | - Teng Han Tan
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
| | - Ian M Collins
- SouthWest Healthcare, Warrnambool, VIC, 3280, Australia
- Faculty of Health, School of Medicine, Deakin University, Warrnambool, VIC, 3280, Australia
| | - Oliver Klein
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia
- Austin Health, Heidelberg, VIC, 3084, Australia
| | - Stephen Barnett
- Royal Melbourne Hospital, Parkville, VIC, 3052, Australia
- Western Hospital, Footscray, VIC, 3011, Australia
| | - Inger Olesen
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- University Hospital Geelong, Geelong, VIC, 3220, Australia
| | - Anne Hamilton
- Royal Women's Hospital, Parkville, VIC, 3052, Australia
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
| | - Oliver Hofmann
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Sean Grimmond
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Anthony T Papenfuss
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
| | - Clare L Scott
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
- Royal Women's Hospital, Parkville, VIC, 3052, Australia
- Australian Rare Cancer Portal, BioGrid Australia, Melbourne Health, Parkville, VIC, 3052, Australia
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
- Royal Melbourne Hospital, Parkville, VIC, 3052, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Holly E Barker
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
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50
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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.
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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.
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