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Lai J, Yang Y, Liu Y, Scharpf RB, Karchin R. Assessing the merits: an opinion on the effectiveness of simulation techniques in tumor subclonal reconstruction. BIOINFORMATICS ADVANCES 2024; 4:vbae094. [PMID: 38948008 PMCID: PMC11213631 DOI: 10.1093/bioadv/vbae094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/28/2024] [Accepted: 06/15/2024] [Indexed: 07/02/2024]
Abstract
Summary Neoplastic tumors originate from a single cell, and their evolution can be traced through lineages characterized by mutations, copy number alterations, and structural variants. These lineages are reconstructed and mapped onto evolutionary trees with algorithmic approaches. However, without ground truth benchmark sets, the validity of an algorithm remains uncertain, limiting potential clinical applicability. With a growing number of algorithms available, there is urgent need for standardized benchmark sets to evaluate their merits. Benchmark sets rely on in silico simulations of tumor sequence, but there are no accepted standards for simulation tools, presenting a major obstacle to progress in this field. Availability and implementation All analysis done in the paper was based on publicly available data from the publication of each accessed tool.
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Affiliation(s)
- Jiaying Lai
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Yi Yang
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Yunzhou Liu
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Robert B Scharpf
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, United States
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21231, United States
| | - Rachel Karchin
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, United States
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, United States
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21231, United States
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, United States
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Lai J, Liu Y, Scharpf RB, Karchin R. Evaluation of simulation methods for tumor subclonal reconstruction. ARXIV 2024:arXiv:2402.09599v1. [PMID: 38410652 PMCID: PMC10896360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Most neoplastic tumors originate from a single cell, and their evolution can be genetically traced through lineages characterized by common alterations such as small somatic mutations (SSMs), copy number alterations (CNAs), structural variants (SVs), and aneuploidies. Due to the complexity of these alterations in most tumors and the errors introduced by sequencing protocols and calling algorithms, tumor subclonal reconstruction algorithms are necessary to recapitulate the DNA sequence composition and tumor evolution in silico. With a growing number of these algorithms available, there is a pressing need for consistent and comprehensive benchmarking, which relies on realistic tumor sequencing generated by simulation tools. Here, we examine the current simulation methods, identifying their strengths and weaknesses, and provide recommendations for their improvement. Our review also explores potential new directions for research in this area. This work aims to serve as a resource for understanding and enhancing tumor genomic simulations, contributing to the advancement of the field.
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Affiliation(s)
- Jiaying Lai
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD
| | - Yunzhou Liu
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD
| | - Robert B. Scharpf
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Rachel Karchin
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD
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3
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Rastegar B, Andersson N, Petersson A, Karlsson J, Chattopadhyay S, Valind A, Jansson C, Durand G, Romerius P, Jirström K, Holmquist Mengelbier L, Gisselsson D. Resolving the Pathogenesis of Anaplastic Wilms Tumors through Spatial Mapping of Cancer Cell Evolution. Clin Cancer Res 2023; 29:2668-2677. [PMID: 37140929 PMCID: PMC10345961 DOI: 10.1158/1078-0432.ccr-23-0311] [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: 02/02/2023] [Revised: 03/31/2023] [Accepted: 05/02/2023] [Indexed: 05/05/2023]
Abstract
PURPOSE While patients with intermediate-risk (IR) Wilms tumors now have an overall survival (OS) rate of almost 90%, those affected by high-stage tumors with diffuse anaplasia have an OS of only around 50%. We here identify key events in the pathogenesis of diffuse anaplasia by mapping cancer cell evolution over anatomic space in Wilms tumors. EXPERIMENTAL DESIGN We spatially mapped subclonal landscapes in a retrospective cohort of 20 Wilms tumors using high-resolution copy-number profiling and TP53 mutation analysis followed by clonal deconvolution and phylogenetic reconstruction. Tumor whole-mount sections (WMS) were utilized to characterize the distribution of subclones across anatomically distinct tumor compartments. RESULTS Compared with non-diffuse anaplasia Wilms tumors, tumors with diffuse anaplasia showed a significantly higher number of genetically distinct tumor cell subpopulations and more complex phylogenetic trees, including high levels of phylogenetic species richness, divergence, and irregularity. All regions with classical anaplasia showed TP53 alterations. TP53 mutations were frequently followed by saltatory evolution and parallel loss of the remaining wild-type (WT) allele in different regions. Morphologic features of anaplasia increased with copy-number aberration (CNA) burden and regressive features. Compartments demarcated by fibrous septae or necrosis/regression were frequently (73%) associated with the emergence of new clonal CNAs, although clonal sweeps were rare within these compartments. CONCLUSIONS Wilms tumors with diffuse anaplasia display significantly more complex phylogenies compared with non-diffuse anaplasia Wilms tumors, including features of saltatory and parallel evolution. The subclonal landscape of individual tumors was constrained by anatomic compartments, which should be considered when sampling tissue for precision diagnostics.
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Affiliation(s)
- Bahar Rastegar
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Pediatrics, Skåne University Hospital, Lund, Sweden
| | - Natalie Andersson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Alexandra Petersson
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Jenny Karlsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Subhayan Chattopadhyay
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Anders Valind
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Pediatrics, Skåne University Hospital, Lund, Sweden
| | - Caroline Jansson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Geoffroy Durand
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Patrik Romerius
- Department of Pediatrics, Skåne University Hospital, Lund, Sweden
| | - Karin Jirström
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | | | - David Gisselsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
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Lu B, Curtius K, Graham TA, Yang Z, Barnes CP. CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples. Genome Biol 2023; 24:144. [PMID: 37340508 DOI: 10.1186/s13059-023-02983-0] [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: 03/24/2022] [Accepted: 06/08/2023] [Indexed: 06/22/2023] Open
Abstract
Phylogenetic trees based on copy number profiles from multiple samples of a patient are helpful to understand cancer evolution. Here, we develop a new maximum likelihood method, CNETML, to infer phylogenies from such data. CNETML is the first program to jointly infer the tree topology, node ages, and mutation rates from total copy numbers of longitudinal samples. Our extensive simulations suggest CNETML performs well on copy numbers relative to ploidy and under slight violation of model assumptions. The application of CNETML to real data generates results consistent with previous discoveries and provides novel early copy number events for further investigation.
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Affiliation(s)
- Bingxin Lu
- Department of Cell and Developmental Biology, University College London, London, UK.
- UCL Genetics Institute, University College London, London, UK.
| | - Kit Curtius
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Trevor A Graham
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Chris P Barnes
- Department of Cell and Developmental Biology, University College London, London, UK.
- UCL Genetics Institute, University College London, London, UK.
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Evolutionary route of nasopharyngeal carcinoma metastasis and its clinical significance. Nat Commun 2023; 14:610. [PMID: 36739462 PMCID: PMC9899247 DOI: 10.1038/s41467-023-35995-2] [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: 08/30/2021] [Accepted: 01/04/2023] [Indexed: 02/06/2023] Open
Abstract
It is critical to understand factors associated with nasopharyngeal carcinoma (NPC) metastasis. To track the evolutionary route of metastasis, here we perform an integrative genomic analysis of 163 matched blood and primary, regional lymph node metastasis and distant metastasis tumour samples, combined with single-cell RNA-seq on 11 samples from two patients. The mutation burden, gene mutation frequency, mutation signature, and copy number frequency are similar between metastatic tumours and primary and regional lymph node tumours. There are two distinct evolutionary routes of metastasis, including metastases evolved from regional lymph nodes (lymphatic route, 61.5%, 8/13) and from primary tumours (hematogenous route, 38.5%, 5/13). The hematogenous route is characterised by higher IFN-γ response gene expression and a higher fraction of exhausted CD8+ T cells. Based on a radiomics model, we find that the hematogenous group has significantly better progression-free survival and PD-1 immunotherapy response, while the lymphatic group has a better response to locoregional radiotherapy.
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Mañas A, Aaltonen K, Andersson N, Hansson K, Adamska A, Seger A, Yasui H, van den Bos H, Radke K, Esfandyari J, Bhave MS, Karlsson J, Spierings D, Foijer F, Gisselsson D, Bexell D. Clinically relevant treatment of PDX models reveals patterns of neuroblastoma chemoresistance. SCIENCE ADVANCES 2022; 8:eabq4617. [PMID: 36306349 PMCID: PMC9616506 DOI: 10.1126/sciadv.abq4617] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Chemotherapy resistance and relapses are common in high-risk neuroblastoma (NB). Here, we developed a clinically relevant in vivo treatment protocol mimicking the first-line five-chemotherapy treatment regimen of high-risk NB and applied this protocol to mice with MYCN-amplified NB patient-derived xenografts (PDXs). Genomic and transcriptomic analyses were used to reveal NB chemoresistance mechanisms. Intrinsic resistance was associated with high genetic diversity and an embryonic phenotype. Relapsed NB with acquired resistance showed a decreased adrenergic phenotype and an enhanced immature mesenchymal-like phenotype, resembling multipotent Schwann cell precursors. NBs with a favorable treatment response presented a lineage-committed adrenergic phenotype similar to normal neuroblasts. Novel integrated phenotypic gene signatures reflected treatment response and patient prognosis. NB organoids established from relapsed PDX tumors retained drug resistance, tumorigenicity, and transcriptional cell states. This work sheds light on the mechanisms of NB chemotherapy response and emphasizes the importance of transcriptional cell states in chemoresistance.
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Affiliation(s)
- Adriana Mañas
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund 22381, Sweden
| | - Kristina Aaltonen
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund 22381, Sweden
| | - Natalie Andersson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund 22185, Sweden
| | - Karin Hansson
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund 22381, Sweden
- Cancer Stem Cell Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Aleksandra Adamska
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund 22381, Sweden
| | - Alexandra Seger
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund 22381, Sweden
| | - Hiroaki Yasui
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund 22185, Sweden
- Department of Gynecologic Oncology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Hilda van den Bos
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, AV, Groningen 9713, Netherlands
| | - Katarzyna Radke
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund 22381, Sweden
| | - Javanshir Esfandyari
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund 22381, Sweden
| | - Madhura Satish Bhave
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund 22381, Sweden
| | - Jenny Karlsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund 22185, Sweden
| | - Diana Spierings
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, AV, Groningen 9713, Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, AV, Groningen 9713, Netherlands
| | - David Gisselsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund 22185, Sweden
- Department of Pathology, Laboratory Medicine, Skane University Hospital, Lund 22184, Sweden
| | - Daniel Bexell
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund 22381, Sweden
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Petersson A, Andersson N, Hau SO, Eberhard J, Karlsson J, Chattopadhyay S, Valind A, Elebro J, Nodin B, Leandersson K, Gisselsson D, Jirström K. Branching Copy-Number Evolution and Parallel Immune Profiles across the Regional Tumor Space of Resected Pancreatic Cancer. Mol Cancer Res 2022; 20:749-761. [PMID: 35149544 PMCID: PMC9381114 DOI: 10.1158/1541-7786.mcr-21-0986] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/05/2022] [Accepted: 02/04/2022] [Indexed: 01/07/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) remains a highly lethal disease. The only option for curative treatment is resection of the tumor followed by standard adjuvant chemotherapy. Yet, early relapse due to chemoresistance is almost inevitable. Herein, we delineated the genetic intratumor heterogeneity in resected PDAC, with the aim to identify evolutionary patterns that may be associated with overall survival (OS) following treatment with curative intent. Potential relationships with the adjacent immune microenvironment were also examined. The genetic and immune landscapes of the regional tumor space were analyzed in nine patients with resected PDAC. Targeted deep sequencing and genome wide SNP array were followed by clonal deconvolution and phylogenetic analysis. A mathematical complexity score was developed to calculate the network extent of each phylogeny. Spatial variation in abundancy and tumor nest infiltration of immune cells was analyzed by double IHC staining. Copy-number heterogeneity was denoted as the major contributing factor to the branching architectures of the produced phylogenetic trees. Increased tree complexity was significantly inversely associated with OS, and larger regional maximum aberrations (higher treetops) were associated with increased PD-L1 expression on tumor cells. Contrastingly, an FREM1 gene amplification, found in one patient, coincided with a particularly vigorous immune response. Findings from this limited case series suggest that complex evolutionary patterns may be associated with a shorter survival in surgically treated patients with PDAC. Some hypothesis-generating associations with the surrounding immune microenvironment were also detected. IMPLICATIONS Evolutionary copy-number patterns may be associated with survival in patients with resected PDAC.
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Affiliation(s)
- Alexandra Petersson
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Natalie Andersson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Sofie Olsson Hau
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Jakob Eberhard
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Jenny Karlsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Subhayan Chattopadhyay
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Anders Valind
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Pediatrics, Skåne University Hospital, Lund, Sweden
| | - Jacob Elebro
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Björn Nodin
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Karin Leandersson
- Cancer Immunology, Department of Translational Medicine, Lund University, Malmö, Sweden
| | - David Gisselsson
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Karin Jirström
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
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