Evolution of late-stage metastatic melanoma is dominated by aneuploidy and whole genome doubling

AbstractAlthough melanoma is initiated by acquisition of point mutations and limited focal copy number alterations in melanocytes-of-origin, the nature of genetic changes that characterise lethal metastatic disease is poorly understood. Here, we analyze the evolution of human melanoma progressing from early to late disease in 13 patients by sampling their tumours at multiple sites and times. Whole exome and genome sequencing data from 88 tumour samples reveals only limited gain of point mutations generally, with net mutational loss in some metastases. In contrast, melanoma evolution is dominated by whole genome doubling and large-scale aneuploidy, in which widespread loss of heterozygosity sculpts the burden of point mutations, neoantigens and structural variants even in treatment-naïve and primary cutaneous melanomas in some patients. These results imply that dysregulation of genomic integrity is a key driver of selective clonal advantage during melanoma progression.

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High prevalence of TP53 loss and whole-genome doubling in early-onset colorectal cancer

Experimental & Molecular Medicine ◽

10.1038/s12276-021-00583-1 ◽

2021 ◽

Author(s):

Jeong Eun Kim ◽

Jaeyong Choi ◽

Chang-Ohk Sung ◽

Yong Sang Hong ◽

Sun Young Kim ◽

...

Keyword(s):

Colorectal Cancer ◽

Early Onset ◽

Large Scale ◽

Late Onset ◽

Age Groups ◽

The Cancer Genome Atlas ◽

Whole Genome ◽

Genome Doubling ◽

Whole Genome Doubling ◽

Early Onset Colorectal Cancer

AbstractThe global incidence of early-onset colorectal cancer (EO-CRC) is rapidly rising. However, the reason for this rise in incidence as well as the genomic characteristics of EO-CRC remain largely unknown. We performed whole-exome sequencing in 47 cases of EO-CRC and targeted deep sequencing in 833 cases of CRC. Mutational profiles of EO-CRC were compared with previously published large-scale studies. EO-CRC and The Cancer Genome Atlas (TCGA) data were further investigated according to copy number profiles and mutation timing. We classified colorectal cancer into three subgroups: the hypermutated group consisted of mutations in POLE and mismatch repair genes; the whole-genome doubling group had early functional loss of TP53 that led to whole-genome doubling and focal oncogene amplification; the genome-stable group had mutations in APC and KRAS, similar to conventional colon cancer. Among non-hypermutated samples, whole-genome doubling was more prevalent in early-onset than in late-onset disease (54% vs 38%, Fisher’s exact P = 0.04). More than half of non-hypermutated EO-CRC cases involved early TP53 mutation and whole-genome doubling, which led to notable differences in mutation frequencies between age groups. Alternative carcinogenesis involving genomic instability via loss of TP53 may be related to the rise in EO-CRC.

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Whole genome doubling confers unique genetic vulnerabilities on tumor cells

10.1101/2020.06.18.159095 ◽

2020 ◽

Cited By ~ 1

Author(s):

Ryan J. Quinton ◽

Amanda DiDomizio ◽

Marc A. Vittoria ◽

Carlos J. Ticas ◽

Sheena Patel ◽

...

Keyword(s):

Spindle Assembly Checkpoint ◽

Human Cancer ◽

Tumor Development ◽

Whole Genome ◽

Sequencing Data ◽

Genetic Traits ◽

Checkpoint Signaling ◽

Genome Doubling ◽

Whole Genome Doubling ◽

Replication Factors

SummaryWhole genome doubling (WGD) occurs early in tumorigenesis and generates genetically unstable tetraploid cells that fuel tumor development. Cells that undergo WGD (WGD+) must adapt to accommodate their abnormal tetraploid state; however, the nature of these adaptations, and whether they confer vulnerabilities that can subsequently be exploited therapeutically, is unclear. Using sequencing data from ∼10,000 primary human cancer samples and essentiality data from ∼600 cancer cell lines, we show that WGD gives rise to common genetic traits that are accompanied by unique vulnerabilities. We reveal that WGD+ cells are more dependent on spindle assembly checkpoint signaling, DNA replication factors, and proteasome function than WGD− cells. We also identify KIF18A, which encodes for a mitotic kinesin, as being specifically required for the viability of WGD+ cells. While loss of KIF18A is largely dispensable for accurate chromosome segregation during mitosis in WGD− cells, its loss induces dramatic mitotic errors in WGD+ cells, ultimately impairing cell viability. Collectively, our results reveal new strategies to specifically target WGD+ cancer cells while sparing the normal, non-transformed WGD− cells that comprise human tissue.

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Plasmids or no plasmids? A comparison between the agilent TapeStation and whole-genome sequencing data in a large-scale bacterial sequencing project

10.26226/morressier.56d5ba27d462b80296c95fe7 ◽

2016 ◽

Author(s):

Sarah Alexander

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Large Scale ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data ◽

Sequencing Project

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Whole-Genome Doubling Affects Pre-miRNA Expression in Plants

Plants ◽

10.3390/plants10051004 ◽

2021 ◽

Vol 10 (5) ◽

pp. 1004

Author(s):

Salvatore Esposito ◽

Riccardo Aversano ◽

Pasquale Tripodi ◽

Domenico Carputo

Keyword(s):

Dna Repair ◽

Mirna Expression ◽

Building Blocks ◽

Nucleotide Metabolism ◽

Integrative Approach ◽

Whole Genome ◽

Solanum Commersonii ◽

Genome Doubling ◽

Whole Genome Doubling ◽

Micro Rnas

Whole-genome doubling (polyploidy) is common in angiosperms. Several studies have indicated that it is often associated with molecular, physiological, and phenotypic changes. Mounting evidence has pointed out that micro-RNAs (miRNAs) may have an important role in whole-genome doubling. However, an integrative approach that compares miRNA expression in polyploids is still lacking. Here, a re-analysis of already published RNAseq datasets was performed to identify microRNAs’ precursors (pre-miRNAs) in diploids (2x) and tetraploids (4x) of five species (Arabidopsis thaliana L., Morus alba L., Brassica rapa L., Isatis indigotica Fort., and Solanum commersonii Dun). We found 3568 pre-miRNAs, three of which (pre-miR414, pre-miR5538, and pre-miR5141) were abundant in all 2x, and were absent/low in their 4x counterparts. They are predicted to target more than one mRNA transcript, many belonging to transcription factors (TFs), DNA repair mechanisms, and related to stress. Sixteen pre-miRNAs were found in common in all 2x and 4x. Among them, pre-miRNA482, pre-miRNA2916, and pre-miRNA167 changed their expression after polyploidization, being induced or repressed in 4x plants. Based on our results, a common ploidy-dependent response was triggered in all species under investigation, which involves DNA repair, ATP-synthesis, terpenoid biosynthesis, and several stress-responsive transcripts. In addition, an ad hoc pre-miRNA expression analysis carried out solely on 2x vs. 4x samples of S. commersonii indicated that ploidy-dependent pre-miRNAs seem to actively regulate the nucleotide metabolism, probably to cope with the increased requirement for DNA building blocks caused by the augmented DNA content. Overall, the results outline the critical role of microRNA-mediated responses following autopolyploidization in plants.

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Estimating sequencing error rates using families

BioData Mining ◽

10.1186/s13040-021-00259-6 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Kelley Paskov ◽

Jae-Yoon Jung ◽

Brianna Chrisman ◽

Nate T. Stockham ◽

Peter Washington ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Exome Sequencing ◽

Genome Sequencing ◽

Variant Calling ◽

Error Rates ◽

Sequencing Error ◽

Whole Genome ◽

Sequencing Data ◽

Sequencing Platform ◽

Whole Exome

Abstract Background As next-generation sequencing technologies make their way into the clinic, knowledge of their error rates is essential if they are to be used to guide patient care. However, sequencing platforms and variant-calling pipelines are continuously evolving, making it difficult to accurately quantify error rates for the particular combination of assay and software parameters used on each sample. Family data provide a unique opportunity for estimating sequencing error rates since it allows us to observe a fraction of sequencing errors as Mendelian errors in the family, which we can then use to produce genome-wide error estimates for each sample. Results We introduce a method that uses Mendelian errors in sequencing data to make highly granular per-sample estimates of precision and recall for any set of variant calls, regardless of sequencing platform or calling methodology. We validate the accuracy of our estimates using monozygotic twins, and we use a set of monozygotic quadruplets to show that our predictions closely match the consensus method. We demonstrate our method’s versatility by estimating sequencing error rates for whole genome sequencing, whole exome sequencing, and microarray datasets, and we highlight its sensitivity by quantifying performance increases between different versions of the GATK variant-calling pipeline. We then use our method to demonstrate that: 1) Sequencing error rates between samples in the same dataset can vary by over an order of magnitude. 2) Variant calling performance decreases substantially in low-complexity regions of the genome. 3) Variant calling performance in whole exome sequencing data decreases with distance from the nearest target region. 4) Variant calls from lymphoblastoid cell lines can be as accurate as those from whole blood. 5) Whole-genome sequencing can attain microarray-level precision and recall at disease-associated SNV sites. Conclusion Genotype datasets from families are powerful resources that can be used to make fine-grained estimates of sequencing error for any sequencing platform and variant-calling methodology.

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Preoperative clinical and tumor genomic features associated with pathologic lymph node metastasis in clinical stage I and II lung adenocarcinoma

npj Precision Oncology ◽

10.1038/s41698-021-00210-2 ◽

2021 ◽

Vol 5 (1) ◽

Author(s):

Raul Caso ◽

James G. Connolly ◽

Jian Zhou ◽

Kay See Tan ◽

James J. Choi ◽

...

Keyword(s):

Lung Adenocarcinoma ◽

Clinical Stage ◽

Multivariable Analysis ◽

Multivariable Logistic Regression Model ◽

Genomic Features ◽

Genome Doubling ◽

Whole Genome Doubling ◽

Metastatic Lung ◽

Treatment Naïve ◽

Patients At Risk

AbstractWhile next-generation sequencing (NGS) is used to guide therapy in patients with metastatic lung adenocarcinoma (LUAD), use of NGS to determine pathologic LN metastasis prior to surgery has not been assessed. To bridge this knowledge gap, we performed NGS using MSK-IMPACT in 426 treatment-naive patients with clinical N2-negative LUAD. A multivariable logistic regression model that considered preoperative clinical and genomic variables was constructed. Most patients had cN0 disease (85%) with pN0, pN1, and pN2 rates of 80%, 11%, and 9%, respectively. Genes altered at higher rates in pN-positive than in pN-negative tumors were STK11 (p = 0.024), SMARCA4 (p = 0.006), and SMAD4 (p = 0.011). Fraction of genome altered (p = 0.037), copy number amplifications (p = 0.001), and whole-genome doubling (p = 0.028) were higher in pN-positive tumors. Multivariable analysis revealed solid tumor morphology, tumor SUVmax, clinical stage, SMARCA4 and SMAD4 alterations were independently associated with pathologic LN metastasis. Incorporation of clinical and tumor genomic features can identify patients at risk of pathologic LN metastasis; this may guide therapy decisions before surgical resection.

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Origin, Conservation, and Loss of Alternative Splicing Events that Diversify the Proteome in Saccharomycotina Budding Yeasts

10.1101/2020.04.13.039594 ◽

2020 ◽

Author(s):

Jennifer E. Hurtig ◽

Minseon Kim ◽

Luisa J. Orlando-Coronel ◽

Jellisa Ewan ◽

Michelle Foreman ◽

...

Keyword(s):

Alternative Splicing ◽

Low Frequency ◽

Common Mechanism ◽

Duplicate Genes ◽

Whole Genome ◽

Genome Doubling ◽

Whole Genome Doubling ◽

Functional Consequences ◽

Alternatively Spliced ◽

Mammalian Genes

AbstractMany eukaryotes use alternative splicing to express multiple proteins from the same gene. However, while the majority of mammalian genes are alternatively spliced, other eukaryotes use this process less frequently. The budding yeast Saccharomyces cerevisiae has been successfully used to study the mechanism of splicing and the splicing machinery, but alternative splicing in yeast is relatively rare and has not been extensively studied. We have recently shown that the alternative splicing of SKI7/HBS1 is widely conserved, but that yeast and a few other eukaryotes have replaced this one alternatively spliced gene with a pair of duplicated unspliced genes as part of a whole genome doubling (WGD). Here we show that other examples of alternative splicing that were previously found to have functional consequences are widely conserved within the Saccharomycotina. We also show that the most common mechanism by which alternative splicing has disappeared is by the replacement of an alternatively spliced gene with duplicate genes. Saccharomycetaceae that diverged before WGD use alternative splicing more frequently than S. cerevisiae. This suggests that the WGD is a major reason for the low frequency of alternative splicing in yeast. We anticipate that whole genome doublings in other lineages may have had the same effect.

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Loss of USP28 and SPINT2 expression promotes cancer cell survival after whole genome doubling

Cellular Oncology ◽

10.1007/s13402-021-00654-5 ◽

2021 ◽

Author(s):

Sara Vanessa Bernhard ◽

Katarzyna Seget-Trzensiok ◽

Christian Kuffer ◽

Dragomir B. Krastev ◽

Lisa-Marie Stautmeister ◽

...

Keyword(s):

Cell Cycle ◽

Dna Damage ◽

Cancer Cell ◽

Cancer Cell Line ◽

Colorectal Cancer Cell Line ◽

Whole Genome ◽

Cancer Evolution ◽

Genome Doubling ◽

Whole Genome Doubling ◽

Frequent Event

Abstract Background Whole genome doubling is a frequent event during cancer evolution and shapes the cancer genome due to the occurrence of chromosomal instability. Yet, erroneously arising human tetraploid cells usually do not proliferate due to p53 activation that leads to CDKN1A expression, cell cycle arrest, senescence and/or apoptosis. Methods To uncover the barriers that block the proliferation of tetraploids, we performed a RNAi mediated genome-wide screen in a human colorectal cancer cell line (HCT116). Results We identified 140 genes whose depletion improved the survival of tetraploid cells and characterized in depth two of them: SPINT2 and USP28. We found that SPINT2 is a general regulator of CDKN1A transcription via histone acetylation. Using mass spectrometry and immunoprecipitation, we found that USP28 interacts with NuMA1 and affects centrosome clustering. Tetraploid cells accumulate DNA damage and loss of USP28 reduces checkpoint activation, thus facilitating their proliferation. Conclusions Our results indicate three aspects that contribute to the survival of tetraploid cells: (i) increased mitogenic signaling and reduced expression of cell cycle inhibitors, (ii) the ability to establish functional bipolar spindles and (iii) reduced DNA damage signaling.

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Excision Dominates Pseudogenization During Fractionation After Whole Genome Duplication and in Gene Loss After Speciation in Plants

Frontiers in Genetics ◽

10.3389/fgene.2020.603056 ◽

2020 ◽

Vol 11 ◽

Author(s):

Zhe Yu ◽

Chunfang Zheng ◽

Victor A. Albert ◽

David Sankoff

Keyword(s):

Whole Genome Duplication ◽

Gene Loss ◽

Genome Duplication ◽

Duplicate Genes ◽

Whole Genome ◽

Coding Sequence ◽

Genome Doubling ◽

Whole Genome Doubling ◽

Synteny Blocks ◽

Genomic Divergence

We take advantage of synteny blocks, the analytical construct enabled at the evolutionary moment of speciation or polyploidization, to follow the independent loss of duplicate genes in two sister species or the loss through fractionation of syntenic paralogs in a doubled genome. By examining how much sequence remains after a contiguous series of genes is deleted, we find that this residue remains at a constant low level independent of how many genes are lost—there are few if any relics of the missing sequence. Pseudogenes are rare or extremely transient in this context. The potential exceptions lie exclusively with a few examples of speciation, where the synteny blocks in some larger genomes tolerate degenerate sequence during genomic divergence of two species, but not after whole genome doubling in the same species where fractionation pressure eliminates virtually all non-coding sequence.

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SECNVs: A Simulator of Copy Number Variants and Whole-Exome Sequences from Reference Genomes

10.1101/824128 ◽

2019 ◽

Cited By ~ 1

Author(s):

Yue Xing ◽

Alan R. Dabney ◽

Xiao Li ◽

Guosong Wang ◽

Clare A. Gill ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Copy Number ◽

Copy Number Variants ◽

Whole Genome ◽

Sequencing Data ◽

Software Applications ◽

Exome Sequencing Data ◽

Whole Exome ◽

Whole Exome Sequencing Data

AbstractCopy number variants are insertions and deletions of 1 kb or larger in a genome that play an important role in phenotypic changes and human disease. Many software applications have been developed to detect copy number variants using either whole-genome sequencing or whole-exome sequencing data. However, there is poor agreement in the results from these applications. Simulated datasets containing copy number variants allow comprehensive comparisons of the operating characteristics of existing and novel copy number variant detection methods. Several software applications have been developed to simulate copy number variants and other structural variants in whole-genome sequencing data. However, none of the applications reliably simulate copy number variants in whole-exome sequencing data. We have developed and tested SECNVs (Simulator of Exome Copy Number Variants), a fast, robust and customizable software application for simulating copy number variants and whole-exome sequences from a reference genome. SECNVs is easy to install, implements a wide range of commands to customize simulations, can output multiple samples at once, and incorporates a pipeline to output rearranged genomes, short reads and BAM files in a single command. Variants generated by SECNVs are detected with high sensitivity and precision by tools commonly used to detect copy number variants. SECNVs is publicly available at https://github.com/YJulyXing/SECNVs.

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