Genome Doubling Research Articles

The oscillation of mitotic kinase governs cell cycle latches in mammalian cells.

The mammalian cell cycle alternates between two phases - S-G2-M with high levels of A- and B-type cyclins (CycA and CycB, respectively) bound to cyclin-dependent kinases (CDKs), and G1 with persistent degradation of CycA and CycB by an activated anaphase promoting complex/cyclosome (APC/C) bound to Cdh1 (also known as FZR1 in mammals; denoted APC/C:Cdh1). Because CDKs phosphorylate and inactivate Cdh1, these two phases are mutually exclusive. This 'toggle switch' is flipped from G1 to S by cyclin-E bound to a CDK (CycE:CDK), which is not degraded by APC/C:Cdh1, and from M to G1 by Cdc20-bound APC/C (APC/C:Cdc20), which is not inactivated by CycA:CDK or CycB:CDK. After flipping the switch, cyclin E is degraded and APC/C:Cdc20 is inactivated. Combining mathematical modelling with single-cell timelapse imaging, we show that dysregulation of CycB:CDK disrupts strict alternation of the G1-S and M-G1 switches. Inhibition of CycB:CDK results in Cdc20-independent Cdh1 'endocycles', and sustained activity of CycB:CDK drives Cdh1-independent Cdc20 endocycles. Our model provides a mechanistic explanation for how whole-genome doubling can arise, a common event in tumorigenesis that can drive tumour evolution.

Abstract B002: Profiling intra-tumor heterogeneity and chromosomal instability in malignant peripheral nerve sheath tumors

Abstract Malignant peripheral nerve sheath tumors (MPNSTs) are rare soft-tissue sarcomas that manifest on peripheral nerves, constituting 2% of all sarcomas. They arise both sporadically and in 8% to 13% of individuals with neurofibromatosis type 1 (NF1), where they represent the major cause of morbidity and mortality. While previous genomic analyses of MPNSTs have been conducted on small cohorts, often limited to single samples per patient and lacking comprehensive resolution, the extent of intra-tumor heterogeneity and the contribution of chromosomal instability to MPNST development remain unclear. To address these limitations, we developed a multi-omics integration pipeline and applied it to integrate bulk Next Generation Sequencing (NGS), single-cell RNA sequencing, single-cell DNA sequencing, spatial transcriptomics (ST), and Laser Capture Microsection (LCM) information. 35 tumor samples were collected from 10 patients with MPNST, and for each sample, data were generated using the above five techniques. Overall, we detected copy-number aberrations recurrently found in MPNSTs, including events such as loss of heterozygosity (LOH), whole genome doubling (WGD) and chromosome 7 and 8 amplifications. Subclonal copy number alterations were called by the Battenberg algorithm, followed by SNV clustering using Dirichlet Process-based methods. Applying the pigeonhole principle, we constructed tumor phylogenetic trees. Intriguingly, our findings indicate that for patient 2.3, primary tumor samples PT_1 and PT_2 displayed a close phylogenetic relationship, while local recurrences LR_2 and LR_3 represent a different branch of the phylogenetic tree. Following stringent quality control and cell type annotation, we leveraged normal cells identified within the snRNA data as controls to infer copy number changes in tumor cells through inferCNV. Notably, in patient 2.16, we identified significant copy number gains on chromosomes 5, 7, 8, and 15. Comparing the inferred copy number changes derived from snRNA with those obtained through Battenberg copy number profiles showed a remarkable congruence, thereby reinforcing the robustness of our results. To reveal communication networks among tumor microenvironment (TME) cells, we used iTalk to visualize ligand-receptor interactions between distinct cell types. For Patient 2.3, macrophages emerged as key players, releasing cytokines such as IL-16 and IL-18, which exerted their influence on receptors in tumor cells. Additionally, T cells engaged in checkpoint factors, including TNFSF4 and CD28, interacting with receptors on tumor cells, such as TRAF2 and LGALS9. Our research revealed that MPNSTs are primarily driven by chromosomal instability and intra-tumor heterogeneity is shaped by TME interactions. We enhanced our understanding of the tumors' evolutionary histories and intra-tumor heterogeneity down to single-cell resolution. By shedding light on the genomic landscape of MPNSTs, we aspire to make profound contributions to the field of sarcoma research, ultimately improving patient outcomes. Citation Format: Yixiao Cheng, Haixi Yan, Maxime Tarabichi, Zhihui Zhang, Chunxu Gao, Tom Lesluyes, Adrienne Flanagan, Peter Van Loo. Profiling intra-tumor heterogeneity and chromosomal instability in malignant peripheral nerve sheath tumors [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr B002.

Abstract IA004: Insights into lung cancer evolution and metastases in TRACERx and PEACE

Abstract TRACERx is a prospective longitudinal cancer evolution programme which investigates the relationship between intratumour heterogeneity and clinical outcomes in non-small cell lung cancer (NSCLC). In an interim cohort of 421 patients with extended follow up, matched primary and metastatic tumour analysis has demonstrated the impact of cancer evolution on patient outcomes. Large dominant subclones in primary tumours were associated with positive subclonal selection, and mutations in specific genes were found to be under significant subclonal, and not clonal, selection. Subclonal genome doubling was identified in 20% of tumours and multiple genome doubling events were identified in 10% of tumours. Patients with tumours containing large recent subclonal expansions had significantly shorter disease-free survival (DFS), and as previously demonstrated, chromosomal instability was associated with poor outcomes, in particular, extrathoracic disease relapse. Metastatic relapse was found to occur late in tumour evolution in 75% of tumours, and early divergence (25% of tumours) was found to occur at predicted tumour volumes below the threshold for further investigation using radiological imaging, suggesting potential implications for clinical intervention. Metastasis-seeding subclones in primary tumours were subject to subclonal expansion, likely reflective of the acquisition of subclonal driver mutations and somatic copy number alterations. ctDNA analyses in this larger cohort demonstrated the value of ctDNA to predict the likelihood of future relapse, but also its use in tracking tumour growth dynamics and emergence of relapse. Patients who develop relapsed disease in TRACERx after surgery are co-recruited into PEACE, a national research autopsy programme. Early findings from PEACE have demonstrated the genomic complexity of cancer relapse and metastatic heterogeneity and the different patterns of cellular migration that aid metastatic dissemination with both primary-to-metastasis and metastasis-to-metastasis seeding. Citation Format: Mariam Jamal-Hanjani. Insights into lung cancer evolution and metastases in TRACERx and PEACE [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr IA004.

Abstract IA001: Molecular archeology of cancer

Abstract Tumor development is driven by changes to the genome and epigenome leading to fitness advantages underlying successive clonal expansions. As somatic genetic and epigenetic changes occur across most or all cell cycles, the cancer (epi)genome carries an archeological record of its past. Over the past years, we have developed several approaches to mine that archeological record from the cancer genome, which we collectively call 'molecular archeology of cancer'. Using these approaches, we are able to infer the subclonal architecture of tumors, and gain key insights into the order and timing of the genomic changes that occurred over their evolutionary history. We have applied these approaches in a large-scale pan-cancer setting, showing that intra-tumor heterogeneity is pervasive across cancers and that the timelines of tumor evolution span multiple years to decades. Key driver events in tumor evolution typically occur early, and copy number gains often accumulate as punctuated bursts, commonly after genome doubling. Late genome doubling is frequent in cancer evolution and is typically followed by an increase in the rate of copy number gains. Genome duplications affect the selection landscape of copy number losses, while only minimally impacting copy number gains. We have recently also started to develop methods that leverage the cancer epigenome to reconstruct the subclonal architecture of cancer, which will open up new avenues to study tumor evolution. Citation Format: Peter Van Loo. Molecular archeology of cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr IA001.

Abstract PR018: Adaptive local fitness landscapes for aneuploid karyotypes

Abstract Aneuploidy, which occurs in most solid tumors, dramatically alters the expression of many genes which in turn has broad phenotypic effects. Recent evidence suggests that specific aneuploid karyotypes confer a selective advantage. However, various questions remain unanswered regarding the magnitude of these selective advantages, as well as the repeatability and predictability of karyotype evolution. We developed ALFA-K (Adaptive Local Fitness landscapes for Aneuploid Karotypes) – the first approach to infer karyotype fitness landscapes in a context-dependent manner. Based on the dynamics of just a few subclones derived from longitudinal single cell sequencing data, our method can extrapolate the fitness of thousands of karyotypes. We validate the predictive power of our method on data from several P53 deficient cell lines which exhibited substantial subclonal evolution across multiple passages in vivo or in vitro. Based on topological analyses of the inferred fitness landscapes we investigated how mis-segregation rate itself shapes the stringency of karyotype evolution and whether karyotype evolution is subject to diminishing returns epistasis, sign epistasis or reciprocal sign epistasis. We adapted metrics from geo-statistics to study the fitness landscape of a P53 deficient 184-hTERT diploid breast epithelial cell line that underwent whole genome doubling (WGD) and found support for the hypothesis that WGD benefits tumor cells by enhancing their robustness against chromosomal instability. The stark phenotypic consequences of karyotype changes emphasize the value of predicting the evolutionary trajectory of karyotype composition when exposing cells to a new environment. Our work contributes to accumulating evidence that karyotype evolution is predictable. Citation Format: Richard J. Beck, Noemi Andor. Adaptive local fitness landscapes for aneuploid karyotypes [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr PR018.

Abstract B011: Lower incidence of small intestinal adenocarcinomas may be due to constrained copy number karyotype and increased immune surveillance

Abstract Aim: To evaluate the genomic profiles of duodenal adenocarcinomas and explore the role of the immune system in the evolution of these cancers. Introduction: Tumours of the small intestine are rare and represent the smallest fraction of all gastrointestinal (GI) cancers despite being the largest organ in the GI tract. As a result, they have not been well characterised at the molecular level, and consequently are often clinically managed similarly to colorectal cancers. Methods: Here we performed shallow whole-genome sequencing (sWGS) on 125 cases of the most common adenocarcinomas in the small intestine, duodenal adenocarcinomas, and compared their somatic copy number aberrations to 880 upper and lower GI primary adenocarcinomas from the TCGA. Furthermore, we reanalysed published whole exome sequencing (WEX) from a further 91 small intestinal carcinomas to assess the immune landscape. Results: In our sWGS cohort, we found that duodenal adenocarcinomas have a significantly lower incidence of genome doubling (20%) than elsewhere in the GI tract (colon=43.6%, stomach=44%, rectum=55%, oesophagus=64.3%). Percentage of genome altered (PGA) is affected by the amount of genome doubling present, by median centering the proportion of the genome altered we could circumvent this. Duodenal cancers also had a significantly lower median centered percentage genome aberrated (mPGA) than colon (p=6.3 × 10-4, es=0.176), rectal (p=3 × 10-5, es=0.279), stomach (p=1.5 × 10-8, es=0.309) and oesophageal (p=1.2 × 10-11, es=0.546) adenocarcinomas. Inter-tumour heterogeneity of copy number alterations was lowest in duodenal cancers compared to other GI cancer types (p<2.22 × 10-16 for all and effect size > 0.7 for all). Within the previously published WEX cohort of small intestinal adenocarcinomas, we observed a higher proportion of clonal mutations that are neoantigens (vs not-neoantigens) in immune escaped tumours than non-escaped tumours (p=0.016) and found that small intestinal tumours are more likely to be immune escaped than colon cancers. Escaped small intestinal tumours were associated with a significantly decreased overall survival compared to non-escaped tumours (HR 2.197 (95% CI, 1.736– 46.63); p=0.009). Further, dNdS analysis indicated strong immune-mediated negative selection on clonal non-synonymous mutations in the immunopeptidome in most tumours. Conclusions: The decreased inter-tumour heterogeneity of karyotypes amongst small intestinal cancers compared to other GI cancers could indicate more restricted routes for karyotype evolution in the small intestine. Our data also suggest a more pertinent role for immune-predation than elsewhere in the GI tract. Together this may explain their lower incidence. Citation Format: Salpie Nowinski, Vickna Balarajah, Ann-Marie Baker, Riku Katainen, Christine Hughes, Qingli Guo, Luis Zapata, Eszter Lakatos, Hemant M. Kocher, Trevor A. Graham. Lower incidence of small intestinal adenocarcinomas may be due to constrained copy number karyotype and increased immune surveillance [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr B011.

Abstract IA010: Molecular archeology of cancer

Abstract Tumor development is driven by changes to the genome leading to fitness advantages underlying successive clonal expansions. As somatic changes occur across most or all cell cycles, the cancer genome carries an archeological record of its past. Over the past years, we have developed several approaches to mine that archeological record from the cancer genome, which we collectively call 'molecular archeology of cancer'. Using these approaches, we are able to infer the subclonal architecture of tumors and gain key insights into the order and timing of the genomic changes that occurred over their evolutionary history. We have applied these approaches in a large-scale pan-cancer setting, showing that intra-tumor heterogeneity is pervasive across cancers and that the timelines of tumor evolution span multiple years to decades. Key driver events in tumor evolution typically occur early, and copy number gains often accumulate as punctuated bursts, commonly after genome doubling. Late genome doubling is frequent in cancer evolution and is typically followed by an increase in the rate of copy number gains. Genome duplications affect the selection landscape of copy number losses, while only minimally impacting copy number gains. Extending our timing framework to time mutational signatures, we find that, as expected, environmentally associated mutations are associated with early tumor development. We also find evidence of episodic APOBEC mutagenesis across many tumors and clear timing patterns in many mutational processes that have unknown origins. Our approaches increase the evolutionary information that can be obtained from tumor genome sequences and, therefore, improve our understanding of the developmental history of cancer. Citation Format: Peter Van Loo. Molecular archeology of cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Damage Repair: From Basic Science to Future Clinical Application; 2024 Jan 9-11; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2024;84(1 Suppl):Abstract nr IA010.

Comparative Transcriptome Analysis and Expression of Genes Associated with Polysaccharide Biosynthesis in Dendrobium officinale Diploid and Tetraploid Plants

Dendrobium officinale Kimura et Migo is a kind of herb with high medicinal, ornamental, and commercial value, and is rich in polysaccharides. Polyploid breeding is an important breeding method for the genome doubling of medicinal species to increase biomass and polysaccharide production. Previous studies have revealed comparative transcriptome analysis and polysaccharide biosynthesis across the growth stages and plant parts, but there have been no studies dissecting such genes and pathways in tetraploid D. officinale. Therefore, this study aimed to unravel the molecular mechanisms of the increase in polysaccharide content in tetraploid D. officinale via the generation of four transcriptomic libraries for protocorm-like bodies and six-month-old seedlings of both diploid and tetraploid D. officinale plants. In this study, a total of 230,786,618 clean reads remained with a total of 34.62 Gb nucleotides generated; 274,403 unigenes were assembled, of which 73.99% were annotated to at least one of the protein databases; and of 17,451 unigenes, 6.35% were annotated to all seven protein databases (NR, NT, KO, Swiss-Prot, FAM, GO, and KOG). Putative genes encoding enzymes related to polysaccharide biosynthetic pathways were determined. RT-qPCR for 11 randomly selected genes involved in polysaccharides indicated consistency with RNA-Seq data and polysaccharide content. The expressions of nine genes were higher in tetraploid than in diploid plants, while the expressions of the other two genes encoding bifunctional enzymes were the opposite. This study has provided a foundation for subsequent works regarding the biosynthetic pathways of metabolites involved in the autoploidy of Dendrobium species in general, and D. officinale in particular.

Alleviated lead toxicity in rice plant by co-augmented action of genome doubling and TiO2 nanoparticles on gene expression, cytological and physiological changes

Lead is a very toxic and futile heavy metal for rice plants because of its injurious effects on plant growth and metabolic processes. Polyploidy or whole genome doubling increases the ability of plants to withstand biotic and abiotic stress. Considering the beneficial effects of nanoparticles and tetraploid rice, this research was conducted to examine the effectiveness of tetraploid and titanium dioxide nanoparticles (TiO2 NPs) in mitigating the toxic effects of lead. A diploid (E22-2x) and it's tetraploid (T-42) rice line were treated with Pb (200 μM) and TiO2 NPs (15 mg L−1). Lead toxicity dramatically reduced shoot length (16 % and 4 %) and root length (17 % and 9 %), biological yield (55 % and 36 %), and photosynthetic activity, as evidenced by lower levels of chlorophyll a and b (30 % and 9 %) in E-22 and T-42 rice cultivars compared to the control rice plants, respectively. Furthermore, lead toxicity amplified the levels of reactive oxygen species (ROS), such as malondialdehyde and H2O2, while decreasing activities of all antioxidant enzymes, such as superoxidase, peroxidase, and glutathione predominately in the diploid cultivar. Transmission electron microscopy and semi-thin section observations revealed that Pb-treated cells in E22-2x had more cell abnormalities than T-42, such as irregularly shaped mitochondria, cell wall, and reduced root cell size. Polyploidy and TiO2 reduced Pb uptake in rice cultivars and expression levels of metal transporter genes such as OsHMA9 and OsNRAMP5. According to the findings, genome doubling alleviates Pb toxicity by reducing Pb accumulation, ROS, and cell damage. Tetraploid rice can withstand the toxic effect of Pb better than diploid rice, and TiO2 NPs can alleviate the toxic impact of Pb. Our study findings act as a roadmap for future research endeavours, directing the focus toward risk management and assessing long-term impacts to balance environmental sustainability and agricultural growth.

Physiology, gene expression, and epiphenotype of two Dianthus broteri polyploid cytotypes under temperature stress.

Increasing evidence supports a major role for abiotic stress response in the success of plant polyploids, which usually thrive in harsh environments. However, understanding the ecophysiology of polyploids is challenging due to interactions between genome doubling and natural selection. Here, we investigated physiological responses, gene expression, and the epiphenotype of two related Dianthus broteri cytotypes-with different genome duplications (4× and 12×) and evolutionary trajectories-to short extreme temperature events (42/28 °C and 9/5 °C). The 12× cytotype showed higher expression of stress-responsive genes (SWEET1, PP2C16, AI5L3, and ATHB7) and enhanced gas exchange compared with 4×. Under heat stress, both ploidies had greatly impaired physiological performance and altered gene expression, with reduced cytosine methylation. However, the 12× cytotype exhibited remarkable physiological tolerance (maintaining gas exchange and water status via greater photochemical integrity and probably enhanced water storage) while down-regulating PP2C16 expression. Conversely, 4× D. broteri was susceptible to thermal stress despite prioritizing water conservation, showing signs of non-stomatal photosynthetic limitations and irreversible photochemical damage. This cytotype also presented gene-specific expression patterns under heat, up-regulating ATHB7. These findings provide insights into divergent stress response strategies and physiological resistance resulting from polyploidy, highlighting its widespread influence on plant function.

Diurnal oscillations of epigenetic modifications are associated with variation in rhythmic expression of homoeologous genes in Brassica napus

BackgroundEpigenetic modifications that exhibit circadian oscillations also promote circadian oscillations of gene expression. Brassica napus is a heterozygous polyploid species that has undergone distant hybridization and genome doubling events and has a young and distinct species origin. Studies incorporating circadian rhythm analysis of epigenetic modifications can offer new insights into differences in diurnal oscillation behavior among subgenomes and the regulation of diverse expressions of homologous gene rhythms in biological clocks.ResultsIn this study, we created a high-resolution and multioscillatory gene expression dataset, active histone modification (H3K4me3, H3K9ac), and RNAPII recruitment in Brassica napus. We also conducted the pioneering characterization of the diurnal rhythm of transcription and epigenetic modifications in an allopolyploid species. We compared the evolution of diurnal rhythms between subgenomes and observed that the Cn subgenome had higher diurnal oscillation activity in both transcription and active histone modifications than the An subgenome. Compared to the A subgenome in Brassica rapa, the An subgenome of Brassica napus displayed significant changes in diurnal oscillation characteristics of transcription. Homologous gene pairs exhibited a higher proportion of diurnal oscillation in transcription than subgenome-specific genes, attributed to higher chromatin accessibility and abundance of active epigenetic modification types. We found that the diurnal expression of homologous genes displayed diversity, and the redundancy of the circadian system resulted in extensive changes in the diurnal rhythm characteristics of clock genes after distant hybridization and genome duplication events. Epigenetic modifications influenced the differences in the diurnal rhythm of homologous gene expression, and the diurnal oscillation of homologous gene expression was affected by the combination of multiple histone modifications.ConclusionsHerein, we presented, for the first time, a characterization of the diurnal rhythm characteristics of gene expression and its epigenetic modifications in an allopolyploid species. Our discoveries shed light on the epigenetic factors responsible for the diurnal oscillation activity imbalance between subgenomes and homologous genes’ rhythmic expression differences. The comprehensive time-series dataset we generated for gene expression and epigenetic modifications provides a valuable resource for future investigations into the regulatory mechanisms of protein-coding genes in Brassica napus.

Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity.

Most computational methods that infer somatic copy number alterations (SCNAs) from bulk sequencing of DNA analyse tumour samples individually. However, the sequencing of multiple tumour samples from a patient's disease is an increasingly common practice. We introduce Refphase, an algorithm that leverages this multi-sampling approach to infer haplotype-specific copy numbers through multi-sample phasing. We demonstrate Refphase's ability to infer haplotype-specific SCNAs and characterise their intra-tumour heterogeneity, to uncover previously undetected allelic imbalance in low purity samples, and to identify parallel evolution in the context of whole genome doubling in a pan-cancer cohort of 336 samples from 99 tumours.

Genomic Characterization of Locally Recurrent Prostate Cancer after Radiation Therapy.

Radiation therapy (RT) is a backbone of treatment for patients with prostate cancer (PCa). However, locally recurrent disease after definitive RT (i.e., radiorecurrent PCa) is not uncommon and is associated with a higher risk of distant metastases and death from PCa. While the genomic landscape of primary PCa is well-characterized, little is known regarding the genomic landscape of radiorecurrent PCa or how this compares to that of primary PCa. We hypothesized that the genomic landscape of radiorecurrent PCa differs significantly from primary PCa and that these differences have clinical relevance. We examined this hypothesis by performing whole exome sequencing (WES) of radiorecurrent PCa. We identified 25 patients with radiorecurrent PCa with available post-RT tissue obtained from biopsy or radical prostatectomy, as well as germline tissue. The tumor and germline tissue for 19 patients successfully underwent WES. We identified genomic variants including single nucleotide variants (SNVs), insertions/deletions, and copy number alterations. Furthermore, we estimated the tumor mutational burden (TMB; number of nonsynonymous mutations per megabase [Mb]) and contribution of individual mutational signatures. We compared our samples to a publicly available large cohort of primary PCa (n = 680) to define genomic alterations unique to radiorecurrent PCa. In the overall cohort of 25 patients, the RT modality included external beam RT (56%), brachytherapy (36%), and combination of both (8%). 40% of patients received upfront androgen deprivation therapy with RT. The median time to local recurrence was 6.5 years. For the 19 radiorecurrent patients with WES data, the median TMB was 2.7 mutations/Mb, which was significantly higher than the median TMB of 0.7 mutation/Mb for primary PCa (P = 0.002 after multivariable adjustment). Radiorecurrent PCa demonstrated an enrichment of short deletions, with a significantly higher deletion/SNV ratio compared to primary PCa (P = 0.006). TP53 was the most frequently mutated gene in radiorecurrent PCa (n = 6), and the TP53 mutation prevalence was significantly higher compared to primary PCa (32% vs 10%, P = 0.016 by Fisher's exact test). TP53 was also determined to be recurrently mutated using MutSigCV (Q = 0.0003). Additionally, 3 samples demonstrated evidence of whole genome doubling. Radiorecurrent PCa has a distinct genomic profile compared to primary PCa, characterized by a higher TMB with an enrichment of short deletions as part of the mutational composition, which may be a scar of nonhomologous end joining subsequent to RT-induced DNA double-stranded breaks. In addition, TP53 mutations may be of functional consequence in radiorecurrent PCa. Further efforts are underway to examine other genomic features apparent in WES data, as well as perform whole transcriptome sequencing to provide complementary insights into radiorecurrent PCa.

The golden bell flower genome provides insights into its evolutionary history and reveals the potential genomic bases of its ecological divergence from weeping forsythia

The golden bell flower (GBF), a beloved flower that blooms in early spring, faces a significant challenge in genetic research and breeding due to the lack of available genomic data. Here, a genome of GBF with a genome size of 735.31 Mb and tiny gaps of 3,782 N were assembled. Our results showed GBF underwent two round of whole genome doubling (WGD) events. The more recent WGD events, along with subsequent structural variations in GBF and weeping forsythia, might lead to the divergence of GBF and weeping forsythia. Analysis of enriched KEGG pathways and Gene Ontology categories of the expanded and contracted genes indicated an increase in the GBF abilities of faster growth and stronger cold and drought tolerance since the separation of the two species. Our results showed that the effective population size (Ne) of the GBF species has been decreasing, declining from 0.352 Mya to 0.018 Mya. However, the stronger cold tolerance of GBF likely helped to alleviate the reduction of Ne during the Pleistocene glacial periods. The expansion of peroxidase (POD) and l-gulonolactone oxidase (GULO) genes and more POD and GULO genes with anaerobic and ABA-induced cis elements in GBF genome might be responsible for the strong waterlogging tolerance of GBF. Our study characterized the evolutionary history of GBF and the genomic bases for the ecological divergenece between GBF and weeping forsythia. Our genome provides genetic resources for future genetic and breeding studies on GBF and its related species.

Genomic Evolution and Transcriptional Changes in the Evolution of Prostate Cancer into Neuroendocrine and Ductal Carcinoma Types.

Prostate cancer is typically of acinar adenocarcinoma type but can occasionally present as neuroendocrine and/or ductal type carcinoma. These are associated with clinically aggressive disease, and the former often arises on a background of androgen deprivation therapy, although it can also arise de novo. Two prostate cancer cases were sequenced by exome capture from archival tissue. Case 1 was de novo small cell neuroendocrine carcinoma and ductal adenocarcinoma with three longitudinal samples over 5 years. Case 2 was a single time point after the development of treatment-related neuroendocrine prostate carcinoma. Case 1 showed whole genome doubling in all samples and focal amplification of AR in all samples except the first time point. Phylogenetic analysis revealed a common ancestry for ductal and small cell carcinoma. Case 2 showed 13q loss (involving RB1) in both adenocarcinoma and small cell carcinoma regions, and 3p gain, 4p loss, and 17p loss (involving TP53) in the latter. By using highly curated samples, we demonstrate for the first time that small-cell neuroendocrine and ductal prostatic carcinoma can have a common ancestry. We highlight whole genome doubling in a patient with prostate cancer relapse, reinforcing its poor prognostic nature.

Expression dosage effects of a small number of genes after the artificial doubling of weeping forsythia

Whole genome doubling (WGD) plays a critical role in plant evolution, yet the mechanisms underlying the maintenance of overall equilibrium following an artificial doubling event, as well as its impact on phenotype and adaptability, remain unclear. By comparing the gene expression of naturally occurring weeping forsythia diploids and colchicine-induced autotetraploids under normal growth conditions and cold stress, we identified gene expression dosage responses resulting from ploidy change. Only a small proportion of effectively expressed genes showed dosage effect, and most genes did not exhibit significant expression differences. However, the genes that showed expression dosage effect were largely random. The autotetraploids had slower overall growth rates, possibly resulting from negative gene dosage effects on zeatin synthesis and multiple metabolic delays caused by other negative dosage genes. Our comparative analysis of cold response genes in diploids and autotetraploids revealed that genes related to “response to abscisic acid” and “cold acclimation” were key factors contributing to greater cold tolerance in the autotetraploids. In particular, gene expression related to “cold acclimation” might mitigate the effects of cold stress. Taken together, our findings suggested that overall gene expression equilibrium following WGD of weeping forsythia autotetraploids was achieved through the inactivation of the majority of duplicated genes. Our research provides new insights into the mechanisms regulating expression dosage balance following polyploidization events.

Comparative analysis of tumor content estimation methods based on simu- lated tumor samples identified their impact on somatic variant detection in cancer whole genome sequencing.

Whole genome sequencing (WGS) in cancer genomics has become widespread with recent technological innovations, and the amount and types of information obtained from WGS are increasing rapidly. Appropriate interpretation of results is becoming increasingly important in clinical applications. This study aimed to evaluate the accuracy of tumor content estimation and its impact on somatic variant detection, using 100 simulated tumor samples covering 10-100% tumor content constructed from the sequencing data of cell line models. Extensive analysis revealed that the estimation results varied among computational analytical methods. Notably, there was a large discrepancy in low tumor content (≤ 30%). The reproducibility decreased in cases wherein chromosome-scale copy number changes were observed in normal cells. The minimum tumor content required to detect somatic alterations was estimated to be 10-30%. Identification of whole genome doubling was achieved with the lowest tumor content, followed by single nucleotide variation/insertion or deletion, structural variation, and copy number variation. Tumor content had a significantly higher impact on the false negatives than the false positives in variant calls. Results should be interpreted cautiously for samples wherein tumor content is a concern. These results can form the basis of developing important guidelines for evaluating cancer WGS.

The fate of extra centrosomes in newly formed tetraploid cells: should I stay, or should I go?

An increase in centrosome number is commonly observed in cancer cells, but the role centrosome amplification plays along with how and when it occurs during cancer development is unclear. One mechanism for generating cancer cells with extra centrosomes is whole genome doubling (WGD), an event that occurs in over 30% of human cancers and is associated with poor survival. Newly formed tetraploid cells can acquire extra centrosomes during WGD, and a generally accepted model proposes that centrosome amplification in tetraploid cells promotes cancer progression by generating aneuploidy and chromosomal instability. Recent findings, however, indicate that newly formed tetraploid cells in vitro lose their extra centrosomes to prevent multipolar cell divisions. Rather than persistent centrosome amplification, this evidence raises the possibility that it may be advantageous for tetraploid cells to initially restore centrosome number homeostasis and for a fraction of the population to reacquire additional centrosomes in the later stages of cancer evolution. In this review, we explore the different evolutionary paths available to newly formed tetraploid cells, their effects on centrosome and chromosome number distribution in daughter cells, and their probabilities of long-term survival. We then discuss the mechanisms that may alter centrosome and chromosome numbers in tetraploid cells and their relevance to cancer progression following WGD.

The protective role of tetraploidy and nanoparticles in arsenic-stressed rice: Evidence from RNA sequencing, ultrastructural and physiological studies

Genome doubling in plants induces physiological and molecular changes to withstand environmental stress. Diploid rice (D-2x) and its tetraploid (T-4x) plants were treated with 25 μM Arsenic (As) and 15 mg L−1 TiO2 nanoparticles (NPs), and results indicated decreased growth and photosynthetic activity with high accumulation of reactive oxygen species (ROS) due to the As-toxicity in rice lines, significantly in D-2x rice plants. The treatment of As-contaminated rice with TiO2 NPs resulted in increased root length (8.17%) and chlorophyll AB (13.28%) and decreased electrolyte leakage (21.76%) and H2O2 (17.65%) contents than its counterpart diploid rice. Moreover, TiO2 NPs improved the activity of peroxidase, catalase, glutathione, and superoxide dismutase and reduced lipid peroxidation due to lower ROS production in D-2x and T-4x under As toxicity. Transcriptome analysis revealed abrupt changes in the expression levels of key signaling heat shock proteins, tubulin, aquaporins, As, and metal transporters under As toxicity in T-4x and D-2x lines. The KEGG and GO studies highlighted the striking distinctions between rice lines under As-stress in glutathione metabolism, H2O2 catabolic process, MAPK signaling pathway, and carotenoid biosynthesis terms, revealing consistency between physiological and molecular results. Root cells from D-2x rice were significantly more distorted by As poisoning than those from 4x rice, and cell organelles, such as mitochondria and endoplasmic reticulum, were changed or deformed. These findings proved the superiority of tetraploid rice lines over their diploid counterpart in coping with As-stress.

New insights on the evolution of nucleolar dominance in newly resynthesized hexaploid wheat Triticum zhukovskyi.

Nucleolar dominance (ND) is a widespread epigenetic phenomenon in hybridizations where nucleolus transcription fails at the nucleolus organizer region (NOR). However, the dynamics of NORs during the formation of Triticum zhukovskyi (GGAu Au Am Am ), another evolutionary branch of allohexaploid wheat, remains poorly understood. Here, we elucidated genetic and epigenetic changes occurring at the NOR loci within the Am , G, and D subgenomes during allopolyploidization by synthesizing hexaploid wheat GGAu Au Am Am and GGAu Au DD. In T. zhukovskyi, Au genome NORs from T. timopheevii (GGAu Au ) were lost, while the second incoming NORs from T. monococcum (Am Am ) were retained. Analysis of the synthesized T. zhukovskyi revealed that rRNA genes from the Am genome were silenced in F1 hybrids (GAu Am ) and remained inactive after genome doubling and subsequent self-pollinations. We observed increased DNA methylation accompanying the inactivation of NORs in the Am genome and found that silencing of NORs in the S1 generation could be reversed by a cytidine methylase inhibitor. Our findings provide insights into the ND process during the evolutionary period of T. zhukovskyi and highlight that inactive rDNA units may serve as a 'first reserve' in the form of R-loops, contributing to the successful evolution of T. zhukovskyi.