Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 156
Filter
1.
ALTEX ; 41(2): 179-201, 2024.
Article in English | MEDLINE | ID: mdl-38629803

ABSTRACT

When The Principles of Humane Experimental Technique was published in 1959, authors William Russell and Rex Burch had a modest goal: to make researchers think about what they were doing in the laboratory - and to do it more humanely. Sixty years later, their groundbreaking book was celebrated for inspiring a revolution in science and launching a new field: The 3Rs of alternatives to animal experimentation. On November 22, 2019, some pioneering and leading scientists and researchers in the field gathered at the Johns Hopkins Bloomberg School of Public Health in Bal-timore for the 60 Years of the 3Rs Symposium: Lessons Learned and the Road Ahead. The event was sponsored by the Johns Hopkins Center for Alternatives to Animal Testing (CAAT), the Foundation for Chemistry Research and Initiatives, the Alternative Research & Development Foundation (ARDF), the American Cleaning Institute (ACI), the International Fragrance Association (IFRA), the Institute for In Vitro Sciences (IIVS), John "Jack" R. Fowle III, and the Society of Toxicology (SoT). Fourteen pres-entations shared the history behind the groundbreaking publication, international efforts to achieve its aims, stumbling blocks to progress, as well as remarkable achievements. The day was a tribute to Russell and Burch, and a testament to what is possible when people from many walks of life - science, government, and industry - work toward a common goal.


William Russell and Rex Burch published their book The Principles of Humane Experimental Technique in 1959. The book encouraged researchers to replace animal experiments where it was possible, to refine experiments with animals in order to reduce their suffering, and to reduce the number of animals that had to be used for experiments to the minimum. Sixty years later, a group of pioneering and leading scientists and researchers in the field gathered to share how the publi­cation came about and how the vision inspired international collaborations and successes on many different levels including new laws. The paper includes an overview of important milestones in the history of alternatives to animal experimentation.


Subject(s)
Animal Experimentation , Animal Testing Alternatives , Animals , Animal Testing Alternatives/methods , Animal Welfare , Research Design
2.
Nat Genet ; 56(1): 60-73, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38049664

ABSTRACT

In this study, the impact of the apolipoprotein B mRNA-editing catalytic subunit-like (APOBEC) enzyme APOBEC3B (A3B) on epidermal growth factor receptor (EGFR)-driven lung cancer was assessed. A3B expression in EGFR mutant (EGFRmut) non-small-cell lung cancer (NSCLC) mouse models constrained tumorigenesis, while A3B expression in tumors treated with EGFR-targeted cancer therapy was associated with treatment resistance. Analyses of human NSCLC models treated with EGFR-targeted therapy showed upregulation of A3B and revealed therapy-induced activation of nuclear factor kappa B (NF-κB) as an inducer of A3B expression. Significantly reduced viability was observed with A3B deficiency, and A3B was required for the enrichment of APOBEC mutation signatures, in targeted therapy-treated human NSCLC preclinical models. Upregulation of A3B was confirmed in patients with NSCLC treated with EGFR-targeted therapy. This study uncovers the multifaceted roles of A3B in NSCLC and identifies A3B as a potential target for more durable responses to targeted cancer therapy.


Subject(s)
Carcinoma, Non-Small-Cell Lung , Lung Neoplasms , Humans , Animals , Mice , Carcinoma, Non-Small-Cell Lung/drug therapy , Carcinoma, Non-Small-Cell Lung/genetics , Lung Neoplasms/drug therapy , Lung Neoplasms/genetics , Mutation , Up-Regulation/genetics , ErbB Receptors/genetics , ErbB Receptors/metabolism , Cytidine Deaminase/genetics , Minor Histocompatibility Antigens/genetics , Minor Histocompatibility Antigens/metabolism
3.
Nature ; 616(7957): 543-552, 2023 04.
Article in English | MEDLINE | ID: mdl-37046093

ABSTRACT

Intratumour heterogeneity (ITH) fuels lung cancer evolution, which leads to immune evasion and resistance to therapy1. Here, using paired whole-exome and RNA sequencing data, we investigate intratumour transcriptomic diversity in 354 non-small cell lung cancer tumours from 347 out of the first 421 patients prospectively recruited into the TRACERx study2,3. Analyses of 947 tumour regions, representing both primary and metastatic disease, alongside 96 tumour-adjacent normal tissue samples implicate the transcriptome as a major source of phenotypic variation. Gene expression levels and ITH relate to patterns of positive and negative selection during tumour evolution. We observe frequent copy number-independent allele-specific expression that is linked to epigenomic dysfunction. Allele-specific expression can also result in genomic-transcriptomic parallel evolution, which converges on cancer gene disruption. We extract signatures of RNA single-base substitutions and link their aetiology to the activity of the RNA-editing enzymes ADAR and APOBEC3A, thereby revealing otherwise undetected ongoing APOBEC activity in tumours. Characterizing the transcriptomes of primary-metastatic tumour pairs, we combine multiple machine-learning approaches that leverage genomic and transcriptomic variables to link metastasis-seeding potential to the evolutionary context of mutations and increased proliferation within primary tumour regions. These results highlight the interplay between the genome and transcriptome in influencing ITH, lung cancer evolution and metastasis.


Subject(s)
Evolution, Molecular , Genome, Human , Lung Neoplasms , Neoplasm Metastasis , Transcriptome , Humans , Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Non-Small-Cell Lung/pathology , Genomics , Lung Neoplasms/genetics , Lung Neoplasms/pathology , Mutation , Neoplasm Metastasis/genetics , Transcriptome/genetics , Alleles , Machine Learning , Genome, Human/genetics
4.
Nature ; 616(7957): 534-542, 2023 04.
Article in English | MEDLINE | ID: mdl-37046095

ABSTRACT

Metastatic disease is responsible for the majority of cancer-related deaths1. We report the longitudinal evolutionary analysis of 126 non-small cell lung cancer (NSCLC) tumours from 421 prospectively recruited patients in TRACERx who developed metastatic disease, compared with a control cohort of 144 non-metastatic tumours. In 25% of cases, metastases diverged early, before the last clonal sweep in the primary tumour, and early divergence was enriched for patients who were smokers at the time of initial diagnosis. Simulations suggested that early metastatic divergence more frequently occurred at smaller tumour diameters (less than 8 mm). Single-region primary tumour sampling resulted in 83% of late divergence cases being misclassified as early, highlighting the importance of extensive primary tumour sampling. Polyclonal dissemination, which was associated with extrathoracic disease recurrence, was found in 32% of cases. Primary lymph node disease contributed to metastatic relapse in less than 20% of cases, representing a hallmark of metastatic potential rather than a route to subsequent recurrences/disease progression. Metastasis-seeding subclones exhibited subclonal expansions within primary tumours, probably reflecting positive selection. Our findings highlight the importance of selection in metastatic clone evolution within untreated primary tumours, the distinction between monoclonal versus polyclonal seeding in dictating site of recurrence, the limitations of current radiological screening approaches for early diverging tumours and the need to develop strategies to target metastasis-seeding subclones before relapse.


Subject(s)
Carcinoma, Non-Small-Cell Lung , Clonal Evolution , Clone Cells , Evolution, Molecular , Lung Neoplasms , Neoplasm Metastasis , Humans , Carcinoma, Non-Small-Cell Lung/pathology , Clone Cells/pathology , Cohort Studies , Disease Progression , Lung Neoplasms/pathology , Neoplasm Metastasis/diagnosis , Neoplasm Metastasis/pathology , Neoplasm Recurrence, Local
5.
Nature ; 616(7955): 159-167, 2023 04.
Article in English | MEDLINE | ID: mdl-37020004

ABSTRACT

A complete understanding of how exposure to environmental substances promotes cancer formation is lacking. More than 70 years ago, tumorigenesis was proposed to occur in a two-step process: an initiating step that induces mutations in healthy cells, followed by a promoter step that triggers cancer development1. Here we propose that environmental particulate matter measuring ≤2.5 µm (PM2.5), known to be associated with lung cancer risk, promotes lung cancer by acting on cells that harbour pre-existing oncogenic mutations in healthy lung tissue. Focusing on EGFR-driven lung cancer, which is more common in never-smokers or light smokers, we found a significant association between PM2.5 levels and the incidence of lung cancer for 32,957 EGFR-driven lung cancer cases in four within-country cohorts. Functional mouse models revealed that air pollutants cause an influx of macrophages into the lung and release of interleukin-1ß. This process results in a progenitor-like cell state within EGFR mutant lung alveolar type II epithelial cells that fuels tumorigenesis. Ultradeep mutational profiling of histologically normal lung tissue from 295 individuals across 3 clinical cohorts revealed oncogenic EGFR and KRAS driver mutations in 18% and 53% of healthy tissue samples, respectively. These findings collectively support a tumour-promoting role for  PM2.5 air pollutants  and provide impetus for public health policy initiatives to address air pollution to reduce disease burden.


Subject(s)
Adenocarcinoma of Lung , Air Pollutants , Air Pollution , Cell Transformation, Neoplastic , Lung Neoplasms , Animals , Mice , Adenocarcinoma of Lung/chemically induced , Adenocarcinoma of Lung/genetics , Air Pollutants/adverse effects , Air Pollutants/analysis , Air Pollution/adverse effects , Air Pollution/analysis , Cell Transformation, Neoplastic/chemically induced , Cell Transformation, Neoplastic/drug effects , Cell Transformation, Neoplastic/genetics , Environmental Exposure , ErbB Receptors/genetics , Lung Neoplasms/chemically induced , Lung Neoplasms/genetics , Particulate Matter/adverse effects , Particulate Matter/analysis , Particle Size , Cohort Studies , Macrophages, Alveolar/drug effects , Alveolar Epithelial Cells/drug effects , Alveolar Epithelial Cells/pathology
6.
Cancer Discov ; 13(6): 1364-1385, 2023 06 02.
Article in English | MEDLINE | ID: mdl-36977461

ABSTRACT

Understanding the evolutionary pathways to metastasis and resistance to immune-checkpoint inhibitors (ICI) in melanoma is critical for improving outcomes. Here, we present the most comprehensive intrapatient metastatic melanoma dataset assembled to date as part of the Posthumous Evaluation of Advanced Cancer Environment (PEACE) research autopsy program, including 222 exome sequencing, 493 panel-sequenced, 161 RNA sequencing, and 22 single-cell whole-genome sequencing samples from 14 ICI-treated patients. We observed frequent whole-genome doubling and widespread loss of heterozygosity, often involving antigen-presentation machinery. We found KIT extrachromosomal DNA may have contributed to the lack of response to KIT inhibitors of a KIT-driven melanoma. At the lesion-level, MYC amplifications were enriched in ICI nonresponders. Single-cell sequencing revealed polyclonal seeding of metastases originating from clones with different ploidy in one patient. Finally, we observed that brain metastases that diverged early in molecular evolution emerge late in disease. Overall, our study illustrates the diverse evolutionary landscape of advanced melanoma. SIGNIFICANCE: Despite treatment advances, melanoma remains a deadly disease at stage IV. Through research autopsy and dense sampling of metastases combined with extensive multiomic profiling, our study elucidates the many mechanisms that melanomas use to evade treatment and the immune system, whether through mutations, widespread copy-number alterations, or extrachromosomal DNA. See related commentary by Shain, p. 1294. This article is highlighted in the In This Issue feature, p. 1275.


Subject(s)
Brain Neoplasms , Melanoma , Humans , Melanoma/pathology , Mutation , Evolution, Molecular , DNA
7.
Stem Cell Reports ; 18(2): 570-584, 2023 02 14.
Article in English | MEDLINE | ID: mdl-36669491

ABSTRACT

Adenomatous polyposis coli (APC) mutation is the hallmark of colorectal cancer (CRC), resulting in constitutive WNT activation. Despite decades of research, targeting WNT signaling in cancer remains challenging due to its on-target toxicity. We have previously shown that the deubiquitinating enzyme USP7 is a tumor-specific WNT activator in APC-truncated cells by deubiquitinating and stabilizing ß-catenin, but its role in gut tumorigenesis is unknown. Here, we show in vivo that deletion of Usp7 in Apc-truncated mice inhibits crypt hyperproliferation and intestinal tumor development. Loss of Usp7 prolongs the survival of the sporadic intestinal tumor model. Genetic deletion, but not pharmacological inhibition, of Usp7 in Apc+/- intestine induces colitis and enteritis. USP7 inhibitor treatment suppresses growth of patient-derived cancer organoids carrying APC truncations in vitro and in xenografts. Our findings provide direct evidence that USP7 inhibition may offer a safe and efficacious tumor-specific therapy for both sporadic and germline APC-mutated CRC.


Subject(s)
Adenomatous Polyposis Coli , Colorectal Neoplasms , Humans , Mice , Animals , Colorectal Neoplasms/drug therapy , Colorectal Neoplasms/genetics , Colorectal Neoplasms/pathology , Ubiquitin-Specific Peptidase 7/genetics , Ubiquitin-Specific Peptidase 7/metabolism , Adenomatous Polyposis Coli/genetics , Carcinogenesis/genetics , Cell Transformation, Neoplastic/genetics , Wnt Signaling Pathway , beta Catenin/genetics , beta Catenin/metabolism
8.
Front Vet Sci ; 9: 946603, 2022.
Article in English | MEDLINE | ID: mdl-36532345

ABSTRACT

Dogs (Canis lupus familiaris) are one of the most common pets around the world but ownership patterns and human-dog interactions have been changing, particularly in developing nations. We conducted household surveys in Costa Rica to characterize dog ownership, the owned dog population, where dogs were confined at night and in the morning, and behaviors regarding selected dog care issues. We also compared these results to similar questionnaires used in Costa Rica over the past 20 years. We found 76% of households in Costa Rica owned at least one dog and on average there were about 1.4 dogs owned per household. These dog ownership rates are higher than previous estimates. The probability of owning a dog was highest on farms and lowest in single family dwellings without a yard, higher among respondents that owned their homes and decreasing with increasing human population density The total number of owned dogs in Costa Rica was estimated to be 2,222,032 (95% confidence intervals: 1,981,497-2,503,751). The sterilization rate for homed dogs in 2020 was approximately 62% (females: 67%, males: 61%) which is higher than the 18% of owned dogs that were sterilized in a 2003 survey. Overall, only 1.2% (95% CI: 0.3-2.5%) of owned dogs slept on the street with a slightly higher proportion on the street at 8 am. The number of owned dogs roaming the streets at night nation-wide was estimated to be 27,208 (95% CI: 7,557-56,619) compared to 43,142 (95% CI: 20,118-73,618) on the street at 8 am. The number of unowned free-roaming dogs in Costa Rica has never been estimated but we can generate some idea of the size of the unowned dog population by determining the proportion of free-roaming dogs on the street wearing collars. There was a negative relationship between human population density and owned dogs being on the street meaning fewer dogs roam the streets in highly populated areas compared to less populated areas. Overall, we identify trends against which future progress can be measured and provide information that are critical in designing effective humane dog management programs in Costa Rica in the future.

9.
FEBS J ; 289(1): 121-139, 2022 01.
Article in English | MEDLINE | ID: mdl-34270864

ABSTRACT

Matrix metalloproteinase-13 (MMP-13) is a uniquely important collagenase that promotes the irreversible destruction of cartilage collagen in osteoarthritis (OA). Collagenase activation is a key control point for cartilage breakdown to occur, yet our understanding of the proteinases involved in this process is limited. Neutrophil elastase (NE) is a well-described proteoglycan-degrading enzyme which is historically associated with inflammatory arthritis, but more recent evidence suggests a potential role in OA. In this study, we investigated the effect of neutrophil elastase on OA cartilage collagen destruction and collagenase activation. Neutrophil elastase induced significant collagen destruction from human OA cartilage ex vivo, in an MMP-dependent manner. In vitro, neutrophil elastase directly and robustly activated pro-MMP-13, and N-terminal sequencing identified cleavage close to the cysteine switch at 72 MKKPR, ultimately resulting in the fully active form with the neo-N terminus of 85 YNVFP. Mole-per-mole, activation was more potent than by MMP-3, a classical collagenase activator. Elastase was detectable in human OA synovial fluid and OA synovia which displayed histologically graded evidence of synovitis. Bioinformatic analyses demonstrated that, compared with other tissues, control cartilage exhibited remarkably high transcript levels of the major elastase inhibitor, (AAT) alpha-1 antitrypsin (gene name SERPINA1), but these were reduced in OA. AAT was located predominantly in superficial cartilage zones, and staining enhanced in regions of cartilage damage. Finally, active MMP-13 specifically inactivated AAT by removal of the serine proteinase cleavage/inhibition site. Taken together, this study identifies elastase as a novel activator of pro-MMP-13 that has relevance for cartilage collagen destruction in OA patients with synovitis.


Subject(s)
Inflammation/genetics , Leukocyte Elastase/genetics , Matrix Metalloproteinase 13/genetics , Osteoarthritis/genetics , alpha 1-Antitrypsin/genetics , Cysteine/genetics , Humans , Inflammation/metabolism , Inflammation/pathology , Matrix Metalloproteinase 3/genetics , Neutrophils/enzymology , Osteoarthritis/metabolism , Osteoarthritis/pathology , Osteochondrodysplasias/genetics , Osteochondrodysplasias/metabolism , Synovitis/genetics , Synovitis/metabolism , Synovitis/pathology , alpha 1-Antitrypsin Deficiency/genetics , alpha 1-Antitrypsin Deficiency/pathology
10.
Nat Ecol Evol ; 6(1): 88-102, 2022 01.
Article in English | MEDLINE | ID: mdl-34949820

ABSTRACT

Genetic intra-tumour heterogeneity fuels clonal evolution, but our understanding of clinically relevant clonal dynamics remain limited. We investigated spatial and temporal features of clonal diversification in clear cell renal cell carcinoma through a combination of modelling and real tumour analysis. We observe that the mode of tumour growth, surface or volume, impacts the extent of subclonal diversification, enabling interpretation of clonal diversity in patient tumours. Specific patterns of proliferation and necrosis explain clonal expansion and emergence of parallel evolution and microdiversity in tumours. In silico time-course studies reveal the appearance of budding structures before detectable subclonal diversification. Intriguingly, we observe radiological evidence of budding structures in early-stage clear cell renal cell carcinoma, indicating that future clonal evolution may be predictable from imaging. Our findings offer a window into the temporal and spatial features of clinically relevant clonal evolution.


Subject(s)
Neoplasms , Clonal Evolution , Humans
11.
Cancer Cell ; 39(11): 1497-1518.e11, 2021 11 08.
Article in English | MEDLINE | ID: mdl-34715028

ABSTRACT

ADAPTeR is a prospective, phase II study of nivolumab (anti-PD-1) in 15 treatment-naive patients (115 multiregion tumor samples) with metastatic clear cell renal cell carcinoma (ccRCC) aiming to understand the mechanism underpinning therapeutic response. Genomic analyses show no correlation between tumor molecular features and response, whereas ccRCC-specific human endogenous retrovirus expression indirectly correlates with clinical response. T cell receptor (TCR) analysis reveals a significantly higher number of expanded TCR clones pre-treatment in responders suggesting pre-existing immunity. Maintenance of highly similar clusters of TCRs post-treatment predict response, suggesting ongoing antigen engagement and survival of families of T cells likely recognizing the same antigens. In responders, nivolumab-bound CD8+ T cells are expanded and express GZMK/B. Our data suggest nivolumab drives both maintenance and replacement of previously expanded T cell clones, but only maintenance correlates with response. We hypothesize that maintenance and boosting of a pre-existing response is a key element of anti-PD-1 mode of action.


Subject(s)
Carcinoma, Renal Cell/drug therapy , Drug Resistance, Neoplasm , Immune Checkpoint Inhibitors/administration & dosage , Kidney Neoplasms/drug therapy , Nivolumab/administration & dosage , Receptors, Antigen, T-Cell/genetics , CD8-Positive T-Lymphocytes , Carcinoma, Renal Cell/genetics , Clinical Trials, Phase II as Topic , Endogenous Retroviruses/genetics , Gene Expression Profiling/methods , Genomics/methods , Humans , Immune Checkpoint Inhibitors/pharmacology , Kidney Neoplasms/genetics , Nivolumab/pharmacology , Prospective Studies , Sequence Analysis, RNA , Single-Cell Analysis , Tumor Escape , Tumor Microenvironment , Exome Sequencing
12.
Cancer Discov ; 11(10): 2456-2473, 2021 10.
Article in English | MEDLINE | ID: mdl-33947663

ABSTRACT

APOBEC3 enzymes are cytosine deaminases implicated in cancer. Precisely when APOBEC3 expression is induced during cancer development remains to be defined. Here we show that specific APOBEC3 genes are upregulated in breast ductal carcinoma in situ, and in preinvasive lung cancer lesions coincident with cellular proliferation. We observe evidence of APOBEC3-mediated subclonal mutagenesis propagated from TRACERx preinvasive to invasive non-small cell lung cancer (NSCLC) lesions. We find that APOBEC3B exacerbates DNA replication stress and chromosomal instability through incomplete replication of genomic DNA, manifested by accumulation of mitotic ultrafine bridges and 53BP1 nuclear bodies in the G1 phase of the cell cycle. Analysis of TRACERx NSCLC clinical samples and mouse lung cancer models revealed APOBEC3B expression driving replication stress and chromosome missegregation. We propose that APOBEC3 is functionally implicated in the onset of chromosomal instability and somatic mutational heterogeneity in preinvasive disease, providing fuel for selection early in cancer evolution. SIGNIFICANCE: This study reveals the dynamics and drivers of APOBEC3 gene expression in preinvasive disease and the exacerbation of cellular diversity by APOBEC3B through DNA replication stress to promote chromosomal instability early in cancer evolution.This article is highlighted in the In This Issue feature, p. 2355.


Subject(s)
APOBEC Deaminases/genetics , Breast Neoplasms/genetics , Carcinoma, Ductal/genetics , Carcinoma, Non-Small-Cell Lung/genetics , Lung Neoplasms/genetics , Animals , Cell Line, Tumor , Chromosomal Instability , DNA Replication , Female , Humans , Mice
13.
Nat Ecol Evol ; 5(7): 1033-1045, 2021 07.
Article in English | MEDLINE | ID: mdl-34002049

ABSTRACT

The genetic evolutionary features of solid tumour growth are becoming increasingly well described, but the spatial and physical nature of subclonal growth remains unclear. Here, we utilize 102 macroscopic whole-tumour images from clear cell renal cell carcinoma patients, with matched genetic and phenotypic data from 756 biopsies. Utilizing a digital image processing pipeline, a renal pathologist marked the boundaries between tumour and normal tissue and extracted positions of boundary line and biopsy regions to X and Y coordinates. We then integrated coordinates with genomic data to map exact spatial subclone locations, revealing how genetically distinct subclones grow and evolve spatially. We observed a phenotype of advanced and more aggressive subclonal growth in the tumour centre, characterized by an elevated burden of somatic copy number alterations and higher necrosis, proliferation rate and Fuhrman grade. Moreover, we found that metastasizing subclones preferentially originate from the tumour centre. Collectively, these observations suggest a model of accelerated evolution in the tumour interior, with harsh hypoxic environmental conditions leading to a greater opportunity for driver somatic copy number alterations to arise and expand due to selective advantage. Tumour subclone growth is predominantly spatially contiguous in nature. We found only two cases of subclone dispersal, one of which was associated with metastasis. The largest subclones spatially were dominated by driver somatic copy number alterations, suggesting that a large selective advantage can be conferred to subclones upon acquisition of these alterations. In conclusion, spatial dynamics is strongly associated with genomic alterations and plays an important role in tumour evolution.


Subject(s)
DNA Copy Number Variations , Neoplasms , Evolution, Molecular , Genomics , Humans , Mutation
14.
Cell ; 184(3): 596-614.e14, 2021 02 04.
Article in English | MEDLINE | ID: mdl-33508232

ABSTRACT

Checkpoint inhibitors (CPIs) augment adaptive immunity. Systematic pan-tumor analyses may reveal the relative importance of tumor-cell-intrinsic and microenvironmental features underpinning CPI sensitization. Here, we collated whole-exome and transcriptomic data for >1,000 CPI-treated patients across seven tumor types, utilizing standardized bioinformatics workflows and clinical outcome criteria to validate multivariable predictors of CPI sensitization. Clonal tumor mutation burden (TMB) was the strongest predictor of CPI response, followed by total TMB and CXCL9 expression. Subclonal TMB, somatic copy alteration burden, and histocompatibility leukocyte antigen (HLA) evolutionary divergence failed to attain pan-cancer significance. Dinucleotide variants were identified as a source of immunogenic epitopes associated with radical amino acid substitutions and enhanced peptide hydrophobicity/immunogenicity. Copy-number analysis revealed two additional determinants of CPI outcome supported by prior functional evidence: 9q34 (TRAF2) loss associated with response and CCND1 amplification associated with resistance. Finally, single-cell RNA sequencing (RNA-seq) of clonal neoantigen-reactive CD8 tumor-infiltrating lymphocytes (TILs), combined with bulk RNA-seq analysis of CPI-responding tumors, identified CCR5 and CXCL13 as T-cell-intrinsic markers of CPI sensitivity.


Subject(s)
Immune Checkpoint Inhibitors/pharmacology , Neoplasms/immunology , T-Lymphocytes/immunology , Biomarkers, Tumor/metabolism , CD8 Antigens/metabolism , Chemokine CXCL13/metabolism , Chromosomes, Human, Pair 9/genetics , Cohort Studies , Cyclin D1/genetics , DNA Copy Number Variations/genetics , Exome/genetics , Gene Amplification , Humans , Immune Evasion/drug effects , Multivariate Analysis , Mutation/genetics , Neoplasms/pathology , Polymorphism, Single Nucleotide/genetics , Receptors, CCR5/metabolism , T-Lymphocytes/drug effects , Tumor Burden/genetics
15.
Nature ; 587(7832): 126-132, 2020 11.
Article in English | MEDLINE | ID: mdl-32879494

ABSTRACT

Chromosomal instability in cancer consists of dynamic changes to the number and structure of chromosomes1,2. The resulting diversity in somatic copy number alterations (SCNAs) may provide the variation necessary for tumour evolution1,3,4. Here we use multi-sample phasing and SCNA analysis of 1,421 samples from 394 tumours across 22 tumour types to show that continuous chromosomal instability results in pervasive SCNA heterogeneity. Parallel evolutionary events, which cause disruption in the same genes (such as BCL9, MCL1, ARNT (also known as HIF1B), TERT and MYC) within separate subclones, were present in 37% of tumours. Most recurrent losses probably occurred before whole-genome doubling, that was found as a clonal event in 49% of tumours. However, loss of heterozygosity at the human leukocyte antigen (HLA) locus and loss of chromosome 8p to a single haploid copy recurred at substantial subclonal frequencies, even in tumours with whole-genome doubling, indicating ongoing karyotype remodelling. Focal amplifications that affected chromosomes 1q21 (which encompasses BCL9, MCL1 and ARNT), 5p15.33 (TERT), 11q13.3 (CCND1), 19q12 (CCNE1) and 8q24.1 (MYC) were frequently subclonal yet appeared to be clonal within single samples. Analysis of an independent series of 1,024 metastatic samples revealed that 13 focal SCNAs were enriched in metastatic samples, including gains in chromosome 8q24.1 (encompassing MYC) in clear cell renal cell carcinoma and chromosome 11q13.3 (encompassing CCND1) in HER2+ breast cancer. Chromosomal instability may enable the continuous selection of SCNAs, which are established as ordered events that often occur in parallel, throughout tumour evolution.


Subject(s)
Chromosomal Instability/genetics , Evolution, Molecular , Karyotype , Neoplasm Metastasis/genetics , Neoplasms/genetics , Chromosomes, Human, Pair 11/genetics , Chromosomes, Human, Pair 8/genetics , Clone Cells/metabolism , Clone Cells/pathology , Cyclin E/genetics , DNA Copy Number Variations/genetics , Female , Humans , Loss of Heterozygosity/genetics , Male , Mutagenesis , Neoplasm Metastasis/pathology , Neoplasms/pathology , Oncogene Proteins/genetics
16.
Nat Commun ; 11(1): 3800, 2020 07 30.
Article in English | MEDLINE | ID: mdl-32733040

ABSTRACT

Frameshift insertion/deletions (fs-indels) are an infrequent but highly immunogenic mutation subtype. Although fs-indels are degraded through the nonsense-mediated decay (NMD) pathway, we hypothesise that some fs-indels escape degradation and elicit anti-tumor immune responses. Using allele-specific expression analysis, expressed fs-indels are enriched in genomic positions predicted to escape NMD, and associated with higher protein expression, consistent with degradation escape (NMD-escape). Across four independent melanoma cohorts, NMD-escape mutations are significantly associated with clinical-benefit to checkpoint inhibitor (CPI) therapy (Pmeta = 0.0039). NMD-escape mutations are additionally found to associate with clinical-benefit in the low-TMB setting. Furthermore, in an adoptive cell therapy treated melanoma cohort, NMD-escape mutation count is the most significant biomarker associated with clinical-benefit. Analysis of functional T cell reactivity screens from personalized vaccine studies shows direct evidence of fs-indel derived neoantigens eliciting immune response, particularly those with highly elongated neo open reading frames. NMD-escape fs-indels represent an attractive target for biomarker optimisation and immunotherapy design.


Subject(s)
Melanoma/genetics , Melanoma/immunology , Nonsense Mediated mRNA Decay/genetics , T-Lymphocytes/immunology , Tumor Escape/genetics , Adoptive Transfer , Antigens, Neoplasm/immunology , Biomarkers, Tumor/genetics , Frameshift Mutation/genetics , Humans , INDEL Mutation/genetics , Immunotherapy, Adoptive , T-Lymphocytes/transplantation , Exome Sequencing
17.
Cell Rep ; 31(5): 107550, 2020 05 05.
Article in English | MEDLINE | ID: mdl-32375028

ABSTRACT

Although thousands of solid tumors have been sequenced to date, a fundamental under-sampling bias is inherent in current methodologies. This is caused by a tissue sample input of fixed dimensions (e.g., 6 mm biopsy), which becomes grossly under-powered as tumor volume scales. Here, we demonstrate representative sequencing (Rep-Seq) as a new method to achieve unbiased tumor tissue sampling. Rep-Seq uses fixed residual tumor material, which is homogenized and subjected to next-generation sequencing. Analysis of intratumor tumor mutation burden (TMB) variability shows a high level of misclassification using current single-biopsy methods, with 20% of lung and 52% of bladder tumors having at least one biopsy with high TMB but low clonal TMB overall. Misclassification rates by contrast are reduced to 2% (lung) and 4% (bladder) when a more representative sampling methodology is used. Rep-Seq offers an improved sampling protocol for tumor profiling, with significant potential for improved clinical utility and more accurate deconvolution of clonal structure.


Subject(s)
Biomarkers, Tumor/genetics , High-Throughput Nucleotide Sequencing , Lung Neoplasms/genetics , Tumor Burden/genetics , Urinary Bladder Neoplasms/genetics , Biopsy/methods , High-Throughput Nucleotide Sequencing/methods , Humans , Lung Neoplasms/pathology , Mutation/genetics , Urinary Bladder Neoplasms/pathology
18.
Animals (Basel) ; 10(3)2020 Mar 17.
Article in English | MEDLINE | ID: mdl-32192138

ABSTRACT

No other animal has a closer mutualistic relationship with humans than the dog (Canis familiaris). Domesticated from the Eurasian grey wolf (Canis lupus), dogs have evolved alongside humans over millennia in a relationship that has transformed dogs and the environments in which humans and dogs have co-inhabited. The story of the dog is the story of recent humanity, in all its biological and cultural complexity. By exploring human-dog-environment interactions throughout time and space, it is possible not only to understand vital elements of global history, but also to critically assess our present-day relationship with the natural world, and to begin to mitigate future global challenges. In this paper, co-authored by researchers from across the natural and social sciences, arts and humanities, we argue that a dog-centric approach provides a new model for future academic enquiry and engagement with both the public and the global environmental agenda.

19.
Nat Genet ; 52(3): 283-293, 2020 03.
Article in English | MEDLINE | ID: mdl-32139907

ABSTRACT

Whole-genome doubling (WGD) is a prevalent event in cancer, involving a doubling of the entire chromosome complement. However, despite its prevalence and prognostic relevance, the evolutionary selection pressures for WGD in cancer have not been investigated. Here, we combine evolutionary simulations with an analysis of cancer sequencing data to explore WGD during cancer evolution. Simulations suggest that WGD can be selected to mitigate the irreversible, ratchet-like, accumulation of deleterious somatic alterations, provided that they occur at a sufficiently high rate. Consistent with this, we observe an enrichment for WGD in tumor types with extensive loss of heterozygosity, including lung squamous cell carcinoma and triple-negative breast cancers, and we find evidence for negative selection against homozygous loss of essential genes before, but not after, WGD. Finally, we demonstrate that loss of heterozygosity and temporal dissection of mutations can be exploited to identify novel tumor suppressor genes and to obtain a deeper characterization of known cancer genes.


Subject(s)
Adenocarcinoma of Lung/genetics , Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Squamous Cell/genetics , Gene Duplication , Genome, Human/genetics , Lung Neoplasms/genetics , Tumor Suppressor Proteins/genetics , Cohort Studies , Computer Simulation , DNA Copy Number Variations , Evolution, Molecular , Humans , Longitudinal Studies , Loss of Heterozygosity , Mutation , Prospective Studies
20.
Animals (Basel) ; 9(9)2019 Aug 29.
Article in English | MEDLINE | ID: mdl-31470523

ABSTRACT

In November 2013, a group of international experts in animal research policy (n = 11) gathered in Vancouver, Canada, to discuss openness and accountability in animal research. The primary objective was to bring together participants from various jurisdictions (United States, Sweden, Australia, New Zealand, Germany, Canada and the United Kingdom) to share practices regarding the governance of animals used in research, testing and education, with emphasis on the governance process followed, the methods of community engagement, and the balance of openness versus confidentiality. During the forum, participants came to a broad consensus on the need for: (a) evidence-based metrics to allow a "virtuous feedback" system for evaluation and quality assurance of animal research, (b) the need for increased public access to information, together with opportunities for stakeholder dialogue about animal research, (c) a greater diversity of views to be represented on decision-making committees to allow for greater balance and (d) a standardized and robust ethical decision-making process that incorporates some sort of societal input. These recommendations encourage aspirations beyond merely imparting information and towards a genuine dialogue that represents a shared agenda surrounding laboratory animal use.

SELECTION OF CITATIONS
SEARCH DETAIL
...