Biology subjects

Robine, N.

Publications and source records attributed to Robine, N..

26 records · Page 2Linked to original sources

bioRxiv2021

Occult polyclonality of preclinical pancreatic cancer models drives in vitro evolution.

Intratumoral heterogeneity (ITH) is a hallmark of cancer. The advent of single-cell technologies has helped uncover ITH in a high-throughput manner in different cancers across varied contexts. Here we apply single-cell sequencing technologies to reveal striking ITH in assumptively oligoclonal pancreatic ductal adenocarcinoma (PDAC) cell lines. Our findings reveal a high degree of both genomic and transcriptomic heterogeneity in established and globally utilized PDAC cell lines, custodial variation induced by growing apparently identical PDAC cell lines in different laboratories, and profound transcriptomic shifts in transitioning from 2D to 3D spheroid growth models. Our findings also call into question the validity of widely available immortalized, non-transformed pancreatic lines as contemporaneous "control" lines in experiments. Further, while patient-derived organoid (PDOs) are known to reflect the cognate in vivo biology of the parental tumor, we identify transcriptomic shifts during ex vivo passage that might hamper their predictive abilities over time. The impact of these findings on rigor and reproducibility of experimental data generated using established preclinical PDAC models between and across laboratories is uncertain, but a matter of concern.

cancer biology↗

bioRxiv2019

Novel patterns of complex structural variation revealed across thousands of cancer genome graphs

Cancer genomes often harbor hundreds of somatic DNA rearrangement junctions, many of which cannot be easily classified into simple (e.g. deletion, translocation) or complex (e.g. chromothripsis, chromoplexy) structural variant classes. Applying a novel genome graph computational paradigm to analyze the topology of junction copy number (JCN) across 2,833 tumor whole genome sequences (WGS), we introduce three complex rearrangement phenomena: pyrgo, rigma, and tyfonas. Pyrgo are "towers" of low-JCN duplications associated with early replicating regions and superenhancers, and are enriched in breast and ovarian cancers. Rigma comprise "chasms" of low-JCN deletions at late-replicating fragile sites in esophageal and other gastrointestinal (GI) adenocarcinomas. Tyfonas are "typhoons" of high-JCN junctions and fold back inversions that are enriched in acral but not cutaneous melanoma and associated with a previously uncharacterized mutational process of non-APOBEC kataegis. Clustering of tumors according to genome graph-derived features identifies subgroups associated with DNA repair defects and poor prognosis.

genomics↗

bioRxiv2019

Deep sequencing of 3 cancer cell lines on 2 sequencing platforms

To test the performance of a new sequencing platform, develop an updated somatic calling pipeline and establish a reference for future benchmarking experiments, we sequenced 3 common cancer cell lines along with their matched normal cell lines to great sequencing depths (up to 278X coverage) on both Illumina HiSeqX and NovaSeq sequencing instruments. Somatic calling was generally consistent between the two platforms despite minor differences at the read level. We designed and implemented a novel pipeline for the analysis of tumor-normal samples, using multiple variant callers. We show that coupled with a high-confidence filtering strategy, it improves the accuracy of somatic calls. We also demonstrate the utility of the dataset by creating an artificial purity ladder to evaluate the somatic pipeline and benchmark methods for estimating purity and ploidy from tumor-normal pairs. The data and results of the pipeline are made accessible to the cancer genomics community.

genomics↗

bioRxiv2019

SCANVIS: a tool for SCoring, ANnotating and VISualing splice junctions

MotivationThe association of splicing signatures with disease is a leading area of study for prognosis, diagnosis and therapy, frequently requiring detailed analysis of splicing events across multiple samples. We present a novel fast-performing annotation-dependent tool called SCANVIS for scoring and annotating splice junctions by gene name, junction type and any frame shifts incurred. SCANVIS has a novel and fast visualization technique that distinguishes annotated splice junctions from unannotated ones in the context of nearby variants and read coverage. It also allows users to merge samples across cohorts, thereby allowing for quick comparisons of splice junctions across diseases and tissue types. ResultsWe show that SCANVIS generates reasonable PSI scores by demonstrating that tissue/cancer types in GTEX and TCGA are well separated and easily predicted from a few thousand SJs. We also show how SCANVIS can be used to map out junctions overlaid with variants and read coverage for one or more samples, with line types and colors delineating frame shifts and junction types. AvailabilitySCANVIS is available for download at https://github.com/nygenome/SCANVIS Contactpagius@nygenome.org

bioinformatics↗

bioRxiv2018

Genetic mechanisms of primary chemotherapy resistance in pediatric acute myeloid leukemia: A report from the TARGET initiative

Acute myeloid leukemias (AML) are characterized by mutations of tumor suppressor and oncogenes, involving distinct genes in adults and children. While certain mutations have been associated with the increased risk of AML relapse, the genomic landscape of primary chemotherapy resistant AML is not well defined. As part of the TARGET initiative, we performed whole-genome DNA and transcriptome (RNA and miRNA) sequencing analysis of pediatric AML with failure of induction chemotherapy. We identified at least three genetic groups of patients with induction failure, including those with NUP98 rearrangements, somatic mutations of WT1 in the absence of NUP98 mutations, and additional recurrent variants including those in KMT2C and MLLT10. Comparison of specimens before and after chemotherapy revealed distinct and invariant gene expression programs. While exhibiting overt therapy resistance, these leukemias nonetheless showed diverse forms of clonal evolution upon chemotherapy exposure. This included selection for mutant alleles of FRMD8, DHX32, PIK3R1, SHANK3, MKLN1, as well as persistence of WT1 and TP53 mutant clones, and elimination or contraction of FLT3, PTPN11, and NRAS mutant clones. These findings delineate genetic mechanisms of primary chemotherapy resistance in pediatric AML, which should inform improved approaches for its diagnosis and therapy.

cancer biology↗

bioRxiv2018

YES1 amplification: a mechanism of acquired resistance to EGFR inhibitors identified by transposon mutagenesis and clinical genomics

In approximately 30% of patients with EGFR-mutant lung adenocarcinomas whose disease progresses on EGFR inhibitors, the basis for acquired resistance remains unclear. We have integrated transposon mutagenesis screening in an EGFR-mutant cell line and clinical genomic sequencing in cases of acquired resistance to identify novel mechanisms of resistance to EGFR inhibitors. The most prominent candidate genes identified by insertions in or near the genes during the screen were MET, a gene whose amplification is known to mediate resistance to EGFR inhibitors, and the gene encoding the Src family kinase YES1. Cell clones with transposon insertions that activated expression of YES1 exhibited resistance to all three generations of EGFR inhibitors and sensitivity to pharmacologic and siRNA-mediated inhibition of YES1. Analysis of clinical genomic sequencing data from cases of acquired resistance to EGFR inhibitors revealed amplification of YES1 in 5 cases, 4 of which lacked any other known mechanisms of resistance. Pre-inhibitor samples, available for 2 of the 5 patients, lacked YES1 amplification. None of 136 post-inhibitor samples had detectable amplification of other Src family kinases (SRC, FYN). YES1 amplification was also found in 2 of 17 samples from ALK fusion-positive lung cancer patients who had progressed on ALK TKIs. Taken together, our findings identify acquired amplification of YES1 as a novel, recurrent, and targetable mechanism of resistance to EGFR inhibition in EGFR-mutant lung cancers, and demonstrate the utility of transposon mutagenesis in discovering clinically relevant mechanisms of drug resistance.\n\nSIGNIFICANCEDespite high response rates to treatment with small molecule inhibitors of EGFR tyrosine kinase activity, patients with EGFR-mutant lung adenocarcinomas eventually develop resistance to these drugs. In many cases, the basis of acquired resistance remains unclear. We have used a transposon mutagenesis screen in an EGFR-mutant cell line and clinical genomic sequencing in cases of acquired resistance to identify amplification of YES1 as a novel and targetable mechanism of resistance to EGFR inhibitors in EGFR-mutant lung cancers.

cancer biology↗

bioRxiv2017

Lancet: genome-wide somatic variant calling using localized colored DeBruijn graphs

Reliable detection of somatic variations is of critical importance in cancer research. Lancet is an accurate and sensitive somatic variant caller which detects SNVs and indels by jointly analyzing reads from tumor and matched normal samples using colored DeBruijn graphs. Extensive experimental comparison on synthetic and real whole-genome sequencing datasets demonstrates that Lancet has better accuracy, especially for indel detection, than widely used somatic callers, such as MuTect, MuTect2, LoFreq, Strelka, and Strelka2. Lancet features a reliable variant scoring system which is essential for variant prioritization and detects low frequency mutations without sacrificing the sensitivity to call longer insertions and deletions empowered by the local assembly engine. In addition to genome-wide analysis, Lancet allows inspection of somatic variants in graph space, which augments the traditional read alignment visualization to help confirm a variant of interest. Lancet is available as an open-source program at https://github.com/nygenome/lancet.

bioinformatics↗

bioRxiv2017

taxMaps - Ultra-comprehensive and highly accurate taxonomic classification of short-read data in reasonable time

High-throughput sequencing is a revolutionary technology for the analysis of metagenomic samples. However, querying large volumes of reads against comprehensive DNA/RNA databases in a sensitive manner can be compute-intensive. Here, we present taxMaps, a highly efficient, sensitive and fully scalable taxonomic classification tool, capable of delivering classification accuracy comparable to that of BLASTn, but at up to 3 orders of magnitude less computational cost. taxMaps is freely available for academic and non-commercial research purposes at https://github.com/nygenome/taxmaps.

bioinformatics↗