Showing papers by "Oliver Hofmann published in 2020"

Pan-cancer analysis of whole genomes

Abstract: Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1,2,3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10,11,12,13,14,15,16,17,18.

Aβ-accelerated neurodegeneration caused by Alzheimer’s-associated ACE variant R1279Q is rescued by angiotensin system inhibition in mice

Abstract: Recent genome-wide association studies identified the angiotensin-converting enzyme gene (ACE) as an Alzheimer's disease (AD) risk locus. However, the pathogenic mechanism by which ACE causes AD is unknown. Using whole-genome sequencing, we identified rare ACE coding variants in AD families and investigated one, ACE1 R1279Q, in knockin (KI) mice. Similar to AD, ACE1 was increased in neurons, but not microglia or astrocytes, of KI brains, which became elevated further with age. Angiotensin II (angII) and angII receptor AT1R signaling were also increased in KI brains. Autosomal dominant neurodegeneration and neuroinflammation occurred with aging in KI hippocampus, which were absent in the cortex and cerebellum. Female KI mice exhibited greater hippocampal electroencephalograph disruption and memory impairment compared to males. ACE variant effects were more pronounced in female KI mice, suggesting a mechanism for higher AD risk in women. Hippocampal neurodegeneration was completely rescued by treatment with brain-penetrant drugs that inhibit ACE1 and AT1R. Although ACE variant-induced neurodegeneration did not depend on β-amyloid (Aβ) pathology, amyloidosis in 5XFAD mice crossed to KI mice accelerated neurodegeneration and neuroinflammation, whereas Aβ deposition was unchanged. KI mice had normal blood pressure and cerebrovascular functions. Our findings strongly suggest that increased ACE1/angII signaling causes aging-dependent, Aβ-accelerated selective hippocampal neuron vulnerability and female susceptibility, hallmarks of AD that have hitherto been enigmatic. We conclude that repurposed brain-penetrant ACE inhibitors and AT1R blockers may protect against AD.

Whole-genome sequencing reveals new Alzheimer's disease-associated rare variants in loci related to synaptic function and neuronal development

Abstract: INTRODUCTION Genome-wide association studies have led to numerous genetic loci associated with Alzheimer’s disease (AD). Whole-genome sequencing (WGS) now permit genome-wide analyses to identify rare variants contributing to AD risk. METHODS We performed single-variant and spatial clustering-based testing on rare variants (minor allele frequency ≤1%) in a family-based WGS-based association study of 2,247 subjects from 605 multiplex AD families, followed by replication in 1,669 unrelated individuals. RESULTS We identified 13 new AD candidate loci that yielded consistent rare-variant signals in discovery and replication cohorts (4 from single-variant, 9 from spatial-clustering), implicating these genes: FNBP1L, SEL1L, LINC00298, PRKCH, C15ORF41, C2CD3, KIF2A, APC, LHX9, NALCN, CTNNA2, SYTL3, CLSTN2. DISCUSSION Downstream analyses of these novel loci highlight synaptic function, in contrast to common AD-associated variants, which implicate innate immunity. These loci have not been previously associated with AD, emphasizing the ability of WGS to identify AD-associated rare variants, particularly outside of coding regions.

Cancer Predisposition Sequencing Reporter (CPSR): a flexible variant report engine for high-throughput germline screening in cancer

Abstract: The value of high-throughput germline genetic testing is increasingly recognized in clinical cancer care. Disease-associated germline variants in cancer patients are important for risk management and surveillance, surgical decisions, and can also have major implications for treatment strategies since many are in DNA repair genes. With the increasing availability of high-throughput DNA sequencing in cancer clinics and research, there is thus a need to provide clinically oriented sequencing reports for germline variants and their potential therapeutic relevance on a per-patient basis. To meet this need we have developed the Cancer Predisposition Sequencing Reporter (CPSR), an open-source computational workflow that generates a structured report of germline variants identified in known cancer predisposition genes, highlighting markers of therapeutic, prognostic, and diagnostic relevance. A fully automated variant classification procedure based on more than 30 refined ACMG criteria represents an integral part of the workflow. Importantly, the set of cancer predisposition genes profiled in the report can be flexibly chosen from more than 40 virtual gene panels established by scientific experts, enabling customization of the report for different screening purposes and clinical contexts. The report can be configured to also list actionable secondary variant findings as recommended by ACMG, as well as the status of low-risk variants from genome-wide association studies in cancer. CPSR demonstrates superior sensitivity and comparable specificity for the detection of pathogenic variants when compared to existing algorithms. Technically, the tool is implemented in Python/R, and is freely available through Docker technology. Source code, documentation, example reports, and installation instructions are accessible via the project GitHub page: https://github.com/sigven/cpsr.

Inotuzumab ozogamicin resistance associated with a novel CD22 truncating mutation in a case of B-acute lymphoblastic leukaemia.

Abstract: Relapsed B-acute lymphoblastic leukaemia (B-ALL) remains a difficult disease to treat and is associated with a poor prognosis. Antibody-based immunotherapy (blinatumomab), antibody-drug conjugates [inotuzumab ozogamicin (InO)] and cellular immunotherapies [chimeric antigen receptor T cells (CAR-T)] have emerged as effective treatment options in patients with relapsed disease. While genomic sequencing studies have uncovered mechanisms of intrinsicand acquired-therapy resistance, a significant proportion of clinical resistance remains to be understood. Here, we describe a patient with relapsed B-ALL who acquired a novel CD22 mutation predicted to result in premature truncation of CD22 arising under selective pressure of InO, an anti-CD22 targeted therapy. A 17-year-old man presented with anaemia (haemoglobin level of 85 g/l) and leucocytosis (68.4 9 10/l) after several weeks of abdominal fullness, lethargy, light headedness, night sweats, bruising and weight loss. Bone marrow (BM) biopsy demonstrated 97% blasts with an immunophenotype consistent with pre B-ALL. Chromosome analysis revealed a normal male karyotype. He was commenced on the French Acute Lymphoblastic Leukaemia Group (FRALLE)-93 protocol and had undetectable measurable residual disease (MRD) by flow cytometry at day 94 (sensitivity <10 ). The patient received consolidation and maintenance as per protocol without major complication. At 1 month after completion of maintenance, he relapsed with a BM aspirate demonstrating 92% blasts, with an immunophenotype and karyotype unchanged from diagnosis. He was treated with blinatumomab achieving a morphological remission with persistent MRD (0 15% of mononuclear cells). He was planned for allogeneic transplantation; however, after a single cycle of blinatumomab, he had overt disease progression with a BM aspirate demonstrating 51% blasts. He was commenced on InO, achieving undetectable MRD after one cycle (sensitivity <10 ); however, after two cycles, his disease progressed with 75% blasts in the BM and an immunophenotype that was still consistent with pre-B-ALL, but was now notably negative for CD22. To understand potential mechanisms contributing to leukaemia progression following InO, we performed whole genome sequencing (WGS) and whole transcriptome RNA-sequencing (WTS) on this relapse sample collected 59 days after first administration of InO (R-InO) (see Supporting Information). Additional genomic findings in R-InO and from WGS-WTS performed at diagnosis and progression after CAR-T are summarised in the Supporting Information (Fig S1A–E, Table S1). WGS identified a truncating mutation in exon 4 of CD22 (NM_001771 3:c.712_713insCT; p.(Val238Alafs*2)) (Fig 1A), the transmembrane glycoprotein target of InO, an anti-CD22 monoclonal antibody conjugated to the DNA-binding cytotoxic calicheamicin that is rapidly internalised to deliver calicheamicin within the cytoplasmic compartment. This mutation was homozygous, occurring within a region of copy neutral loss of heterozygosity on chromosome 19q (Fig S1B) and was present in a high proportion of the cancer cell fraction given a variant allele frequency (VAF) of 51 1% in a sample with an estimated tumour purity of 56%. The site of the mutation in CD22 (valine 238) occurs between the second (d2) and third (d3) extracellular immunoglobulin (Ig)-like domains, inducing a frameshift in the CD22 mRNA sequence that is predicted to result in an aberrant reading frame, introducing a premature stop codon after an additional two amino acids and prior to the downstream Ig-like domains (d3–d7), transmembrane domain and the cytoplasmic immunoreceptor tyrosine-based inhibitory motif (ITIM), which normally mediates CD22 activity through recruitment of inhibitory phosphatases that facilitate dephosphorylation of stimulatory co-receptors. The observation that 99 6% of leukaemic blasts were now CD22 negative by flow cytometry (Fig 1B) is consistent with this truncating mutation leading to loss of surface CD22 expression on leukaemic blasts. WTS performed on the R-InO sample demonstrated expression of the mutant allele, suggesting at least partial avoidance of nonsense mediated decay (Fig S1D). In order to investigate when the CD22 mutation emerged in this patient, we performed sensitive allele-specific droplet digital polymerase chain reaction (ddPCR) for the CD22 Val238Alafs*2 mutation using the Bio-Rad Droplet Digital PCR system (Bio-Rad, Hercules, CA, USA) (Fig 1B). The CD22 Val238Alafs*2 mutation was detected at 49 0% VAF in R-InO, consistent with the allele fraction estimated by WGS, but was undetectable to an assay limit of detection of 0 01% in five prior BM samples, including three with high blast burden: diagnosis, first relapse after maintenance (where blasts were CD22-positive) and disease progression after blinatumomab. Correspondence