PanCancer analysis of somatic mutations in repetitive regions reveals recurrent mutations in snRNA U2

Current somatic mutation callers are biased against repetitive regions, preventing the identification of potential driver alterations in these loci. We developed a mutation caller for repetitive regions, and applied it to study repetitive non protein-coding genes in more than 2200 whole-genome cases. We identified a recurrent mutation at position c.28 in the gene encoding the snRNA U2. This mutation is present in B-cell derived tumors, as well as in prostate and pancreatic cancer, suggesting U2 c.28 constitutes a driver candidate associated with worse prognosis. We showed that the GRCh37 reference genome is incomplete, lacking the U2 cluster in chromosome 17, preventing the identification of mutations in this gene. Furthermore, the 5'-flanking region of WDR74, previously described as frequently mutated in cancer, constitutes a functional copy of U2. These data reinforce the relevance of non-coding mutations in cancer, and highlight current challenges of cancer genomic research in characterizing mutations affecting repetitive genes.© 2022. The Author(s)

Cell Dispersal Influences Tumor Heterogeneity and Introduces a Bias in NGS Data Interpretation

Short and long distance cell dispersal can have a marked effect on tumor structure, high cellular motility could lead to faster cell mixing and lower observable intratumor heterogeneity. Here we evaluated a model for cell mixing that investigates how short-range dispersal and cell turnover will account for mutational proportions. We show that cancer cells can penetrate neighboring and distinct areas in a matter of days. In next generation sequencing runs, higher proportions of a given cell line generated frequencies with higher precision, while mixtures with lower amounts of each cell line had lower precision manifesting in higher standard deviations. When multiple cell lines were co-cultured, cellular movement altered observed mutation frequency by up to 18.5%. We propose that some of the shared mutations detected at low allele frequencies represent highly motile clones that appear in multiple regions of a tumor owing to dispersion throughout the tumor. In brief, cell movement will lead to a significant technical (sampling) bias when using next generation sequencing to determine clonal composition. A possible solution to this drawback would be to radically decrease detection thresholds and increase coverage in NGS analyses. © 2017 The Author(s)

Intravascular Large B-Cell Lymphoma Genomic Profile Is Characterized by Alterations in Genes Regulating NF-κB and Immune Checkpoints.

Intravascular large B-cell lymphoma (IVLBCL) is an uncommon lymphoma with an aggressive clinical course characterized by selective growth of tumor cells within the vessels. Its pathogenesis is still uncertain and there is little information on the underlying genomic alterations. In this study, we performed a clinicopathologic and next-generation sequencing analysis of 15 cases of IVLBCL using a custom panel for the detection of alterations in 68 recurrently mutated genes in B-cell lymphomagenesis. Six patients had evidence of hemophagocytic syndrome. Four patients presented concomitantly a solid malignancy. Tumor cells outside the vessels were observed in 7 cases, 2 with an overt diffuse large B-cell cell lymphoma. In 4 samples, tumor cells infiltrated lymphatic vessel in addition to blood capillaries. Programmed death-ligand 1 (PD-L1) was positive in tumor cells in 4 of 11 evaluable samples and in macrophages intermingled with tumor cells in 8. PD-L1 copy number gains were identified in a higher proportion of cases expressing PD-L1 than in negative tumors. The most frequently mutated gene was PIM1 (9/15, 60%), followed by MYD88L265P and CD79B (8/15, 53% each). In 6 cases, MYD88L265P and CD79B mutations were detected concomitantly. We also identified recurrent mutations in IRF4 , TMEM30A , BTG2 , and ETV6 loci (4/15, 27% each) and novel driver mutations in NOTCH2 , CCND3 , and GNA13 , and an IRF4 translocation in 1 case each. The mutational profile was similar in patients with and without evidence of hemophagocytic syndrome and in cases with or without dissemination of tumor cells outside the vessels. Our results confirm the relevance of mutations in B-cell receptor/nuclear factor-κB signaling and immune escape pathways in IVLBCL and identify novel driver alterations. The similar mutational profile in tumors with extravascular dissemination suggests that these cases may also be considered in the spectrum of IVLBCL

Molecular map of chronic lymphocytic leukemia and its impact on outcome

Recent advances in cancer characterization have consistently revealed marked heterogeneity, impeding the completion of integrated molecular and clinical maps for each malignancy. Here, we focus on chronic lymphocytic leukemia (CLL), a B cell neoplasm with variable natural history that is conventionally categorized into two subtypes distinguished by extent of somatic mutations in the heavy-chain variable region of immunoglobulin genes (IGHV). To build the ‘CLL map,’ we integrated genomic, transcriptomic and epigenomic data from 1,148 patients. We identified 202 candidate genetic drivers of CLL (109 new) and refined the characterization of IGHV subtypes, which revealed distinct genomic landscapes and leukemogenic trajectories. Discovery of new gene expression subtypes further subcategorized this neoplasm and proved to be independent prognostic factors. Clinical outcomes were associated with a combination of genetic, epigenetic and gene expression features, further advancing our prognostic paradigm. Overall, this work reveals fresh insights into CLL oncogenesis and prognostication

The application of sediment fingerprinting to floodplain and lake sediment cores: assumptions and uncertainties evaluated through case studies in the Nene Basin, UK

Purpose: Fine sediment has been shown to be a major cause of the degradation of lakes and rivers and, as a result, research has been directed towards the understanding of fine sediment dynamics and the minimisation of sediment inputs. The use of tracers within a sediment fingerprinting framework has become a heavily used technique to investigate the sources of fine sediment pressures. When combined with the use of historically deposited sediment, the technique provides the opportunity to reconstruct past changes to the environment. However, alterations to tracer signatures during sediment transport and storage are a major potential source of uncertainty associated with tracer use. At present, few studies have quantified the uncertainties associated with tracer use. Materials and methods: This paper investigated uncertainty by determining the differences between sediment provenance predictions obtained using lithogenic radionuclide, geochemical and mineral magnetic signatures when fingerprinting lake and floodplain sedimentary deposits. It also investigated the potential causes of the observed differences. Results and discussion: A reservoir core was fingerprinted with the least uncertainty, with tracer group predictions ∼28 % apart and a consistent down-core trend in changing sediment provenance produced. When fingerprinting an on-line lake core and four floodplain cores, differences between tracer group predictions were as large as 100 %; the down-core trends in changing sediment provenance were also different. The differences between tracer group predictions could be attributed to the organic matter content and particle size of the sediment. There was also evidence of the in-growth of bacterially derived magnetite and chemical dissolution affecting the preservation of tracer signatures. Simple data corrections for sediment organic matter content and particle size did not result in significantly greater agreement between the predictions of the different tracer groups. Likewise, the inclusions of weightings for tracer discriminatory efficiency and within-source variability had minimal effects on the fingerprinting results. Conclusions: This paper highlights the importance of tracer selection and the consideration of recognising tracer non-conservatism when using lake and floodplain sediment deposits to reconstruct anthropogenic changes to the environment and changing sediment dynamics. It was recommended that future research focus on the assessment of uncertainty using the artificial mixing of sediment source samples, the limitation of the fingerprinting to narrow particle size fractions and the development of specific particle size and organic matter correction factors for each tracer

Different prognostic impact of recurrent gene mutations in chronic lymphocytic leukemia depending on IGHV gene somatic hypermutation status: a study by ERIC in HARMONY

Recent evidence suggests that the prognostic impact of gene mutations in patients with chronic lymphocytic leukemia (CLL) may differ depending on the immunoglobulin heavy variable (IGHV) gene somatic hypermutation (SHM) status. In this study, we assessed the impact of nine recurrently mutated genes (BIRC3, EGR2, MYD88, NFKBIE, NOTCH1, POT1, SF3B1, TP53, and XPO1) in pre-treatment samples from 4580 patients with CLL, using time-to-first-treatment (TTFT) as the primary end-point in relation to IGHV gene SHM status. Mutations were detected in 1588 (34.7%) patients at frequencies ranging from 2.3-9.8% with mutations in NOTCH1 being the most frequent. In both univariate and multivariate analyses, mutations in all genes except MYD88 were associated with a significantly shorter TTFT. In multivariate analysis of Binet stage A patients, performed separately for IGHV-mutated (M-CLL) and unmutated CLL (U-CLL), a different spectrum of gene alterations independently predicted short TTFT within the two subgroups. While SF3B1 and XPO1 mutations were independent prognostic variables in both U-CLL and M-CLL, TP53, BIRC3 and EGR2 aberrations were significant predictors only in U-CLL, and NOTCH1 and NFKBIE only in M-CLL. Our findings underscore the need for a compartmentalized approach to identify high-risk patients, particularly among M-CLL patients, with potential implications for stratified management

Combined PARP and ATR inhibition potentiates genome instability and cell death in ATM-deficient cancer cells.

The poly (ADP-ribose) polymerase (PARP) inhibitor olaparib is FDA approved for the treatment of BRCA-mutated breast, ovarian and pancreatic cancers. Olaparib inhibits PARP1/2 enzymatic activity and traps PARP1 on DNA at single-strand breaks, leading to replication-induced DNA damage that requires BRCA1/2-dependent homologous recombination repair. Moreover, DNA damage response pathways mediated by the ataxia-telangiectasia mutated (ATM) and ataxia-telangiectasia mutated and Rad3-related (ATR) kinases are hypothesised to be important survival pathways in response to PARP-inhibitor treatment. Here, we show that olaparib combines synergistically with the ATR-inhibitor AZD6738 (ceralasertib), in vitro, leading to selective cell death in ATM-deficient cells. We observe that 24 h olaparib treatment causes cells to accumulate in G2-M of the cell cycle, however, co-administration with AZD6738 releases the olaparib-treated cells from G2 arrest. Selectively in ATM-knockout cells, we show that combined olaparib/AZD6738 treatment induces more chromosomal aberrations and achieves this at lower concentrations and earlier treatment time-points than either monotherapy. Furthermore, single-agent olaparib efficacy in vitro requires PARP inhibition throughout multiple rounds of replication. Here, we demonstrate in several ATM-deficient cell lines that the olaparib and AZD6738 combination induces cell death within 1-2 cell divisions, suggesting that combined treatment could circumvent the need for prolonged drug exposure. Finally, we demonstrate in vivo combination activity of olaparib and AZD6738 in xenograft and PDX mouse models with complete ATM loss. Collectively, these data provide a mechanistic understanding of combined PARP and ATR inhibition in ATM-deficient models, and support the clinical development of AZD6738 in combination with olaparib

On frequency averaging for spectral analysis in speech recognition

Many speech recognition systems use logarithmic filter-bank energies or a linear transformation of them to represent the speech signal. Usually, each of those energies is routinely computed as a weighted average of the periodogram samples that lie in the corresponding frequency band. In this work, we attempt to gain an insight into the statistical properties of the frequency-averaged periodogram (FAP) from which those energies are samples. Thus, we have shown that the FAP is statistically and asymptotically equivalent to a multiwindow estimator that arises from the Thomson’s optimization approach and uses orthogonal sinusoids as windows. The FAP and other multiwindow estimators are tested in a speech recognition application, observing the influence of several design factors. Particularly, a technique that is computationally simple like the FAP’s one, and which is equivalent to use multiple cosine windows, appears as an alternative to be taken into considerationPeer Reviewe

On frequency averaging for spectral analysis in speech recognition

Many speech recognition systems use logarithmic filter-bank energies or a linear transformation of them to represent the speech signal. Usually, each of those energies is routinely computed as a weighted average of the periodogram samples that lie in the corresponding frequency band. In this work, we attempt to gain an insight into the statistical properties of the frequency-averaged periodogram (FAP) from which those energies are samples. Thus, we have shown that the FAP is statistically and asymptotically equivalent to a multiwindow estimator that arises from the Thomson’s optimization approach and uses orthogonal sinusoids as windows. The FAP and other multiwindow estimators are tested in a speech recognition application, observing the influence of several design factors. Particularly, a technique that is computationally simple like the FAP’s one, and which is equivalent to use multiple cosine windows, appears as an alternative to be taken into considerationPeer Reviewe