Detection of somatic mutations in human leukocyte antigen (HLA) genes using whole-exome sequencing (WES) is hampered by the high polymorphism of the HLA loci, which prevents alignment of sequencing ...reads to the human reference genome. We describe a computational pipeline that enables accurate inference of germline alleles of class I HLA-A, B and C genes and subsequent detection of mutations in these genes using the inferred alleles as a reference. Analysis of WES data from 7,930 pairs of tumor and healthy tissue from the same patient revealed 298 nonsilent HLA mutations in tumors from 266 patients. These 298 mutations are enriched for likely functional mutations, including putative loss-of-function events. Recurrence of mutations suggested that these 'hotspot' sites were positively selected. Cancers with recurrent somatic HLA mutations were associated with upregulation of signatures of cytolytic activity characteristic of tumor infiltration by effector lymphocytes, supporting immune evasion by altered HLA function as a contributory mechanism in cancer.
Effective anti-tumour immunity in humans has been associated with the presence of T cells directed at cancer neoantigens, a class of HLA-bound peptides that arise from tumour-specific mutations. They ...are highly immunogenic because they are not present in normal tissues and hence bypass central thymic tolerance. Although neoantigens were long-envisioned as optimal targets for an anti-tumour immune response, their systematic discovery and evaluation only became feasible with the recent availability of massively parallel sequencing for detection of all coding mutations within tumours, and of machine learning approaches to reliably predict those mutated peptides with high-affinity binding of autologous human leukocyte antigen (HLA) molecules. We hypothesized that vaccination with neoantigens can both expand pre-existing neoantigen-specific T-cell populations and induce a broader repertoire of new T-cell specificities in cancer patients, tipping the intra-tumoural balance in favour of enhanced tumour control. Here we demonstrate the feasibility, safety, and immunogenicity of a vaccine that targets up to 20 predicted personal tumour neoantigens. Vaccine-induced polyfunctional CD4
and CD8
T cells targeted 58 (60%) and 15 (16%) of the 97 unique neoantigens used across patients, respectively. These T cells discriminated mutated from wild-type antigens, and in some cases directly recognized autologous tumour. Of six vaccinated patients, four had no recurrence at 25 months after vaccination, while two with recurrent disease were subsequently treated with anti-PD-1 (anti-programmed cell death-1) therapy and experienced complete tumour regression, with expansion of the repertoire of neoantigen-specific T cells. These data provide a strong rationale for further development of this approach, alone and in combination with checkpoint blockade or other immunotherapies.
Neoantigens, which are derived from tumour-specific protein-coding mutations, are exempt from central tolerance, can generate robust immune responses
and can function as bona fide antigens that ...facilitate tumour rejection
. Here we demonstrate that a strategy that uses multi-epitope, personalized neoantigen vaccination, which has previously been tested in patients with high-risk melanoma
, is feasible for tumours such as glioblastoma, which typically have a relatively low mutation load
and an immunologically 'cold' tumour microenvironment
. We used personalized neoantigen-targeting vaccines to immunize patients newly diagnosed with glioblastoma following surgical resection and conventional radiotherapy in a phase I/Ib study. Patients who did not receive dexamethasone-a highly potent corticosteroid that is frequently prescribed to treat cerebral oedema in patients with glioblastoma-generated circulating polyfunctional neoantigen-specific CD4
and CD8
T cell responses that were enriched in a memory phenotype and showed an increase in the number of tumour-infiltrating T cells. Using single-cell T cell receptor analysis, we provide evidence that neoantigen-specific T cells from the peripheral blood can migrate into an intracranial glioblastoma tumour. Neoantigen-targeting vaccines thus have the potential to favourably alter the immune milieu of glioblastoma.
We find two chemically distinct populations separated relatively cleanly in the Fe/H-Mg/Fe plane, but also distinguished in other chemical planes, among metal-poor stars (primarily with metallicities ...) observed by the Apache Point Observatory Galactic Evolution Experiment (APOGEE) and analyzed for Data Release 13 (DR13) of the Sloan Digital Sky Survey. These two stellar populations show the most significant differences in their X/Fe ratios for the -elements, C+N, Al, and Ni. In addition to these populations having differing chemistry, the low metallicity high-Mg population (which we denote "the HMg population") exhibits a significant net Galactic rotation, whereas the low-Mg population (or "the LMg population") has halo-like kinematics with little to no net rotation. Based on its properties, the origin of the LMg population is likely an accreted population of stars. The HMg population shows chemistry (and to an extent kinematics) similar to the thick disk, and is likely associated with in situ formation. The distinction between the LMg and HMg populations mimics the differences between the populations of low- and high- halo stars found in previous studies, suggesting that these are samples of the same two populations.
The biological function of Z-DNA and Z-RNA, nucleic acid structures with a left-handed double helix, is poorly understood
. Z-DNA-binding protein 1 (ZBP1; also known as DAI or DLM-1) is a nucleic ...acid sensor that contains two Zα domains that bind Z-DNA
and Z-RNA
. ZBP1 mediates host defence against some viruses
by sensing viral nucleic acids
. RIPK1 deficiency, or mutation of its RIP homotypic interaction motif (RHIM), triggers ZBP1-dependent necroptosis and inflammation in mice
. However, the mechanisms that induce ZBP1 activation in the absence of viral infection remain unknown. Here we show that Zα-dependent sensing of endogenous ligands induces ZBP1-mediated perinatal lethality in mice expressing RIPK1 with mutated RHIM (Ripk1
), skin inflammation in mice with epidermis-specific RIPK1 deficiency (RIPK1
) and colitis in mice with intestinal epithelial-specific FADD deficiency (FADD
). Consistently, functional Zα domains were required for ZBP1-induced necroptosis in fibroblasts that were treated with caspase inhibitors or express RIPK1 with mutated RHIM. Inhibition of nuclear export triggered the Zα-dependent activation of RIPK3 in the nucleus resulting in cell death, which suggests that ZBP1 may recognize nuclear Z-form nucleic acids. We found that ZBP1 constitutively bound cellular double-stranded RNA in a Zα-dependent manner. Complementary reads derived from endogenous retroelements were detected in epidermal RNA, which suggests that double-stranded RNA derived from these retroelements may act as a Zα-domain ligand that triggers the activation of ZBP1. Collectively, our results provide evidence that the sensing of endogenous Z-form nucleic acids by ZBP1 triggers RIPK3-dependent necroptosis and inflammation, which could underlie the development of chronic inflammatory conditions-particularly in individuals with mutations in RIPK1 and CASP8
.
Transcription in all cellular organisms is performed by multisubunit, DNA-dependent RNA polymerases that synthesize RNA from DNA templates. Previous sequence and structural studies have elucidated ...the importance of shared regions common to all multisubunit RNA polymerases. In addition, RNA polymerases contain multiple lineage-specific domain insertions involved in protein–protein and protein–nucleic acid interactions. We have created comprehensive multiple sequence alignments using all available sequence data for the multisubunit RNA polymerase large subunits, including the bacterial β and β′ subunits and their homologs from archaebacterial RNA polymerases, the eukaryotic RNA polymerases I, II, and III, the nuclear–cytoplasmic large double-stranded DNA virus RNA polymerases, and plant plastid RNA polymerases. To overcome technical difficulties inherent to the large-subunit sequences, including large sequence length, small and large lineage-specific insertions, split subunits, and fused proteins, we created an automated and customizable sequence retrieval and processing system. In addition, we used our alignments to create a more expansive set of shared sequence regions and bacterial lineage-specific domain insertions. We also analyzed the intergenic gap between the bacterial β and β′ genes.
Prediction of HLA epitopes is important for the development of cancer immunotherapies and vaccines. However, current prediction algorithms have limited predictive power, in part because they were not ...trained on high-quality epitope datasets covering a broad range of HLA alleles. To enable prediction of endogenous HLA class I-associated peptides across a large fraction of the human population, we used mass spectrometry to profile >185,000 peptides eluted from 95 HLA-A, -B, -C and -G mono-allelic cell lines. We identified canonical peptide motifs per HLA allele, unique and shared binding submotifs across alleles and distinct motifs associated with different peptide lengths. By integrating these data with transcript abundance and peptide processing, we developed HLAthena, providing allele-and-length-specific and pan-allele-pan-length prediction models for endogenous peptide presentation. These models predicted endogenous HLA class I-associated ligands with 1.5-fold improvement in positive predictive value compared with existing tools and correctly identified >75% of HLA-bound peptides that were observed experimentally in 11 patient-derived tumor cell lines.
The Escherichia coli transcription system is the best characterized from a biochemical and genetic point of view and has served as a model system. Nevertheless, a molecular understanding of the ...details of E. coli transcription and its regulation, and therefore its full exploitation as a model system, has been hampered by the absence of high-resolution structural information on E. coli RNA polymerase (RNAP). We use a combination of approaches, including high-resolution X-ray crystallography, ab initio structural prediction, homology modeling, and single-particle cryo-electron microscopy, to generate complete atomic models of E. coli core RNAP and an E. coli RNAP ternary elongation complex. The detailed and comprehensive structural descriptions can be used to help interpret previous biochemical and genetic data in a new light and provide a structural framework for designing experiments to understand the function of the E. coli lineage-specific insertions and their role in the E. coli transcription program.
Comprehensive multiple sequence alignments of the multisubunit DNA-dependent RNA polymerase (RNAP) large subunits, including the bacterial β and β′ subunits and their homologs from archaebacterial ...RNAPs, eukaryotic RNAPs I–III, nuclear–cytoplasmic large double-stranded DNA virus RNAPs, and plant plastid RNAPs, were created Lane, W. J. and Darst, S. A. (2009). Molecular evolution of multisubunit RNA polymerases: sequence analysis. In press. The alignments were used to delineate sequence regions shared among all classes of multisubunit RNAPs, defining common, fundamental RNAP features as well as identifying highly conserved positions. Here, we present a systematic, detailed structural analysis of these shared regions and highly conserved positions in terms of the RNAP structure, as well as the RNAP structure/function relationship, when known.
The incidence of nipple-sparing mastectomy is rising, but no single incision type has been proven to be superior. This study systematically evaluated the rate and efficacy of various nipple-sparing ...mastectomy incision locations, focusing on nipple-areola complex necrosis and reconstructive method.
A systematic literature review was performed according to the Preferred Reporting Items for Systematic Review and Meta-Analyses guidelines identifying studies on nipple-sparing mastectomy where incision type was described. Pooled descriptive statistics meta-analysis of overall (nipple-areola complex) necrosis rate and nipple-areola complex necrosis by incision type was performed.
Fifty-one studies (9975 nipple-sparing mastectomies) were included. Thirty-two incision variations were identified and categorized into one of six groups: inframammary fold, radial, periareolar, mastopexy/prior scar/reduction, endoscopic, and other. The most common incision types were inframammary fold 3634 nipple-sparing mastectomies (37.8 percent) and radial 3575 nipple-sparing mastectomies (37.2 percent). Meta-analysis revealed an overall partial nipple-areola complex necrosis rate of 4.62 percent (95 percent CI, 3.14 to 6.37 percent) and a total nipple-areola complex necrosis rate of 2.49 percent (95 percent CI, 1.87 to 3.21 percent). Information on overall nipple-areola complex necrosis rate by incision type was available for 30 of 51 studies (4645 nipple-sparing mastectomies). Periareolar incision had the highest nipple-areola complex necrosis rate (18.10 percent). Endoscopic and mastopexy/prior scar/reduction incisions had the lowest rates of necrosis at 4.90 percent and 5.79 percent, respectively, followed by the inframammary fold incision (6.82 percent). The rate of single-stage implant reconstruction increased during this period.
For nipple-sparing mastectomy, the periareolar incision maintains the highest necrosis rate because of disruption of the nipple-areola complex blood supply. The inframammary fold incision has become the most popular incision, demonstrating an acceptable complication profile.
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