No abstract

Predicting peptide binding affinity with human leukocyte antigen (HLA) is a crucial step in developing powerful antitumor vaccine for cancer immunotherapy. Currently available methods work quite well in predicting peptide binding affinity with HLA alleles such as HLA-A*0201, HLA-A*0101, and HLA-B*0702 in terms of sensitivity and specificity. However, quite a few types of HLA alleles that are present in the majority of human populations including HLA-A*0202, HLA-A*0203, HLA-A*6802, HLA-B*5101, HLA-B*5301, HLA-B*5401, and HLA-B*5701 still cannot be predicted with satisfactory accuracy using currently available methods. Furthermore, currently the most popularly used methods for predicting peptide binding affinity are inefficient in identifying neoantigens from a large quantity of whole genome and transcriptome sequencing data. Here we present a Position Specific Scoring Matrix (PSSM)-based software called PSSMHCpan to accurately and efficiently predict peptide binding affinity with a broad coverage of HLA class I alleles. We evaluated the performance of PSSMHCpan by analyzing 10-fold cross-validation on a training database containing 87 HLA alleles and obtained an average area under receiver operating characteristic curve (AUC) of 0.94 and accuracy (ACC) of 0.85. In an independent dataset (Peptide Database of Cancer Immunity) evaluation, PSSMHCpan is substantially better than the popularly used NetMHC-4.0, NetMHCpan-3.0, PickPocket, Nebula, and SMM with a sensitivity of 0.90, as compared to 0.74, 0.81, 0.77, 0.24, and 0.79. In addition, PSSMHCpan is more than 197 times faster than NetMHC-4.0, NetMHCpan-3.0, PickPocket, sNebula, and SMM when predicting neoantigens from 661 263 peptides from a breast tumor sample. Finally, we built a neoantigen prediction pipeline and identified 117 017 neoantigens from 467 cancer samples of various cancers from TCGA. PSSMHCpan is superior to the currently available methods in predicting peptide binding affinity with a broad coverage of HLA class I alleles.

Circulating tumor cells (CTCs) slough off primary tumor tissues and are swept away by the circulatory system. These CTCs can remain in circulation or colonize new sites, forming metastatic clones in distant organs. Recently, CTC analyses have been successfully used as effective clinical tools to monitor tumor progression and prognosis. With advances in next-generation sequencing (NGS) and single-cell sequencing (SCS) technologies, scientists can obtain the complete genome of a CTC and compare it with corresponding primary and metastatic tumors. CTC sequencing has been successfully applied to monitor genomic variations in metastatic and recurrent tumors, infer tumor evolution during treatment, and examine gene expression as well as the mechanism of the epithelial-mesenchymal transition. However, compared with cancer biopsy sequencing and circulating tumor DNA sequencing, the sequencing of CTC genomes and transcriptomes is more complex and technically difficult. Challenges include enriching pure tumor cells from a background of white blood cells, isolating and collecting cells without damaging or losing DNA and RNA, obtaining unbiased and even whole-genome and transcriptome amplification material, and accurately analyzing CTC sequencing data. Here, we review and summarize recent studies using NGS on CTCs. We mainly focus on CTC genome and transcriptome sequencing and the biological and potential clinical applications of these methodologies. Finally, we discuss challenges and future perspectives of CTC sequencing.

The goal of this work was to investigate the molecular profiles and metastasis markers in Chinese patients with gastric carcinoma (GC). In total, we performed whole exome sequencing (WES) on 74 GC patients with tumor and adjacent normal formalin-fixed, paraffin-embedded (FFPE) tissue samples. The mutation spectrum of these samples showed a high concordance with TCGA and other studies on GC. PTPRT is significantly associated with metastasis of GC, suggesting its predictive role in metastasis of GC. Patients carrying BRCA2 mutations tend not to metastasize, which may be related to their sensitivity to chemotherapy. Mutations in MACF1, CDC27, HMCN1, CDH1 and PDZD2 were moderately enriched in peritoneal metastasis (PM) samples. Furthermore, we found two genomic regions (1p36.21 and Xq26.3) were associated with PM of GC, and patients with amplification of 1p36.21 and Xq26.3 have a worse prognosis (P = 0.002, 0.01, respectively). Our analysis provides GC patients with potential markers for single and combination therapies.

Background: A-to-I RNA-editing mediated by ADAR (adenosine deaminase acting on RNA) enzymes that converts adenosine to inosine in RNA sequence can generate mutations and alter gene regulation in metazoans. Previous studies have shown that A-to-I RNA-editing plays vital roles in mouse embryogenesis. However, the RNA-editing activities in early human embryonic development have not been investigated.

Although evolutionarily just as ancient as IgM, it has been thought for many years that IgD is not present in birds. Based on the recently sequenced genomes of 48 bird species as well as high-throughput transcriptome sequencing of immune-related tissues, we demonstrate in this work that the ostrich (Struthio camelus) possesses a functional δ gene that encodes a membrane-bound IgD H chain with seven CH domains. Furthermore, δ sequences were clearly identified in many other bird species, demonstrating that the δ gene is widely distributed among birds and is only absent in certain bird species. We also show that the ostrich possesses two μ genes (μ1, μ2) and two υ genes (υ1, υ2), in addition to the δ and α genes. Phylogenetic analyses suggest that subclass diversification of both the μ and υ genes occurred during the early stages of bird evolution, after their divergence from nonavian reptiles. Although the positions of the two υ genes are unknown, physical mapping showed that the remaining genes are organized in the order μ1-δ-α-μ2, with the α gene being inverted relative to the others. Together with previous studies, our data suggest that birds and nonavian reptile species most likely shared a common ancestral IgH gene locus containing a δ gene and an inverted α gene. The δ gene was then evolutionarily lost in selected birds, whereas the α gene lost in selected nonavian reptiles. The data obtained in this study provide significant insights into the understanding of IgH gene evolution in tetrapods.

The original model showed good performance in the Dutch validation population. The updated models resulted in more accurate ALN metastasis prediction and could be useful preoperative tools in selecting low-risk patients for omission of axillary surgery.

26Triple-negative breast cancer (TNBC) represents the most aggressive breast cancer 27 subtype, which recently attracts great interest for immune therapeutic development. In 28 this context, in-depth understanding of TNBC immune landscape is highly demanded. 29 Here we report single-cell RNA sequencing results of 9683 tumor-infiltrated immune 30 cells isolated from 14 treatment naïve TNBC tumors, where 22 immune cell subsets, 31 including T cells, macrophages, B cells, and DCs have been characterized. We 32 identify a new T cell subset, CD8 + CXCL8 + naïve T cell, which associates with poor 33 survival. A novel immune cell subset comprised of TCR + macrophages, is found to be 34 widely distributed in TNBC tumors. Further analyses reveal an up-regulation of 35 molecules associated with TCR signaling and cytotoxicity in these immune cells, 36 indicating TCR signaling activation. Altogether, our study provides a valuable 37 resource to understand the immune ecosystem of TNBC. The novel immune cell 38 subsets reported herein might be functionally important in cancer immunity. 39 40 SIGNIFICANCE：This work demonstrates a single-cell transcriptome atlas of 41 immune cells in treatment naïve TNBC tumors, revealing novel immune cell subsets. 42This study provides a valuable resource to understand the immune ecosystem of 43 TNBC, which will be helpful for the immunotherapeutic strategy design of TNBC. 44 45 85TNBC tumors are typically more aggressive and difficult to treat than hormone 86 receptor-positive tumors, and are associated with a higher risk of early relapse. The 87 lack of estrogen receptor, progesterone receptor, and HER2 expression precludes the 88 use of targeted therapies, and the only approved systemic treatment option is 89 chemotherapy. Responses to chemotherapy occur, but are often short lived and 90 frequently accompanied by considerable toxicity. Gene profiling studies reveal that 91 TNBCs are highly heterogeneous and a large proportion of them demonstrate DNA 92 Repair Deficiency Signature (18)(19)(20). Recent data showed impressive activity of 93 PD-1/PD-L1 blockade therapy in metastatic TNBC patients who were chemotherapy 94 naïve, suggesting early intervention of immunotherapy can bring more benefit (21). 95Clinical trials applying checkpoint inhibitors in the neo-adjuvant setting of TNBC are 96 ongoing. Although need to be confirmed in a larger cohort, these results are consistent 97 with the notion that immunotherapy agents are most efficient at low tumor burden and 98 in patients naïve of immune-modulatory chemotherapy agents. To better understand 99 the immune ecosystem of TNBC, we analyzed the full-length single-cell RNA 100 sequencing data of 9,683 tumor-infiltrated immune cells isolated from treatment naïve 101 TNBC tumors. We identified 22 unique immune cell subsets, including T cells, 102 macrophages, B cells, and DCs. Using combined expression and TCR-based analyses, 103 we were able to indicate the function and developmental path of T cell subsets. We 104 found a novel T c...