Overall, we conclude that FGA performs comparable to or better than AS in predicting immunotherapy response in individual cancers, suggesting that it is the overall genome affected by CNAs (rather than the individual CNA length or mechanism of formation) that drives the observed CNA-immunotherapy response associations. 224, 389400 (2011). Bioinformatics 37, 24612463 (2021). These encouraging results strongly promote enthusiasm for immunotherapy and underscore a basic fact that at least in a subset of cancer patients, the suppressed immune system can still recognize tumor cells and be reactivated against these if sufficient co-stimulatory signals are delivered. Szklarczyk, D. et al. For pancreatic cancer-specific analyses, TCGA and other open-access databases or datasets without overlapping samples were integrated for further bioinformatic analyses. Intriguingly, TIME factors were identified to have more global coverage and prognostic significance across multiple cancer types compared with ICPs, thus offering more general targetability in clinical therapy. Immunotherapy 9, 681692 (2017). Cancer 9, 29382945 (2018). The function of programmed cell death 1 and its ligands in regulating autoimmunity and infection. Their results show that, at the pan-cancer level, a higher AS was associated with worse survival following immunotherapy among patients with low TMB (defined as the bottom 80% of TMB in each cancer type). Hoge, A. C. H. et al. Nat. These trackers help us to provide a personalized user experience by improving the quality of your preference management options, and by enabling the interaction with external networks and platforms. Annu. Since almost all ICPs and TIME factors were upregulated in PAAD, pancreatic adenocarcinoma was chosen for further detailed investigation, particularly the assessment of the potential combined targetability of ICPs and TIME factors. ICD is capable to elicit antitumor immunity via dead cell-associated antigens, and the molecular properties of ICD have been verified to largely overlap with TIME factors. SCI was established in 1900 to the current. 4, 143ra199 (2012). Neuro-Oncology. Sistigu, A. et al. Nat. If you don't find the journal then it doesn't have one. As FGA combines both chromosomal and focal CNAs, if the association between CNAs and immunotherapy response is driven by the overall genomic instability, one would expect FGA to perform at least as well as AS in predicting immunotherapy response. In addition, to investigate whether mutation of specific genes may contribute to the survival difference following immunotherapy, we performed a differential gene mutation frequency analysis among high FGA0.2 (or AS0.2) group versus low FGA0.2 (or AS0.2) group in the two cancer types in the Samstein et al.s cohort with the largest sample size, i.e., melanoma and non-small cell lung cancer. However, on the other hand, the average values of elbow points across different cancer types of both AS and FGA are 0.17, which is very close to the cutoff of 0.2 used above. PubMed Central Each dot represents the individual expression of a distinct tumor or normal sample. 29, 20522060 (2018). Med. We found that none of the genes had significantly differential mutation frequencies between the high FGA0.2 (or AS0.2) versus low FGA0.2 (or AS0.2) patients after multiple testing correction (Supplementary Table 2). Breast Cancer Res. d Correlation of ICPs and effector T-cell signatures in pancreatic cancer. Open Access funding provided by the National Institutes of Health (NIH). b Summary of expression profiles of TIME factors in multiple cancer types. The landscape of somatic copy-number alteration across human cancers. ), China Postdoctoral Science Foundation (2016T90413 and 2015M581693 to X.H. Sharma, P., Hu-Lieskovan, S., Wargo, J. N. Engl. Rev. Tian-Gen Chang or Eytan Ruppin. Only journals listed in the Science Citation Index Expanded (SCIE) and Social Sciences Citation Index (SSCI) receive an Impact Factor. Ghebeh, H. et al. 1). Considering the expression spectrum and prognostic uncertainty of ICPs in cancer, the widespread application of ICP inhibitors is perhaps unrealistic. Prominent examples are pancreatic cancer19, cholangiocarcinoma (CHOL)20, and gastric cancer21, and this issue has not been resolved to date22,23. Learn more about Stack Overflow the company, and our products. Eng. Our results indicated the prevalence of deregulation of both ICPs and TIME factors in varying types of malignancies, which exerted enormous influence on the prognosis of patients. Science Citation Index covers 9,000+ journals across 177 scientific disciplines. conceived the project and supervised the study. Ariyan, C. E. et al. Oncol. GEPIA generated dot plots profiling the tissue-wise expression patterns of MET across multiple cancer types (TCGA tumor) and paired normal tissue samples (TCGA normal+GTEx normal). Oncol. Immunol. Discover more about utilizing AI for precision oncology in a Behind the Paper post from Author Istvan Petak. Sign up for the Nature Briefing: Cancer newsletter what matters in cancer research, free to your inbox weekly. This landscape included inframe mutation, missense mutation, truncating mutating, fusion, amplification, deep deletion, and no alterations (Fig. Tomczak, K., Czerwinska, P. & Wiznerowicz, M. The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge. 4c, d). Article Confirmation Of Your Paper Being Published. 1a). Did an AI-enabled drone attack the human operator in a simulation environment? GEPIA generated the pair-wise gene expression correlations between two lists of signature genes in pancreatic cancer (TCGA tumor), using the Spearman method after normalized by GAPDH. & Baek, J. G. Oversampling method using outlier detectable generative adversarial network. Ma, Y., Galluzzi, L., Zitvogel, L. & Kroemer, G. Autophagy and cellular immune responses. 193, 839846 (2001). Safety and activity of anti-PD-L1 antibody in patients with advanced cancer. Ann. The combined score ranked from 0 to 1, with 1 indicating the highest possible confidence. Our data analysis revealed that significant KaplanMeier survival analysis always corresponded to significant multivariate analysis in individual cancer types and vice versa. AACR Project GENIE: powering precision medicine through an International Consortium. 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The ISSN of this journal is N/A. Galluzzi, L., Buque, A., Kepp, O., Zitvogel, L. & Kroemer, G. Immunological effects of conventional chemotherapy and targeted anticancer agents. Further information can be found in our privacy policy. Combination cancer immunotherapy and new immunomodulatory targets. 5, 122 (2020). 2b); Similarly, the HRs between high and low FGA0.2 groups were 1.32 and 1.35, respectively, among high-TMB versus low-TMB patients (Fig. SCI is a multidisciplinary citation index. Panaretakis, T. et al. Ann. Journal Rankings on Oncology - Scimago Journal & Country Rank DNA-based copy number analysis confirms genomic evolution of PDX models. You can decide for yourself which categories you want to deny or allow. 3). To obtain J. Exp. The following allows you to customize your consent preferences for any tracking technology used Through this web page, researchers can check the impact factor, total citation, journal quartile, and journal aim & scope. However, instead of identifying immunotherapies as ineffective, the observed resistance may indicate that both the influence and stimulation on TIME factors cannot meet the minimal requirements for reinvigorating of the immune system. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Chen, L. & Han, X. Anti-PD-1/PD-L1 therapy of human cancer: past, present, and future. This is why bona fide immune interventions in specific circumstances can improve the chemotherapeutic efficacy to some extent. Neuro-Oncology Impact Factor IF 2022|2021|2020 - BioxBio Further analysis indicated significant deregulation of the expression levels of other different ICPs in the majority of malignancies (Fig. npj Precision Oncology - Vrije Universiteit Amsterdam what is the impact factor of "npj Precision Oncology" [closed], CEO Update: Paving the road forward with AI and community at the center, Building a safer community: Announcing our new Code of Conduct, AI/ML Tool examples part 3 - Title-Drafting Assistant, We are graduating the updated button styling for vote arrows, What is the relationship between impact factor and journal ranking. Med. For instance, CD73 and CD39, identified as ATP homeostasis factors in this study, have also been identified as potential ICPs. Patients with or without different alterations of ICPs and TIME factors were individually collected and subjected to PFS analysis. Nature 541, 417420 (2017). AS were calculated using ASCETS v.1.1 at https://github.com/beroukhim-lab/ascets with the following command line: where x is the CNA calling cutoff, defined as the threshold at which a CNA event is counted if |log2 copy ratio|> x. FGA was calculated as the ratio between the sum of the lengths of the genomic segments with |log2 copy ratio|>x, and the sum of the lengths of all measured segments: CNA events, which were used to calculate AS and FGA, were first called using |log2 copy ratio| cutoffs ranging from 0.01 to 0.5 with a step size of 0.01. We used the elbow method, which was developed to identify a cutoff point that optimally distinguishes between two qualitative, discrete states15. 33, 19741982 (2015). All journals covered in this database are reviewed for sufficiently high quality each year. In total, 1660 multivariate Cox models as part of the leave-one-out cross-validation analysis are constructed with AS0.1 or AS0.2 or FGA0.1 or FGA0.2 (binned at the candidate binarization percentile), TMB (binned at the 80th percentile), and ICB drug class. Extreme amenability of topological groups and invariant means. Journal Impact. 2b). b Contribution of integrated alterations of ICPs and TIME factors to PFS in pancreatic cancer. Spearman correlation analysis was used to analyze the pair-wise gene expression correlations between ICPs and TIME factors, and results with p value <0.01 were selected. GEPIA generated the KaplanMeier OS map comparing the groups with different expression levels of ICPs in multiple cancer types (TCGA tumors). 4. Similarly, it was found that colorectal cancer might also achieve significant HR>1 with a sample size of ~600 patients in both cohorts (Supplementary Table 1). OS, PFS, DFS, and DSS in pancreatic cancer were individually investigated to compare the prognostic differences between altered and unaltered groups, and the Log rank test was used for hypothesis testing. to help us achieve the features and activities described below. Topalian, S. L. Targeting immune checkpoints in cancer therapy. https://doi.org/10.1126/science.aaf8399 (2017). 6, i.e., the Samstein et al.s cohort1 from MSK-IMPACT. 13, 5461 (2007). To test if differential tumor purity across different cancer types may contribute to the variation of elbow points in individual cancer types, we investigated the relationship between elbow points and average tumor purity. Nat. In fact, ICB represents a specific treatment category that has seen some of the highest FDA and regulatory approvals across many cancer types within a relatively short timein the past over 5 years based on large randomized trials proving survival benefit even as single agents, whether biomarker-driven or not. Gentili, M. et al. A few questions still need to be urgently addressed in the near future: For instance, how should ICD and ICB be scheduled? The ICPs investigated in this study included the most well-established PD-L1, PD-L2, CD80, CD86, VTCN1, C10orf54, HHLA2, TNFRSF14, CD155, CD112, CD200, LGALS9, ICOSL, CD137L, CD252, CD70, GITRL, and CD48111. Science 349, 12321236 (2015). npj Precision Oncology Impact-Faktor IF 2022-2023 | Analyse, Trend However, although ICB is frontline therapy for many cancers, increasing numbers of studies have shown that the positive response rate from patients receiving drugs that target ICPs remains quite low in several specific malignancies. At the beginning, the secreted ATP favors the recruitment and activation of antigen-presenting cells (APCs) by P2RY2 and P2RX736. Quail, D. F. & Joyce, J. PubMed Central Smyth, M. J., Ngiow, S. F., Ribas, A. Nat. Science 350, 972978 (2015). 24, 319333 (2013). The latest impact factor of JCO Precision Oncology and all the other SCI journals was released on 30th June 2022 by Clarivate. Science 348, 5661 (2015). PubMed When attacked by cytotoxic T lymphocytes, cancer cells are able to utilize IFNG in TIME to activate their own signaling pathway related to signal transducers and activators of transcription (STATs), which in turn upregulates PD-L1 expression and suppresses incoming immune attacks14,81,82,83. The multivariable HRs of binarized ASEP (with adjustment of TMB and ICB drug class) in individual cancer types were, on average, greater than those obtained using AS0.1 ( mean HR=0.21, P=0.08; Fig. Onc.) Onc. . 1 Answer. For instance, a previous study reported that CDK4, a serinethreonine kinase involved in cell cycle progression and tumor growth, also plays a critical role in antitumor immunity by regulating PD-L1 expression113, and thus it was also included in this study. These included four datasets, such as Pancreatic Adenocarcinoma (ICGC, Nature 2012)117, Pancreatic Adenocarcinoma (QCMG, Nature 2016)118, Pancreatic Adenocarcinoma (TCGA, PanCancer Atlas)119, and Pancreatic Cancer (UTSW, Nat. Intriguingly, a very recent study by Huang et al.111 has reported that CALR genetically couples with many ICPs in pancreatic cancer, which is actually the first time to reveal the direct molecular connection between ICD and ICP. 7, 818831 (2017). All rights reserved. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. The Hormel Institute, University of Minnesota. Differential regulation of PD-L1 expression by immune and tumor cells in NSCLC and the response to treatment with atezolizumab (anti-PD-L1). Kepp, O. et al. Kowanetz, M. et al. KaplanMeier survival analysis was performed using the R packages survminer v.0.4.9 and survival v.3.3.1, and HR and P values were calculated with univariable Cox proportional hazard regression using the coxph() function19. It says on the website that the journal has been indexed by ESCI (Emerging Science Citation Index). Nat. For example, MUC1, a cell surface TIME factor found on epithelial cells, is found associated with HDGF where they share 26 variants in 769 patient samples. See more details on, https://www.nature.com/npjprecisiononcology/. Front. 6 was |log2 copy ratio|>0.1, the cutoff of |log2 copy ratio|>0.2 in calculating AS and/or FGA was more frequently used (e.g., refs. Nat. (3) ICPs were found to be deregulated and significantly influenced prognosis (e.g., LGG and KIRC). what is the impact factor of "npj Precision Oncology" Sci. T.-G.C., Y.C., and E.D.S. J. Exp. Brahmer, J. R. et al. NPJ Precision Oncology provides a venue for the publication of recent research contributions in the swiftly growing aras of Oncology and Cancer Research. MESO and UVM in TCGA were excluded from the analyses because of data incompleteness. You are using a browser version with limited support for CSS. Given that ICPs can serve as a part rather than the opposite side of TIME factors, it may not be necessary to differentiate between ICPs and TIME factors in the future, but rather, they should be targeted together.