For pancreatic cancer-specific analyses, TCGA and other open-access databases or datasets without overlapping samples were integrated for further bioinformatic analyses. Cell Death Differ. Segmented copy-number data were downloaded from AACR Project GENIE v.7.1. 3a). Kepp, O. et al. 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. MESO and UVM in TCGA were excluded from the analyses because of data incompleteness. Neuro-Oncology Impact Factor IF 2022|2021|2020 - BioxBio 6 (which calls chromosome-level CNAs using the cutoff of |log2 copy ratio|>0.1; denoted as AS0.1). Year: Impact Factor (IF) Total Articles . Paired Wilcoxon test P values are displayed. Edited. 366, 24552465 (2012). If material is not included in the articles Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. Rev. Science 334, 15731577 (2011). Journal Impact. Natl Acad. Yamazaki, T. et al. and T.T. This study published in NPJ Precision Oncology describes a computational method to select the most effective targeted therapies for cancer patients based on the individual molecular profile of their tumor. What to report as impact factor for a journal that had one the year I submitted my manuscript, but not in the year of publication? Vacchelli, E. et al. MantelCox test was used for the hypothesis tests, and the Cox proportional hazard ratio was included in the survival plots. 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. Disrupted epigenetics of the gene encoding PD-L1 (CD247) resulted in high PD-L1 expression in tumor cells, which was associated with poor immune infiltration, sclerotic/desmoplastic stroma, and mesenchymal molecular features64. Year: Impact Factor (IF) Total Articles: Total Cites . Enter journal title, issn or abbr in this box to search. 2b). The immune-related signatures of 28 investigated TIL types were collected according to Charoentong et al.125, and the relative abundances of TILs in different cancer types were inferred using gene set variation analysis based on the gene expression profile. We hence reasoned that an arbitrary threshold could never be optimal for all datasets and searched for an unbiased approach for threshold calling. Genomic investigation of co-targeting tumor immune microenvironment and immune checkpoints in pan-cancer immunotherapy. Sci. Here, our results revealed the prognostic significance of TIME factors in multiple cancers and their close relationship with ICPs, implicating tumors use both ICPs and TIME factors to escape from immune surveillance. As a pan-cancer KaplanMeier survival analysis (as performed in ref. 2, 14031404 (2016). J. Powered by, Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature, Targeting ACE2-BRD4 in Cancer and COVID-19, Advancing human and canine cancer care: analysis of the largest clinico-genomics canine cancer dataset as a hypothesis generation for cancer drug discovery, Artificial Intelligence Reveals Features Associated with Breast Cancer Neoadjuvant Chemotherapy Responses from Multi-stain Histopathologic Images, Racial and ethnic disparities in a real-world precision oncology data registry, Urine cell-free DNA multi-omics to detect MRD and predict survival in bladder cancer patients, Ovarian cancer specific homologous recombination deficiency score, MatchMiner: an open-source platform for cancer precision medicine, Expression of a proliferation signature predicts sensitivity to genotoxic chemotherapy in oligometastatic colorectal cancer. Nat. 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. This ultimately results in immunological resistance and poor prognosis. Data for the Samstein et al.1 cohort (MSK-IMPACT) were downloaded from cBioPortal at http://www.cbioportal.org/study?id= tmb_mskcc_2018. Clin. Instead, sample size limitation may be a critical factor for specific cancer types, as suggested by our power analysis. Topalian, S. L., Drake, C. G. & Pardoll, D. M. Immune checkpoint blockade: a common denominator approach to cancer therapy. reported that the tumor aneuploidy score (AS), defined as the fraction of chromosome arms with arm-level CNAs in a sample, which was called using a loose cutoff of |log2 copy ratio|>0.1, is significantly predictive of survival following immunotherapy in low-TMB patients, but not in high-TMB patients, in a pan-cancer analysis6. Cancer Genome Atlas Research, N. et al. 9f), PANX1 (Fig. Cold Spring Harb. Despite of such potential importance and promising prospect, directly targeting TIME regulators in a simple and feasible way is still not easy to achieve, except in a gene-silencing or editing-based strategy. Onc. This model assumes that the data is generated from two Gaussian distributions with different means and variances, and that each data point belongs to one of the two distributions with a certain probability. 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. Slider with three articles shown per slide. Article Compact visualization of cases originated from four studies with multiple genetic alterations of ICPs and TIME factors were individually shown by cBioPortal as indicated, including the cases with inframe mutation, missense mutation, truncating mutation, fusion, amplification, deep deletion or/and no alterations, and not profiled ones. Investig. Immunol. New functions for the matrix metalloproteinases in cancer progression. Specifically, the HRs between high and low AS0.2 groups were 1.23 and 1.34, respectively, among high-TMB versus low-TMB patients (Fig. Connect and share knowledge within a single location that is structured and easy to search. Impact Factor is the most common scientometric index, which is defined by the number of citations of papers in two preceding years divided by the number of papers published in those years. McGrail, D. J. et al. 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. J. Stay Tuned! We are always looking for inspiration, feedback, and collaborators. 2). Biankin, A. V. et al. Hoge, A. C. H. et al. Furthermore, the released HMGB1 stimulates the synthesis of pro-inflammatory factors, APC maturation, and presentation of tumor antigens by TLR439. In situ immune response after neoadjuvant chemotherapy for breast cancer predicts survival. Article Chang, TG., Cao, Y., Shulman, E.D. Recently, Spurr et al. ICB is not sufficient for cancer immunotherapy. Topalian, S. L. Targeting immune checkpoints in cancer therapy. 8, 152 (2020). So far, to neutralize their immunosuppressive effects and maximize the immunostimulatory functions of anticancer drugs, the chemotherapeutic drug gemcitabine has been combined with ipilimumab in preclinical models107. However, considering the substantial shortcomings in the induction of ICD for cancer therapy, a combination of ICD inducers and ICP-targeted drugs may be an optimal counterplan to help cancer patients in the foreseeable future8,15,103,104,105. 2c). 208, 491503 (2011). c Contribution of integrated alterations of ICPs and TIME factors to DFS in pancreatic cancer. Google Scholar. For instance, cancer cells can alter the outside microenvironment through characteristic metabolic patterns (e.g., Warburg effect and glutaminolysis), thus inactivating cancer-infiltrating immune cells66,67,68,69,70,71. 9b), ANXA1 (Fig. Science 349, 12321236 (2015). NPJ Precis. A number of prominent researchers considered this journal to publish their scholarly documents including Hongyang Wang, Kym F. Faull, Himisha Beltran, Tracy T. Batchelor and Eleftherios P. Diamandis. Corresponding to the different stimuli, there are many types of death of cancer cells, such as apoptosis, necroptosis, autophagy, ferroptosis, and pyroptotic cell death87,88,89. Oncoimmunology 6, e1386829 (2017). ISSN 2397-768X (online), Optimizing cancer immunotherapy response prediction by tumor aneuploidy score and fraction of copy number alterations, CT radiomic signature predicts survival and chemotherapy benefit in stage I and II HPV-associated oropharyngeal carcinoma, Deep computational image analysis of immune cell niches reveals treatment-specific outcome associations in lung cancer, HRD effects on first-line adjuvant chemotherapy and PARPi maintenance therapy in Chinese ovarian cancer patients, High-throughput proteomics profiling-derived signature associated with chemotherapy response and survival for stage II/III colorectal cancer, Deep learning generates synthetic cancer histology for explainability and education, Histological transformation to gliosarcoma with combined BRAF/MEK inhibition in, PD-1 blockade potentiates neoadjuvant chemotherapy in NSCLC via increasing CD127, ML-based sequential analysis to assist selection between VMP and RD for newly diagnosed multiple myeloma, Extraordinary clinical response to ibrutinib in low-grade ovarian cancer guided by organoid drug testing, Refined high-content imaging-based phenotypic drug screening in zebrafish xenografts, A framework for artificial intelligence in cancer research and precision oncology, Development and testing of a polygenic risk score for breast cancer aggressiveness, Immunosuppression for immune-related adverse events during checkpoint inhibition: an intricate balance, Dramatic, durable response to therapy in g, Potential utility of risk stratification for multicancer screening with liquid biopsy tests, Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature, Phase I study of sapanisertib with carboplatin and paclitaxel in mTOR pathway altered solid malignancies, Complete response to alectinib in ALK-fusion metastatic salivary ductal carcinoma, Self-supervised attention-based deep learning for pan-cancer mutation prediction from histopathology. Impact factor: 10.123 Q1 (Oncology (30/245)) Scopus Journal Metrics (2021) SJR: 0.000 SNIP: 2.143 CiteScore: 9.1 Rank within the category: Medicine - Oncology Quartile: Q1 CiteScore percentile: 85% CiteScore rank: 54 out of 360 Rank within the category: Biochemistry, Genetics and Molecular Biology - Cancer Research Quartile: Q1 Science Citation Index covers 9,000+ journals across 177 scientific disciplines. Nat. Doxorubicin downregulates cell surface B7-H1 expression and upregulates its nuclear expression in breast cancer cells: role of B7-H1 as an anti-apoptotic molecule. Thank you for visiting nature.com. SNIP score for npj Precision Oncology is 2. e Correlation of TIME factors and effector T-cell signatures in pancreatic cancer. Pharm. Robust antitumor responses result from local chemotherapy and CTLA-4 blockade. Research Impact Score*: 4.1 Impact Factor: 10.092 Citescore: 9.1 Research Ranking (Medicine) 1001 Number of Best scientists*: 125 Documents by best scientists*: 64 Journal Information ISSN: 2397-768X Publisher: Editors-in-Chief: Trever Bivona Journal & Submission Website: https://www.nature.com/npjprecisiononcology/ Aims & Scope of the Journal 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. 13, 10501059 (2007). Only journals listed in the Science Citation Index Expanded (SCIE) and Social Sciences Citation Index (SSCI) receive an Impact Factor. 2, 401404 (2012). 2015)120. The latest impact factors list will release in june 2023. . In conclusion, TIME factors are promising cancer immunotherapeutic targets, and a TIME factor-targeting strategy should be synergized with ICB to fully harness the power of TIME and obtain a maximum clinical benefit for the future cancer immunotherapy. More importantly, clinical decisions to use these drugs, especially dual CTLA-4 and PD-1 blockade, should consider their potential to induce high-grade immune-related adverse events. Oral Oncol. Semantics of the `:` (colon) function in Bash when used in a pipe? Jia-Shiong Chen, Cheng-Han Chou, Chia-Nan Chen, Nina G. Steele, Eileen S. Carpenter, Marina Pasca di Magliano, Tolga Turan, Sarah Kongpachith, Michele Ceccarelli, Charlotte Pilard, Marie Ancion, Michael Herfs, Szonja Anna Kovcs, Jnos Tibor Fekete & Balzs Gyrffy, Hanne Vos, Kathleen Lambein, Ann Smeets, Juan Dubrot, Peter P. Du, Robert T. Manguso, npj Precision Oncology Therefore, larger sample sizes are required to evaluate, and ultimately use these measures within individual cancer types. This study aimed to assess the potential merits and feasibility of combinational targeting ICPs and TIME in cancer immunotherapy. All rights reserved. Nat. JCO Precision Oncology - Scimago Journal & Country Rank E.R. As a result, anti-PD1/PD-L1 has become one of the most successful immune therapies, and the expression of PD-L1 in tumor cells was identified as a crucial biomarker for the efficacy of ICP therapy65. Nucleic Acids Res. Did an AI-enabled drone attack the human operator in a simulation environment? Garcia-Diaz, A. et al. ISSN 2397-768X (online). Article Open Access 27 Mar 2023. Hence, widely applicable inducers of ER stress, autophagy, necroptosis, or viral mimicry have been employed as ICD activators15,34,48,49,50,51,52,53. For Authors | JAMA Oncology | JAMA Network 29, 20522060 (2018). Red blocks represent TIME factors unfavorable to survival, blue blocks represent TIME factors favorable to survival, and the ones with outer wireframe indicate significant influence. Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors. Commun. Springer Nature is the publisher of npj Precision Oncology. ), Major Scientific Project of Zhejiang Lab (2018DG0ZX01 to T.L. Why is Bb8 better than Bc7 in this position? 4b). npj series. Front Cell Dev. Quantification of aneuploidy in targeted sequencing data using ASCETS. Biotechnol. {\mathrm{R}} \;{\hbox{-}}{\mathrm{i}}\;{\mathrm{genie}}{\_}{\mathrm{msk}}{\_}{\mathrm{cna}}{\_}{\mathrm{hg19}}.{\mathrm{seg}}\;{\hbox{-}}{\mathrm{c}}\;{\mathrm{genomic}}{\_}{\mathrm{arm}}{\_}{\mathrm{coordinates}}{\_}{\mathrm{hg19}}. The detailed study process, including the study design, collection, analysis, and interpretation of the data and the writing of the paper, was not affected by the sponsoring foundations. Nat. Rudd, P. M., Elliott, T., Cresswell, P., Wilson, I. This method has been found to be effective in determining optimal parameter thresholds in a variety of data-driven optimization tasks including the determination of the number of clusters, determination of the number of principal components, and with relevance to our goal, determination of the threshold on a receiver operating characteristic curve16,17,18. Publishers note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Timothy Rajakumar, MD, PhD & Bruno Steinkraus, PhD, Copyright 2023 Springer Nature All rights reserved. Cell death in the maintenance and abrogation of tolerance: the five Ws of dying cells. You are using a browser version with limited support for CSS. 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. Enter journal title, issn or abbr in this box to search. It also indicated the feasibility of combined treatment to boost a controllable anticancer immune response to overcome immunotherapeutic resistance in clinical applications. Nat. Adalsteinsson, V. A. et al. STRING generated known and predicted proteinprotein interactions between ICPs and TIME factors, including direct (physical) binding and indirect (functional) association, stemmed from interactions aggregated from primary databases, knowledge transfer between organisms, and computational prediction.