keyword
https://read.qxmd.com/read/38503874/correction-an-immunogenomic-exome-landscape-of-triple-positive-primary-antiphospholipid-patients
#1
A Guffroy, L Jacquel, Y Seeleuthner, N Paul, V Poindron, F Maurier, V Delannoy, A C Voegeli, P Zhang, B Nespola, A Molitor, M J Apithy, P Soulas-Sprauel, T Martin, R E Voll, S Bahram, V Gies, J L Casanova, A Cobat, B Boisson, R Carapito, A S Korganow
No abstract text is available yet for this article.
March 19, 2024: Genes and Immunity
https://read.qxmd.com/read/38493947/single-cell-and-multi-omics-analyses-highlight-cancer-associated-fibroblasts-induced-immune-evasion-and-epithelial-mesenchymal-transition-for-smoking-bladder-cancer
#2
JOURNAL ARTICLE
Jiajin Wu, Fang Gao, Rui Meng, Huiqin Li, Zhenguang Mao, Yanping Xiao, Qiuyi Pu, Mulong Du, Zhengdong Zhang, Qiang Shao, Rui Zheng, Meilin Wang
Tobacco carcinogens are recognized as critical hazard factors for bladder tumorigenesis, affecting the prognosis of patients through aromatic amines components. However, the specific function of tobacco carcinogens and systematic assessment models in the prognosis of bladder cancer remains poorly elucidated. We retrieved bladder cancer specific tobacco carcinogens-related genes from Comparative Toxicogenomic Database, our Nanjing Bladder Cancer cohort and TCGA database. Gene×gene interaction method was utilized to establish a prognostic signature...
March 15, 2024: Toxicology
https://read.qxmd.com/read/38420407/the-global-landscape-of-immune-derived-lncrna-signature-in-colorectal-cancer
#3
JOURNAL ARTICLE
Mengying Zhang, Yifei Wu, Jingyi Mou, Yang Yao, Pengbo Wen, Xin Liu, Shipeng Shang, Xingxing Kang, Jiaqi Tian, Yan Liu, Enhui Lv, Liang Wang
BACKGROUND: Colorectal cancer (CRC) is a highly heterogeneous cancer. This heterogeneity has an impact on the efficacy of immunotherapy. Long noncoding RNAs (lncRNAs) have been found to play regulatory functions in cancer immunity. However, the global landscape of immune-derived lncRNA signatures has not yet been explored in colorectal cancer. METHODS: In this study, we applied DESeq2 to identify differentially expressed lncRNAs in colon cancer. Next, we performed an integrative analysis to globally identify immune-driven lncRNA markers in CRC, including immune-associated pathways, tumor immunogenomic features, tumor-infiltrating immune cells, immune checkpoints, microsatellite instability (MSI) and tumor mutation burden (TMB)...
February 29, 2024: Heliyon
https://read.qxmd.com/read/38359792/single-cell-transcriptome-landscape-of-circulating-cd4-t%C3%A2-cell-populations-in-autoimmune-diseases
#4
JOURNAL ARTICLE
Yoshiaki Yasumizu, Daiki Takeuchi, Reo Morimoto, Yusuke Takeshima, Tatsusada Okuno, Makoto Kinoshita, Takayoshi Morita, Yasuhiro Kato, Min Wang, Daisuke Motooka, Daisuke Okuzaki, Yamami Nakamura, Norihisa Mikami, Masaya Arai, Xuan Zhang, Atsushi Kumanogoh, Hideki Mochizuki, Naganari Ohkura, Shimon Sakaguchi
CD4+ T cells are key mediators of various autoimmune diseases; however, their role in disease progression remains unclear due to cellular heterogeneity. Here, we evaluated CD4+ T cell subpopulations using decomposition-based transcriptome characterization and canonical clustering strategies. This approach identified 12 independent gene programs governing whole CD4+ T cell heterogeneity, which can explain the ambiguity of canonical clustering. In addition, we performed a meta-analysis using public single-cell datasets of over 1...
February 14, 2024: Cell Genom
https://read.qxmd.com/read/38358031/diversity-of-major-histocompatibility-complex-mhc-and-natural-killer-cell-receptor-nkr-genes-and-their-interactions-in-domestic-horses
#5
JOURNAL ARTICLE
Jana Bubenikova, Martin Plasil, Jan Futas, Karla Stejskalova, Marie Klumplerova, Jan Oppelt, Franz Suchentrunk, Pamela A Burger, Petr Horin
The immunogenome is the part of the genome that underlies immune mechanisms and evolves under various selective pressures. Two complex regions of the immunogenome, major histocompatibility complex (MHC) and natural killer cell receptor (NKR) genes, play an important role in the response to selective pressures of pathogens. Their importance is expressed by their genetic polymorphism at the molecular level, and their diversity associated with different types of diseases at the population level. Findings of associations between specific combinations of MHC/NKR haplotypes with different diseases in model species suggest that these gene complexes did not evolve independently...
February 2024: HLA
https://read.qxmd.com/read/38268001/mrna-based-precision-targeting-of-neoantigens-and-tumor-associated-antigens-in-malignant-brain-tumors
#6
JOURNAL ARTICLE
Vrunda Trivedi, Changlin Yang, Kelena Klippel, Oleg Yegorov, Christina von Roemeling, Lan Hoang-Minh, Graeme Fenton, Elizabeth Ogando-Rivas, Paul Castillo, Ginger Moore, Kaytora Long-James, Kyle Dyson, Bently Doonan, Catherine Flores, Duane A Mitchell
BACKGROUND: Despite advancements in the successful use of immunotherapy in treating a variety of solid tumors, applications in treating brain tumors have lagged considerably. This is due, at least in part, to the lack of well-characterized antigens expressed within brain tumors that can mediate tumor rejection; the low mutational burden of these tumors that limits the abundance of targetable neoantigens; and the immunologically "cold" tumor microenvironment that hampers the generation of sustained and productive immunologic responses...
January 25, 2024: Genome Medicine
https://read.qxmd.com/read/38267542/an-immunogenomic-exome-landscape-of-triple-positive-primary-antiphospholipid-patients
#7
JOURNAL ARTICLE
A Guffroy, L Jacquel, Y Seeleuthner, N Paul, V Poindron, F Maurier, V Delannoy, A C Voegeli, P Zhang, B Nespola, A Molitor, M J Apithy, P Soulas-Sprauel, T Martin, R E Voll, S Bahram, V Gies, J L Casanova, A Cobat, B Boisson, R Carapito, A S Korganow
Primary antiphospholipid syndrome is characterized by thrombosis and autoantibodies directed against phospholipids or associated proteins. The genetic etiology of PAPS remains unknown. We enrolled 21 patients with thromboembolic events associated to lupus anticoagulant, anticardiolipin and anti β2 glycoprotein1 autoantibodies. We performed whole exome sequencing. Data were compared to public databases and to a control cohort of 873 non-autoimmune patients. We performed whole exome sequencing and a systematic variant-based analysis in genes associated with thrombosis, in candidate genes previously associated with APS or inborn errors of immunity...
January 24, 2024: Genes and Immunity
https://read.qxmd.com/read/38170124/a-novel-prognostic-predictor-of-immune-microenvironment-and-therapeutic-response-in-clear-cell-renal-cell-carcinoma-based-on-angiogenesis-immune-related-gene-signature
#8
JOURNAL ARTICLE
Guixin Ding, Tianqi Wang, Gonglin Tang, Qingsong Zou, Gang Wu, Jitao Wu
BACKGROUND: Clear cell renal cell carcinoma (ccRCC), the most common type of RCC, typically produces no symptoms initially. Patients with ccRCC are at increased risk of developing advanced metastatic disease due to the absence of dependable and effective prognostic biomarkers. Therefore, it is particularly urgent to find optimal stratification of patients with ccRCC to distinguish the clinical benefits of different malignant degrees. Angiogenesis has a profound impact on the malignant behavior of renal cancer cells, and anti-angiogenic drugs have been applied to metastatic renal cancer patients...
January 15, 2024: Heliyon
https://read.qxmd.com/read/38149253/utilizing-immunogenomic-approaches-to-prioritize-targetable-neoantigens-for-personalized-cancer-immunotherapy
#9
REVIEW
Ravi K Shah, Erin Cygan, Tanya Kozlik, Alfredo Colina, Anthony E Zamora
Advancements in sequencing technologies and bioinformatics algorithms have expanded our ability to identify tumor-specific somatic mutation-derived antigens (neoantigens). While recent studies have shown neoantigens to be compelling targets for cancer immunotherapy due to their foreign nature and high immunogenicity, the need for increasingly accurate and cost-effective approaches to rapidly identify neoantigens remains a challenging task, but essential for successful cancer immunotherapy. Currently, gene expression analysis and algorithms for variant calling can be used to generate lists of mutational profiles across patients, but more care is needed to curate these lists and prioritize the candidate neoantigens most capable of inducing an immune response...
2023: Frontiers in Immunology
https://read.qxmd.com/read/38137116/a-prediction-model-for-deciphering-intratumoral-heterogeneity-derived-from-the-microglia-macrophages-of-glioma-using-non-invasive-radiogenomics
#10
JOURNAL ARTICLE
Yunyang Zhu, Zhaoming Song, Zhong Wang
Microglia and macrophages play a major role in glioma immune responses within the glioma microenvironment. We aimed to construct a prognostic prediction model for glioma based on microglia/macrophage-correlated genes. Additionally, we sought to develop a non-invasive radiogenomics approach for risk stratification evaluation. Microglia/macrophage-correlated genes were identified from four single-cell datasets. Hub genes were selected via lasso-Cox regression, and risk scores were calculated. The immunological characteristics of different risk stratifications were assessed, and radiomics models were constructed using corresponding MRI imaging to predict risk stratification...
December 1, 2023: Brain Sciences
https://read.qxmd.com/read/38062499/comprehensive-characterization-of-adipogenesis-related-genes-in-colorectal-cancer-for-clinical-significance-and-immunogenomic-landscape-analyses
#11
JOURNAL ARTICLE
Jing Han, Shangshang Li, Qiong Zhan, Yuchao Hu, Chaoxiang Zhong, Jie Yang, Zhengcai Qiu
OBJECTIVE: Colorectal cancer (CRC) is a major global health concern, necessitating the identification of biomarkers and molecular subtypes for improved clinical management. This study aims to evaluate the clinical value of adipogenesis-related genes and molecular subtypes in CRC. METHODS: A comprehensive analysis of adipogenesis-related genes in CRC was performed using publicly available datasets (TCGA and GEO database) and bioinformatics tools. Unsupervised cluster analysis was employed to identify the molecular subtypes of CRC, while LASSO regression analysis was utilized to develop a risk prognostic model...
December 7, 2023: Lipids in Health and Disease
https://read.qxmd.com/read/38042584/recent-advances-in-immunopeptidomic-based-tumor-neoantigen-discovery
#12
JOURNAL ARTICLE
Wei Meng, Robert D Schreiber, Cheryl F Lichti
The role of aberrantly expressed proteins in tumors in driving immune-mediated control of cancer has been well documented for more than five decades. Today, we know that both aberrantly expressed normal proteins as well as mutant proteins (neoantigens) can function as tumor antigens in both humans and mice. Next-generation sequencing (NGS) and high-resolution mass spectrometry (MS) technologies have made significant advances since the early 2010s, enabling detection of rare but clinically relevant neoantigens recognized by T cells...
2023: Advances in Immunology
https://read.qxmd.com/read/38026206/mirs-an-ai-scoring-system-for-predicting-the-prognosis-and-therapy-of-breast-cancer
#13
JOURNAL ARTICLE
Chen Huang, Min Deng, Dongliang Leng, Baoqing Sun, Peiyan Zheng, Xiaohua Douglas Zhang
Tumor-infiltrating immune cells (TIICs) and metastasis are crucial characteristics for tumorigenesis. However, the potential role of their combination in breast cancer (BRCA) remains elusive. Herein, on the basis of quantifying TIICs and tumor metastasis together, we established a precise prognostic scoring system named metastatic and immunogenomic risk score (MIRS) using a neural network model. MIRS showed better performance when compared with other published signatures. MIRS stratifies patients into a high risk subtype (MIRShigh ) and a low risk subtype (MIRSlow )...
November 17, 2023: IScience
https://read.qxmd.com/read/38017322/elucidation-of-novel-snps-affecting-immune-response-to-classical-swine-fever-vaccination-in-pigs-using-immunogenomics-approach
#14
JOURNAL ARTICLE
Satish Kumar, Bharat Bhushan, Amit Kumar, Manjit Panigrahi, Jaya Bharati, Soni Kumari, Kaisa Kaiho, Santanu Banik, A Karthikeyan, Rajni Chaudhary, G K Gaur, Triveni Dutt
The host genetic makeup plays a significant role in causing the within-breed variation among individuals after vaccination. The present study was undertaken to elucidate the genetic basis of differential immune response between high and low responder Landlly (Landrace X Ghurrah) piglets vis-à-vis CSF vaccination. For the purpose, E2 antibody response against CSF vaccination was estimated in sampled animals on the day of vaccination and 21-day post-vaccination as a measure of humoral immune response. Double-digestion restriction associated DNA (ddRAD) sequencing was undertaken on 96 randomly chosen Landlly piglets using Illumina HiSeq platform...
November 29, 2023: Veterinary Research Communications
https://read.qxmd.com/read/37993659/globally-shared-tcr-repertoires-within-the-tumor-infiltrating-lymphocytes-of-patients-with-metastatic-gynecologic-cancer
#15
JOURNAL ARTICLE
Taehoon Kim, Hyeonseob Lim, Soyeong Jun, Junsik Park, Dongin Lee, Ji Hyun Lee, Jung-Yun Lee, Duhee Bang
Gynecologic cancer, including ovarian cancer and endometrial cancer, is characterized by morphological and molecular heterogeneity. Germline and somatic testing are available for patients to screen for pathogenic variants in genes such as BRCA1/2. Tissue expression levels of immunogenomic markers such as PD-L1 are also being used in clinical research. The basic therapeutic approach to gynecologic cancer combines surgery with chemotherapy. Immunotherapy, while not yet a mainstream treatment for gynecologic cancers, is advancing, with Dostarlimab recently receiving approval as a treatment for endometrial cancer...
November 22, 2023: Scientific Reports
https://read.qxmd.com/read/37985959/unveiling-the-immunogenomic-landscape-of-cholangiocarcinoma-identifying-new-prognostic-markers-and-therapeutic-targets-based-on-ccl5-expression
#16
JOURNAL ARTICLE
Jing Wang, Dan Xiang, Zhe Dai, Jialong Zhu, Yuanyang Du, Gongbo Fu, Xiaoyuan Chu
BACKGROUND: Cholangiocarcinoma (CCA) stands as an aggressive malignancy of the biliary tract. The interplay between the tumor and immune system plays a pivotal role in disease progression and treatment outcomes. Hence, the present study aimed to extensively explore the immunogenomic landscape of CCA, with the objective of unveiling unique molecular and immunological signatures that could guide personalized therapeutic approaches. METHODS: The study collected data from The Cancer Genome Atlas databases, performed gene set variation analysis for the chemokine ligand 5 (CCL5) high/low expression group, conducted principal component analysis, gene set enrichment analysis enrichment and mutation pattern analysis, generated a heatmap, and performed cox regression analysis...
November 20, 2023: Journal of Gene Medicine
https://read.qxmd.com/read/37985530/pan-cancer-analyses-of-senescence-related-genes-in-extracellular-matrix-characterization-in-cancer
#17
JOURNAL ARTICLE
Bo Yan, Pan Liao, Liqiu Shi, Ping Lei
PURPOSE: The aged microenvironment plays a crucial role in tumor onset and progression. However, it remains unclear whether and how the aging of the extracellular matrix (ECM) influences cancer onset and progression. Furthermore, the mechanisms and implications of extracellular matrix senescence-related genes (ECM-SRGs) in pan-cancer have not been investigated. METHODS: We collected profiling data from over 10,000 individuals, covering 33 cancer types, 750 small molecule drugs, and 24 immune cell types, for a thorough and systematic analysis of ECM-SRGs in cancer...
November 20, 2023: Discover. Oncology
https://read.qxmd.com/read/37972940/immunogenomics-of-cholangiocarcinoma
#18
JOURNAL ARTICLE
Virag Gehl, Colm J O'Rourke, Jesper B Andersen
The development of cholangiocarcinoma spans years, if not decades, during which the immune system becomes corrupted and permissive to primary tumor development and metastasis. This involves subversion of local immunity at tumor sites, as well as systemic immunity and the wider host response. While immune dysfunction is a hallmark of all cholangiocarcinoma, the specific steps of the cancer-immunity cycle that are perturbed differ between patients. Heterogeneous immune functionality impacts the evolutionary development, pathobiological behavior and therapeutic response of these tumors...
November 16, 2023: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://read.qxmd.com/read/37971722/nivolumab-for-patients-with-high-risk-oral-leukoplakia-a-nonrandomized-controlled-trial
#19
JOURNAL ARTICLE
Glenn J Hanna, Alessandro Villa, Shuvro P Nandi, Ruichao Shi, Anne ONeill, Mofei Liu, Charles T Quinn, Nathaniel S Treister, Herve Y Sroussi, Piamkamon Vacharotayangul, Laura A Goguen, Donald J Annino, Eleni M Rettig, Vickie Y Jo, Kristine S Wong, Patrick Lizotte, Cloud P Paweletz, Ravindra Uppaluri, Robert I Haddad, Ezra E W Cohen, Ludmil B Alexandrov, William N William, Scott M Lippman, Sook-Bin Woo
IMPORTANCE: Proliferative verrucous leukoplakia (PVL) is an aggressive oral precancerous disease characterized by a high risk of transformation to invasive oral squamous cell carcinoma (OSCC), and no therapies have been shown to affect its natural history. A recent study of the PVL immune landscape revealed a cytotoxic T-cell-rich microenvironment, providing strong rationale to investigate immune checkpoint therapy. OBJECTIVE: To determine the safety and clinical activity of anti-programmed cell death 1 protein (PD-1) therapy to treat high-risk PVL...
November 16, 2023: JAMA Oncology
https://read.qxmd.com/read/37950640/optimal-population-specific-hla-imputation-with-dimension-reduction
#20
JOURNAL ARTICLE
Venceslas Douillard, Nayane Dos Santos Brito Silva, Sonia Bourguiba-Hachemi, Michel S Naslavsky, Marilia O Scliar, Yeda A O Duarte, Mayana Zatz, Maria Rita Passos-Bueno, Sophie Limou, Pierre-Antoine Gourraud, Élise Launay, Erick C Castelli, Nicolas Vince
Human genomics has quickly evolved, powering genome-wide association studies (GWASs). SNP-based GWASs cannot capture the intense polymorphism of HLA genes, highly associated with disease susceptibility. There are methods to statistically impute HLA genotypes from SNP-genotypes data, but lack of diversity in reference panels hinders their performance. We evaluated the accuracy of the 1000 Genomes data as a reference panel for imputing HLA from admixed individuals of African and European ancestries, focusing on (a) the full dataset, (b) 10 replications from 6 populations, and (c) 19 conditions for the custom reference panels...
November 11, 2023: HLA
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