4.8 Article

Immunometabolic coevolution defines unique microenvironmental niches in ccRCC

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Oncology

Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness

Yize Li et al.

Summary: By integrating histopathologic, proteogenomic, and metabolomic analyses, this study reveals the inter- and intratumoral heterogeneity of clear cell renal cell carcinomas (ccRCCs). It identifies high-risk disease subsets based on tumor grade, BAP1 mutation, genome instability, hypermethylation, and protein glycosylation signature. RNA sequencing provides insights into gene signatures and potential targeted therapies, while in vitro cell line studies validate the efficacy of inhibiting identified phosphoproteome targets.

CANCER CELL (2023)

Article Biochemical Research Methods

Spatially resolved isotope tracing reveals tissue metabolic activity

Lin Wang et al.

Summary: Isotope imaging enables quantification of metabolic activity in mammalian tissues with spatial resolution, revealing metabolic heterogeneity in the kidney and brain and spatial gradients in metabolic processes.

NATURE METHODS (2022)

Article Multidisciplinary Sciences

PHGDH heterogeneity potentiates cancer cell dissemination and metastasis

Matteo Rossi et al.

Summary: The loss of phosphoglycerate dehydrogenase (PHGDH) has been found to increase cancer metastasis. Heterogeneous or low expression of PHGDH in primary tumors of breast cancer patients is associated with decreased metastasis-free survival time. Loss of PHGDH activates the hexosamine-sialic acid pathway through its interaction with the glycolytic enzyme phosphofructokinase, leading to increased cell migration and invasion.

NATURE (2022)

Article Genetics & Heredity

Spatiotemporal evolution of the clear cell renal cell carcinoma microenvironment links intra-tumoral heterogeneity to immune escape

Mahdi Golkaram et al.

Summary: This study on ccRCC patients revealed that increased ITH is associated with a constellation of genetic and microenvironmental features, as well as neoantigen depletion, impacting the response to ICI treatment. These findings have implications for the development of biomarkers for ICI response in the future.

GENOME MEDICINE (2022)

Article Oncology

A Targetable Myeloid Inflammatory State Governs Disease Recurrence in Clear-Cell Renal Cell Carcinoma

Phillip M. Rappold et al.

Summary: This study identifies myeloid inflammation as a key driver of disease recurrence in localized clear-cell renal cell carcinoma (ccRCC) and suggests that effector T-cell gene signatures are not associated with disease recurrence. Targeting immunosuppressive myeloid inflammation significantly reduces metastatic development in an immunocompetent mouse model.

CANCER DISCOVERY (2022)

Article Biotechnology & Applied Microbiology

MIRTH: Metabolite Imputation via Rank-Transformation and Harmonization

Benjamin A. Freeman et al.

Summary: This study describes a method called Metabolite Imputation via Rank-Transformation and Harmonization (MIRTH) that can impute unmeasured metabolite abundances by modeling metabolite covariation across different datasets. MIRTH successfully recovers masked metabolite abundances and suggests that latent information about unmeasured metabolites exists within existing metabolomics data, which can be used to generate new hypotheses and simplify metabolomic workflows.

GENOME BIOLOGY (2022)

Article Medicine, Research & Experimental

Tobacco smoking induces metabolic reprogramming of renal cell carcinoma

James Reigle et al.

Summary: The study identified a TS-related metabolic subtype of ccRCC with vulnerabilities that can be targeted for precision medicine. A gene expression signature based on this subtype provided prognostic stratification of ccRCC tumors independent of genomic alterations. Metallomic analysis revealed disrupted metal homeostasis in ccRCC, emphasizing the importance of studying effects of metals from e-cigarettes and environmental exposures.

JOURNAL OF CLINICAL INVESTIGATION (2021)

Review Cell Biology

Ferroptosis: mechanisms, biology and role in disease

Xuejun Jiang et al.

Summary: Ferroptosis, as a form of regulated cell death driven by iron-dependent phospholipid peroxidation, has seen significant growth in research in recent years. Studies have focused on molecular mechanisms, regulation, and functions of ferroptosis, linking this cell death modality to various pathologies and proposing its roles in normal physiology and potential therapeutic targeting.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2021)

Article Multidisciplinary Sciences

1-Methylnicotinamide is an immune regulatory metabolite in human ovarian cancer

Marisa K. Kilgour et al.

Summary: Immune regulatory metabolites in the tumor microenvironment, such as 1-methylnicotinamide (MNA), play a key role in modulating T cell responses. Despite the elevated levels of MNA in T cells infiltrating tumors, the enzyme catalyzing MNA transfer is restricted to fibroblasts and tumor cells. Functionally, MNA induces T cells to secrete tumor-promoting cytokines, suggesting it as a potential immunotherapy target for human cancer treatment.

SCIENCE ADVANCES (2021)

Article Multidisciplinary Sciences

CTLA-4 blockade drives loss of Treg stability in glycolysis-low tumours

Roberta Zappasodi et al.

Summary: By blocking CTLA-4, metabolic fitness and immune cell infiltration in tumours, especially those with low glycolytic activity, can be enhanced. This improves therapeutic outcomes, particularly in tumours with defective glycolysis, by destabilizing T-reg cells and promoting the activity of tumour-specific CD8(+) T cells.

NATURE (2021)

Article Medicine, General & Internal

Nivolumab plus Cabozantinib versus Sunitinib for Advanced Renal-Cell Carcinoma

T. K. Choueiri et al.

Summary: The study demonstrates that nivolumab plus cabozantinib has significant advantages over sunitinib in the treatment of previously untreated advanced renal-cell carcinoma, including progression-free survival, overall survival, and likelihood of response.

NEW ENGLAND JOURNAL OF MEDICINE (2021)

Article Multidisciplinary Sciences

Cell-programmed nutrient partitioning in the tumour microenvironment

Bradley Reinfeld et al.

Summary: The study found that in the tumor microenvironment, different cell types have varying abilities to access and consume glucose and glutamine, with nutrient partitioning being programmed in a cell-intrinsic manner through mTORC1 signaling and the expression of genes related to glucose and glutamine metabolism.

NATURE (2021)

Article Multidisciplinary Sciences

Metabolic heterogeneity confers differences in melanoma metastatic potential

Alpaslan Tasdogan et al.

NATURE (2020)

Article Multidisciplinary Sciences

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

Haley M. Amemiya et al.

SCIENTIFIC REPORTS (2019)

Article Biochemistry & Molecular Biology

A clonal expression biomarker associates with lung cancer mortality

Dhruva Biswas et al.

NATURE MEDICINE (2019)

Article Multidisciplinary Sciences

LC-MS based metabolomic profiling for renal cell carcinoma histologic subtypes

Lun Jing et al.

SCIENTIFIC REPORTS (2019)

Article Biochemical Research Methods

Strelka2: fast and accurate calling of germline and somatic variants

Sangtae Kim et al.

NATURE METHODS (2018)

Article Medicine, General & Internal

Nivolumab plus Ipilimumab versus Sunitinib in Advanced Renal-Cell Carcinoma

R. J. Motzer et al.

NEW ENGLAND JOURNAL OF MEDICINE (2018)

Article Biochemistry & Molecular Biology

A Landscape of Metabolic Variation across Tumor Types

Ed Reznik et al.

CELL SYSTEMS (2018)

Article Biochemistry & Molecular Biology

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

Kyle Ellrott et al.

CELL SYSTEMS (2018)

Review Cell Biology

Role of Histamine in Modulating the Immune Response and Inflammation

Anna Claudia Calvielli Castelo Branco et al.

MEDIATORS OF INFLAMMATION (2018)

Review Oncology

Sphingolipid metabolism in cancer signalling and therapy

Besim Ogretmen

NATURE REVIEWS CANCER (2018)

Article Biochemistry & Molecular Biology

Allele-Specific HLA Loss and Immune Escape in Lung Cancer Evolution

Nicholas McGranahan et al.

Article Medicine, Research & Experimental

Addressing metabolic heterogeneity in clear cell renal cell carcinoma with quantitative Dixon MRI

Yue Zhang et al.

JCI INSIGHT (2017)

Article Oncology

An Integrated Metabolic Atlas of Clear Cell Renal Cell Carcinoma

A. Ari Hakimi et al.

CANCER CELL (2016)

Article Biochemistry & Molecular Biology

FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing

Ronglai Shen et al.

NUCLEIC ACIDS RESEARCH (2016)

Review Nutrition & Dietetics

Impact of Obesity and Metabolic Syndrome on Immunity

Catherine J. Andersen et al.

ADVANCES IN NUTRITION (2016)

Article Biotechnology & Applied Microbiology

The Ensembl Variant Effect Predictor

William McLaren et al.

GENOME BIOLOGY (2016)

Article Biochemistry & Molecular Biology

Molecular and Genetic Properties of Tumors Associated with Local Immune Cytolytic Activity

Michael S. Rooney et al.

Article Biochemistry & Molecular Biology

Metabolic Competition in the Tumor Microenvironment Is a Driver of Cancer Progression

Chih-Hao Chang et al.

Article Biochemical Research Methods

Robust enumeration of cell subsets from tissue expression profiles

Aaron M. Newman et al.

NATURE METHODS (2015)

Article Medicine, General & Internal

Nivolumab versus Everolimus in Advanced Renal-Cell Carcinoma

R. J. Motzer et al.

NEW ENGLAND JOURNAL OF MEDICINE (2015)

Article Biochemistry & Molecular Biology

The Molecular Signatures Database Hallmark Gene Set Collection

Arthur Liberzon et al.

CELL SYSTEMS (2015)

Article Multidisciplinary Sciences

Fructose-1,6-bisphosphatase opposes renal carcinoma progression

Bo Li et al.

NATURE (2014)

Review Multidisciplinary Sciences

Metabolic control of cell death

Douglas R. Green et al.

SCIENCE (2014)

Article Biotechnology & Applied Microbiology

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love et al.

GENOME BIOLOGY (2014)

Article Biochemical Research Methods

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin et al.

BIOINFORMATICS (2013)

Article Multidisciplinary Sciences

Comprehensivemolecular characterization of clear cell renal cell carcinoma

Chad J. Creighton et al.

NATURE (2013)

Article Medicine, General & Internal

Pazopanib versus Sunitinib in Metastatic Renal-Cell Carcinoma

Robert J. Motzer et al.

NEW ENGLAND JOURNAL OF MEDICINE (2013)

Article Multidisciplinary Sciences

Inferring tumour purity and stromal and immune cell admixture from expression data

Kosuke Yoshihara et al.

NATURE COMMUNICATIONS (2013)

Article Ecology

A general and simple method for obtaining R2 from generalized linear mixed-effects models

Shinichi Nakagawa et al.

METHODS IN ECOLOGY AND EVOLUTION (2013)

Article Biochemical Research Methods

Software for Computing and Annotating Genomic Ranges

Michael Lawrence et al.

PLOS COMPUTATIONAL BIOLOGY (2013)

Article Biochemical Research Methods

SomaticSniper: identification of somatic point mutations in whole genome sequencing data

David E. Larson et al.

BIOINFORMATICS (2012)

Article Biochemical Research Methods

RSeQC: quality control of RNA-seq experiments

Liguo Wang et al.

BIOINFORMATICS (2012)

Article Biochemistry & Molecular Biology

Ferroptosis: An Iron-Dependent Form of Nonapoptotic Cell Death

Scott J. Dixon et al.

Article Biochemistry & Molecular Biology

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

Daniel C. Koboldt et al.

GENOME RESEARCH (2012)

Article Biochemical Research Methods

Fiji: an open-source platform for biological-image analysis

Johannes Schindelin et al.

NATURE METHODS (2012)

Article Medicine, General & Internal

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

Marco Gerlinger et al.

NEW ENGLAND JOURNAL OF MEDICINE (2012)

Article Biochemistry & Molecular Biology

Molecular Basis for the Substrate Stereoselectivity in Tryptophan Dioxygenase

Luciana Capece et al.

BIOCHEMISTRY (2011)

Article Biochemical Research Methods

phangorn: phylogenetic analysis in R

Klaus Peter Schliep

BIOINFORMATICS (2011)

Article Biochemical Research Methods

survcomp: an R/Bioconductor package for performance assessment and comparison of survival models

Markus S. Schroeder et al.

BIOINFORMATICS (2011)

Article Oncology

Chromosomal Instability Confers Intrinsic Multidrug Resistance

Alvin J. X. Lee et al.

CANCER RESEARCH (2011)

Article Multidisciplinary Sciences

Tumour evolution inferred by single-cell sequencing

Nicholas Navin et al.

NATURE (2011)

Article Genetics & Heredity

A framework for variation discovery and genotyping using next-generation DNA sequencing data

Mark A. DePristo et al.

NATURE GENETICS (2011)

Article Biochemistry & Molecular Biology

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

Aaron McKenna et al.

GENOME RESEARCH (2010)

Article Multidisciplinary Sciences

The patterns and dynamics of genomic instability in metastatic pancreatic cancer

Peter J. Campbell et al.

NATURE (2010)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Article Multidisciplinary Sciences

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

David A. Barbie et al.

NATURE (2009)

Article Multidisciplinary Sciences

Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing

Peter J. Campbell et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Multidisciplinary Sciences

Genomic Analysis of the Clonal Origins of Relapsed Acute Lymphoblastic Leukemia

Charles G. Mullighan et al.

SCIENCE (2008)

Article Biochemistry & Molecular Biology

Molecules in focus: Indoleamine 2,3-dioxygenase

Nicholas J. C. King et al.

INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY (2007)

Article Biochemistry & Molecular Biology

The UCSC Table Browser data retrieval tool

D Karolchik et al.

NUCLEIC ACIDS RESEARCH (2004)