Topic 189

cancer tumor patients patient prognostic survival alterations cancers microenvironment clinical profiling genomic collection signature tumours tumour breast presence metastasis vulnerabilities metastatic analysis comprehensive progression poor amplification samples biology prognosis prostate them status had subtype lymph potential therapeutic pathological lcm m2 gene clinico overall immunohistochemistry characteristics imminent found tp53 score co strategy marker 17 pertinence laser focusing idc microdissection 54 derived attractive subset malignant 19q kaplan meier oncogenic 1p correlated m1 distinct subtypes immunoglobulin remarkable primary phenotypes macrophage statement advanced lymphatic epithelial associated profile 85 lineage mutation highly classified setting atrx pik3ca disparate dependencies was 3000 aggressive morevover mutational variant but

29 items. Top items listed below.

Human Prostate Cancer-Associated Macrophage Subtypes with Prognostic Potential Revealed by Single-cell Transcriptomics 189 148 14 9 3

Genome profiles of lymphovascular breast cancer cells reveal multiple clonally differentiated outcomes with multi-regional LCM and G&T-seq 189 14 9 3

Identification of stromal genes differentially expressed in lobular breast cancer highlights role for pregnancy-associated-plasma protein-A 189 14 9 3

Inflammatory state of lymphatic vessels and miRNA profiles associated with relapse in ovarian cancer patients 189 14 10 9

Patients Derived Short-Term Glioma Culture: Identification of Aggressive, Drug Resistant Phenotype 189 14 10 9

CBX2 and CBX7 antagonistically regulate metabolic reprogramming in breast cancer 189 14 9 3

A subset of pediatric thalamic gliomas share a distinct DNA methylation profile, H3K27me3 loss and frequent alteration of EGFR 189 14 9

CDKN2C homozygous loss identifies a distinct subtype of TP53/RB1-wildtype leiomyosarcoma with frequent CIC genomic alterations and 1p/19q-codeletion 189 9

A pan-cancer analysis of the frequency of DNA alterations across cell cycle activity levels 189 15 9

Expression of Toll like Receptor 4 in the ductal epithelial cells of the Breast tumor microenvironment is correlated with the invasiveness of the tumor 189 98 14 10 3

A Boolean Model of the Formation of Tumour Associated Macrophages in an in-vitro Model of Chronic Lymphocytic Leukaemia 189 14 10 3

Lineage transcription factors co-regulate subtype-specific genes providing a roadmap for systematic identification of small cell lung cancer vulnerabilities 189 31 9 3

Personalized Cancer Therapy Prioritization Based on Driver Alteration Co-occurrence Patterns 189 112 14 4

Intracellular Optical Doppler Phenotypes of Chemosensitivity in Human Epithelial Ovarian Cancer 189 152 14 10

Relationship between stemness and transcriptionally-inferred PI3K activity in human breast cancer 189 126 14 10

Detection of HER2 expression and its structural alterations in gastric cancer tissues infected with cagA+ H. pylori 189 15 10

CCM 1 determines YAP/TAZ signaling dependent metastatic hallmarks of prostate cancer cells 189 108 14 3

Targeted surveillance strategies for efficient detection of novel antibiotic resistance variants 189 97 52 12

The Clinical Kinase Index: Prioritizing Understudied Kinases as Targets for the Treatment of Cancer 189 14 9

Multiplexing Mutation Rate Assessment: Determining Pathogenicity of Msh2 Variants in S. cerevisiae 189 97 4

The pathognomonic FOXL2 C134W mutation alters DNA binding specificity 189 31 9 3

Persistent cell proliferation signals correlates with increased glycolysis in tumor hypoxia microenvironment across cancer types 186 9

Alternative Lengthening of Telomeres is not synonymous with mutations in ATRX/DAXX 189 97

The Primary Tumor Immune Microenviornment Status Predicts the Response to Immunotherapy and Overall Survival in Breast Cancer 14 10 9

A multi-layered systems approach for renal cell carcinoma 14 9

TCGA Pan-Cancer genomic analysis of Alternative Lengthening of Telomeres (ALT) related genes 9

Stroma transcriptomic and proteomic profile of prostate cancer metastasis xenograft models reveals conservation of bonemicroenvironment signatures 152 14 9 3

"3G" Trial: An RNA Editing Signature for Guiding Gastric Cancer Chemotherapy 112 9 4

Relationship Between Neuroendocrine and Immune Gene Expression in Small Cell Lung Cancer 14 9 3

Aging interacts with tumor biology to produce major changes in the immune tumor microenvironment 14 9 3

Convergent network effects along the axis of gene expression during prostate cancer progression 14 9

The Molecular Landscape of Asian Breast Cancers Reveals Clinically Relevant Population-Specific Differences 14 9

Characterizing the tumor microenvironment of metastatic ovarian cancer by single cell transcriptomics 148 14 9 3

Global computational alignment of tumor and cell line transcriptional profiles 43 14 9 4

RRM2B is frequently amplified across multiple tumor types: non-oncogenic addiction and therapeutic opportunities 142 14 9 3

Metastatic signaling of hypoxia-related genes across TCGA Pan-Cancer types 186 14 9 3

Comparative study of transcriptomics-based scoring metrics for the epithelial-hybrid-mesenchymal spectrum 98 14 9 4

Genetic timestamping of plasma cells in vivo reveals homeostatic population turnover 189

Machine learning-based investigation of the cancer protein secretory pathway 112 14 9 4

Identification of the associated expression patterns as potential predictive markers for cancer prognosis 112 9

ARID2 deficiency promotes tumor progression and is associated with higher sensitivity to PARP inhibition in lung cancer 142 14 9 3

Integrative omics data analysis uncovers biomarker genes and potential candidate drugs for G3 medulloblastoma 112 14 9

The clinical and molecular significance associated with STING signaling in estrogen receptor-positive early breast cancer 14 10 3

Systems biomedicine of primary and metastatic colorectal cancer reveals potential therapeutic targets 98 14 9 3

Molecular characterization of unusual G10P genomic constellations and evidence of zooanthroponosis in bovines 189 121 12 5

An Integrative Analysis of the Age-Associated Genomic, Transcriptomic and Epigenetic Landscape across Cancers 87 9

Comprehensive analysis of prognostic immune-related genes in the tumor microenvironment of lung adenocarcinoma 14 9

Prostate cancer peripheral blood NK cells show enhanced CD9, CD49a, CXCR4, CXCL8, MMP-9 production, and secrete monocyte-recruiting and polarizing factors 189 27 10 3

The landscape of interactions between cancer polygenic risk scores and somatic alterations in cancer cells 97 9 4

Patient-derived glioblastoma cells (GBM) exhibit distinct biomechanical profiles associated with altered activity in the cytoskeleton regulatory pathway 152 14 9 3

Hormone Receptor-status Prediction in Breast Cancer Using Gene Expression Profiles and Their Macroscopic Landscape 9 4

Single-cell analysis of patient-derived PDAC organoids reveals cell state heterogeneity and a conserved developmental hierarchy 152 14 9 3

Analysis of single-cell RNA-seq data from ovarian cancer samples before and after chemotherapy links stress-related transcriptional profile withchemotherapy resistance 14 9

Integrated genomics and comprehensive validation reveal novel drivers of genomic evolution in esophageal adenocarcinoma 14 9 3

Autoantibody landscape of advanced prostate cancer 189 14

Transcriptome sequencing and multi-plex imaging of prostate cancer microenvironment reveals a dominant role for monocytic cells in progression 148 14 9 3

Comparative analysis of genome-wide DNA methylation identifies patterns that associate with conserved transcriptional programs in osteosarcoma 87 9

ATM Inhibition Synergizes with Fenofibrate in High Grade Serous Ovarian Cancer Cells 126 14 10 9 3

A single cell atlas of the healthy breast tissues reveal clinically relevant clusters of breast epithelial cells 7

Epigenetic downregulation of HER2 during EMT leads to tumor resistance to HER2-targeted therapies in breast cancer 98 14 10 3

Plasticity as an Underlying Mechanism of Tumor Heterogeneity in Breast Cancer 152 14 9

The capacity of the ovarian cancer tumor microenvironment to integrate inflammation signaling conveys a shorter disease-free interval 14 10 9 3

Single cell analysis of colorectal cancer identifies mitogen-activated protein kinase as a key driver of tumor cell plasticity 152 148 142 14 9 3

Biomarker-guided treatment strategies for ovarian cancer identified from a heterogeneous panel of patient-derived tumor xenografts 126 14 10 9

Identification of oncolytic vaccinia restriction factors in canine high-grade mammary tumor cells using single-cell transcriptomics 14 9

TimeTeller: a New Tool for Precision Circadian Medicine and Cancer Prognosis 112 14 4

Molecular characterization of triple negative breast cancer formaldehyde-fixed paraffin-embedded samples by data independent acquisition proteomics 45 14 9

A novel role for the tumor suppressor gene ITF2 in lung tumorigenesis and chemotherapy response 186 14 9 3

Systematic analysis of aberrances of ferroptosis reveals its potential functional roles in cancer 14 9 3

Molecular and clinical characterization of 5mC regulators in glioma: results of a multicenter study 14 9

USP19 modulates cancer cell migration and invasion and acts as a novel prognostic marker in patients with early breast cancer 108 14 3

A novel hypoxia gene signature indicates prognosis and reveals the multi-omics molecular landscape of tumour tissue in patients with hepatocellular carcinoma 14 9

Mobile Element Insertions and Associated Structural Variants in Longitudinal Breast Cancer Samples 97 9

Calumenin contributes to epithelial-mesenchymal transition and predicts poor survival in glioma 98 7

Integrative analysis of mutated genes and mutational processes reveals seven colorectal cancer subtypes 97 9 4

The landscape of metabolic pathway dependencies in cancer cell lines 186 9 3

TRAF4 inhibits bladder cancer progression by promoting BMP/SMAD signalling pathway 98 14 3

Exploring the effects of genetic variation on gene regulation in cancer in the context of 3D genome structure 89 19 9 4

Primary platinum resistance and immune exclusion in ovarian carcinomas with high expression of the homologous recombination mediator RAD51 138 14 10 9

Single-cell RNA-sequencing of peripheral neuroblastic tumors reveals an aggressive transitional cell state at the junction of an adrenergic-mesenchymal transdifferentiation trajectory 152 14 9 3

PRER: A Patient Representation with Pairwise Relative Expression of Proteins on Biological Networks 184 7 4

Epigenetic regulation of differentially expressed genes between various glioma types 31 9

NDRG1 expression is an independent prognostic factor in inflammatory breast cancer 14 10 9

A deep learning approach for tissue spatial quantification and genomic correlations of histopathological images 131 26 9 4

Profiles and clinical significance of immune cell infiltration in pancreatic adenocarcinoma 9

Transcriptional profiling reveals a subset of human breast tumors that retain wt TP53 but display mutant p53-associated features 142 14 9 3

RIPK2 Stabilizes c-Myc and is an Actionable Target for Inhibiting Prostate Cancer Metastasis 108 14 10 3

Divergent resistance mechanisms to immunotherapy explains response in different skin cancers. 173 14 10 3

Integration of Biodynamic Imaging and RNA-seq predicts chemotherapy response in canine diffuse large B-cell lymphoma 112 14 9 4

The functional and phenotypic diversity of single T-cell infiltrates in human colorectal cancer as correlated with clinical outcome 14 9 3

Functional mapping of androgen receptor enhancer activity 31 9 3

Oecophyllibacter saccharovorans gen. nov. sp. nov., a bacterial symbiont of the weaver ant Oecophylla smaragdina 189 121 12 5

Tumor Edge-to-Core Transition Promotes Malignancy in Primary-to-Recurrent Glioblastoma Progression in a PLAGL1/CD109-mediated mechanism 14 3

Large scale analysis of smoking-induced changes in the tumor immune microenvironment 14 9

Integration of machine learning and genome-scale metabolic modeling identifies multi-omics biomarkers for radiation resistance 112 14 4

Human papillomavirus type 16 sub-lineages and integration in cancer 7

Gene expression profiles of inflammatory breast cancer reveal high heterogeneity across the epithelial-hybrid-mesenchymal spectrum 98 14 9 4

Tumor-on-a-chip platform to interrogate the role of macrophages in tumor progression 14 10 3

Mutational processes impact the evolution of anti-EGFR antibody resistance in colorectal cancer 14 10 9

Predicting Tumor Response to Drugs based on Gene-Expression Biomarkers of Sensitivity Learned from Cancer Cell Lines 7 4