Yanding Zhao
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View article: Spatial Proximity of Immune Cell Pairs to Cancer Cells in the Tumor Microenvironment as Biomarkers for Patient Stratification
Spatial Proximity of Immune Cell Pairs to Cancer Cells in the Tumor Microenvironment as Biomarkers for Patient Stratification Open
Background/Objectives: The tumor microenvironment (TME) plays a critical role in cancer progression by shaping immune responses and influencing patient outcomes. We hypothesized that the relative proximity of specific immune cell pairs to …
View article: Three-dimensional genome landscape of primary human cancers
Three-dimensional genome landscape of primary human cancers Open
Genome conformation underlies transcriptional regulation by distal enhancers, and genomic rearrangements in cancer can alter critical regulatory interactions. Here we profiled the three-dimensional genome architecture and enhancer connecto…
View article: EcDNA-borne PVT1 fusion stabilizes oncogenic mRNAs
EcDNA-borne PVT1 fusion stabilizes oncogenic mRNAs Open
Summary Extrachromosomal DNA (ecDNA) amplifications are prevalent drivers of human cancers. We show that ecDNAs exhibit elevated structural variants leading to gene fusions that produce oncogene fusion transcripts. The long noncoding RNA (…
View article: Autoantibody hotspots reveal origin and impact of immunogenic XIST ribonucleoprotein complex
Autoantibody hotspots reveal origin and impact of immunogenic XIST ribonucleoprotein complex Open
Four out of five patients with autoimmune diseases are women. The XIST ribonucleoprotein (RNP) complex, comprising the female-specific long noncoding RNA XIST and over 100 associated proteins, may drive several autoimmune diseases that dis…
View article: Enhancing transcription–replication conflict targets ecDNA-positive cancers
Enhancing transcription–replication conflict targets ecDNA-positive cancers Open
Extrachromosomal DNA (ecDNA) presents a major challenge for cancer patients. ecDNA renders tumours treatment resistant by facilitating massive oncogene transcription and rapid genome evolution, contributing to poor patient survival 1–7 . A…
View article: Single-cell chromatin accessibility reveals malignant regulatory programs in primary human cancers
Single-cell chromatin accessibility reveals malignant regulatory programs in primary human cancers Open
To identify cancer-associated gene regulatory changes, we generated single-cell chromatin accessibility landscapes across eight tumor types as part of The Cancer Genome Atlas. Tumor chromatin accessibility is strongly influenced by copy nu…
View article: Rampant transcription replication conflict creates therapeutic vulnerability in extrachromosomal DNA containing cancers
Rampant transcription replication conflict creates therapeutic vulnerability in extrachromosomal DNA containing cancers Open
Extrachromosomal DNA (ecDNA) presents a major challenge for precision medicine, contributing to poor survival for patients with oncogene-amplified tumours. EcDNA renders tumours resistant to targeted treatments by facilitating massive tran…
View article: Xist ribonucleoproteins promote female sex-biased autoimmunity
Xist ribonucleoproteins promote female sex-biased autoimmunity Open
View article: Exploration of glycosyltransferases mutation status in cervical cancer reveals PARP14 as a potential prognostic marker
Exploration of glycosyltransferases mutation status in cervical cancer reveals PARP14 as a potential prognostic marker Open
View article: Supplementary Tables 1-8 from MYC Activity Inference Captures Diverse Mechanisms of Aberrant MYC Pathway Activation in Human Cancers
Supplementary Tables 1-8 from MYC Activity Inference Captures Diverse Mechanisms of Aberrant MYC Pathway Activation in Human Cancers Open
Table S1. TCGA samples included in study. Table S2. Gene weights of MYC signatures. Table S3. Pre-ranked Gene Set Enrichment Analysis results of cancer type-specific MYC activity signatures. Table S4. MYC AUC characteristics. Table S5. Rec…
View article: Supplementary Figures 1-5 from MYC Activity Inference Captures Diverse Mechanisms of Aberrant MYC Pathway Activation in Human Cancers
Supplementary Figures 1-5 from MYC Activity Inference Captures Diverse Mechanisms of Aberrant MYC Pathway Activation in Human Cancers Open
S1. Characteristics of MYC signatures. S2. MYC activity scores capture MYC pathway activity. S3. Diverse mechanisms of MYC alterations captured by MYC activity scores. S4. Prognostic relevance of MYC score. S5. High MYC activity is associa…
View article: Data from A Leukocyte Infiltration Score Defined by a Gene Signature Predicts Melanoma Patient Prognosis
Data from A Leukocyte Infiltration Score Defined by a Gene Signature Predicts Melanoma Patient Prognosis Open
Melanoma is the most aggressive type of skin cancer in the United States with an increasing incidence. Melanoma lesions often exhibit high immunogenicity, with infiltrating immune cells playing important roles in regression of tumors occur…
View article: Supplementary Figures 1-5 from MYC Activity Inference Captures Diverse Mechanisms of Aberrant MYC Pathway Activation in Human Cancers
Supplementary Figures 1-5 from MYC Activity Inference Captures Diverse Mechanisms of Aberrant MYC Pathway Activation in Human Cancers Open
S1. Characteristics of MYC signatures. S2. MYC activity scores capture MYC pathway activity. S3. Diverse mechanisms of MYC alterations captured by MYC activity scores. S4. Prognostic relevance of MYC score. S5. High MYC activity is associa…
View article: Data from A Leukocyte Infiltration Score Defined by a Gene Signature Predicts Melanoma Patient Prognosis
Data from A Leukocyte Infiltration Score Defined by a Gene Signature Predicts Melanoma Patient Prognosis Open
Melanoma is the most aggressive type of skin cancer in the United States with an increasing incidence. Melanoma lesions often exhibit high immunogenicity, with infiltrating immune cells playing important roles in regression of tumors occur…
View article: Supplementary Tables 1-7 from A Leukocyte Infiltration Score Defined by a Gene Signature Predicts Melanoma Patient Prognosis
Supplementary Tables 1-7 from A Leukocyte Infiltration Score Defined by a Gene Signature Predicts Melanoma Patient Prognosis Open
Table S1. Summary of the datasets Table S2. Immune related genes' correlation with ImmuneScore Table S3. 25 genes PC1 loading coefficient Table S4. Primary tumor mutation's association with LIS Table S5. Metastatic tumor mutation's associa…
View article: Supplementary Tables 1-7 from A Leukocyte Infiltration Score Defined by a Gene Signature Predicts Melanoma Patient Prognosis
Supplementary Tables 1-7 from A Leukocyte Infiltration Score Defined by a Gene Signature Predicts Melanoma Patient Prognosis Open
Table S1. Summary of the datasets Table S2. Immune related genes' correlation with ImmuneScore Table S3. 25 genes PC1 loading coefficient Table S4. Primary tumor mutation's association with LIS Table S5. Metastatic tumor mutation's associa…
View article: Supplementary Tables 1-8 from MYC Activity Inference Captures Diverse Mechanisms of Aberrant MYC Pathway Activation in Human Cancers
Supplementary Tables 1-8 from MYC Activity Inference Captures Diverse Mechanisms of Aberrant MYC Pathway Activation in Human Cancers Open
Table S1. TCGA samples included in study. Table S2. Gene weights of MYC signatures. Table S3. Pre-ranked Gene Set Enrichment Analysis results of cancer type-specific MYC activity signatures. Table S4. MYC AUC characteristics. Table S5. Rec…
View article: Supplementary figures 1-3 from A Leukocyte Infiltration Score Defined by a Gene Signature Predicts Melanoma Patient Prognosis
Supplementary figures 1-3 from A Leukocyte Infiltration Score Defined by a Gene Signature Predicts Melanoma Patient Prognosis Open
Figure S1. LIS reflects immune cell infiltration in melanoma microenvironment. Figure S2. LIS is associated with clinical factors and provided prognostic value in addition to clinical information in melanoma. Figure S3. LIS is predictive o…
View article: Supplementary figures 1-3 from A Leukocyte Infiltration Score Defined by a Gene Signature Predicts Melanoma Patient Prognosis
Supplementary figures 1-3 from A Leukocyte Infiltration Score Defined by a Gene Signature Predicts Melanoma Patient Prognosis Open
Figure S1. LIS reflects immune cell infiltration in melanoma microenvironment. Figure S2. LIS is associated with clinical factors and provided prognostic value in addition to clinical information in melanoma. Figure S3. LIS is predictive o…
View article: Data from MYC Activity Inference Captures Diverse Mechanisms of Aberrant MYC Pathway Activation in Human Cancers
Data from MYC Activity Inference Captures Diverse Mechanisms of Aberrant MYC Pathway Activation in Human Cancers Open
c-MYC (MYC) is deregulated in more than 50% of all cancers. While MYC amplification is the most common MYC-deregulating event, many other alterations can increase MYC activity. We thus systematically investigated MYC pathway activity acros…
View article: Data from MYC Activity Inference Captures Diverse Mechanisms of Aberrant MYC Pathway Activation in Human Cancers
Data from MYC Activity Inference Captures Diverse Mechanisms of Aberrant MYC Pathway Activation in Human Cancers Open
c-MYC (MYC) is deregulated in more than 50% of all cancers. While MYC amplification is the most common MYC-deregulating event, many other alterations can increase MYC activity. We thus systematically investigated MYC pathway activity acros…
View article: Random Forest model reveals the interaction between N6-methyladenosine modifications and RNA-binding proteins
Random Forest model reveals the interaction between N6-methyladenosine modifications and RNA-binding proteins Open
RNA-binding proteins (RBPs) have critical roles in N6-methyladenosine (m6A) modification process. We designed a Random Forest (RF) model to systematically analyze the interaction among RBPs and m6A modifications by integrating the binding …
View article: Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP-1 shapes 3D enhancer landscapes
Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP-1 shapes 3D enhancer landscapes Open
View article: Xist ribonucleoproteins promote female sex-biased autoimmunity
Xist ribonucleoproteins promote female sex-biased autoimmunity Open
SUMMARY Autoimmune diseases disproportionately affect females more than males. The XX sex chromosome complement is strongly associated with susceptibility to autoimmunity. Xist long noncoding RNA (lncRNA) is expressed only in females to ra…
View article: The steroid hormone estriol (E3) regulates epigenetic programming of fetal mouse brain and reproductive tract
The steroid hormone estriol (E3) regulates epigenetic programming of fetal mouse brain and reproductive tract Open
Background Estriol (E 3 ) is a steroid hormone formed only during pregnancy in primates including humans. Although E 3 is synthesized at large amounts through a complex pathway involving the fetus and placenta, it is not required for the m…
View article: Influence of T Cell-Mediated Immune Surveillance on Somatic Mutation Occurrences in Melanoma
Influence of T Cell-Mediated Immune Surveillance on Somatic Mutation Occurrences in Melanoma Open
Background Neoantigens are presented on the cancer cell surface by peptide-restricted human leukocyte antigen (HLA) proteins and can subsequently activate cognate T cells. It has been hypothesized that the observed somatic mutations in tum…
View article: Computational modeling of chromatin accessibility identified important epigenomic regulators
Computational modeling of chromatin accessibility identified important epigenomic regulators Open
View article: Additional file 6 of Computational modeling of chromatin accessibility identified important epigenomic regulators
Additional file 6 of Computational modeling of chromatin accessibility identified important epigenomic regulators Open
Additional file 6: Suppl. Table 1. Dataset summary. For each HM and TF, its ENCODE accession number, experimental targets and the cell line origin are provided.
View article: Additional file 2 of The steroid hormone estriol (E3) regulates epigenetic programming of fetal mouse brain and reproductive tract
Additional file 2 of The steroid hormone estriol (E3) regulates epigenetic programming of fetal mouse brain and reproductive tract Open
Additional file 2: Table S1. PCR primers. Table S2. The genes with altered expression patterns in the female offspring uteri after prenatal exposure to estriol (E3 v.s CT). Table S3. A The hypomethylated genes in the female offspring uteri…
View article: Additional file 1 of The steroid hormone estriol (E3) regulates epigenetic programming of fetal mouse brain and reproductive tract
Additional file 1 of The steroid hormone estriol (E3) regulates epigenetic programming of fetal mouse brain and reproductive tract Open
Additional file 1: Fig. S1 Prenatal exposure of estriol (E3) alters the global gene expression profile of the female offspring uteri. A) Grouping of altered genes in E3-treated animals compared to vehicle-treated groups according to biolog…