A5104032862- Cancer Genomics and Diagnostics
- Cancer Immunotherapy and Biomarkers
- Immunotherapy and Immune Responses
- Single-cell and spatial transcriptomics
- vaccines and immunoinformatics approaches
- T-cell and B-cell Immunology
- Genomics and Rare Diseases
- Monoclonal and Polyclonal Antibodies Research
- Axon Guidance and Neuronal Signaling
- Genetic factors in colorectal cancer
- DNA Repair Mechanisms
- Hedgehog Signaling Pathway Studies
- Cancer-related molecular mechanisms research
- Lung Cancer Treatments and Mutations
- Cancer Diagnosis and Treatment
- Hippo pathway signaling and YAP/TAZ
- Cancer, Hypoxia, and Metabolism
- PARP inhibition in cancer therapy
- Wnt/β-catenin signaling in development and cancer
- CRISPR and Genetic Engineering
- Protein Degradation and Inhibitors
- Peptidase Inhibition and Analysis
- Cancer, Lipids, and Metabolism
- Ubiquitin and proteasome pathways
- Inflammatory mediators and NSAID effects
ShanghaiTech University
2022-2024
University of Chinese Academy of Sciences
2022-2024
Center for Excellence in Molecular Cell Science
2022-2024
Chinese Academy of Sciences
2022-2024
Extrachromosomal DNA (ecDNA) is a type of circular and tumor specific genetic element. EcDNA has been reported to display open chromatin structure, facilitate oncogene amplification material unequal segregation, associated with poor cancer patients' prognosis. The ability immune evasion typical feature for progression, however the intrinsic factors that determine remain poorly understood. Here we show presence ecDNA markers evasion, obtaining could be one mechanisms employed by cells escape...
Copy number alterations (CNAs) are a predominant source of genetic in human cancer and play an important role progression. However comprehensive understanding the mutational processes signatures CNA is still lacking. Here we developed mechanism-agnostic method to categorize based on various fragment properties, which reflect consequences mutagenic can be extracted from different types data, including whole genome sequencing (WGS) single nucleotide polymorphism (SNP) array. The 14 have been...
Neoantigens derived from somatic DNA alterations are ideal cancer-specific targets. In recent years, the combination therapy of PD-1/PD-L1 blockers and neoantigen vaccines has shown clinical efficacy in original blocker non-responders. However, not all mutations result immunogenicity among cancer cells efficient tools to predict neoepitopes still urgently needed. Here, we present Seq2Neo pipeline, which provides a one-stop solution for neoepitope feature prediction using raw sequencing data....
Abstract Major histocompatibility complex (MHC) class II molecules play a pivotal role in antigen presentation and CD4+ T cell response. Accurate prediction of the immunogenicity MHC II-associated antigens is critical for vaccine design cancer immunotherapies. However, current computational methods are limited by insufficient training data algorithmic constraints, rules that govern which peptides truly recognized existing receptors remain poorly understood. Here, we build transfer...
Abstract DNA methylation analysis has been applied to determine the primary site of cancer; however, robust and accurate prediction cancer types with a minimum number sites is still significant scientific challenge. To build an type tool sites, we internally benchmarked different selection ranking procedures, as well classification models. We used The Cancer Genome Atlas dataset (26 8296 samples) train test models independent (17 2738 for model validation. A deep neural network using...
Metastasis is the leading cause of high ovarian-cancer-related mortality worldwide. Three major processes constitute whole metastatic cascade: invasion, intravasation, and extravasation. Tumor cells often reprogram their metabolism to gain advantages in proliferation survival. However, whether how those metabolic alterations contribute invasiveness tumor has yet be fully understood. Here we performed a genome-wide CRISPR-Cas9 screening identify genes participating cell dissemination revealed...
Abstract Immunoediting includes three temporally distinct stages, termed elimination, equilibrium, and escape, has been proposed to explain the interactions between cancer cells immune system during evolution of cancer. However, status immunoediting in remains unclear, existence neoantigen depletion untreated debated. Here we developed a distribution pattern-based method for quantifying neoantigen-mediated negative selection evolution. The can provide robust reliable quantification signal...
Abstract Homologous recombination deficiency (HRD) renders cancer cells vulnerable to unrepaired double-strand breaks and is an important therapeutic target as exemplified by the clinical efficacy of poly ADP-ribose polymerase (PARP) inhibitors well platinum chemotherapy drugs applied HRD patients. However, it remains a challenge predict status precisely economically. Copy number alteration (CNA), pervasive trait human cancers, can be extracted from variety data sources, including whole...
Lymph nodes metastases are common in patients with lung cancer. Additionally, those often at a higher risk for death from tumor than tumor-free lymph nodes. Somatic DNA alterations key drivers of cancer, and copy number (CNAs) major types alteration that promote cancer progression. Here, we performed genome-wide analysis, identified novel lung-cancer-metastasis-related gene, EFNA4. The EFNA4 genome locus was significantly amplified, mRNA expression up-regulated compared normal tissue, also...
TCfinder is a tumor cell identification tool, based on pathway activity and deep neural network (DNN). Across different platforms of scRNA-seq datasets, demonstrates robust efficiency. It outperforms existing tools performs under sparse data. freely available as an R package at: https://github.com/XSLiuLab/TCfinder. Traditional RNA sequencing (RNA-seq) bulk tumors only obtains the average information gene expression [1], thus unable to precisely delineate microenvironment infiltrating...
Abstract Neoantigens derived from somatic DNA alterations are ideal cancer-specific targets. In recent years, the combination therapy of PD-1/PD-L1 blockers and neoantigen vaccines shows clinical efficacy in original blocker non-responders. However, not all mutations can result immunogenicity cancer cells, efficient tools for predicting neoepitope still urgently needed. Here we present Seq2Neo pipeline, which provides a one-stop solution features prediction raw sequencing data, neoantigens...
Abstract Lymph nodes metastases are common in patients with lung cancer. And those often at a higher risk for death from tumor than tumor-free lymph nodes. So-matic DNA alterations key drivers of cancer, and copy number (CNAs) major type alteration that promotes cancer progression. Here, we performed genome-wide analysis, identified novel metastasis related gene, EFNA4. EFNA4 genome locus was significantly amplified mRNA expression up-regulated compared normal tissue, also node without...
Abstract Immunoediting, which includes three temporally distinct stages, termed elimination, equilibrium, and escape, has been proposed to explain the interactions between cancer cells immune system during evolution of cancer. However status immunoediting in remains unclear, existence neoantigen depletion signal untreated debated. Here we developed a distribution pattern based method for quantifying mediated negative selection evolution. Our provides robust reliable quantification an...
Abstract Copy number alterations (CNAs) are a predominant source of genetic in human cancer and play an important role progression. However comprehensive understanding the mutational processes signatures CNA is still lacking. Here we developed mechanism-agnostic method to categorize based on various fragment properties, which reflect consequences mutagenic can be extracted from different types data, including whole genome sequencing (WGS) SNP array. The 14 have been 2778 pan-cancer analysis...
Abstract Extrachromosomal DNA (ecDNA) is a type of circular and tumor specific genetic element. EcDNA has been reported to display open chromatin structure, facilitate oncogene amplification material unequal segregation, associated with poor cancer patients’ prognosis. The ability immune evasion typical feature for progression, however the intrinsic factors that determine remain poorly understood. Here we show presence ecDNA markers evasion, obtaining could be one mechanisms employed by...