Computational immunogenomic approaches to predict response to cancer immunotherapies

V Addala, F Newell, JV Pearson, A Redwood… - Nature Reviews …, 2024 - nature.com
Cancer immunogenomics is an emerging field that bridges genomics and immunology. The
establishment of large-scale genomic collaborative efforts along with the development of …

EBV-associated diseases: Current therapeutics and emerging technologies

S Chakravorty, B Afzali, M Kazemian - Frontiers in immunology, 2022 - frontiersin.org
EBV is a prevalent virus, infecting> 90% of the world's population. This is an oncogenic virus
that causes~ 200,000 cancer-related deaths annually. It is, in addition, a significant …

Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer

I Joanito, P Wirapati, N Zhao, Z Nawaz, G Yeo, F Lee… - Nature …, 2022 - nature.com
The consensus molecular subtype (CMS) classification of colorectal cancer is based on bulk
transcriptomics. The underlying epithelial cell diversity remains unclear. We analyzed …

[HTML][HTML] Transcriptome analysis reveals tumor microenvironment changes in glioblastoma

Y Hoogstrate, K Draaisma, SA Ghisai, L van Hijfte… - Cancer cell, 2023 - cell.com
A better understanding of transcriptional evolution of IDH-wild-type glioblastoma may be
crucial for treatment optimization. Here, we perform RNA sequencing (RNA-seq)(n= 322 test …

Targeting IRG1 reverses the immunosuppressive function of tumor-associated macrophages and enhances cancer immunotherapy

YJ Chen, GN Li, XJ Li, LX Wei, MJ Fu, ZL Cheng… - Science …, 2023 - science.org
Immune-responsive gene 1 (IRG1) encodes aconitate decarboxylase (ACOD1) that
catalyzes the production of itaconic acids (ITAs). The anti-inflammatory function of IRG1/ITA …

Feasibility of functional precision medicine for guiding treatment of relapsed or refractory pediatric cancers

AM Acanda De La Rocha, NE Berlow, M Fader… - Nature Medicine, 2024 - nature.com
Children with rare, relapsed or refractory cancers often face limited treatment options, and
few predictive biomarkers are available that can enable personalized treatment …

Spatial transcriptomics reveals distinct and conserved tumor core and edge architectures that predict survival and targeted therapy response

R Arora, C Cao, M Kumar, S Sinha, A Chanda… - Nature …, 2023 - nature.com
The spatial organization of the tumor microenvironment has a profound impact on biology
and therapy response. Here, we perform an integrative single-cell and spatial transcriptomic …

Identification of the novel exhausted T cell CD8+ markers in breast cancer

H Liu, A Dong, AM Rasteh, P Wang, J Weng - Scientific Reports, 2024 - nature.com
Cancer is one of the most concerning public health issues and breast cancer is one of the
most common cancers in the world. The immune cells within the tumor microenvironment …

Genomic predictors of response to PD-1 inhibition in children with germline DNA replication repair deficiency

A Das, S Sudhaman, D Morgenstern, A Coblentz… - Nature medicine, 2022 - nature.com
Cancers arising from germline DNA mismatch repair deficiency or polymerase proofreading
deficiency (MMRD and PPD) in children harbour the highest mutational and microsatellite …

The collagen landscape in cancer: profiling collagens in tumors and in circulation reveals novel markers of cancer‐associated fibroblast subtypes

J Thorlacius‐Ussing, C Jensen, NI Nissen… - The Journal of …, 2024 - Wiley Online Library
Cancer‐associated fibroblasts (CAFs) deposit and remodel collagens in the tumor stroma,
impacting cancer progression and efficacy of interventions. CAFs are the focus of new …