CIBERSORT analysis of TCGA and METABRIC identifies subgroups with better outcomes in triple negative breast cancer

KE Craven, Y Gökmen-Polar, SS Badve - Scientific Reports, 2021 - nature.com
Studies have shown that the presence of tumor infiltrating lymphocytes (TILs) in Triple
Negative Breast Cancer (TNBC) is associated with better prognosis. However, the molecular …

Benchmarking of methods for DNA methylome deconvolution

K De Ridder, H Che, K Leroy, B Thienpont - Nature Communications, 2024 - nature.com
Defining the number and abundance of different cell types in tissues is important for
understanding disease mechanisms as well as for diagnostic and prognostic purposes …

Oncolytic immunotherapy with nivolumab in muscle-invasive bladder cancer: a phase 1b trial

R Li, NY Villa, X Yu, JO Johnson, G Borjas, J Dhillon… - Nature medicine, 2024 - nature.com
There is a critical unmet need for safe and efficacious neoadjuvant treatment for cisplatin-
ineligible patients with muscle-invasive bladder cancer. Here we launched a phase 1b study …

Bone marrow microenvironments that contribute to patient outcomes in newly diagnosed multiple myeloma: A cohort study of patients in the Total Therapy clinical trials

SA Danziger, M McConnell, J Gockley, MH Young… - PLoS …, 2020 - journals.plos.org
Background The tumor microenvironment (TME) is increasingly appreciated as an important
determinant of cancer outcome, including in multiple myeloma (MM). However, most …

Genetic variation of putative myokine signaling is dominated by biological sex and sex hormones

LM Velez, C Van, T Moore, Z Zhou, C Johnson… - Elife, 2022 - elifesciences.org
Skeletal muscle plays an integral role in coordinating physiological homeostasis, where
signaling to other tissues via myokines allows for coordination of complex processes. Here …

Transcriptomic classification of diffuse large B-cell lymphoma identifies a high-risk activated B-cell-like subpopulation with targetable MYC dysregulation

ME Stokes, K Wenzl, CC Huang, M Ortiz… - Nature …, 2024 - nature.com
Immunochemotherapy has been the mainstay of treatment for newly diagnosed diffuse large
B-cell lymphoma (ndDLBCL) yet is inadequate for many patients. In this work, we perform …

Progress and challenge for computational quantification of tissue immune cells

Z Chen, A Wu - Briefings in Bioinformatics, 2021 - academic.oup.com
Tissue immune cells have long been recognized as important regulators for the
maintenance of balance in the body system. Quantification of the abundance of different …

Multi-omics reveal immune microenvironment alterations in multiple myeloma and its precursor stages

Y Cheng, F Sun, DV Alapat, V Wanchai, D Mery… - Blood Cancer …, 2024 - nature.com
Tumor immune microenvironmental alterations occur early in multiple myeloma (MM)
development. In this study, we aim to systematically characterize the tumor immune …

Follicular lymphoma comprises germinal center–like and memory-like molecular subtypes with prognostic significance

C Laurent, P Trisal, B Tesson, S Seth, A Beyou… - Blood, 2024 - ashpublications.org
A robust prognostic and biological classification for newly diagnosed follicular lymphoma
(FL) using molecular profiling remains challenging. FL tumors from patients treated in the …

[PDF][PDF] Single-cell mapper (scMappR): using scRNA-seq to infer the cell-type specificities of differentially expressed genes

DJ Sokolowski, M Faykoo-Martinez… - NAR genomics and …, 2021 - academic.oup.com
RNA sequencing (RNA-seq) is widely used to identify differentially expressed genes (DEGs)
and reveal biological mechanisms underlying complex biological processes. RNA-seq is …