High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer

S Salcher, G Sturm, L Horvath, G Untergasser… - Cancer cell, 2022 - cell.com
Non-small cell lung cancer (NSCLC) is characterized by molecular heterogeneity with
diverse immune cell infiltration patterns, which has been linked to therapy sensitivity and …

Challenges and perspectives in computational deconvolution of genomics data

LX Garmire, Y Li, Q Huang, C Xu, SA Teichmann… - Nature …, 2024 - nature.com
Deciphering cell-type heterogeneity is crucial for systematically understanding tissue
homeostasis and its dysregulation in diseases. Computational deconvolution is an efficient …

Enrichment of oral-derived bacteria in inflamed colorectal tumors and distinct associations of Fusobacterium in the mesenchymal subtype

BS Younginger, O Mayba, J Reeder, DR Nagarkar… - Cell Reports …, 2023 - cell.com
While the association between colorectal cancer (CRC) features and Fusobacterium has
been extensively studied, less is known of other intratumoral bacteria. Here, we leverage …

Transcriptome profiling for precision cancer medicine using shallow nanopore cDNA sequencing

A Mock, M Braun, C Scholl, S Fröhling, C Erkut - Scientific Reports, 2023 - nature.com
Transcriptome profiling is a mainstay of translational cancer research and is increasingly
finding its way into precision oncology. While bulk RNA sequencing (RNA-seq) is widely …

Localized skin inflammation during cutaneous leishmaniasis drives a chronic, systemic IFN-γ signature

C Farias Amorim, F O. Novais, BT Nguyen… - PLoS neglected …, 2021 - journals.plos.org
Cutaneous leishmaniasis is a localized infection controlled by CD4+ T cells that produce IFN-
γ within lesions. Phagocytic cells recruited to lesions, such as monocytes, are then exposed …

OpenPBTA: The Open Pediatric Brain Tumor Atlas

JA Shapiro, KS Gaonkar, SJ Spielman, CL Savonen… - Cell genomics, 2023 - cell.com
Pediatric brain and spinal cancers are collectively the leading disease-related cause of
death in children; thus, we urgently need curative therapeutic strategies for these tumors. To …

Comprehensive transcriptomic analysis shows disturbed calcium homeostasis and deregulation of T lymphocyte apoptosis in inclusion body myositis

M Johari, A Vihola, J Palmio, M Jokela, PH Jonson… - Journal of …, 2022 - Springer
Objective Inclusion body myositis (IBM) has an unclear molecular etiology exhibiting both
characteristic inflammatory T-cell activity and rimmed-vacuolar degeneration of muscle …

Seminoma subtypes differ in the organization and functional state of the immune microenvironment

AV Savelyeva, KE Medvedev - 3 Biotech, 2023 - Springer
Seminoma is the most common type of testicular germ cell tumors (TGCTs) among 15–44
years old men. Seminoma treatments include orchiectomy, platinum-based chemotherapy …

Identification and verification of microtubule associated genes in lung adenocarcinoma

YH Wei, CZ Yang, JM Wei, WT Li, YW Qin, GN Liu - Scientific Reports, 2023 - nature.com
Associated with high morbidity and mortality, lung adenocarcinoma (LUAD) is lacking in
effective prognostic prediction and treatment. As chemotherapy drugs commonly used in …

Tumour immune characterisation of primary triple-negative breast cancer using automated image quantification of immunohistochemistry-stained immune cells

S Roostee, D Ehinger, M Jönsson, B Phung… - Scientific Reports, 2024 - nature.com
The tumour immune microenvironment (TIME) in breast cancer is acknowledged with an
increasing role in treatment response and prognosis. With a growing number of immune …