Fred Kolling

Common viral infections seed regionally distinct resident memory T cells in the human CNS

The paper identifies regionally distinct CD8+ resident memory T cells in the human CNS shaped by viral infections using single-cell RNA sequencing and T cell receptor analysis.

Epithelial-Mesenchymal Transition is Associated with Altered Immune Composition and Cytotoxic Function in Triple-Negative Breast Cancer

This study shows that EMT progression in breast cancer correlates with reduced immune cell infiltration and function, including decreased cytotoxic T cells and altered B cell composition.

Mucosal-associated invariant T cells support IL-15-dependent Treg response in skin injury and promote resolution of skin inflammation

This study identifies MAIT cells as regulators of Treg responses in skin inflammation, showing their ability to resolve inflammation through IL-15-dependent mechanisms.

Multi-site Assessment of Methods for Cell Preservation Upstream of Single Cell RNA Sequencing

This study evaluates three cell preservation methods for scRNA-seq across multiple sites, showing concordant cell type results but platform-specific gene expression differences and better granulocyte retention with preservation methods.

RAD: A Read-structure Agnostic Demultiplexer for Single-Cell Long-Read Sequencing and Analysis

RAD is a demultiplexer for single-cell long-read sequencing that improves speed and sensitivity over existing methods while supporting complex read structures.

Differential Transcript Usage Reveals Isoform-Level Remodeling of Tumor Biology in Clear Cell Renal Cell Carcinoma

The paper identifies isoform-level changes in ccRCC using DTU analysis, revealing subgroups with distinct survival outcomes and potential biomarkers.

Retroelement Hypomethylation Links Hypoxia Signaling, Immune Phenotypes, and Survival in Clear Cell Renal Cell Carcinoma

This study identifies RE methylation subtypes in ccRCC linked to immune phenotypes and survival, validated across multiple cohorts.

Myeloid Cell States in Influenza-Associated Pulmonary Aspergillosis Are Shaped by Iron Overload and Metabolic Reprogramming

This study identifies iron overload and metabolic reprogramming in myeloid cells as drivers of susceptibility to Aspergillus fumigatus in influenza-associated pulmonary aspergillosis.

Mapping breast cancer lineage in radiation and immunotherapy using the REMAP mouse

The paper introduces REMAP, a mouse model for tracking breast cancer lineage, and shows how treatment affects tumor evolution and immune response.

Single-cell RNA sequencing of peripheral blood cells identifies transcriptomic signatures in Parkinson's disease

This study uses single-cell RNA sequencing to identify immune cell-specific gene expression signatures and sex differences in Parkinson's disease patients compared to healthy controls.

Optimizing Protocols for MicroRNA Profiling of Infant and Toddler Stool

This study compares RNA extraction and preservation protocols for miRNA profiling in infant and toddler stool, finding that RNAlater and Zymo DNA/RNA Shield yield similar high-quality RNA with comparable human miRNA profiles.

Vicarious trauma primes innate immunity and reconfigures human brain networks

This study examines how vicarious trauma affects human brain networks and immune responses through fMRI, autonomic physiology, and gene expression in monocytes.

A streamlined and comprehensive protocol for the generation and multi-omic analysis of human monocyte-derived macrophages

This paper presents a streamlined protocol for generating and multi-omic analyzing human macrophages from frozen PBMCs, showing their phenotypic stability and compatibility with snRNA-seq.

Anti-CD206 CAR T Cell Treatment Restores Fibrosis-Induced Loss of Dermal White Adipose Tissue

The paper demonstrates that anti-CD206 CAR T cells restore dermal white adipose tissue in systemic sclerosis by targeting CD206+ macrophages and reversing their effects on adipose-derived stem cells.

Continuous DNA Methylation Deconvolution-Based Surrogate for B-Cell Differentiation State in CLL

The paper develops a continuous DNA methylation metric (B-Index) to classify CLL subtypes and identifies epigenetic signals linked to B-cell differentiation and tumor burden.

The essential role of connective-tissue cells during axolotl limb regeneration

This study shows connective-tissue cells are essential for axolotl limb regeneration, making up 75% of blastema cells and requiring specific signaling for regeneration.

Hierarchal single-cell lineage tracing reveals differential fate commitment of CD8 T-cell clones in response to acute infection.

This study uses single-cell lineage tracing to show that CD8 T-cell clones exhibit differential fate commitment during acute infection, with some clones adopting memory or effector biases over time.

Endocrine persistence in ER+ breast cancer is accompanied by metabolic vulnerability in oxidative phosphorylation

This study identifies mitochondrial oxidative phosphorylation as a metabolic vulnerability in endocrine-tolerant persister ER+ breast cancer cells, suggesting therapeutic targeting of mitochondrial function could prevent recurrence.

Integrative Co-Registration of Elemental Imag-ing and Histopathology for Enhanced Spatial Multimodal Analysis of Tissue Sections through TRACE

TRACE co-registers elemental imaging and histopathology to enable spatial analysis of tissue sections through a web application.

Buckling instability underlies vertebral segmentation during axolotl tail regeneration

The paper shows that vertebral segmentation during axolotl tail regeneration occurs via a buckling instability mechanism, distinct from the somite-based process in embryonic development.

Genomic analysis of Cryaa-R49C and Cryab-R120G knockin mutant mice: 10-year follow-up

The paper reexamines the genetic background of Cryaa-R49C and Cryab-R120G knockin mutant mice 10 years after conversion to the C57Bl/6 background using SNP analysis.