M. Hafner

Transformer-based modeling of Clonal Selection and Expression Dynamics (TraCSED) reveals resistance signatures in breast cancer

TraCSED identifies resistance pathways in breast cancer by analyzing scRNA-seq data and clonal selection dynamics over time.

A Multiparametric Analysis Reveals Differential Behavior of Spheroid Cultures on Distinct Ultra-Low Attachment Plates Types

This study compares spheroid formation and behavior across six ultra-low attachment plate types using four human cell lines, finding size and eccentricity differences that suggest plate type impacts experimental outcomes.

A comprehensive analysis of Transcribed Ultra Conserved Regions uncovers important regulatory functions of novel non-coding transcripts in gliomas.

This study analyzes Transcribed Ultra Conserved Regions (TUCRs) in gliomas, identifying uc.110 as a tumor enhancer that promotes malignancy via the WNT pathway.

Mature microRNA-binding protein QKI promotes microRNA-mediated gene silencing

The paper identifies QKI as a novel microRNA-binding protein that enhances AGO2/let-7b-mediated gene silencing and suppresses tumor growth.

Constitutive protein degradation induces acute cell death via proteolysis products

This study shows proteasome-generated peptides from degraded proteins induce cell death by neutralizing IAPs, explaining the efficacy of proteolysis-modulating drugs like thalidomide analogs and bortezomib.

Mitochondrial Matrix Protease ClpP Agonists inhibit Cancer Stem Cell Function in Breast Cancer Cells by Disrupting Mitochondrial Homeostasis

This study shows that ClpP agonists inhibit breast cancer stem cell function by disrupting mitochondrial homeostasis and multiple metabolic pathways.

MKP-1 modulates Ubiquitination/Phosphorylation of TLR signaling

This study shows MKP-1 modulates TRAF6 ligase activity by regulating DUBs, leading to altered ubiquitination and phosphorylation in TLR signaling.

RTK-dependent inducible degradation of mutant PI3K alpha drives GDC-0077 (Inavolisib) efficacy

The paper shows that GDC-0077 and taselisib degrade mutant PI3K alpha via HER2-dependent mechanisms, enhancing efficacy in PIK3CA-mutant breast cancer.

Proteomic profiling of breast cancer cell lines and models

The paper performs proteomic profiling of 61 breast cancer cell lines, identifies molecular subtypes, and makes datasets publicly available for drug response prediction and therapeutic marker discovery.

Multiple Capsid Protein Binding Sites Mediate Selective Packaging of the Alphavirus Genomic RNA

The paper identifies multiple Cp binding sites on alphavirus genomic RNA that mediate selective packaging, challenging the role of the previously proposed packaging signal.

Anti-inflammatory Activity of Lefamulin in a Lipopolysaccharide-Induced Lung Neutrophilia Model

This study shows lefamulin reduces lung neutrophilia in mice, with effects similar to dexamethasone.

G9a methyltransferase governs cell identity in the lung and is required for KRAS G12D tumor development and propagation

This study shows G9a methyltransferase regulates Wnt signaling in lung development and tumor progression by controlling β-catenin transcriptional activity, and its inhibition prevents KrasG12D lung cancer.

Accelerating iterative deconvolution and multiview fusion by orders of magnitude

This paper introduces faster deconvolution and multiview fusion methods, achieving speedups of 10 to several thousand-fold over previous approaches.

Multi-omics profiling establishes the polypharmacology of FDA Approved CDK4/6 inhibitors and the potential for differential clinical activity

This study compares the mechanisms of three FDA-approved CDK4/6 inhibitors and finds significant differences in their transcriptional, proteomic, and cellular effects, suggesting potential for differential clinical use.

A multi-center study on factors influencing the reproducibility of in vitro drug-response studies

This study investigates factors affecting the reproducibility of in vitro drug-response assays across multiple centers, identifying context-sensitive factors that impact results.

CD95/Fas ligand mRNA is toxic to cells

The paper shows that full-length CD95L mRNA is toxic to cells and induces apoptosis through sRNA processing independent of Dicer and Drosha, suggesting a new role for RNAi in cell fate regulation.

6mer seed toxicity in tumor suppressive microRNAs

The paper identifies 6mer seed sequences in miRNAs that are toxic to cancer cells, showing that tumor suppressive miRNAs use these toxic seeds to kill cancer cells.

The splicing factor U2AF1 contributes to cancer progression through a non-canonical role in translation regulation

This study identifies a non-canonical role of U2AF1 in translation regulation, showing that the S34F mutation enhances interleukin 8 synthesis, promoting cancer progression.

Many si/shRNAs can kill cancer cells by targeting multiple survival genes through an off-target mechanism

The paper shows that many si/shRNAs targeting CD95 or CD95L induce cancer cell death via an off-target mechanism called DISE by eliminating survival genes.