Markku T Varjosalo

Conjunctive Targeting Links Drug Synergy to Emergent Proteome Structural States

This paper introduces CoPPRA, a structural proteomics method to analyze drug combinations in AML, revealing peptide-level accessibility changes linked to conjunctive targeting.

Chemical Proteomics of Residual Acute Myeloid Leukemia Cells Reveals Therapeutic Vulnerabilities

This study uses CoPISA and proteomics to analyze venetoclax-azacitidine response in AML cells, identifying adaptive vulnerabilities like NRP2.

A novel method for obtaining epileptic brain tissue for omic analyses using electrodes from a clinical stereoelectroencephalography study

This paper describes a method to obtain brain tissue for omic analyses using SEEG electrodes, showing concordant transcriptomic and proteomic findings across different epileptic zones.

β4-integrins safeguard nuclear mechanics to suppress prostate cancer progression

This study identifies β4-integrins as critical for maintaining nuclear mechanics and integrity in prostate cancer, linking cell-ECM adhesion to genome stability and patient survival.

Multi-layered regulatory networks driving human dopaminergic neuron differentiation

The paper integrates multi-omics data to identify regulatory networks driving human dopaminergic neuron differentiation and highlights key transcription factors and enhancer-associated regulators.

Efficient NK cell transduction with VSV-G-pseudotyped lentiviral vectors

This study optimizes VSV-G-pseudotyped lentiviral transduction of NK cells by improving activation, construct design, and enhancer use, achieving high efficiency without compromising cell function.

A phosphorylation switch in PAGE4 drives MED12-mutant fibroid pathogenesis

The paper identifies a phosphorylation switch in PAGE4 as a key mechanism in MED12-mutant fibroid pathogenesis, revealing its role in rewiring the interactome and transcriptional machinery.

Automated MagNet Enrichment Unlocks Deep and Cost-Effective LC-MS Plasma Proteomics

The paper compares plasma protein enrichment methods, finding MagNet significantly increases protein identifications and enables cost-effective, high-throughput LC-MS proteomics.

The non-catalytic ϵ DNA polymerase subunit is an NPF motif recognition protein

This study identifies POLE2 as a general NPF-motif receptor, revealing its role in recruiting proteins involved in replication, DNA repair, and transcription through SLiM-mediated interactions.

ISG15 Differentially Modulates Clade Ib and II MPXV Infection in MEF cells

This study shows ISG15 modulates Clade Ib and II MPXV infection differently in MEF cells, with clade-specific effects on viral replication and immune evasion.

T cell correction pipeline for Inborn Errors of Immunity

This paper presents a T cell gene correction pipeline using CRISPR/Cas9 and HDR to correct monogenic mutations in IEI models, achieving up to 80% bi-allelic editing with no detectable off-target effects.

FINCA disease mouse model exhibits altered behaviour and immune response

The paper describes a FINCA mouse model with mild hyperactivity and altered immune response, identifying Rho GTPase signaling as a key pathway affected by the p.Asp148Tyr variant in NHLRC2.

Human skeletal muscle possesses both reversible proteomic signatures and a retained proteomic memory after repeated resistance training

This study shows that resistance training induces reversible and retained proteomic changes in human skeletal muscle, suggesting a proteomic memory of muscle growth.

Fetal-like reversion in the regenerating intestine is regulated by mesenchymal Asporin

The paper shows that mesenchymal Asporin mediates fetal-like reprogramming in regenerating intestinal epithelium by modulating Tgfβ signaling through CD44.

The novel SCN5A-P1891A mutation is associated with left ventricular hypertrabeculation and links Nav1.5 to cardiomyocyte proliferation and disrupted 3D cardiac tissue formation

This study identifies a novel SCN5A mutation linked to left ventricular hypertrabeculation and shows its impact on cardiomyocyte proliferation and 3D cardiac tissue formation.

Distinct functions for the paralogous RBM41 and U11/U12-65K proteins in the minor spliceosome

This study identifies RBM41 as a paralog of U11/U12-65K in the minor spliceosome, showing distinct roles in splicing and spliceosome dynamics.

Analysis of human brain tissue derived from DBS surgery

The paper describes a method to collect brain tissue from DBS surgical instruments for transcriptomic and proteomic analysis, showing it provides reliable data comparable to traditional brain tissue samples.

Physical and functional interactome atlas of human receptor tyrosine kinases

The paper maps the interactome and substrates of human receptor tyrosine kinases using AP-MS, BioID, and kinase assays, revealing interactions and functions of both well-known and understudied RTKs.

Rapid genome editing by CRISPR-Cas9-POLD3 fusion

The paper evaluates DNA repair protein-Cas9 fusions for improving CRISPR editing efficiency, finding that most require optimization for specific cell types and genomic loci.

Human Transcription Factor and Protein Kinase Gene Fusions in Human Cancer

The paper analyzes oncogenic gene fusions in cancer, finding that 30% of detected fusions produce functional proteins, primarily involving kinases and transcription factors, which deregulate cellular signaling.

A second hybrid-binding domain modulates the activity of Drosophila ribonuclease H1

The paper investigates the role of a second hybrid-binding domain in Drosophila RNase H1, showing it enhances catalytic activity and processivity by facilitating dissociation of the active site from the product.

DUX4 regulates oocyte to embryo transition in human

This study shows that DUX4 regulates the oocyte-to-embryo transition in humans by activating enhancers and promoting genome reprogramming.

Maturation of Neuronal Activity in Caudalized Human Brain Organoids

This study describes a protocol to generate hindbrain-like human brain organoids with mature, functional neurons and reports their response to Zika virus and anticonvulsants.

Molecular atlas of postnatal mouse heart development

This study provides a molecular atlas of postnatal mouse heart development by integrating transcriptomics, proteomics, and metabolomics data to identify metabolism-related mechanisms linked to the loss of cardiac regeneration.

Haploinsufficiency of A20 impairs protein-protein interactome and leads into caspase-8-dependent enhancement of NLRP3 inflammasome activation

This study identifies a novel mutation in A20 causing haploinsufficiency and shows it impairs the protein-protein interactome, leading to enhanced NLRP3 inflammasome activation through caspase-8.

An integrated approach to comprehensively map the molecular context of proteins

The paper develops an integrated approach combining AP-MS and BioID to map protein interactions and molecular contexts across the human proteome.