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Deep thermal profiling for detection of functional proteoform groups

Applying thermal proteome profiling to acute B cell childhood leukemia cell lines combined with deep peptide fractionation and a graph-based clustering algorithm allows inference of functional proteoform groups and their association with drug response.

Nils Kurzawa
Isabelle Rose Leo
Rozbeh Jafari
ResearchOpen Access20 Mar 2023
Nature Chemical Biology

Volume: 19, P: 962-971
Functional proteoform group deconvolution reveals a broader spectrum of ibrutinib off-targets

This study refines ibrutinib’s target landscape by resolving drug targets while accounting for functional proteoform groups, identifying off-targets linked to immunomodulation and cellular processes and identifying variability in CLL patient responses, establishing a framework to understand drug interactions in precision medicine.

Isabelle Rose Leo
Elena Kunold
Rozbeh Jafari
ResearchOpen Access25 Feb 2025
Nature Communications

Volume: 16, P: 1-17
Integrative multi-omics and drug response profiling of childhood acute lymphoblastic leukemia cell lines

Childhood acute lymphoblastic leukemia is characterised by a range of genetic aberrations. Here, the authors use multi-omics profiling of ALL cell lines to connect molecular phenotypes and drug responses to provide an interactive resource of drug sensitivity.

Isabelle Rose Leo
Luay Aswad
Rozbeh Jafari
ResearchOpen Access30 Mar 2022
Nature Communications

Volume: 13, P: 1-19
Proteogenomics refines the molecular classification of chronic lymphocytic leukemia

Proteomics can be used to refine cancer classification. Here, the authors characterise chronic lymphocytic leukaemia patients by proteogenomics, and identified a subtype of patients with poor prognosis associated with aberrant B cell receptor signalling.

Sophie A. Herbst
Mattias Vesterlund
Sascha Dietrich
ResearchOpen Access20 Oct 2022
Nature Communications

Volume: 13, P: 1-18
Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia

High hyperploidy is a common feature in childhood B-cell precursor acute lymphoblastic leukemia. Here, the authors perform proteogenomic and Hi-C analyses of this leukemia and the ETV6/RUNX1 subtype and show that CTCF and cohesin expression are low in hyperdiploid cases and transcriptional dysregulation in relation to topologically associating domain borders in some of these cases.

Minjun Yang
Mattias Vesterlund
Kajsa Paulsson
ResearchOpen Access03 Apr 2019
Nature Communications

Volume: 10, P: 1-15
CETSA screening identifies known and novel thymidylate synthase inhibitors and slow intracellular activation of 5-fluorouracil

Drugs therapeutic efficacy relies on their capability of binding the relevant targets in a physiological environment, which has so far been hard to measure. Here, the authors present a compound library screen based on a target engagement assay that reports on protein stability upon ligands binding in cell.

Helena Almqvist
Hanna Axelsson
Pär Nordlund
ResearchOpen Access24 Mar 2016
Nature Communications

Volume: 7, P: 1-11
Prediction model for drug response of acute myeloid leukemia patients

Quang Thinh Trac
Yudi Pawitan
Trung Nghia Vu
ResearchOpen Access24 Mar 2023
npj Precision Oncology

Volume: 7, P: 1-10
SETD8 inhibition targets cancer cells with increased rates of ribosome biogenesis

Matilde Murga
Gema Lopez-Pernas
Oscar Fernández-Capetillo
ResearchOpen Access28 Sept 2024
Cell Death & Disease

Volume: 15, P: 1-11
Targeting autophagy as a therapeutic strategy in pediatric acute lymphoblastic leukemia

Henri Colyn Bwanika
Isabelle Rose Leo
Katja Pokrovskaja Tamm
ResearchOpen Access18 Feb 2024
Scientific Reports

Volume: 14, P: 1-13
Preclinical efficacy of azacitidine and venetoclax for infant KMT2A-rearranged acute lymphoblastic leukemia reveals a new therapeutic strategy

Laurence C. Cheung
Carlos Aya-Bonilla
Rishi S. Kotecha
ResearchOpen Access15 Nov 2022
Leukemia

Volume: 37, P: 61-71
Inhibition of the ubiquitin-proteasome system by an NQO1-activatable compound

Tatiana A. Giovannucci
Florian A. Salomons
Nico P. Dantuma
ResearchOpen Access06 Oct 2021
Cell Death & Disease

Volume: 12, P: 1-19
The cellular thermal shift assay for evaluating drug target interactions in cells

Interaction between a drug and its protein target results in a shift in thermal stability of that protein. The cellular thermal shift assay–CETSA–exploits this to characterize intracellular drug-protein engagement.

Rozbeh Jafari
Helena Almqvist
Daniel Martinez Molina
Protocols07 Aug 2014
Nature Protocols

Volume: 9, P: 2100-2122
Delineating functional and molecular impact of ex vivo sample handling in precision medicine

Nona Struyf
Albin Österroos
Tom Erkers
ResearchOpen Access19 Feb 2024
npj Precision Oncology

Volume: 8, P: 1-7

Search

Deep thermal profiling for detection of functional proteoform groups

Functional proteoform group deconvolution reveals a broader spectrum of ibrutinib off-targets

Integrative multi-omics and drug response profiling of childhood acute lymphoblastic leukemia cell lines

Proteogenomics refines the molecular classification of chronic lymphocytic leukemia

Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia

CETSA screening identifies known and novel thymidylate synthase inhibitors and slow intracellular activation of 5-fluorouracil

Prediction model for drug response of acute myeloid leukemia patients

SETD8 inhibition targets cancer cells with increased rates of ribosome biogenesis

Targeting autophagy as a therapeutic strategy in pediatric acute lymphoblastic leukemia

Preclinical efficacy of azacitidine and venetoclax for infant KMT2A-rearranged acute lymphoblastic leukemia reveals a new therapeutic strategy

Inhibition of the ubiquitin-proteasome system by an NQO1-activatable compound

The cellular thermal shift assay for evaluating drug target interactions in cells

Delineating functional and molecular impact of ex vivo sample handling in precision medicine

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