Achim Treumann

Achim Treumann
KBI Biopharma BV · Analytical Formulation Sciences

PhD

About

135
Publications
38,168
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
3,157
Citations
Citations since 2017
51 Research Items
1461 Citations
2017201820192020202120222023050100150200250300350
2017201820192020202120222023050100150200250300350
2017201820192020202120222023050100150200250300350
2017201820192020202120222023050100150200250300350
Introduction
Achim Treumann is Director of Analytical Formulation Sciences and Site Head of KBI Biopharma in Leuven, Belgium. In addition to his interest in proteins, their structure, function and modifications, Achim is interested in the organisation and analysis of data.
Additional affiliations
March 2019 - present
KBI Biopharma BVBA
Position
  • Managing Director
July 2012 - February 2019
Newcastle University
Position
  • Managing Director
February 2008 - February 2012
Centre for Excellence in Life Sciences
Position
  • Scientific Manager, North East Proteome Analysis Facility

Publications

Publications (135)
Article
Full-text available
Systematic quantification of phosphoprotein within cell signaling networks in solid tissues remains challenging and precise quantification in large scale samples has great potential for biomarker identification and validation. We developed a reverse phase protein array (RPPA) based phosphor-antibody characterization approach by taking advantage of...
Article
Full-text available
Coral reefs are facing unprecedented mass bleaching and mortality events due to marine heatwaves and climate change. To avoid extirpation, corals must adapt. Individual variation in heat tolerance and its heritability underpin the potential for coral adaptation. However, the magnitude of heat tolerance variability within coral populations is largel...
Article
Full-text available
Background It is not enough to optimize proteomics assays. It is critical those assays are robust to operating conditions. Without robust assays, proteomic biomarkers are unlikely to translate readily into the clinic. This study outlines a structured approach to the identification of a robust operating window for proteomics assays and applies that...
Preprint
Full-text available
Background: Systematic quantification of phosphoprotein within cell signaling networks in solid tissues remains challenging and precise quantification in large scale samples has great potential for biomarker identification and validation. Methods: We developed a reverse phase protein array (RPPA) based phosphor-antibody characterization workflow by...
Article
Full-text available
Coral cover on tropical reefs has declined during the last three decades due to the combined effects of climate change, destructive fishing, pollution, and land use change. Drastic reductions in greenhouse gas emissions combined with effective coastal management and conservation strategies are essential to slow this decline. Innovative approaches,...
Preprint
Full-text available
Background: It is not enough to optimize proteomics assays. It is critical those assays are robust to operating conditions. Without robust assays, proteomic biomarkers are unlikely to translate readily into the clinic. This study outlines a structured approach to the identification of a robust operating window for proteomics assays and applies that...
Preprint
Full-text available
Coral cover on tropical reefs has declined during the last three decades due to the combined effects of climate change, destructive fishing, pollution, and land use change. Drastic reductions in greenhouse gas emissions combined with effective coastal management and conservation strategies are essential to slow this decline. Innovative approaches,...
Article
Full-text available
During the preimplantation period of pregnancy in eutherian mammals, transcriptional and proteomic changes in the uterine endometrium are required to facilitate receptivity to an implanting blastocyst. These changes are mediated, in part, by proteins produced by the developing conceptus (inner cell mass and extraembryonic membranes). We hypothesize...
Preprint
During the pre-implantation period of pregnancy in eutherian mammals, changes to the uterine endometrium are required (both at the transcriptional and protein level) to facilitate the endometrium becoming receptive to an implanting embryo. We know that the developing bovine conceptus (embryo and extraembryonic membranes) produce proteins during thi...
Article
Full-text available
Advances in liquid chromatography‐mass spectrometry have facilitated the incorporation of proteomic studies to many biology experimental workflows. Data‐Independent Acquisition platforms, such as SWATH, offer several advantages for label‐free quantitative assessment of complex proteomes over Data‐Dependent Acquisition (DDA) approaches. However, SWA...
Preprint
Full-text available
Advances in liquid chromatography-mass spectrometry have facilitated the incorporation of proteomic studies to many biology experimental workflows. In particular, the introduction of Data-Independent Acquisition platforms, such as SWATH, offers several advantages for label-free quantitative assessment of complex proteomes over Data-Dependent Acquis...
Article
Full-text available
Liquid chromatography coupled with mass spectrometric detection is one of the major technologies used for protein sequencing, identification, and quantification. This review provides an introduction of the current state-of-the-art technology in peptide profiling using nano-liquid chromatography–mass spectrometry applied to large-scale protein or pr...
Article
Full-text available
Mutations in pre-mRNA processing factors (PRPFs) cause autosomal-dominant retinitis pigmentosa (RP), but it is unclear why mutations in ubiquitously expressed genes cause non-syndromic retinal disease. Here, we generate transcriptome profiles from RP11 (PRPF31-mutated) patient-derived retinal organoids and retinal pigment epithelium (RPE), as well...
Article
Full-text available
The original version of this Article omitted the following from the Acknowledgements: 'This work was support by EPSRC grant EP/K504336/1 and Leverhulme Trust grant RPG-2016-017.' This has been corrected in both the PDF and HTML versions of the Article.
Data
Figure S1. Brightfield images of organoids. Example images of organoids cultured in pooled and single conditions from each cell line tested. Scale bar = 500 μM.
Data
Figure S4. TEM and electrophysiological analysis. (A): Transmission electron micrographs of single and (B) pooled retinal organoids at day 150. Abbreviations: OLM, outer limiting membrane; IS, inner segment; PC, primary cilium; M, mitochondria; OS, outer segment. Scale bar far left = 2 μm, scale bar middle and right = 500 nm. (C): 25 representative...
Data
Figure S5. Factorial experimental design. (A): Table showing design of factorial experiment 1. (B): Table showing design of factorial experiment 2. (C): Chart showing overlapping coverage of cell number and BMP4 between the two experiments.
Data
Figure S2. Relative organoid size during the differentiation process. Error bars = SEM. Significance assessed by one way ANOVA with Tukey's multiple comparisons test.
Data
Figure S6. Response of iPSC‐derived‐retinal organoids to moxifloxacin treatment. (A): Hematoxylin and eosin staining of retinal organoids, left = untreated control and right = Moxifloxacin 100 μg/ml. Red asterisk = disorganization and gaps in laminated structure (Scale bar = 100 μm; n = 3). (B): LDH tests of retinal organoids treated with Moxifloxa...
Data
Table S1. The DNA sequence of oligonucleotides used in the qRT‐PCR analysis.
Data
Table S2. Summary of antibodies used in this study.
Data
Figure S3. Schematic chart showing the development of iPSC derived retinal organoids and RPE spheres at day 60 of differentiation. Abbreviations: RPE, RPE spheres; NR, retinal organoids with neural retina (no RPE), NR+ RPE, retinal organoids with RPE; undefined, organoids that did not contain any neural retina or RPE cells, n = 3.
Data
Table S5. (A): Table showing significant single interactions on gene expression for design 2. (B): Table showing two way interactions for design 2.
Data
Table S3. Mann–Whitney U test on spiking activity.
Data
Table S4. (A): Table showing significant single interactions on gene expression for design 1. (B): Table showing two way interactions for design 1.
Article
Full-text available
Type II DNA topoisomerases (EC 5.99.1.3) are enzymes that catalyse topological changes in DNA in an ATP dependent manner. Strand passage reactions involve passing one double stranded DNA duplex (transported helix) through a transient enzyme-bridged break in another (gated helix). This activity is required for a range of cellular processes including...
Article
Full-text available
Carbon dioxide is vital to the chemistry of life processes including metabolism, cellular homoeostasis, and pathogenesis. CO2 is generally unreactive but can combine with neutral amines to form carbamates on proteins under physiological conditions. The most widely known examples of this are CO2 regulation of ribulose 1,5-bisphosphate carboxylase/ox...
Article
Full-text available
The availability of in vitro models of the human retina in which to perform pharmacological and toxicological studies is an urgent and unmet need. An essential step for developing in vitro models of human retina is the ability to generate laminated, physiologically functional and light-responsive retinal organoids from renewable and patient specifi...
Article
BACKGROUND AND AIMS: Elevated urinary 11-dehydro thromboxane B 2 (TxB 2 ), a measure of thromboxane A 2 formation in vivo, predicts future atherothrombotic events. To further understand this relationship, the genetic determinants of 11-dehydro TxB 2 and their associations with cardiovascular morbidity were investigated in this study. METHODS: Genom...
Article
Background and aims: Elevated urinary 11-dehydro thromboxane B2 (TxB2), a measure of thromboxane A2 formation in vivo, predicts future atherothrombotic events. To further understand this relationship, the genetic determinants of 11-dehydro TxB2 and their associations with cardiovascular morbidity were investigated in this study. Methods: Genome-...
Article
Full-text available
It is widely known that numerous adaptive responses of drought-stressed plants are stimulated by chemical messengers known as phytohormones. Jasmonic acid (JA) is one such kind of phytohormone. But there are very few reports revealing its direct implication in drought related responses or its cross-talk with other phytohormones. In this study, we c...
Chapter
Muscle tissue poses a particular challenge to proteomic analysis due to a very wide range of protein abundances arising from the dominant expression of myofilament-related proteins. We address this issue by describing proteomic analysis with liquid chromatography–mass spectrometry (LC-MS) and sequential window acquisition of all theoretical mass sp...
Article
Full-text available
The bifunctional protein kinase-endoribonuclease Ire1 initiates splicing of the mRNA for the transcription factor Hac1 when unfolded proteins accumulate in the endoplasmic reticulum. Activation of Saccharomyces cerevisiae Ire1 coincides with autophosphorylation of its activation loop at S840, S841, T844, and S850. Mass spectrometric analysis of Ire...
Article
Full-text available
The androgen receptor (AR) is the main driver of prostate cancer (PC) development and progression, and the primary therapeutic target in PC. To date, two functional ubiquitination sites have been identified on AR, both located in its C-terminal ligand binding domain (LBD). Recent reports highlight the emergence of AR splice variants lacking the LBD...
Article
Full-text available
This data article contains the results of molecular dynamics (MD) simulations performed to assess the stability of the previously computed complex between the hCES1 structure and the Amplex Red (AR) substrate [1] and to compare the dynamic behavior of this complex with that of the corresponding hCES1-deacetylAR product. The study involves both stan...
Article
Full-text available
Background: Necrotising enterocolitis (NEC) and late onset sepsis (LOS) are the leading causes of death among preterm infants in the developed world. This study aimed to explore the serum proteome and metabolome longitudinally in preterm infants with NEC or LOS, matched to controls. Methods: Nineteen patients (10 cases, 9 controls) were included...
Article
Full-text available
Amplex Red is a fluorescent probe that is widely used to detect hydrogen peroxide (H2O2) in a reaction where it is oxidised to resorufin by horseradish peroxidase (HRP) as a catalyst. This assay is highly rated amongst other similar probes thanks to its superior sensitivity and stability. However, we report here that Amplex Red is readily converted...
Article
Full-text available
Smallholder rice cultivation productivity is directly related to alleviating hunger and poverty. Biotic and abiotic stresses increasingly subvert the process, and drought is the most common stress. A mechanistic understanding of plant response to drought could lead to the use of gene-based markers to generate drought-tolerant rice. Such an understa...
Article
Full-text available
The proteomics field has shifted over recent years from two-dimensional gel electrophoresis (2-DE)-based approaches to SDS-PAGE or gel-free workflows because of the tremendous developments in isotopic labeling techniques, nano-liquid chromatography, and high-resolution mass spectrometry. However, 2-DE still offers the highest resolution in protein...
Article
Full-text available
Mitochondrial function is an important determinant of the ageing process; however, the mitochondrial properties that enable longevity are not well understood. Here we show that optimal assembly of mitochondrial complex I predicts longevity in mice. Using an unbiased high-coverage high-confidence approach, we demonstrate that electron transport chai...
Article
Treatment with tyrosine kinase inhibitors (TKIs) including trastuzumab has revolutionized the management of HER2-positive breast cancer. Recent evaluation of clinical trial data suggests that a subset of HER2/ER double-positive cancers may not receive significant benefit from the TKI therapy. Here we investigate the cross talk between HER2 and ER i...
Article
Full-text available
There is increasing interest in establishing the roles that lysine acetylation of non nuclear proteins may exert in modulating cell function. Lysine deacetylase 8 (KDAC8), for example, has been suggested to interact with α-actin and control the differentiation of smooth muscle cells. However, a direct role of smooth muscle non nuclear protein acety...
Article
Full-text available
Platelets have been implicated in colon cancer metastasis and prognosis but the underlying molecular mechanisms remain unclear. We evaluated the role of the different MAPK pathways in platelet-stimulated matrix metalloproteinase-9 (MMP-9) generation and colon cancer invasion. In addition, proteins released during platelet-tumour cell interactions w...
Article
The proteomics field has shifted during the last years from two-dimensional gel electrophoresis (2-DE)-based approaches to SDS-PAGE or gel free workflows due to the tremendous developments in isotopic labelling techniques, nano-liquid chromatography (LC) and high resolution mass spectrometry (MS). However, 2-DE still offers the highest resolution i...
Article
Full-text available
14-3-3 proteins are ubiquitous molecular chaperones with important roles in brain development and neuronal function. Altered expression of 14-3-3 proteins has been reported in several neurologic and neurodegenerative disorders and identifying 14-3-3 binding proteins may provide important insights into the physiologic and pathophysiologic roles of t...
Article
Isobaric peptide termini labeling (IPTL) is a recently introduced approach to the chemical labeling of peptides with isotopic reagents. Peptides derived from two different samples are labeled at the N terminus and at the C terminus with isotopically labeled reagents that have identical mass differences. To obtain isobaric peptides, labeling is carr...