MSCA 博士生职位：基于质谱的蛋白质组学分析及 β-catenin 翻译后修饰研究

University of Milan Project Title: MS-based proteomic profiling of unmodified and modified β-catenin- and β-catenin-peptide binder-sequences to decipher the role of protein PTMs in the IDR-mediated β-catenin interactome Objectives: 1. Develop and benchmark quantitative MS-based proteomic strategies to resolve PTM-dependent β-catenin interaction networks, integrating affinity-based interactomics with perturbation-driven proteomic readouts. 2. Define how individual and combinatorial PTMs—including S/T phosphorylation and R methylation—rewire β-catenin/IDR interaction networks and propagate into measurable cellular proteomic responses. 3. Establish quantitative proteomic signatures linking defined molecular perturbations of the β-catenin system to interaction-network remodeling and downstream pathway states, thereby distinguishing direct PTM-dependent interactions from secondary cellular responses. Project Overview: Recent evidence shows that PRMT2 directly methylates β-catenin, promoting its proteasomal degradation and thereby attenuating downstream transcriptional activity. This places arginine methylation upstream in the regulation of β-catenin protein stability and provides a compelling mechanistic foundation for investigating β-catenin methylation and its crosstalk with phosphorylation. Building on these findings, this project will investigate how specific PTMs—and defined combinations of PTMs—encode different molecular and cellular states of the β-catenin regulatory network. Rather than considering PTMs exclusively as determinants of individual protein–protein interactions, the project will use β-catenin as a model system for developing a quantitative proteomics framework capable of connecting molecular PTM states, interaction-network remodeling, and cellular responses. Peptide-array pulldown assays and quantitative mass spectrometry-based proteomics will initially identify β-catenin interactions that are sensitive to phosphorylation, arginine methylation, or combinations of these modifications. Quantitative experimental designs will then determine the magnitude, specificity, and reproducibility of PTM-dependent interaction changes, allowing the construction of PTM-resolved interaction signatures rather than binary lists of interactors. The Maric lab (JMU, WP2) will provide expertise in peptide-array screening, assisting in the design and setup of the pulldown workflow and validation of β-catenin-binding IDR sequences. The Conibear lab (TUW, WP3) will synthesize defined S/T phosphorylated and R-methylated peptide variants and semi-synthetic β-catenin constructs, enabling systematic exploration of individual and combinatorial PTM states. A central technological component of the project will be developed in the Bonaldi lab (UMI), where advanced quantitative proteomics will be used not simply to cat logue β-catenin-associated proteins, but to determine how experimentally controlled PTM states reshape interaction networks. MS-based workflows for comparative interactomics across multiple molecular states will be integrated with proteome-level responses to targeted perturbations of the corresponding regulatory machinery. In particular, perturbation of selected kinases/phosphatases and PRMT-dependent pathways will provide an orthogonal cellular layer through which interaction-level observations can be tested. Comparing molecularly defined PTM states with cellular perturbation signatures will make it possible to identify coherent regulatory modules and prioritize PTM-dependent interactions that are functionally propagated through the β-catenin pathway. This strategy extends the concept of a PTM “barcode”: rather than defining a barcode solely as a combination of chemical modifications, PTM barcodes will be represented by multidimensional quantitative signatures comprising modification state, interaction-network configuration, and downstream proteomic response. Integration with structural studies (Madl, MUG) will provide a mechanistic interpretation of selected PTM-sensitive interactions, while integration with bioinformatic approaches (Pritišanac, HZM) will enable network-level analysis, prioritization of regulatory modules, and identification of proteomic signatures associated with specific β-catenin states. The resulting framework will reveal the molecular logic through which IDR-associated PTMs regulate β-catenin while establishing a transferable experimental strategy for interrogating dynamic, PTM-controlled signaling networks using quantitative and perturbational proteomics. Finally, selected regulatory mechanisms will be challenged pharmacologically, including perturbation of kinase/phosphatase and PRMT activities. Proteomic responses to these perturbations will be compared with the experimentally derived β-catenin PTM signatures, providing a route from molecular mechanism to pharmacologically actionable network states and potentially revealing intervention points relevant to pathological β-catenin signaling, including cancer. Contribution to the overall research program: Establishes a quantitative and perturbation-based proteomics framework connecting defined PTM states with IDR-mediated interaction plasticity and downstream cellular responses. The project will generate PTM-resolved interaction and proteomic signatures that guide the design of synthetic variants and binders while providing experimentally testable models of β-catenin regulatory states. Skills and research profile: The doctoral candidate will acquire an interdisciplinary profile at the interface of quantitative proteomics, protein interaction biology, and PTM-dependent signaling. Training will include advanced quantitative MS-based proteomics, affinity/interactome profiling, experimental design for multi-condition proteomics, analysis of PTM-dependent protein interaction networks, cellular perturbation experiments, and integration of molecular and proteome-wide datasets. A particular emphasis will be placed on using quantitative proteomics as a hypothesis-generating and mechanistic technology, moving from protein identification toward quantitative signatures, regulatory networks, and experimentally testable models of pathway states, to be investigated/tested during the student’s secondment Salary: The position is funded by the Horizon Europe MSCA-DN project FlexCAT (Grant Agreement No. 101311592) for three years. To meet the doctoral program requirements of SEMM, a fourth-year extension will be covered by a salary aligned with the standard SEMM PhD candidate scale. The selected candidate will be offered a competitive salary comprising a Living Allowance (adjusted by the country correction coefficient), a Mobility Allowance, and, if applicable, a Family Allowance. All allowances are subject to applicable social security contributions and taxation. Planned secondment: Host: PMC; Supervisor: Dr. Sanne van Neerven; Length: 3 months Purpose: Cell-based perturbation of β-catenin regulatory pathways and generation of matched samples for quantitative proteomic profiling, enabling validation of PTM-dependent interaction signatures in a cellular context. Enrolment in Doctoral degree(s): UMI/SEMM (https://semm.it/)

Requirements / required education level / degree: Master Degree or equivalent

Requirements / required education level / discipline: Chemistry

Requirements / skills: Applicants of any nationality are welcome to apply. To be eligible for recruitment as an MSCA Doctoral Candidate, applicants must fulfil the following criteria at the date of recruitment: • Education – you do not hold a doctoral degree and hold (or will shortly complete) a science Master’s degree (see individual project requirements), with excellent results, qualifying you for admission to the doctoral program of the respective host institution. The successful candidate must fulfil the admission requirements of the respective doctoral programme and will be enrolled in a doctoral programme during the project. • Mobility - you must not have resided or carried out your main activity (work, studies, etc.) in recruiting beneficiary’s country for more than 12 months during the 36 months before your recruitment. Compulsory national service, holidays/short stays and time spent obtaining refugee status under the Geneva Convention4 are not considered for this purpose. • Language & communication – excellent command of spoken and written English (min. B2 level). Ability to communicate results clearly to diverse audiences, both in writing and verbally. • Motivation – motivation for multidisciplinary, international doctoral research, hands-on experimental work, mandatory academic/industy secondment(s), to publish research findings in international journals, present results at conferences and contribute to project deliverables. Willingness to contribute to project network-wide activities, communication, training events, and dissemination efforts. • Technical skills – specific to the individual DC project (see individual project descriptions).

Requirements / specific requirements: Skills and research profile: The doctoral candidate will acquire an interdisciplinary profile at the interface of quantitative proteomics, protein interaction biology, and PTM-dependent signaling. Training will include advanced quantitative MS-based proteomics, affinity/interactome profiling, experimental design for multi-condition proteomics, analysis of PTM-dependent protein interaction networks, cellular perturbation experiments, and integration of molecular and proteome-wide datasets. A particular emphasis will be placed on using quantitative proteomics as a hypothesis-generating and mechanistic technology, moving from protein identification toward quantitative signatures, regulatory networks, and experimentally testable models of pathway states, to be investigated/tested during the student’s secondment.

Requirements / required languages / language: ENGLISH

Requirements / required languages / language level: Excellent

Research experience / main research field: Chemistry

Research experience / years of research experience: 1 - 4

Additional information / selection process: Applications will be assessed for eligibility and scientific/academic quality. Shortlisted applicants will be invited to interview. The final selection will follow the open, transparent and merit-based recruitment principles of MSCA.

Work location / nr job positions: 1

Work location / job organisation institute: University of Milan

Work location / job country: Italy

Work location / job city: Milan

Hiring contact / organisation institute: University of Milan

Hiring contact / organisation institute type: Higher Education Institute

Hiring contact / country: Italy

Hiring contact / city: Milan

Hiring contact / website: https://phd-recruiting.medunigraz.at/

Application / how to apply: website

Application / application website: https://phd-recruiting.medunigraz.at/

EU funding / framework programme: Horizon Europe - MSCA

EU funding / cofund nr job position: 1

EU funding / sesam agreement number: 101311592

Research field / main research field: Chemistry

Research field / sub research field: Biochemistry

Researcher profile: First Stage Researcher (R1)

Positions: PhD Positions

Contract: Temporary

Job status: Full-time

Application deadline (as exported; timezone unverified): 2026-10-31T22:59:00