PhD student in Immunology

UMR 5164 (CNRS/UB) IMMUNOCONCEPT Laboratory - UNIVERSITY OF BORDEAUX Candidat pour une thèse de science pour septembre/octobre 2024, qui est donc financée sur 3 ans

Job description

Title of the structure : Immunoconcept Laboratory
Name and surname of the person in charge of the structure: Julie Déchanet Merville
Immediate supervisor (if different from the head of the structure) : Hannah Kaminski
Geographical location of the position (full address):
UMR 5164 (CNRS/UB) IMMUNOCONCEPT Laboratory
UNIVERSITY OF BORDEAUX
Carreire site, North zone, Building 1B
146 Rue Léo Saignat
33076 Bordeaux Cedex
Contact person for any information: Hannah Kaminski ; hkaminski@immuconcept.org
Job title: PhD student in Immunology
BAP: Life Science
Job type: PhD
Vacancy date: 01/09/2024 (3-year fixed-term contract)
Quota of working time: 100%.
Proposed gross salary:  3 397,77 € per month (adapted regarding the candidate’s degree)


Main mission(s) or project(s) to be accomplished :

  • To develop and use innovative techniques necessary for the characterisation of immune response in humans.
  • Participate in the writing of original articles and reviews produced in the framework of the project.
  • Present results at team meetings
  • Work of bibliography
  • Training proposed by the university (new techniques, software use, etc..)


Key activities:

  • Develop and update here/his knowledge about her/his project by regular bibliography
  • Develops, experiments and implements innovative techniques for the functional and molecular analysis of immune cells in humans
    (based on flow cytometry, measurement of gene expression by PCR, tissue labelling, mouse experiments, biochemical techniques such as Westernblot immunoprecipitation ELISA)
  • Regular meeting with hers/his thesis director
  • Defines and implements the logistics and requirements necessary for the application of new technologies in the research protocols
  • Ensures the quality and reliability of the results and takes the necessary steps in case of problems
  • Ordering of reagents and consumables needed by the project


Related activities:

  • Discusses procedures with project investigators and technical staff involved
  • Provide the necessary analysis to propose solutions
  • Present research results in an appropriate form (oral presentations and reports)


Work environment and context, particular constraints linked to the position :

  • The PhD student will be recruited with 100% time on HORUS.
  • He/she will also work closely with the scientific team of the project (mainly her/his director as well as other researchers, teacher-researchers associated with HORUS and engineer depending on the common projects linked to HORUS)).
  • He/she will work with biological samples from patients (tissues or PBMC) potentially infected with CMV and from mice infected with CMV.


Presentation of the project :
Organ transplantation is the treatment of choice for treating end-stage organ failure, but the immunosuppressive drugs used to prevent graft rejection expose patients to an increased risk of opportunistic infections, with cytomegalovirus (CMV) being a prominent concern. To enhance our understanding of this issue, we established a European consortium named ‘HORUS,’ with Hannah Kaminski as the coordinator, funded by Horizon Europe, to collaboratively work on characterizing viral and immunological signatures associated with infection control.
The HORUS project (Horizon Europe funding – health cluster, destination “Tackling diseases”) aims to improve our understanding of the “host-virus” relationship between cytomegalovirus (CMV) and solid organ transplant recipients to discover signatures integrating viral, clinical and immunological characteristics associated with CMV control. The ultimate goal is to decrease the incidence of CMV, better manage difficult-to-treat infections, avoid the use of unnecessary antiviral therapies, and discover new molecules that can specifically target the CMV immune response without increasing the risk of acute rejection.

This project will address three unresolved questions:


Job description :

  1. How to identify host-virus interactions that impact on the incidence of CMV infection after solid organ transplantation?
  2. How to identify the host-virus interaction associated with effective control of CMV infection?
  3. How to improve the prevention and management of CMV infection using immunomodulatory regimens that

enhance the immune response to CMV?

The 5-year project has 16 partners from 7 European countries: France, Belgium, Germany, Czech Republic, Spain, Italy and Switzerland. The consortium includes academics, companies, hospitals and technology transfer centres.


The PhD project will be a 3 year-project based on

  • the analysis by flow cytometry of patients’ samples recruited in HORUS cohort to contribute to identify signatures associated with CMV control,
  • in vitro study and potentially, in vivo study with mice model, analysing gd T cell response to CMV both in patients with preformed immunity (called CMV positive patients) and in naïve patients (called CMV negative patients).


1. Assessment of gd T cells function of R+ patients
We postulate that immune cells in CMV positive patients who develop CMV reactivation will have a more dysfunctional profile than R+ patients without CMV infection (Kaminski H, JASN 2021). Dysfunctional and non-dysfunctional gd T cells will be similarly analyzed after activation with CMV-infected cells. Full functional characterization of activated T cells will be performed using intracytoplasmic detection of IFNg, TNFa, MIP1b, IL-2, and cell surface expression of CD107 and CD40L after stimulation by flow cytometry. We will determine which inhibitory receptors or metabolic pathways are involved in dysfunction using ex-vivo blocking antibodies, pharmacological inhibitors, and CRISPR-Cas9 gene knock-down.
Finally, we will decipher full transcriptome of dysfunctional versus functional gd T cells after cell-sorting by cytometry and bulk RNASeq.


2. Assessment of naïve γδ T cells responding to CMV
Preliminary data from our team suggest the existence of a natural repertoire of innate naïve γδ T cells responding to CMV in healthy individuals with negative CMV serology (CMV-negative individuals), who are at the highest risk of CMV disease post-transplantation. These cells and their response to CMV have not been studied previously, although the presence of CMV-responsive T lymphocytes in CMV-negative individuals may have a significant impact on the subsequent response and control of CMV infection after transplantation.γδ T cells responding to CMV will be characterized in more detail at the transcriptional level (RNASeq), phenotypic level (NK-type receptors, checkpoint
molecules, cytotoxicity by flow cytometry), and functional level (cytokine and chemokine production). Since γδ T cells exhibit adaptive properties and an effector/memory phenotype when studied in CMV-positive individuals, our in vitro co-cultures will help us understand the transition from a polyclonal innate repertoire to an adaptive mono/oligoclonal repertoire of CMV-responsive γδ Tcells. Concurrently, an ex vivo analysis of γδ T cells in CMV negative patients from the patient cohort included in HORUS, experiencing CMV infection post-transplantation, will be conducted at various time points before and during infection, with a focus on transcriptional aspects. Candidate pathways involved in activation will be blocked using specific antibodies or inhibitors, emphasizing those targeted by current
immunosuppression (TCR signaling, mTOR pathway, cytokine receptor signaling) to compare the ability of naïve T cells to respond in the context of immunosuppression compared to conventional αβ T cells. Once the molecules or pathways involved in the early stages of γδ T cell activation are validated in vitro, we will validate them in vivo using mice deficient for these molecules/pathways. Naïve γδ T cells from knockout mice and wild-type mice will be adoptively transferred into CD3KO mice to assess their ability to protect CD3KO mice from CMV-induced mortality.

On-call duty: no

Requested profile

• Skills required:

Degree or level of qualification

  • master 2 degree in Immunology

Knowledge :

  • Solid knowledge in immunology
  • Solid training in cellular and molecular biology, immunolabelling techniques, and biochemical analysis techniques
  • Good English level
  • Work in a biosafety laboratory
  • good level of using software as Prism, Flowjo and Excel
  • Ability to work in a team
  • Organisational skills
  • Ability to analyse and summarise
  • Rigour, good interpersonal skills and discretion (confidentiality)
  • Ability to adapt to different working methods and techniques

If applicable, experience required :

  • Not applicable

Contacts for job interviews

Hannah Kaminski hkaminski@immuconcept.org
Julie Déchanet-Merville jdechanet@immuconcept.org