data scientist job offer
Reference: DS0124
Contract type: Full time position,fix-term contract
Location: Bordeaux, France

 

You like to play with large multi-omics datasets and analyze spatial information ? You have an interest in the biological processes involved in the response to cancer immunotherapies ? Keep reading and apply!


 

About Explicyte


Explicyte is a preclinical and translational contract research organization specialized in immuno-oncology. Our mission is to support academics, biotechs and pharmas in the discovery of novel targets and novel cancer immunotherapies.

With a team of 25, we’re a human-sized company, which brings under the same roof cell biologists, immunologists, medical oncologists and bioinformaticians. Focused on sponsors’ projects, our activity also involves in-house R&D and external collaborations, which led to the publication of 30+ papers in high impact-factor journals.

Based in Bordeaux, our lab is located at the Bergonié Comprehensive Cancer Center, where we work in close contact with medical oncology teams. We believe Explicyte is a place to learn, grow, and have impact in the fight against cancer.

More about us

 

Your position


To strengthen our translational research activities and benefit our partners, we are currently looking for an experienced Data Scientist.

In your role, you will be accountable for data mining & analysis in relation to sponsors’ and R&D studies. You will play with data from various biological samples (e.g. FFPE tumor samples, Peripheral Blood Mononuclear Cells, tumor immune infiltrates, plasmas, etc.), captured through a wide range of tools and platforms such as Immunohistochemistry (IHC)/Immunohistofluorescence (IHF), spatial transcriptomics, flow cytometry, gene expression profiling (RNAseq, TCRseq, scRNAseq) or proteomics and metabolomics.

You will interact with the translational team, and will report to the Chief Technology Officer.

What you will find at Explicyte

 

Your skills & traits



  • Post-graduate degree (MSc/PhD) in computational biology, in bioinformatics, or biostatistics

  • Strong experience in multi-omics data analysis, using genomic, transcriptomic, and other -omics datasets

  • Proficiency in R programming language (markdown, shiny…) is mandatory. Other languages (Python, Groovy, mySQL…) are a plus

  • Expertise in analysis softwares, such as Inform, Qupath, FlowJo, CellRanger

  • Knowledge of basic and multivariate statistics is required

  • Ability to conceptualize desired tables and graphs and codebase as needed

  • Experience in cloud computing (AWS, Azure etc…) and database development (mySQL)

  • Ability to adapt activities and priorities to challenging deliverables

  • Fluency in written and oral English

  • Good interpersonal and collaborative skills


Your missions & responsibilities



  • Understand the biological issues and the questions asked

  • Interact with the Data Science Director, the Study Managers or the collaborating teams for the optimal definition of the analysis criteria

  • Collect, process, analyze and compare large-scale datasets from various origins (images, genomics, proteomics, metabolomics, etc.)

  • Use pre-existing bioinformatics tools and develop new ones as needed to enable data mining and analysis (large-scale data analysis and integration, supervised or unsupervised learning, statistics, genomic analysis, modeling, deep learning, etc.)

  • Provide documentation of procedures to describe the analytical strategies

  • Run data analysis reports to support teams to provide study deliverables that meet project’s requirements and deadlines

  • Have a theoretical understanding of data analysis algorithms, and be up to date with literature review to be at the forefront of developments in data analysis methods


Apply now! 


 

Predictive value of tumor microenvironment on pathologic response to neoadjuvant chemotherapy in patients with undifferentiated pleomorphic sarcomas.
In this retrospective study led by Pr. Antoine Italiano (Bergonié & Gustave Roussy Comprehensive Cancer Centers) based on the NEOSARCOMICS trial, we investigated whether microenvironment features of undifferentiated pleomorphic sarcomas (UPS) - an aggressive subtype of soft tissue sarcoma - could predict response to neoadjuvant anthracycline-based chemotherapy.


  • Microenvironment features & prognosis without neoadjuvant therapy: We applied a multiplexed immunohistofluorescence (mIHF) panel on tumor samples from 47 patients with UPS who underwent surgical resection. We found that patients with poor survival had fewer infiltrated immune cells (especially CD8+ cells and M1 macrophages), while patients with better overall survival tended to feature high tumor infiltration.

  • Microenvironment features & response to neoadjuvant therapy: We then analyzed the gene expression of baseline samples from 24 patients with resectable UPS, who were treated with neoadjuvant chemotherapy. We found that a good response was associated with a high proliferation and low immune infiltration phenotype. This finding was confirmed with the multiplex mIHF panel: patients who poorly respond to neoadjuvant therapy feature high immune infiltration. Plasma proteomics confirmed the upregulation of cell cycle pathways in low immune infiltration patients.


These results suggest that immune infiltration status can serve to stratify UPS patients before surgical resection. Patients with high immune infiltration benefit from a better prognosis from the start and may respond poorly to chemotherapy. However, neoadjuvant therapy may improve the prognosis of immune-low UPS patients.

Read paper in the Journal Hematology & Oncology

Single cell spatial transcriptomics CRO Oncology Immunotherapy US EU France Japan
Explicyte is the first immuno-oncology CRO in Europe equipped with the 10x Xenium platform for single-cell spatial transcriptomics!  Training by the 10x Genomics team started! Why is it exciting for immuno-oncology?

“For our translational and data science team, the Xenium platform opens unexplored avenues for analyzing tumors and their microenvironment in response to various cancer modalities, including immunotherapies.

For our sponsors, gaining a deep understanding of the gene expression profiles and spatial distribution of individual cells within a tumor specimen can provide unique insights into understanding tumor biology, and mechanisms at play in anti-cancer response or resistance to treatment. It creates opportunities to identify new targets and biomarkers to predict clinical outcomes for cancer patients.

As a researcher, I’m eager to watch tumor cells, immune cells, cancer-associated fibroblasts with the Xenium eye, and to witness the single-cell architecture of immune infiltrates and tertiary lymphoid structures. We are truly excited as we enter a new era of cancer discovery."

Alban Bessede, CEO of Explicyte Immuno-Oncology.

 

About the 10x Xenium platform:

  • Compatible with standard tumor specimens (frozen & FFPE)

  • TME architecture is visualized at subcellular level with a 5000-gene panel

  • Single-cell analysis & segmentation with AI-driven algorithm


 

Learn about our services for target identification & biomarker discovery in immuno-oncology.
Identification of microenvironment features associated with primary resistance to anti-PD-1/PD-L1 + antiangiogenesis in gastric cancer through spatial transcriptomics and plasma proteomics
In this study led by Pr. Antoine Italiano (Bergonié & Gustave Roussy Comprehensive Cancer Centers), 49 patients with advanced gastric cancer were treated with avelumab (a PD-1/PD-L1 inhibitor) in combination with the anti-angiogenic drug regorafenib (a multi-kinase tyrosine inhibitor). Despite encouraging efficacy results, a significant subset of patients did not respond to this therapeutic regimen.

Explicyte utilized spatial transcriptomics to profile the expression of over 18,000 protein-coding genes across six tumors from both responding and non-responding patients from the REGOMUNE & REGONIVO studies (both combining regorafenib with immune checkpoint inhibition). In the immune compartments of resistant patients, the CD163 gene was found to be overexpressed, alongside an enrichment in M2 macrophages. Non-responding patients also exhibited a strong upregulation of the S100A10 protein in tumor cells—a protein involved in macrophage chemotaxis.

We then developed two immunohistofluorescence (IHF) panels to validate these findings via digital pathology in 43 tumor biopsies. The results confirmed the abundance of M2 macrophages in resistant patients, with a significant increase in the M2/M1 ratio, and the overexpression of S100A10 in tumor cells among patients with poor responses.

Finally, plasma biomarkers were investigated using an Olink proteomic panel. Several cytokines (CSF-1, IL-4, IL-8, and TWEAK) associated with macrophage infiltration were found to be upregulated in patients with worse outcomes.

Altogether, this paper highlights the central role of M2 macrophages in the resistance to anti-PD-1/PD-L1 immunotherapy combined with anti-angiogenic therapy in gastric cancers and provides perspectives for novel diagnostic and therapeutic approaches.

 

Read paper in Molecular Cancer

banner webinar TLS modulation explicyte
Since 2021, Explicyte has developed a specific expertise in Tertiary Lymphoid Structure (TLS) detection and scoring by digital pathology. Hosted by Alban Bessede, PhD, CEO of Explicyte, this 45-minute webinar dedicated to TLS modulation in cancer immunotherapy will feature 2 presentations:

Tertiary lymphoid structures as modulators of anti-tumor immunity: what do we know and where are we headed?


Tullia C. Bruno, PhD - UPMC Hillman Cancer Center / University of Pittsburgh

Following a PhD thesis on intratumoral T cells at Johns Hopkins in 2010, Tullia Bruno started working on the role of B cells in the TME during her postdoctoral fellowship at the University of Colorado Denver. In 2015, she joined the University of Pittsburgh as an Assistant Professor to investigate the role of intratumoral B cell function within TLS in solid tumors. Focused on translational research and the development of novel immunotherapies, she is also a faculty member in the Tumor Microenvironment Center and the Cancer Immunology and Immunotherapy Program at the UPMC Hillman Cancer Center.

Predictive role of TLS for cancer immunotherapy: current insights and perspectives


Pr Antoine Italiano, MD, PhD - Institut Bergonié & Gustave Roussy Comprehensive Cancer Centers

Author of 500+ peer-reviewed publications, Pr. Italiano has been the Principal Investigator of 50+ clinical trials over the past 5 years, investigating the resistance mechanisms to cancer immunotherapies in solid tumors. Trained as a medical oncologist in France, he obtained a PhD in Molecular & Cell Biology in 2008. He then joined the laboratory of Cristina Antonescu for a post-doctoral fellowship at the MSKCC (New York, USA). He is currently leading Early Phase Trials and Sarcoma Units at Institut Bergonié (Bordeaux, France) and the head of the Precision Medicine unit at Gustave Roussy (Villejuif, France).

More about Explicyte's capacities for TLS detection & scoring in patient specimens

Register for the webinar

Reshaping the tumor microenvironment of cold soft-tissue sarcomas with oncolytic viral therapy: a phase 2 trial of intratumoral JX-594 combined with avelumab and low-dose cyclophosphamide
In soft tissue sarcomas, the presence of tertiary lymphoid structures (TLS) is known to increase sensitivity to immune checkpoint inhibitors. In a clinical trial conducted at the Institut Bergonié, Prof. Antoine Italiano and colleagues studied the combination of an oncolytic virus and metronomic chemotherapy with the aim of remodeling the tumor microenvironment of patients with TLS-negative soft-tissue sarcoma, thereby improving their sensitivity to the PD-L1 inhibitor Avelumab.

As part of this study, tumor biopsies and plasma samples were supported and processed by Explicyte teams, for staining and Olink-based proteomics, respectively. Our results confirm that intratumoral administration of the oncolytic virus JX-584 can alter the immune landscape of the tumor microenvironment, potentially converting cold tumors into immunogenic tumors.

Read the article

Faecalibaterium prausnitzii strain EXL01 boosts efficacy of immune checkpoint inhibitors
We're happy to showcase a collaboration just published in OncoImmunology. Since 2016, French biotech Exeliom Bioscience has been advancing therapeutic programs targeting the gut microbiota in Crohn's disease and various types of cancer, based on the immuno-modulatory bacterium Faecalibacterium prausnitzii (oral drug EXL01). In this paper, we supported Exeliom Bioscience in the generation of in vivo and vitro data to decipher the mechanism of action of EXL01.

The in vivo study, based on the MCA205 syngeneic tumor model, demonstrates that oral supplementation with EXL1 restores the efficacy of anti-PD-L1 immunotherapy in animals with antibiotics-induced gut dysbiosis. The subsequent in vitro investigation, based on the MLR assay, showed that the EXL1 strain boosts the activation of both dendritic cells and T cells in the presence of anti-PD-L1 antibody.

Read the paper

Tor geants 2024 explicyte
From the 8th to the 14th of September, Gregory Lebras will run 330km in the Aosta Valley, in Italy. Enlisted for the TOR330 - TOR DES GÉANTS ultra-endurance trail together with 1,100 competitors, this anesthetist nurse at the Institut Bergonié Comprehensive Cancer Center aims to raise funds to support sarcoma research. Over 7 days, he will encourage his audience to make donations to the not-for-profit association "La Course du Petit Prince".

"We actively participate in the RHU Condor, a research consortium that receives funds from "La Course du Petit Prince" for the development of novel immunotherapies against soft-tissue sarcoma. So when we learned about the initiative of Gregory, we felt compelled to be part of it. Gregory is currently running over 10h per week, he's dedicated, fun, and generous. It just clicked. I can tell we are very proud sponsors !" Alban Bessede, CEO of Explicyte.

 

https://youtu.be/ejnRb2Acr3Y?si=qovB7lJ2FTELxqxj

 

Make a donation

2024 ASCO meeting abstract Explicyte
Alban Bessede, CEO of Explicyte, and Antoine Italiano, MD at the Institut Bergonié, were in Chicago in early June at the 2024 ASCO meeting to present a recent piece of research performed in partnership with 3 French Comprehensive Cancer Centers: Institut Gustave Roussy (Paris), Institut Bergonié (Bordeaux), and Institut Claudius Regaud (Toulouse).

In this phase II trial of Regorafenib (anti-VEGFR therapy) combined with avelumab (anti-PD-L1 immunotherapy) in soft-tissue sarcoma patients with cold tumors (TLS-negative), we found a positive effect of this combotherapy in terms of anti-tumor immunity mobilization and 6-month progression-free survival (PFS).

Read abstract

translational research in immuno-oncology cancer immunotherapies
Over the past 5 years, our translational team released major papers in the field of cancer immunotherapy, in collaboration with French oncologists from the Institut Bergonié and Gustave Roussy Comprehensive Cancer Centers. Here are 5 key papers to highlight what we've learned:




In Clinical Cancer Research (2024): TROP2 is a biomarker of resistance to immune checkpoint inhibition in NSCLC


In patients with advanced Non-Small Cell Lung Cancer (NSCLC) treated with PD-L1 inhibitor atezolizumab, the overexpression of trophoblast cell surface antigen 2 (TROP2) is associated with poorer progression-free survival. TROP2High patients are more likely to benefit from a combination of immunotherapy and anti-TROP2 agents.

Technologies used: Plasma Proteomics, Bulk Transcriptomics, Digital Pathology (IF), Spatial Transcriptomics

Read paper




In Clinical Cancer Research (2023): IDO1 is a potential therapeutic target for NSCLC patients with inflamed tumor microenvironment and/or TLS


By analyzing NSCLC tumor samples from 891 patients treated with immune checkpoint inhibitors or chemotherapy, we evidenced that IDO1 expression was associated with a favorable clinical outcome (ORR, PFS, OS) upon ICI but not chemotherapy. We also demonstrated that IDO1 is overexpressed within inflamed tumors and noticeably in Tertiary Lymphoid Structures (TLS). These results strongly suggest that targeting the immunosuppressive IDO1 enzyme could be beneficial in patients with inflamed tumors.

Technologies used: T-cell Killing Assay, Germinal Center Reaction Assay, Bulk Transcriptomics, Digital Pathology (IHC/IF), Spatial Transcriptomics

Read paper




In Annals of Oncology (2022): Acetaminophen negatively impacts cancer immunotherapy efficacy


Metabolomic analysis of plasma samples collected before cancer patients underwent immunotherapy revealed that the presence of Acetaminophen (APAP) correlates with a limited response to immune checkpoint blockade. This negative impact was validated in two independent prospective cohorts and further strengthened by preclinical evidence, both in vitro and in vivo. Altogether, our findings suggest that the use of Acetaminophen, one of the most widely used drugs, limits cancer immunotherapy efficacy and should be taken with caution.

Technology used: Flow cytometry, Plasma Proteomics, In Vitro Assays, In Vivo Experiments

Read paper




In Nature Cancer (2021): The presence of mature TLS is a predictive biomarker of anti-PD1/PD-L1 axis  blockers efficacy in patients with advanced cancer


We analyzed the presence of Tertiary Lymphoid Structures (TLS) in tumor samples from 328 patients with solid tumors treated with anti-PD1 or anti-PD-L1 monoclonal antibodies. We found that the presence of mature TLS is predictive of improved clinical outcome (objective response, progression-free survival, overall survival).

Technology used: Digital Pathology

Read paper




In Annals of Oncology (2021): Elevated LIF level in serum is a predictive biomarker of resistance to immune checkpoint inhibition


Using Olink-based proteomics, we analyzed the plasma samples of 387 patients with advanced cancer treated with immune checkpoint inhibitors. High levels of Leukemia inhibitory factor (LIF) emerged as indicative of poor clinical outcome. The study identifies LIF as a potential target to improve the efficacy of cancer immunotherapies.

Technology used: Plasma Proteomics

Read paper




 

That's it for now! If you wish to get a full picture of our scientific production, please take a look here.

And if you have a translational research project in mind, let's talk about it. We'll be happy to help.

 
SITC 2024
Imane Nafia, Chief Scientific Officer at Explicyte, will attend the 39th Annual Meeting of the Society for Immunotherapy of Cancer - SITC (Houston USA, November 6-10, 2024) to share some new developments and translational research work. Her abstract title:

Ovarian cancer ascites exhibit an impaired immune environment - immunosuppressive & protumoral – detrimental to the immune response
TROP2 lung cancer
New paper in Clinical Cancer Research!  The result of a joint work between Bergonié Institute, Gustave Roussy Institute and Explicyte.

Relying on precious patient samples and cutting-edge technologies, the teams involved discovered that Trophoblast cell-surface antigen 2 (TROP2), well-known as an attractive target for antibody-drug conjugate (ADC)-based therapy, is a strong predictor of resistance to immunotherapy, but not to chemotherapy, in patients with advanced lung cancer.

Pr. Antoine Italiano (Bergonié and Gustave Roussy Institutes) supervised the entire study, which follows on previous research on tertiary lymphoid structures (more here). He shares his views on this outstanding work.

Read the article here, entitled “TROP2 is associated with primary resistance to immune checkpoint inhibition in patients with advanced non-small cell lung cancer”.

 

Why is TROP2 getting so much attention today?

Pr. Italiano: TROP2 emerges as a pivotal player in the realm of cancer research and therapy due to its overexpression in various cancer types (breast, lung, etc.). This high expression positions TROP2 as a promising biomarker for cancer detection but also as a prime target for therapeutic intervention.

The compelling narrative surrounding TROP2 is gaining further strength with the positive results of numerous studies evaluating the safety and efficacy of ADCs specifically designed to target TROP2. Tangible results have been achieved in breast, urothelial, and non-small cell lung cancer (NSCLC). These studies validate TROP2 targeting as a robust and successful strategy in the ongoing pursuit of effective cancer therapies.

In light of these substantial findings, TROP2 emerges as a beacon of hope and a focal point for future advances in cancer diagnosis and treatment.

 

What is the main result of your study? Can you comment on the link between TROP2 expression and the tumor microenvironment characteristics?

Pr. Italiano: The reason for the TROP2 upregulation in cancer cells remains unclear; however, it is postulated that TROP2 plays a crucial role in regulating cell proliferation and invasion. This suggests that its overexpression could selectively drive tumor progression. Notably, preclinical data support this hypothesis, demonstrating that TROP2 overexpression stimulates tumor growth, while TROP2 knockdown inhibits it.

Moreover, preclinical findings indicated that surface expression of TROP2 in lung cancer cells could impact the functionality of cancer cell reactive T cells, leading to apoptosis of CD8+ T cells. Intrigued by these observations, we sought to investigate the influence of TROP2 expression on treatment outcomes of NSCLC patients undergoing immunotherapy.

Our analysis of large independent patient cohorts revealed an association between TROP2 overexpression, NSCLC microenvironment, and response to immune checkpoint inhibitors. Specifically, NSCLC with low TROP2 expression had the highest abundance of immune cells, including T cells, cytotoxic lymphocytes, and B cells. Conversely, high expression of TROP2 was linked to primary resistance to immune checkpoint inhibitors. To our knowledge, this study represents the first correlation between TROP2 expression levels, tumor microenvironment, and patient outcomes.

 

What is the impact of this research on the clinical development of TROP2 ADC candidates?

Pr. Italiano: TROP2 targeting appears to be a very promising therapeutic strategy for patients with advanced NSCLC. Compelling results from the reference study (TROPION-Lung01) Phase III trial show the effectiveness of the main TROP2 ADC (Datopotamab deruxtecan, Dato-DXd) compared to Docetaxel, the current standard of care in chemotherapy, in NSCLC patients treated with at least one prior line of therapy.

Recent data indicate that combining TROP2 targeting with PD-1/PD-L1 inhibition yields promising responses and presents no new safety signals in patients with previously untreated advanced or metastatic NSCLC lacking actionable genomic alterations.

Building on our results, we hypothesize that patients most likely to benefit from this therapeutic strategy are those with high TROP2 expression. Notably, our finding of a strong correlation between circulating levels of TROP2 and its expression by tumor cells suggests that selection of these patients can be achieved non-invasively through a simple blood test.

This groundbreaking approach not only strengthens the potential of TROP2 as a key therapeutic target, but also introduces a practical and accessible method of patient stratification, paving the way for personalized and effective treatments at the forefront of NSCLC management.

 

How did Explicyte contribute to this major discovery?     

Pr. Italiano: The collaboration with Explicyte teams played a pivotal role in the success of this study. Explicyte offers a unique and comprehensive immuno-oncology platform, seamlessly integrating robust analytical technologies, for groundbreaking testing of cancer immunotherapies. This includes cutting-edge capabilities in gene sequencing, spatial transcriptomics, multiplex immunofluorescence, plasma proteomics, and more.

Explicyte being installed within Bergonié Institute, this proximity allows our clinical and research teams to foster close collaborations with them. Undeniably, this proximity favors a synergistic approach to advance our understanding of cancer immunotherapies and translate these findings into meaningful clinical applications. The invaluable contributions offered by these collaborative efforts underscore the strength of our partnership in driving innovative advances in the field of immuno-oncology.

 

What are the remaining challenges to radically change the outcome of NSCLC?

Pr. Italiano: NSCLC poses a myriad of challenges due to its heterogeneous nature. A significant breakthrough lies in the development and validation of a platinum-free first-line regimen for patients with advanced NSCLC, free of adverse effects.

Our results present a compelling proposition in this regard. Combining TROP2 ADC with immune checkpoint inhibitors emerges as a promising strategy, while introducing a paradigm shift in how we approach the treatment of advanced NSCLC. To the extent that it eliminates platinum from the therapeutic landscape, it holds the promise of significantly improving the quality of life of patients facing this complex and demanding disease.
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