Identification of clinically relevant T cell receptors for personalized T cell therapy using combinatorial algorithms.

A central challenge in developing personalized cancer cell immunotherapy is the identification of tumor-reactive T cell receptors (TCRs). By exploiting the distinct transcriptomic profile of tumor-reactive T cells relative to bystander cells, we build and benchmark TRTpred, an antigen-agnostic in silico predictor of tumor-reactive TCRs. We integrate TRTpred with an avidity predictor to derive a combinatorial algorithm of clinically relevant TCRs for personalized T cell therapy and benchmark it in patient-derived xenografts.

Response to tumor-infiltrating lymphocyte adoptive therapy is associated with preexisting CD8+ T-myeloid cell networks in melanoma.

Adoptive cell therapy (ACT) using ex vivo-expanded tumor-infiltrating lymphocytes (TILs) can eliminate or shrink metastatic melanoma, but its long-term efficacy remains limited to a fraction of patients. Using longitudinal samples from 13 patients with metastatic melanoma treated with TIL-ACT in a phase 1 clinical study, we interrogated cellular states within the tumor microenvironment (TME) and their interactions. We performed bulk and single-cell RNA sequencing, whole-exome sequencing, and spatial proteomic analyses in pre- and post-ACT tumor tissues, finding that ACT responders exhibited higher basal tumor cell-intrinsic immunogenicity and mutational burden. Compared with nonresponders, CD8+ TILs exhibited increased cytotoxicity, exhaustion, and costimulation, whereas myeloid cells had increased type I interferon signaling in responders. Cell-cell interaction prediction analyses corroborated by spatial neighborhood analyses revealed that responders had rich baseline intratumoral and stromal tumor-reactive T cell networks with activated myeloid populations. Successful TIL-ACT therapy further reprogrammed the myeloid compartment and increased TIL-myeloid networks. Our systematic target discovery study identifies potential T-myeloid cell network-based biomarkers that could improve patient selection and guide the design of ACT clinical trials.

A phase 1 trial of adoptive transfer of vaccine-primed autologous circulating T cells in ovarian cancer.

We have previously shown that vaccination with tumor-pulsed dendritic cells amplifies neoantigen recognition in ovarian cancer. Here, in a phase 1 clinical study ( NCT01312376 /UPCC26810) including 19 patients, we show that such responses are further reinvigorated by subsequent adoptive transfer of vaccine-primed, ex vivo-expanded autologous peripheral blood T cells. The treatment is safe, and epitope spreading with novel neopeptide reactivities was observed after cell infusion in patients who experienced clinical benefit, suggesting reinvigoration of tumor-sculpting immunity.

TCR sequencing and cloning methods for repertoire analysis and isolation of tumor-reactive TCRs.

T cell receptor (TCR) technologies, including repertoire analyses and T cell engineering, are increasingly important in the clinical management of cellular immunity in cancer, transplantation, and other immune diseases. However, sensitive and reliable methods for repertoire analyses and TCR cloning are still lacking. Here, we report on SEQTR, a high-throughput approach to analyze human and mouse repertoires that is more sensitive, reproducible, and accurate as compared with commonly used assays, and thus more reliably captures the complexity of blood and tumor TCR repertoires. We also present a TCR cloning strategy to specifically amplify TCRs from T cell populations. Positioned downstream of single-cell or bulk TCR sequencing, it allows time- and cost-effective discovery, cloning, screening, and engineering of tumor-specific TCRs. Together, these methods will accelerate TCR repertoire analyses in discovery, translational, and clinical settings and permit fast TCR engineering for cellular therapies.

Cancer vaccines based on whole-tumor lysate or neoepitopes with validated HLA binding outperform those with predicted HLA-binding affinity.

Antigen selection and prioritization represent crucial determinants of vaccines' efficacy. Here, we compare two personalized dendritic cell-based vaccination strategies using whole-tumor lysate or neoantigens. Data in mouse and in cancer patients demonstrate that peptide vaccines using neoantigens predicted on the sole basis of in silico peptide-major histocompatibility complex (MHC) binding affinity underperform relative to whole-tumor-lysate vaccines. In contrast, effective in vitro peptide-MHC binding affinity and peptide immunogenicity significantly improve the prioritization of tumor-rejecting neoepitopes and result in more efficacious vaccines.

A Real-Time Comparison of Four Particulate Matter Size Fractions in the Personal Breathing Zone of Paris Subway Workers: A Six-Week Prospective Study.

We developed a Bayesian spline model for real-time mass concentrations of particulate matter (PM10, PM2.5, PM1, and PM0.3) measured simultaneously in the personal breathing zone of Parisian subway workers. The measurements were performed by GRIMM, a gravimetric method, and DiSCmini during the workers' work shifts over two consecutive weeks. The measured PM concentrations were analyzed with respect to the working environment, the underground station, and any specific events that occurred during the work shift. Overall, PM0.3 concentrations were more than an order of magnitude lower compared to the other PM concentrations and showed the highest temporal variation. The PM2.5 levels raised the highest exposure concern: 15 stations out of 37 had higher mass concentrations compared to the reference. Station PM levels were not correlated with the annual number of passengers entering the station, the year of station opening or renovation, or the number of platforms and tracks. The correlation with the number of station entrances was consistently negative for all PM sizes, whereas the number of correspondence concourses was negatively correlated with PM0.3 and PM10 levels and positively correlated with PM1 and PM2.5 levels. The highest PM10 exposure was observed for the station platform, followed by the subway cabin and train, while ticket counters had the highest PM0.3, PM1, and PM2.5 mass concentrations. We further found that compared to gravimetric and DiSCmini measurements, GRIMM results showed some discrepancies, with an underestimation of exposure levels. Therefore, we suggest using GRIMM, calibrated by gravimetric methods, for PM sizes above 1µm, and DiSCmini for sizes below 700 nm.

Application of the Bayesian spline method to analyze real-time measurements of ultrafine particle concentration in the Parisian subway.

BACKGROUND: Air pollution in subway environments is a growing concern as it often exceeds WHO recommendations for indoor air quality. Ultrafine particles (UFP), for which there is still no regulation nor a standardized exposure monitoring method, are the strongest contributor to this pollution when the number concentration is used as exposure metric. OBJECTIVES: We aimed to assess the real-time UFP number concentration in the personal breathing zone (PBZ) of three types of underground Parisian subway professionals and analyze it using a novel Bayesian spline approach. Consecutively, we investigated the effect of job, week day, subway station, worker location, and some further events on UFP number concentrations. METHODS: The data collection procedure originated from a longitudinal study and lasted for a total duration of 6 weeks (from October 7 to November 15, 2019, i.e. two weeks per type of subway professionals). Time-series were built from the real-time particle number concentration (PNC) measured in the PBZ of professionals during their work-shifts. Complementarily, contextual information expressed as Station, Environment, and Event variables were extracted from activity logbooks completed for every work-shift. A Bayesian spline approach was applied to model the PNC within a Bayesian framework as a function of the mentioned contextual information. RESULTS: Overall, the Bayesian spline method suited a real-time personal PNC data modeling approach. The model enabled estimating the differences in UFP exposure between subway professionals, stations, and various locations. Our results suggest a higher PNC closer to the subway tracks, with the highest PNC on subway station platforms. Studied event and week day variables had a lesser influence. CONCLUSION: It was shown that the Bayesian spline method is suitable to investigate individual exposure to UFP in underground subway settings. This method is informative for better documenting the magnitude and variability of UFP exposure, and for understanding the determinants in view of further regulation and control of this exposure.