Histological stratification in metastatic non-small cell lung cancer (NSCLC) is essential to properly guide therapy. Morphological evaluation remains the basis for subtyping and is completed by ...additional immunohistochemistry labelling to confirm the diagnosis, which delays molecular analysis and utilises precious sample. Therefore, we tested the capacity of convolutional neural networks (CNNs) to classify NSCLC based on pathologic HES diagnostic biopsies. The model was estimated with a learning cohort of 132 NSCLC patients and validated on an external validation cohort of 65 NSCLC patients. Based on image patches, a CNN using InceptionV3 architecture was trained and optimized to classify NSCLC between squamous and non-squamous subtypes. Accuracies of 0.99, 0.87, 0.85, 0.85 was reached in the training, validation and test sets and in the external validation cohort. At the patient level, the CNN model showed a capacity to predict the tumour histology with accuracy of 0.73 and 0.78 in the learning and external validation cohorts respectively. Selecting tumour area using virtual tissue micro-array improved prediction, with accuracy of 0.82 in the external validation cohort. This study underlines the capacity of CNN to predict NSCLC subtype with good accuracy and to be applied to small pathologic samples without annotation.
Tumors poorly infiltrated by T cells are more resistant to immunogenic chemotherapies and checkpoint inhibition than highly infiltrated tumors. Using murine models, we found that CCR6
type 3 innate ...lymphoid cells (ILC3s) can trigger an increase in the number of T cells infiltrating a tumor. Shortly after administration of cisplatin chemotherapy, production of the chemokine CCL20 and proinflammatory cytokine IL-1β at the tumor site led to the recruitment and activation of ILC3s. Within the tumor, ILC3 production of the chemokine CXCL10 was responsible for the recruitment of CD4
and CD8
T lymphocytes to the tumor. ILC3-dependent infiltration of T cells was essential for antitumor immune responses and increased the efficacy of checkpoint inhibition. Thus, we reveal an essential role of CCL20 and IL-1β, which promote ILC3-dependent antitumor immunity and enhance tumor sensitivity to immunotherapy.
BackgroundT follicular helper cells (Tfh) are essential to shape B cell response during germinal center formation. Tfh accumulation has been reported in various human cancers, with positive or ...negative prognostic roles. However, the mechanisms explaining the accumulation of Tfh and their role in cancer remain obscure.MethodsIn vitro differentiated and mouse cell sorted Tfh phenotype was evaluated by flow cytometry and quantitative PCR (qPCR). Antitumor effect of Tfh was evaluated by adoptive transfer in different tumor-bearing mice models. The involvement of immune cells, cytokines and chemokines was evaluated, using depleting antibodies. Chemokines and cytokines expression and production were evaluated by qPCR and ELISA. In human, the impact of immune cells and chemokines on survival was evaluated by analyzing transcriptomic data from public databases and from our own patient cohorts.ResultsIn this study, we show that Tfh exert an antitumor immune effect in a CD8+-dependent manner. Tfh produce interleukin-21, which sustains proliferation, viability, cytokine production and cytotoxic functions of exhausted T cells. The presence of Tfh is required for efficacy of antiprogrammed cell death ligand-1 therapy. Tfh accumulate in the tumor bed and draining lymph nodes in different mouse cancer models. This recruitment is due to the capacity of transforming growth factor β to drive Chemokine (C-X-C motif) Ligand 13 expression, a chemoattractant of Tfh, by intratumor CD8+ T cells. Accumulation of Tfh and exhausted CD8+ T cells predicts cancer outcome in various cancer types. In patients treated with anti-programmed cell death-1 mAb, accumulation of Tfh and CD8+ at the tumor site is associated with outcome.ConclusionThis study provides evidence that CD8+/Tfh crosstalk is important in shaping antitumor immune response generated by immunotherapy.
Tumor immune infiltrates are associated with tumor prognosis in many cancer types. However, their capacity to predict the efficacy of checkpoint inhibitors is poorly documented. We generate three ...signatures that evaluate in different ways these infiltrates: lymphoid- and myeloid-alone signatures, and a combined signature of both named the TIL (tumor-infiltrating lymphocyte) transcriptomic signature. We evaluate these signatures in The Cancer Genome Atlas Program (TCGA) Pan-Cancer cohort and four cohorts comprising patients with melanoma, lung, and head and neck cancer treated with anti-PD-1 or anti-CTLA-4 therapies. We observe using TCGA Pan-Cancer cohort that this TIL or lymphoid-alone signature accurately estimates prognosis in most cancer types and outperforms histological TIL evaluation or myeloid signature alone. Both TIL and lymphoid signatures are correlated with response rate to immunotherapy. Combining lymphoid signature or TIL with tumor mutational burden generates a score that is highly efficient in predicting response to immunotherapy. In different series of patients treated with checkpoint inhibitors for non-small cell lung cancer, head and neck cancer, and melanoma, we observed that TIL or lymphoid signature were associated with outcome. These data demonstrate that a simple TIL or lymphoid signature could be used as a Pan-Cancer prognostic and predictive biomarker to estimate patient survival under checkpoint inhibitors.
Abstract
Purpose
The vast majority of research studies that have described the links between DNA damage repair or homologous recombination deficiency (HRD) score, and tumor biology, have concerned ...either triple negative breast cancers or cancers with mutation of
BRCA 1/2.
We hypothesized that ER + /HER2- early breast tumors without
BRCA 1/2
mutation could have high HRD score and aimed to describe their genomic, transcriptomic, and immune landscapes.
Patients and methods
In this study, we reported
BRCA 1/2
mutational status, HRD score, and mutational signature 3 (S3) expression, in all early breast cancer (eBC) subtypes from the TCGA database, with a particular focus in ER + /HER2-. In this subtype, bioinformatics analyses of tumor transcriptomic, immune profile, and mutational landscape were performed, according to HRD status. Overall survival (OS), progression free-interval (PFI), and variables associated with outcome were also evaluated.
Results
Among the 928 tumor samples analyzed, 46 harbored
BRCA 1/2
mutations, and 606 were ER + /HER2- (of which 24 were
BRCA 1/2
mutated). We found a subset of
BRCA
-proficient ER + /HER2— eBC, with high HRD score. These tumors displayed significantly different immune, mutational, and tumor molecular signatures landscapes, compared to
BRCA
-mutated and
BRCA
-proficient HRD-low tumors. Outcome did not significantly differ between these 3 groups, but biological factors associated with survival are not the same across the 3 entities.
Conclusion
This study highlights possible novel biological differences among ER + /HER2- breast cancer related to HRD status. Our results could have important implications for translational research and/or the design of future clinical trials, but require prospective clinical evaluation.
Immunotherapy has allowed major advances in oncology in the past years, in particular with the development of immune checkpoint inhibitors, but the clinical benefits are still limited, particularly ...in colorectal cancer (CRC). Our scientific approach is based on the search for innovative immunotherapy with a final goal that aims to induce an effective antitumor immune response in CRC. Here, we focused on a multikinase inhibitor, H89. We carried out
experiments based on syngeneic mouse models of colon cancer in BALB/c mice and chemically colon tumorigenesis. Flow cytometry, RNAseq, RT-qPCR, antibody-specific immune cell depletion, and Western blot were used to identify the immune cell type involved in the preventive and antitumor activity of H89. We demonstrated that H89 delays colon oncogenesis and prevents tumor growth. This latter effect seems to involve NK cells. H89 also inhibits colon tumor growth in a T-cell-dependent manner. Analysis of the immune landscape in the tumor microenvironment showed an increase of CD4
Th1 cells and CD8
cytotoxic T cells but a decrease of CD4
T
cell infiltration. Mechanistically, we showed that H89 could promote naïve CD4
T-cell differentiation into Th1, a decrease in T
differentiation, and an increase in CD8
T-cell activation and cytotoxicity
. Furthermore, H89 induced overexpression of genes involved in antitumor immune response, such as IL-15RA, which depletion counteracts the antitumor effect of H89. We also found that H89 regulated Akt/PP2A pathway axis, involved in TCR and IL-15 signaling transduction. Our findings identify the H89 as a potential strategy for immune system activation leading to the prevention and treatment of CRC.
(1) Background: Immunosuppression is a key barrier to effective anti-cancer therapies, particularly in triple-negative breast cancer (TNBC), an aggressive and difficult to treat form of breast ...cancer. We investigated here whether the combination of doxorubicin, a standard chemotherapy in TNBC with glyceryltrinitrate (GTN), a nitric oxide (NO) donor, could overcome chemotherapy resistance and highlight the mechanisms involved in a mouse model of TNBC. (2) Methods: Balb/C-bearing subcutaneous 4T1 (TNBC) tumors were treated with doxorubicin (8 mg/Kg) and GTN (5 mg/kg) and monitored for tumor growth and tumor-infiltrating immune cells. The effect of treatments on MDSCs reprogramming was investigated ex vivo and in vitro. (3) Results: GTN improved the anti-tumor efficacy of doxorubicin in TNBC tumors. This combination increases the intra-tumor recruitment and activation of CD8
lymphocytes and dampens the immunosuppressive function of PMN-MDSCs PD-L1
. Mechanistically, in PMN-MDSC, the doxorubicin/GTN combination reduced STAT5 phosphorylation, while GTN +/- doxorubicin induced a ROS-dependent cleavage of STAT5 associated with a decrease in FATP2. (4) Conclusion: We have identified a new combination enhancing the immune-mediated anticancer therapy in a TNBC mouse model through the reprograming of PMN-MDSCs towards a less immunosuppressive phenotype. These findings prompt the testing of GTN combined with chemotherapies as an adjuvant in TNBC patients experiencing treatment failure.
BackgroundSingle agent PD-1/PD-L1 inhibition are not effective in metastatic colorectal cancer with microsatellite stable tumors. However, signal of efficacy was shown using combotherapy of ...anti-PD-L1 and anti-CTLA-4 in multitreated patients and the combination with FOLFOX regimen could lead to a potential positive effect on antitumor immune response. We report here the immune response observed following immunomonitoring of patients before and during MEDITREME trial.MethodsMEDITREME was a single arm phase II trial which aimed at evaluating efficacy and safety of mFOLFOX in combination with durvalumab and tremelimumab. We studied the phenotypic and functional immune response at inclusion and after 15 days (C2), 5 (C5) and 12 (C12) weeks of treatment by flow cytometry and the specific T response by ELISPOT. These immune parameters could be linked to survival data (RECIST criteria, progression free-survival) to highlight factors that may be prognostic of treatment response.One patient with a complete response allowed further a more detailed analysis of antitumoral immune response by single cell (sc) RNA- and TCR-sequencing, ELISPOT and flow cytometry analyses of the blood and tumor infiltrated immune cells.ResultsComputational cytometry analyses showed that high baseline levels of Th2, Tc2 and PDL1+ MDSC were associated with non-responder patients. Conversely, a high baseline level of activated T cells secreting IFNg and TNFa and a high level of activated T cells expressing ICOS and high level of CD45RA+ Treg after a treatment cycle were associated with responder patients. Concerning specific T cells response, TERT response at C2 and C5 was associated with responder patients and with high PFS.ScRNA sequencing performed on CD8 cells isolated from blood and tumor samples from the patient with a complete response showed an accumulation of polyfunctional CD8 T cells in tumor with high level of expression of effector cytokine and cytotoxic molecules. TCR sequencing analysis underlined the expansion of multiple clonotypes in TILS with some similarly between clone found in TILS and blood at the time of surgery. Moreover, we showed that only in TILs and blood at surgery charged multiple TCR clones predicted to recognize similar antigen. Finally, we generated the 14 predicted CD8 neoantigen peptides thanks to tumor exome sequencing and found that blood T cells and TILs response against neoantigens.ConclusionsImmunomonitoring has allowed us to associate peripheral immune parameters with treatment efficacy. ScRNA sequencing underlines the ability of the treatment to induce a specific immune response against neoantigens in a complete responder patient.AcknowledgementsThanks to AstraZeneca for their financial support.Trial RegistrationClinicalTrialsgov Identifier: NCT03202758Ethics ApprovalEudra-CT registration number2016-005006-19
Metastatic breast cancer (MBC) is frequently managed by platinum-based chemotherapy during the disease course. The real benefit of these treatments is uncertain at advanced stages of the disease and ...in non-triple-negative subtypes. Since homologous recombination deficiency (HRD) could inform about tumor sensitivity to DNA-damaging agents, we aimed to determine biomarkers of genomic instability, and their link with platinum efficacy. In this single-center study, we report BRCA1/2 mutational status, HRD score and signature 3 levels, all obtained by tumor exome sequencing, in 86 patients with various subtypes of MBC and who received platinum-based chemotherapy. Overall response rate, disease control rate, PFS and PFS2/PFS1 ratio were evaluated to assess platinum-based chemotherapy efficacy. Among the 86 tumor samples analyzed, 7 harbored BRCA1/2 mutations. We found a subset of BRCA-proficient MBC with high HRD score or high S3 levels, comparable to BRCA-mutated tumors. However, these patients with high HRD score or high S3 tumor level do not seem to benefit more from platinum-based chemotherapy than the others, in terms of response rates and/or PFS, regardless of BC molecular subtype. By multivariate analysis, only the absence of liver metastases was independently associated with significantly better PFS on platinum-based chemotherapy. However, some of our exploratory analyses reveal that certain methods, when optimized, seem to associate with platinum benefit. Tumor exome sequencing methodology for quantifying HRD has to be approached systematically, and further validated and standardized prior to its clinical use. Further studies are warranted to confirm these results to guide platinum use in MBC.
Microsatellite stable colorectal cancers (MSS-CRC) are resistant to anti-PD-1/PD-L1 therapy but the combination of immune checkpoints inhibitors (ICI) could be a clue to reverse resistance. Our aim ...was to evaluate ex vivo the capacity of the combination of atezolizumab (anti-PD-L1) and tiragolumab (anti-TIGIT) to reactivate the immune response of tumor infiltrating lymphocytes (TILs) in MSS-CRC. We analysed CRC tumor tissue and the associated blood sample in parallel. For each patient sample, extensive immunomonitoring and cytokine production were tested. We generated an ex vivo assay to study immune reactivity following immune stimulation with checkpoint inhibitors of tumor cell suspensions. Three microsatellite instable (MSI) and 13 MSS-CRC tumors were analysed. To generalize our observations, bioinformatics analyses were performed on public data of single cell RNA sequencing of CRC TILs and RNA sequencing data of TCGA. Atezolizumab alone could only reactivate T cells from MSI tumors. Atezolizumab and tiragolumab reactivated T cells in 46% of MSS-CRC samples. Reactivation by ICK was observed in patients with higher baseline frequency of Th1 and Tc1 cells, and was also associated with higher baseline T cell polyfunctionality and higher CD96 expression. We showed that a high frequency of CD96 expression on T cells could be a surrogate marker of atezolizumab and tiragolumab efficacy. Together these data suggest that the association of atezolizumab and tiragolumab could restore function of CD4 and CD8 TILs in MSS-CRC and could be tested in a clinical trial in colorectal cancer patients with MSS status.
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