CAR-tropic extracellular vesicles carry tumor-associated antigens and modulate CAR T cell functionality

Abstract Tumor-derived extracellular vesicles (EVs) are active contributors in metastasis and immunosuppression in tumor microenvironment. At least some of the EVs carry tumor surface molecules such as tumor-associated antigens (TAAs) and/or checkpoint inhibitors, and potentially could interact with T cells or CAR T cells. Upon contact with T cells, EVs could alter their phenotype and functions by triggering signaling through TCR or CAR reprogramming them to escape immune response. We hypothesize that EVs that possess TAA on the surface will probably interact with CAR T cells which can recognize and bind corresponding TAA. This interaction between EVs and CAR T cells may change the outcome of CAR T-based cancer immunotherapy since it should affect CAR T cells. Also, EVs could serve as adjuvants and antigenic components of antitumor vaccines. Herein, we isolated EVs from B cell precursor leukemia cell line (pre-B ALL) Nalm-6 and demonstrated that recognition and binding of CD19+EVs with CD19-CAR T cells strongly depends on the presence of CD19 antigen. CD19+EVs induce secretion of pro-inflammatory cytokines (IL-2 and IFN-y) and upregulated transcription of activation-related genes (IFNG, IFNGR1, FASLG, IL2) in CD19-CAR T cells. Tumor necrosis factor receptor superfamily (TNFRSF4 and TNFRSF9) and T-cell exhaustion markers (CTLA4, LAG3, TIM3 and PDCD1LG2) were also upregulated in CD19-CAR T cells after incubation with CD19+EVs. Long-term cultivation of CD19+ or PD-L1+EVs with CD19-CAR T cells led to increased terminal differentiation and functional exhaustion according to elevated expression of PD-1, TIGIT, CD57. In summary, our results suggest that chronic exposure of CD19-CAR T cells to CD19+EVs mediates activation and systemic exhaustion in antigen-specific manner, and this negative effect is accompanied by the impaired cytotoxic activity in vitro

CAR-tropic extracellular vesicles carry tumor-associated antigens and modulate CAR T cell functionality

AbstractTumor-derived extracellular vesicles (EVs) are active contributors in metastasis and immunosuppression in tumor microenvironment. At least some of the EVs carry tumor surface molecules such as tumor-associated antigens (TAAs) and/or checkpoint inhibitors, and potentially could interact with T cells or CAR T cells. Upon contact with T cells, EVs could alter their phenotype and functions by triggering signaling through TCR or CAR reprogramming them to escape immune response. We hypothesize that EVs that possess TAA on the surface will probably interact with CAR T cells which can recognize and bind corresponding TAA. This interaction between EVs and CAR T cells may change the outcome of CAR T-based cancer immunotherapy since it should affect CAR T cells. Also, EVs could serve as adjuvants and antigenic components of antitumor vaccines. Herein, we isolated EVs from B cell precursor leukemia cell line (pre-B ALL) Nalm-6 and demonstrated that recognition and binding of CD19+EVs with CD19-CAR T cells strongly depends on the presence of CD19 antigen. CD19+EVs induce secretion of pro-inflammatory cytokines (IL-2 and IFN-y) and upregulated transcription of activation-related genes (IFNG, IFNGR1, FASLG, IL2) in CD19-CAR T cells. Tumor necrosis factor receptor superfamily (TNFRSF4 and TNFRSF9) and T-cell exhaustion markers (CTLA4, LAG3, TIM3 and PDCD1LG2) were also upregulated in CD19-CAR T cells after incubation with CD19+EVs. Long-term cultivation of CD19+ or PD-L1+EVs with CD19-CAR T cells led to increased terminal differentiation and functional exhaustion according to elevated expression of PD-1, TIGIT, CD57. In summary, our results suggest that chronic exposure of CD19-CAR T cells to CD19+EVs mediates activation and systemic exhaustion in antigen-specific manner, and this negative effect is accompanied by the impaired cytotoxic activity in vitro.</jats:p

&lt;i&gt;FGFR3, TERT, ТР53&lt;/i&gt; mutations and the &lt;i&gt;FGFR3&lt;/i&gt; gene expression in bladder cancer as prognostic markers

Background. Bladder cancer (BC) is a common urological cancer, 75 % of which are non-muscle invasive BC. After removal of the primary tumor, the adequate classification of malignancy and the defining of tumor progression risk remains an important issue, since it is associated with frequency of cystoscopy and choice of the BCG- or chemotherapy management.Objective: improve the algorithms of prognosis in intermediate-risk patients with non-muscle-invasive bladder cancer with the consideration of molecular characteristics of the primary tumor.Materials and methods. We studied 125 BC samples; mutations in the FGFR3, PIK3CA, TERT, and TP53 genes were determined by polymerase chain reaction and Sanger sequencing, as well as the expression of the FGFR3, EGFR, ERBB2, FOXA1, and GATA3 genes using realtime polymerase chain reaction.Results. Somatic mutations in the studied loci were detected in 65.6 % of the samples, five new mutations were identified. A decrease of the mutation frequency in the FGFR3 and TERT genes was shown, an increase — TP53 in order (Ta—T1/low G) &gt; (T1/high G) &gt; (&gt;T2/any G). The largest area under the ROC curve (0.807 ± 0.092, р = 0.004) was demonstratedfor the prognostic classifier with the independent variables: mutation in FGFR3 and/or TERT; mutation TP53; overexpression of the FGFR3 gene. The FGFR3, TERT mutations and/or FGFR3 overexpression in the absence of TP53 mutation indicates minimally invasive primary tumor. On the contrary, harboring TP53 mutation indicate the features of muscle-invasive BC at the genetic level. Using this algorithm, we reclassified 21 of T1G3 BC cases as having characteristics associated with non-invasive tumor in 43 %, and invasive BC in 57 % of patients.Conclusion. The aforementioned prognostic model could be used as additional laboratory test in assessing the malignancy and progression risk of non-muscle invasive BC.</jats:p

Combining chromosome conformation capture and exome sequencing for simultaneous detection of structural and single-nucleotide variants

Abstract Background Effective molecular diagnosis of congenital diseases hinges on comprehensive genomic analysis, traditionally reliant on various methodologies specific to each variant type—whole exome or genome sequencing for single nucleotide variants (SNVs), array CGH for copy-number variants (CNVs), and microscopy for structural variants (SVs). Methods We introduce a novel, integrative approach combining exome sequencing with chromosome conformation capture, termed Exo-C. This method enables the concurrent identification of SNVs in clinically relevant genes and SVs across the genome and allows analysis of heterozygous and mosaic carriers. Enhanced with targeted long-read sequencing, Exo-C evolves into a cost-efficient solution capable of resolving complex SVs at base-pair accuracy. Results Applied to 66 human samples Exo-C achieved 100% recall and 73% precision in detecting chromosomal translocations and SNVs. We further benchmarked its performance for inversions and CNVs and demonstrated its utility in detecting mosaic SVs and resolving diagnostically challenging cases. Conclusions Through several case studies, we demonstrate how Exo-C’s multifaceted application can effectively uncover diverse causative variants and elucidate disease mechanisms in patients with rare disorders