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Oct 13, 2023

A ablação de RASA2 em células T aumenta a sensibilidade ao antígeno e

Nature volume 609, páginas 174–182 (2022) Cite este artigo

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A eficácia das terapias adotivas de células T para o tratamento do câncer pode ser limitada por sinais supressivos de fatores extrínsecos e pontos de controle inibitórios intrínsecos1,2. A edição genética direcionada tem o potencial de superar essas limitações e melhorar a função terapêutica das células T3,4,5,6,7,8,9,10. Aqui, realizamos várias telas knock-out de CRISPR em todo o genoma sob diferentes condições imunossupressoras para identificar genes que podem ser direcionados para prevenir a disfunção das células T. Essas telas convergiram para RASA2, uma proteína ativadora de RAS GTPase (RasGAP) que identificamos como um ponto de verificação de sinalização em células T humanas, que é regulado negativamente após a estimulação aguda do receptor de células T e pode aumentar gradualmente com a exposição crônica ao antígeno. A ablação de RASA2 melhorou a sinalização de MAPK e a atividade citolítica de células T do receptor de antígeno quimérico (CAR) em resposta ao antígeno alvo. As estimulações repetidas de antígeno tumoral in vitro revelaram que as células T deficientes em RASA2 apresentam aumento da ativação, produção de citocinas e atividade metabólica em comparação com as células de controle, e apresentam uma vantagem marcante na morte persistente de células cancerígenas. As células CAR T nocauteadas para RASA2 tiveram uma vantagem competitiva de aptidão sobre as células de controle na medula óssea em um modelo de leucemia em camundongos. A ablação de RASA2 em vários modelos pré-clínicos de receptor de células T e terapias de células CAR T prolongou a sobrevida em camundongos xenoenxertados com tumores líquidos ou sólidos. Juntos, nossas descobertas destacam o RASA2 como um alvo promissor para melhorar tanto a persistência quanto a função efetora em terapias de células T para o tratamento do câncer.

As células CAR T foram transformadoras em um subconjunto de malignidades hematológicas agressivas, e as células T transgênicas do receptor de células T (TCR) (células TCR T) mostraram resultados promissores em estudos clínicos de fase inicial para tumores sólidos1. No entanto, muitos cânceres, especialmente tumores sólidos, não respondem às terapias atuais com células T ou progridem rapidamente após a resposta inicial. Dentro da massa tumoral, o microambiente imunossupressor representa uma barreira substancial à eficácia da imunidade antitumoral2,11. Além disso, a exposição persistente ao antígeno pode levar à disfunção das células T, destacando a necessidade de equilibrar a função efetora e a persistência de longo prazo nas células T modificadas3,12. A manipulação direcionada de genes selecionados está sendo testada como uma estratégia para aumentar a eficácia das terapias adotivas com células T5,6,7. No entanto, os alvos gênicos ideais nas células T humanas não foram explorados sistematicamente. As telas CRISPR em larga escala podem acelerar a descoberta de perturbações genéticas que podem aumentar a eficácia das células T modificadas3,8,9,10. Anteriormente, desenvolvemos uma plataforma de descoberta em células T humanas primárias e a aplicamos para identificar novos reguladores genéticos da proliferação de células T13. Aqui descrevemos telas genéticas imparciais realizadas sob várias condições imunossupressoras comumente encontradas no microambiente tumoral (TME) que revelaram a ablação do gene RASA2 como uma estratégia para as células T superarem vários sinais inibitórios. Descobrimos que a ablação de RASA2 aumenta a sensibilidade ao antígeno e melhora a função efetora e a persistência das células CAR T e TCR T. Finalmente, mostramos que a ablação de RASA2 em células T antígeno-específicas pode melhorar o controle do tumor e prolongar a sobrevida em vários modelos pré-clínicos de tumores líquidos e sólidos.

Os pontos de verificação intrínsecos de células T e TME supressivas podem interferir na eficácia das células T manipuladas direcionadas a tumores sólidos14. Desenvolvemos uma abordagem sistemática para identificar perturbações genéticas que poderiam tornar as células T resistentes a uma variedade de sinais inibitórios encontrados no TME. Anteriormente, usamos CGS-21680, um agonista de adenosina13, para simular sinalização inibitória elevada de adenosina A2A em resposta a altos níveis de adenosina no TME hipóxico15. Aqui, estendemos essa estratégia para modelar vários desafios para a função das células T no TME. Para modelar os sinais intrínsecos do ponto de controle, focamos nos inibidores da sinalização de cálcio e calcineurina (tacrolimus e ciclosporina), que é uma via crítica para a ativação de células T que é frequentemente suprimida em células T infiltrantes tumorais16. Para imitar um sinal inibitório extrínseco proeminente no TME, usamos TGFβ, uma citocina supressiva canônica que limita a função das células T nos tumores17. Finalmente, como as células reguladoras T (células Treg) são mediadores importantes da disfunção das células T em vários tipos de tumor18, adaptamos nossa plataforma de triagem para analisar as interações célula-célula e, assim, revelar genes que conferem resistência à supressão das células T efetoras pelas células Treg.

1.5) between 5 (blue) and all 6 (pink) of the screens are labelled. Bar height is the number of shared genes among the screens, connected by dots in the lower panel (n = 4 human donors for stimulated (stim) and Treg cell screens, n = 2 for adenosine, cyclosporine and tacrolimus, and n = 1 for the TGFβ screen). c,d, log2 fold change (FC) for individual guide RNAs (vertical lines); background shows the overall guide distribution in greyscale. c, Guides targeting RASA2 (pink) across all suppressive conditions. d, Guides targeting RasGAP family members other than RASA2 were not enriched consistently in either direction, whereas guides targeting the RasGEF RASGRP1 were depleted from dividing cells as expected. e, Distribution of CFSE staining in RASA2-KO versus control (Ctrl; non-targeting guide RNA) T cells across all suppressive conditions. f, Cancer cell growth during in vitro cancer cell-killing assay under suppressive conditions. AUC, area under the growth curve. n = 2 donors in triplicate, shape denotes donor. g, Suppression assay confirms that RASA2 ablation rendered T cells resistant to Treg cell suppression of proliferation in vitro. Bars show the CD8+ cell count 4 days after stimulation (n = 4 donors per group; mean ± s.e.m.; **P < 0.01 and ***P < 0.001, two-sided paired Student's t-test). h, RASA2 ablation rendered T cells resistant to Treg cell suppression compared with control T cells in an in vitro cancer cell-killing assay for one representative donor out of four (summary statistics shown in Extended Data Fig. 2g). Line is the mean and shaded area is 95% confidence interval for 3 technical replicates./p>1.54) were defined as hits for the shared hits analysis to generate Fig. 1b and Extended Data Fig. 1c and are detailed in Supplementary Table 1. To define suppressive condition-specific hits, the sgRNA counts in CFSE-low (highly dividing) cells were compared to the stimulation only (stim) condition using MAGeCK software as above. Results of this analysis are provided in Supplementary Table 2. For the quality metric of screens by dropout analysis of essential genes, we used essential genes as determined by DepMap19 and GSEA for gene-level log2 fold change. For analysis of expression of screen hits in primary human T cells the DICE database was used, averaging the expression of both activated CD4+ and CD8+ T cells20./p>1010 photons s–1 or when mice demonstrated signs of distress described in our IACUC protocol such as respiratory distress, hunched posture, lesions unresponsive to treatment, 15–20% weight loss, impaired or decreased mobility, neurologic signs that interfere with normal function or reduced grooming. These limits were not exceeded in any of the experiments. Mice were injected intraperitoneally with 1 × 106 LM7-GFP-ffluc osteosarcoma tumour cells. Seven days later, mice were injected intraperitoneally with 1 × 105 CAR T cells. The experiment was performed twice with CAR T cells generated from two different healthy donors. For the second experiment, mice that had long-term tumour-free survival (n = 1 for control KO, n = 3 for RASA2 KO) were re-challenged with an intraperitoneal injection of 1 × 106 LM7-GFP-ffluc tumor cells at day 174. Tumour burden was monitored by bioluminescence imaging as above./p> 1.5, methods) across the screen conditions (x-axis) including hits unique to each individual screen. Shared hits for each subset are detailed in Supplementary Table 1. d, Heatmap of the pairwise Pearson's correlation coefficient for gene-level z-scores for all screen conditions. e, Volcano plots showing p-value (MAGeCK RRA one-sided test and methods) on the y-axis and gene-level z-scores on the x-axis, comparing highly dividing cells in each suppressive condition to highly dividing in the vehicle condition. Highlighted are genes found to be specific to adenosine and TGFβ screens, selected for further validation. f, Gene targets from screens were selected as either general (PAN) or more specific to certain suppressive contexts and were knocked out individually in T cells. CFSE stained, Cas9 RNP-electroporated edited T cells were stimulated and cultured in the different suppressive conditions. Percent of cells proliferating for each gene KO compared to control cells are displayed for each suppressive condition (n = 2 donors, 2 sgRNAs per gene target in triplicates. We highlighted gene KOs found to confer significant resistance in predicted conditions (adenosine, TGFB, and calcium/calcineurin inhibitors – Tacrolimus, and Cyclosporine), using a cut-off of FDR adjusted p-value < 0.05. For clarity, displayed are the significant p-values for gene targets according to their suppressive screen condition of origin, but results for all genes across conditions are detailed in Supplementary Table 3). As expected, ADORA2A, TGFBR1 and TGFBR2, FKBP1A, and PPIA KOs conferred resistance in the adenosine, TGFB, Tacrolimus, and Cyclosporine conditions, respectively. PDE4C and NKX2-6 KOs were found to confer relatively selective resistance in the adenosine condition, and NFKB2 KO was found to increase resistance in the calcineurin inhibitor (tacrolimus and cyclosporine) conditions. TMEM222, while scoring very highly in the screens, did not increase proliferative advantage in this arrayed validation (dots are individuals replicates, black vertical lines are the mean, *p < 0.05, **p < 0.01, ***p < 0.001 and ***p < 0.0001 for two-sided unpaired Student's t-test). g, Log fold change (LFC) of guides targeting RasGAP genes or the RasGEF RASGRP1, across the different suppressive screen conditions shown here. h, Expression levels (scaled to minimum of 0 and a maximum of 1) of the RasGAP family members available in the BioGPS dataset27, including RASA2, across healthy human tissues revealed RASA2 as selectively expressed in CD8+/4+ human T cells. Data also shown for RASGRP1, a RasGEF with defined roles in TCR signaling and an expression pattern strikingly similar to that of RASA2./p>

1, as determined by DESeq2 analysis (methods). c, d Gene set enrichment analysis (GSEA) of oxidative phosphorylation (c) and glycolysis (d) ranked genes, based on DESeq2, higher rank indicates enrichment in RASA2 KO over CTRL. p-value is shown as determined by a two-sided permutation-test. Top up-regulated genes in each enrichment are listed to the right of each panel e, GSEA of oxidative phosphorylation genes correlated with RASA2 expression in immune cells in the GEO expression database, as retrieved by correlationAnalyzeR (methods). Genes are ranked by the Pearson correlation coefficients between RASA2 and the query gene, p-value by two-sided permutation test, after FDR adjustment. f, Selected examples of expression of RASA2 and two mitochondrial fitness genes, MRPL27 (left panel) and MRPL14 (right panel) across GEO datasets from immune cells. Shown at the top is the Pearson's correlation coefficient (R) and FDR adjusted p-value (padj) for each scatter plot. Values represent expression after variance stabilizing transformation (VST). g, Expression of RASA2 in stimulated T cells compared to unstimulated T cells, as measured by published single-cell RNA-Seq dataset, for two human donors13. h, i, Expression of Rasa2 compared to Pdcd1 in published RNA-Seq datasets from models of T cell exhaustion in murine T cells. Expression was scaled for a maximum of 1 and a minimum of 0 for each gene in each dataset (For LCMV samples in (h): n = 2 mice for Naive group, n = 3 mice for exhaustion group; for OVA samples, error bars are mean ± SEM (i): n = 3 mice for all groups, error bars are mean ± SEM). j, Log fold change (LFC) values for RASA2 sgRNAs in CRISPRa and CRISPRi screens for cytokine production42 (MAGeCK's gene-level FDR listed for RASA2 in each screen). k, Western blot for level of RASA2 expression following RASA2 transgene or control (CTRL) transduction in two T cell donors. l, Normalized values for T cell expansion based on cell counts for T cells with RASA2 transgene versus GFP control (n = 3 human T cell donors, mean ± SEM, shape denotes donor). m, histogram for one example donor from cells described in (l), stained and FACS analyzed for CD69 activation marker. n, Summary data for CD69 levels in two T cell donors transduced with the RASA2 transgene versus control (n = 2 human T cell donors, shape denotes donor)./p>

 0.05 for two-sided Wilcoxon test, shape denotes donor)./p>

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