The DOI matches its Crossref record; 47 of the 47 references it cites were found in a registry or an index; none of the 28 sources its claims cite is checked for support yet.
Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion
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Abstract
Resistance to immune checkpoint inhibitors (ICIs) is a key challenge in cancer therapy. To elucidate underlying mechanisms, we developed Perturb-CITE-sequencing (Perturb-CITE-seq), enabling pooled clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 perturbations with single-cell transcriptome and protein readouts. In patient-derived melanoma cells and autologous tumor-infiltrating lymphocyte (TIL) co-cultures, we profiled transcriptomes and 20 proteins in ~218,000 cells under ~750 perturbations associated with cancer cell-intrinsic ICI resistance (ICR). We recover known mechanisms of resistance, including defects in the interferon-γ (IFN-γ)-JAK/STAT and antigen-presentation pathways in RNA, protein and perturbation space, and new ones, including loss/downregulation of CD58. Loss of CD58 conferred immune evasion in multiple co-culture models and was downregulated in tumors of melanoma patients with ICR. CD58 protein expression was not induced by IFN-γ signaling, and CD58 loss conferred immune evasion without compromising major histocompatibility complex (MHC) expression, suggesting that it acts orthogonally to known mechanisms of ICR. This work provides a framework for the deciphering of complex mechanisms by large-scale perturbation screens with multimodal, single-cell readouts, and discovers potentially clinically relevant mechanisms of immune evasion.
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“Other enriched perturbations included CD47, CD58, CDH19 and (Fig. 2d,e).”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Pooled screens identify mechanisms of immune evasion
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“co-cultures of T cells and cancer cells resulted in dose- (TIL:cancer cell ratio) and time-dependent cancer cell killing”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Patient-derived co-cultures for pooled perturbation screens
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“Loss of CD58 conferred immune evasion in multiple co-culture models”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Abstract
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“we developed Perturb-CITE-seq, enabling pooled CRISPR-Cas9 perturbations with single-cell transcriptome and protein read-outs.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Abstract
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“we find that loss or downregulation of CD58 confers immune evasion to T cell (and in part to Natural Killer (NK) cells) mediated killing”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > INTRODUCTION
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“was downregulated in tumors of melanoma patients with ICR.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Abstract
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“CD58 loss conferred immune evasion without compromising MHC expression”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Abstract
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“We recover known mechanisms of resistance, including defects in the IFNγ-JAK/STAT and antigen-presentation pathways in RNA, protein and perturbation space, and novel ones, including loss/downregulation of CD58.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Abstract
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“In patient-derived melanoma cells and autologous tumor infiltrating lymphocyte (TIL) co-cultures, we profiled transcriptomes and 20 proteins in ~218,000 cells under ~750 perturbations associated with cancer cell-intrinsic ICR.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Abstract
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“co-culture showed dose-dependent lysis of cancer cells with 30.96%, 58.35 % and 75.0% killing at 1:1, 2:1 and 4:1 ratios, respectively”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Pooled screens identify mechanisms of immune evasion
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“we identified sgRNAs that are depleted by day 7 and day 14 prior to any treatment or co-culture (Fig. 2a, Extended Data Fig. 3b-d, Supplementary Table 2). These included expected genes such as MYC.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Pooled screens identify mechanisms of immune evasion
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“CD58 expression was not significantly regulated by IFNγ”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Abstract
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“and novel ones, including loss/downregulation of CD58.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Abstract
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“Indeed, defects in the IFNγ-JAK/STAT nodes led to increased CD58 RNA and protein expression”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Loss of CD58 is an orthogonal mechanism of immune evasion
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“Perturbation of any major known node of this pathway down-regulated a coherent regulatory program in co-culture”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Perturb-CITE-Seq identifies immune evasion programs/modules
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“Loss of CD58 also conferred resistance to NK cell mediated killing”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Loss/downregulation of CD58 confers cancer immune evasion
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“Notably, in our Perturb-CITE-Seq data CD58 KO did not significantly alter the level of the B2M transcript or MHC Class I protein (encoded by HLA-A)”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Loss of CD58 is an orthogonal mechanism of immune evasion
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“Perturbations of the IFNγ-JAK/STAT module strongly increased the Overall Expression of the ICR signature (JAK1 p-value = 1.3e-10, IFNGR2 p-value = 1.4e-8, IFNGR1 p-value = 3.3e-5, STAT1 p-value = 9.6e-5, statistics by Welch’s t test, Methods)”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Perturb-CITE-Seq identifies immune evasion programs/modules
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“The perturbations also altered the expression of the ICR program, which we originally defined in patients1, in both co-culture (Fig. 4e) and in response to IFN γ treatment (Fig. 4f).”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Perturb-CITE-Seq identifies immune evasion programs/modules
What the sources say
- Not checked yetcites [1] Dixit, A. et al. Perturb-seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens. Cell 167, 1853–1866 (2016). source
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“Embedding cells by either protein (Fig. 3a) or RNA (Fig. 3e) profiles alone separated by treatment conditions.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Multi-modal single-cell readouts of immune evasion
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“Perturbations of different nodes within IFNγ pathway led to highly converging molecular phenotypes, irrespective of the level of the defect.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > DISCUSSION
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“yet only some of the protein-level differences between treatments were observed at the level of the individual corresponding transcript”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Multi-modal single-cell readouts of immune evasion
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“consistent with prior reports12, induction of CD49f, which encodes an integrin associated with epithelial-to-mesenchymal transition (EMT).”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Multi-modal single-cell readouts of immune evasion
What the sources say
- Not checked yetcites [12] Pan, D. et al. A major chromatin regulator determines resistance of tumor cells to T cell-mediated killing. Science 359, 770–775 (2018). source
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“The regulatory model can be parsed into eight major co-functional modules of perturbations that similarly impact one or more of four major gene co-regulated programs”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Perturb-CITE-Seq identifies immune evasion programs/modules
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“we examined the regulation matrix after excluding perturbations in the IFNγ-JAK/STAT pathway genes (Fig. 4c), and recovered novel regulators and mechanisms of immune evasion”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Perturb-CITE-Seq identifies immune evasion programs/modules
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“First, Perturb-CITE-Seq data readily identified major known clinical mechanisms of immune evasion, especially perturbations and their associated cell programs in the IFNγ pathway and downregulation or defects of the antigen-presentation axis.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > DISCUSSION
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“stimulation with IFNγ (at 1 ng or 10 ng/mL) did not increase protein abundance of CD58”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Loss of CD58 is an orthogonal mechanism of immune evasion
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“Both CD58 KO and B2M KO cells had a strong competitive advantage over CD274 KO and parental cell lines”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Loss/downregulation of CD58 confers cancer immune evasion
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“Compared to malignant cells from treatment-naïve patients, ICI resistant patients had a significantly lower expression of CD58”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Loss of CD58 is an orthogonal mechanism of immune evasion
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“Across all Perturb-CITE-Seq screens, we analyzed 218,331 high quality single-cell RNA and protein profiles spanning the co-culture (73,114 cells), IFNγ (87,590), and control (57,627) conditions”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Multi-modal single-cell readouts of immune evasion
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“This results in 141, 183, and 181 gene-level targets (of 248 total target genes) for the control, IFNγ, and co-culture conditions, respectively.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > METHODS > Computational model for Perturb-CITE-Seq analysis
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“High Cas9 activity in Cas9 transgenic line.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Extended Data
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“there was strong down-regulation of several proteins with potential roles in modifying the response to immunotherapies exclusively in co-culture conditions, including CXCR4 (CD184), c-KIT (CD117) and KDR (CD309)23,24”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Multi-modal single-cell readouts of immune evasion
What the sources say
- Not checked yetcites [23] Pardoll, D. M. The blockade of immune checkpoints in cancer immunotherapy. Nat. Rev. Cancer 12, 252–264 (2012). source
- Not checked yetcites [24] Restifo, N. P., Dudley, M. E. & Rosenberg, S. A. Adoptive immunotherapy for cancer: harnessing the T cell response. Nat. Rev. Immunol. 12, 269–281 (2012). source
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“Using flow-cytometry, we confirmed that stimulation with low- or high-dose IFNγ resulted in higher levels of PD-L1 protein in CD58 KO cell lines compared to parental control”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Loss of CD58 is an orthogonal mechanism of immune evasion
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“Comparing RNA profiles between conditions also highlighted genes involved in antigen presentation, chemokines and immune modulators”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Multi-modal single-cell readouts of immune evasion
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“In contrast, other perturbations, such as KO of CDK6, MYC, ILF2, DNMT1, or ACSL3, repressed the ICR signature”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Perturb-CITE-Seq identifies immune evasion programs/modules
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“These include SERPINE2 and TGFB2, CD9 protein, CD59 protein, and both CD58 transcript and CD58 protein”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Perturb-CITE-Seq identifies immune evasion programs/modules
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“as did deletion of TMEM173, encoding STING (STimulator of INterferon Genes), which activates a type I interferon response25”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Perturb-CITE-Seq identifies immune evasion programs/modules
What the sources say
- Not checked yetcites [25] Chen, Q., Sun, L. & Chen, Z. J. Regulation and function of the cGAS-STING pathway of cytosolic DNA sensing. Nat. Immunol. 17, 1142–1149 (2016). source
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“Our Perturb-CITE-Seq data also suggested that CD58 KO led to increased expression of PD-L1”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Loss of CD58 is an orthogonal mechanism of immune evasion
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“Importantly CD58 is not activated by the IFNγ-JAK/STAT pathway”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Loss/downregulation of CD58 confers cancer immune evasion
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“A permutation test was used to score marker genes associated with each cluster shown in (a)35. Score (y axis, permutation test, Methods) of marker genes (x axis) associated with the distinct cluster marked by an arrow in (a), include canonical T cell markers.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Extended Data
What the sources say
- Not checked yetcites [35] Pedregosa, F. et al. Scikit-learn: machine learning in Python. J. Mach. Learn. Res. 12, 2825–2830 (2011).
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In the paper
“Cell complexity affects scRNA-Seq profiles.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Extended Data
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In the paper
“Limited relation between the cell cycle and immune pressure or phenotype.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Extended Data
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In the paper
“Comparable growth of control and KO cells. Ratio of viable cells relative to timepoint 0 (y axis) for control and B2M KO, CD58 KO or CD274 KO melanoma cells from patient 2686 (x axis).”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Extended Data
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“We previously identified an ICR signature, which is predictive of intrinsic resistance to ICI, in a subset of malignant cells in patients with metastatic melanoma using scRNA-seq9.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > INTRODUCTION
What the sources say
- Not checked yetcites [9] Jerby-Arnon, L. et al. A cancer cell program promotes T cell exclusion and resistance to checkpoint blockade. Cell 175, 984–997 (2018). source
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In the paper
“and discovers potentially clinically relevant mechanisms of immune evasion.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Abstract
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In the paper
“Notably, there is no known mouse homolog of CD58, emphasizing the value of performing such screens in human models10.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Pooled screens identify mechanisms of immune evasion
What the sources say
- Not checked yetcites [10] Patel, S. J. et al. Identification of essential genes for cancer immunotherapy. Nature 548, 537–542 (2017). source
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In the paper
“This work provides framework for deciphering complex mechanisms by large-scale perturbation screens with multi-modal single-cell readouts”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Abstract
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In the paper
“suggesting that it acts orthogonal to known mechanisms of ICR.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Abstract
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In the paper
“The screens were highly reproducible across triplicate samples”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Pooled screens identify mechanisms of immune evasion
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In the paper
“identifies mechanisms of immune evasion that are in part orthogonal to previously described mechanisms in patients.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > INTRODUCTION
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In the paper
“and CD58’s role in immune evasion may therefore be distinct from defects in the IFNγ-JAK/STAT pathway.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Perturb-CITE-Seq identifies immune evasion programs/modules
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In the paper
“Together, these data suggest that downregulation or loss of CD58 represents a clinically relevant immune evasion mechanism that is orthogonal to previously described ones involving defects in antigen presentation and IFNγ response.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Loss of CD58 is an orthogonal mechanism of immune evasion
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In the paper
“Inclusion as covariates of cell quality (defined as the total number of UMIs in each cell) and cell cycle state (assigned with Scanpy’s implementation of scoring cell cycle genes34) improved the fit.”
- Also stated in: § Extended Data · plain
“Improved model fit following accounting for cell state as a covariate.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > METHODS > Computational model for Perturb-CITE-Seq analysis
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In the paper
“Importantly, we excluded the possibility that these differences were due to differences in proliferation rates, (Extended Data Fig. 7d) or apoptotic potential of different KO models (Extended Data Fig. 7e).”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Loss/downregulation of CD58 confers cancer immune evasion
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In the paper
“It is likely that the induction of these genes is not through the IFNγ-JAK/STAT pathway.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Perturb-CITE-Seq identifies immune evasion programs/modules
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In the paper
“Dose-response killing in the co-culture experiment validates target killing range.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Extended Data
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In the paper
“suggesting that CD58 is not induced via the IFNγ pathway.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Loss of CD58 is an orthogonal mechanism of immune evasion
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In the paper
“Overall, our results suggest that genes functionally impacting susceptibility to T cell mediated killing (based on genetic perturbation in the viability screen) are concordantly regulated at the protein and RNA level.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Multi-modal single-cell readouts of immune evasion
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In the paper
“As we previously showed1, detection of a sgRNA in a cell does not necessarily mean that this cell is perturbed, either because the sgRNA has not perturbed the gene, or the perturbation does not have an impact.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > A computational framework for analysis of Perturb-CITE-Seq
What the sources say
- Not checked yetcites [1] Dixit, A. et al. Perturb-seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens. Cell 167, 1853–1866 (2016). source
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In the paper
“Importantly, genes that were hits in the viability screen partitioned into different functional modules, thus highlighting the effect of the same (converging) or distinct (divergent) mechanism, which could not be distinguished by a viability screen alone.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Perturb-CITE-Seq identifies immune evasion programs/modules
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In the paper
“suggesting that upregulation of PD-L1 could contribute to immune evasion in CD58 KO in T cell co-culture.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Loss of CD58 is an orthogonal mechanism of immune evasion
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In the paper
“Thus, single-cell RNA and protein profiles provide rich relevant phenotypes for assessing the impact of CRISPR perturbations.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Multi-modal single-cell readouts of immune evasion
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In the paper
“Thus, CD58 loss may represent a resistance mechanism distinct from IFNγ-JAK/STAT pathway inactivation.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Loss/downregulation of CD58 confers cancer immune evasion
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In the paper
“We developed a computational framework to model the effects of genetic perturbations on both RNA and protein profiles of individual genes”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > A computational framework for analysis of Perturb-CITE-Seq
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In the paper
“Validation of CRISPR/Cas9 KO (and unperturbed control) melanoma cells.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Extended Data
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“We performed pooled Perturb-CITE-Seq screens of the ICR program genes in a patient-derived tumor-TIL co-culture model, targeting 248 genes of the ICR signature (744 targeting guides) and profiling single-cell transcriptomes and 20 surface proteins in >218,000 cells.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > INTRODUCTION
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In the paper
“and we validate this finding in additional patient models and in clinical scRNA-seq data of patients with ICR.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > INTRODUCTION
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In the paper
“We developed an integrated analytical framework and recover the known landscape of clinically relevant immune resistance mutations along with novel ones.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > INTRODUCTION
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In the paper
“perturbations of B2M, HLA-A, JAK1, JAK2, STAT1, IFNGR1 and IFNGR2 (Fig. 2d,e, Extended Data Fig. 3e,f, Supplementary Table 2) conferred immune evasion, consistent with clinical mechanisms of resistance to immunotherapy7–9.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Pooled screens identify mechanisms of immune evasion
What the sources say
- Not checked yetcites [7] Zaretsky, J. M. et al. Mutations associated with acquired resistance to PD-1 blockade in melanoma. N. Engl. J. Med. 375, 819–829 (2016). source
- Not checked yetcites [8] Sade-Feldman, M. et al. Resistance to checkpoint blockade therapy through inactivation of antigen presentation. Nat. Commun. 8, 1136 (2017). source
- Not checked yetcites [9] Jerby-Arnon, L. et al. A cancer cell program promotes T cell exclusion and resistance to checkpoint blockade. Cell 175, 984–997 (2018). source
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In the paper
“Tumor cell lysis was highly reproducible and specific to T cell receptor (TCR)/MHC Class I interactions”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Patient-derived co-cultures for pooled perturbation screens
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In the paper
“At the protein level, we observe increases in MHC proteins and PD-L1 (CD274) in IFNγ-treated vs. control cells; a global increase in MHC proteins in co-culture vs. control cells”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Multi-modal single-cell readouts of immune evasion
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“the CD58 KO conferred a different molecular phenotype than IFNγ-JAK/STAT pathway perturbations, belonged to a distinct module, and did not impact the expression of antigen presentation genes”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Loss/downregulation of CD58 confers cancer immune evasion
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“MaMel-134 TILs produce IFNγ, TNFa, and Granzyme-B.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Extended Data
plainSingle case- Asserted: passes — The authors put it forward as true.
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In the paper
“integrating RNA and protein measurements for joint analysis (Methods) highlighted gene programs that are either common across conditions, or unique to different conditions (Fig. 3i), with the co-cultured cells uniquely enriched for induction of immune escape pathway genes and the ICR signature.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Multi-modal single-cell readouts of immune evasion
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“CD58 emerged as a compelling mechanism of immune evasion: KO of CD58 conferred resistance to T cell killing in the viability screen and CD58 RNA/protein were down regulated in cells surviving TIL co-culture.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Loss/downregulation of CD58 confers cancer immune evasion
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Conversely, neither B2M nor HLA-A KO impacted CD58 protein levels in our Perturb-CITE-Seq screen”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Loss of CD58 is an orthogonal mechanism of immune evasion
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“Using flow-cytometry, we show that compared to parental cells, CD58 KO did not alter expression of MHC proteins at baseline or their induction in response to IFNγ”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Loss of CD58 is an orthogonal mechanism of immune evasion
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“The Perturb-CITE-Seq model correctly reconstructed impacts of genes known to affect resistance to immunotherapy, especially the effect of perturbing the IFNγ response machinery (Fig. 4b), along with novel pathways.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Perturb-CITE-Seq identifies immune evasion programs/modules
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“In particular, CD58, CD47, and IFNGR1 (CD119) protein levels were reduced in co-culture, concordant with enrichment of their genetic KO in the viability screen”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Multi-modal single-cell readouts of immune evasion
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“Proportion of mKATE2+ cells prior to selection (x axis) and survival after puromycin selection (y axis) in 2686 melanoma Cas9 transgenic cells transduced with the ICR library. Line: Linear regression, Pearson R2=0.90.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Extended Data
plaincorrelationalSingle case- Asserted: passes — The authors put it forward as true.
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In the paper
“Empirically, adding a second iteration had only a very modest effect on sgRNA/target assignments.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > METHODS > Computational model for Perturb-CITE-Seq analysis
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In the paper
“The downregulated program included key components of antigen presentation and associated machinery (e.g., PSMB4, PSMB8, PSMB9, PSMA4, HLA-A,B,C gene and protein, HLA-E, HLA-F, HLAD-DPB1), chemokines associated with anti-tumor immunity (CXCL1, CXCL2, CXCL8, CXCL10, CXCL11), inflammatory cytokines (STAT3, IL1B, IL6), interferon response elements (STAT1, IRF1, IRF3, IFITM3, IFIT6), surface checkp”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Perturb-CITE-Seq identifies immune evasion programs/modules
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“In all models, CD58 KO and B2M KO conferred resistance (Fig. 5b-d) while PD-L1 KO sensitized cells to T cell mediated killing”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Loss/downregulation of CD58 confers cancer immune evasion
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In the paper
“Within each condition, both the cell cycle (G1/0, S, G2/M) (Fig. 3f) and complexity (Extended Data Fig. 4c) impacted RNA profiles”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Multi-modal single-cell readouts of immune evasion
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Several programs, including cell cycle regulation, DNA repair, and antigen presentation, were shared across conditions, whereas immune escape programs were uniquely recovered in co-culture data, and interferon response genes in IFNγ stimulation”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Multi-modal single-cell readouts of immune evasion
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In the paper
“TILs from 2686 retain ability to induce IFNγ and TNFa, and OKT-3 reactivation leads to an increase in Granzyme-B production compared to TILs grown in IL2 alone.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Extended Data
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In the paper
“Overall, the viability screen recovered known immune evasion mechanisms in a dose-dependent manner, and identified several novel candidates.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Pooled screens identify mechanisms of immune evasion
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“For example, in the co-culture condition, a single iteration of EM adjusts the assignment of 1,741 targets to near zero (confidence that the cell contains an effective sgRNA < 25%), while an additional iteration only adjusted 97 target-cell assignments.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > METHODS > Computational model for Perturb-CITE-Seq analysis
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“MaMel-80 TILs produce IFNγ, TNFa, and Granzyme-B.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Extended Data
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In the paper
“CITE profiles of 20 cell surface proteins do not reflect cell cycle phases (d) or UMI count (e).”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Extended Data
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In the paper
“Comparable induction of apoptosis in response to Staurosporin and resistance to DTIC in control and KO melanoma cells.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Extended Data
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In the paper
“CD58 perturbation in co-culture does not affect B2M and HLA expression at the RNA and protein level but induces CD274.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Extended Data
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- Rests on an assumption: The patient-derived melanoma-TIL co-culture with IFNγ pretreatment models T cell-mediated immune selection in human melanoma.
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In the paper
“G2M program learned from control dataset.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Extended Data
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In the paper
“CD58 (also known as LFA3) is an understudied adhesion molecule, typically expressed on antigen-presenting cells, that binds CD2 on T cell and Natural Killer (NK) cells22.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Pooled screens identify mechanisms of immune evasion
What the sources say
- Not checked yetcites [22] Arulanandam, A. R. et al. The CD58 (LFA-3) binding site is a localized and highly charged surface area on the AGFCC’C” face of the human CD2 adhesion domain. Proc. Natl Acad. Sci. USA 90, 11613–11617 (1993). source
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In the paper
“Recent studies revealed that activated T cells also express SIRPa and that interaction with CD47 results in increased T cell activation and cytokine production20, which may impact the potential clinical benefit of CD47-blockade21.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Pooled screens identify mechanisms of immune evasion
What the sources say
- Not checked yetcites [20] Myers, L. M. et al. A functional subset of CD8+ T cells during chronic exhaustion is defined by SIRPα expression. Nat. Commun. 10, 794 (2019). source
- Not checked yetcites [21] Zhang, W. et al. Advances in anti-tumor treatments targeting the CD47/SIRPα Axis. Front. Immunol. 11, 18 (2020).
hedgeddirect- Asserted: passes — The authors put it forward as true.
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In the paper
“A proof-of-concept study using ECCITE-seq5 demonstrated simultaneous detection of protein, RNA, and guide RNAs in individual cells and was applied at a small scale without the analytical framework required for large scale screens.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > INTRODUCTION
What the sources say
- Not checked yetcites [5] Mimitou, E. P. et al. Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells. Nat. Methods 16, 409–412 (2019). source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“Clinically relevant mechanisms of include mutations in beta-2-microglobulin (B2M) resulting in loss of MHC Class I presentation, downregulation of the antigen presentation machinery, and mutations in the IFNγ-JAK/STAT pathway that impair response to T cell mediated anti-tumor activity7–9.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > INTRODUCTION
What the sources say
- Not checked yetcites [7] Zaretsky, J. M. et al. Mutations associated with acquired resistance to PD-1 blockade in melanoma. N. Engl. J. Med. 375, 819–829 (2016). source
- Not checked yetcites [8] Sade-Feldman, M. et al. Resistance to checkpoint blockade therapy through inactivation of antigen presentation. Nat. Commun. 8, 1136 (2017). source
- Not checked yetcites [9] Jerby-Arnon, L. et al. A cancer cell program promotes T cell exclusion and resistance to checkpoint blockade. Cell 175, 984–997 (2018). source
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“CRISPR/Cas9 KO screens in murine models or engineered human cell lines testing tumor-T cell interactions identified putative novel mechanisms of immune evasion involving chromatin regulators10, TNFα signaling11, SOX412, PTPN213, and APLNR10, yet their clinical relevance is unclear.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > INTRODUCTION
What the sources say
- Not checked yetcites [10] Patel, S. J. et al. Identification of essential genes for cancer immunotherapy. Nature 548, 537–542 (2017). source
- Not checked yetcites [11] Kearney, C. J. et al. Tumor immune evasion arises through loss of TNF sensitivity. Sci. Immunol. 3, eaar3451 (2018).
- Not checked yetcites [12] Pan, D. et al. A major chromatin regulator determines resistance of tumor cells to T cell-mediated killing. Science 359, 770–775 (2018). source
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“However, many relevant phenotypes are functionally best understood at protein level, and are reflected differently at the RNA and protein level, thus requiring expansion of prior Perturb-Seq schemes.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > INTRODUCTION
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In the paper
“CD47 is a “don’t eat me” signal on tumor cells that interacts with SIRPa on phagocytic cells; and blockade of the CD47/SIRPa axis improves tumor control in vivo19.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Pooled screens identify mechanisms of immune evasion
What the sources say
- Not checked yetcites [19] Veillette, A. & Chen, J. SIRPα–CD47 immune checkpoint blockade in anticancer therapy. Trends Immunol. 39, 173–184 (2018). source
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“While ICIs produce durable responses in some patients most patients either do not benefit or develop resistance over time.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > INTRODUCTION
What the sources say
- Not checked yetcites [6] Sharma, P. & Allison, J. P. The future of immune checkpoint therapy. Science 348, 56–61 (2015). source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“Taken together, our Perturb-CITE-Seq analysis rediscovered key mechanisms of immune evasion, organized them into modules and related them to the genes and programs they impact, as well as recovered new modules that may confer immune evasion beyond defects in the IFNγ-JAK/STAT pathway and antigen presentation.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Perturb-CITE-Seq identifies immune evasion programs/modules
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In the paper
“Thus, multiple transcripts and proteins implicated in modifying the response to immunotherapies are directly regulated by the IFNγ-JAK/STAT axis, suggesting that some of these mechanisms are a consequence of defective IFNγ-JAK/STAT signaling, rather than independent modes of resistance.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Perturb-CITE-Seq identifies immune evasion programs/modules
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In the paper
“Furthermore, PD-L1 is upregulated in CD58 KO, suggesting that CD58 loss could confer immune evasion directly (reduced adhesion) or indirectly (inhibitory PD-L1)”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > DISCUSSION
hedgedconditional- Asserted: passes — The authors put it forward as true.
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In the paper
“Our study presents a large-scale CRISPR/Cas9 screen with multi-modal single-cell readouts, providing a general approach, as well as addressing a critical clinical challenge in a unique patient-derived cell culture model system.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > DISCUSSION
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In the paper
“Melanoma cells tested repeatedly negative for contamination with mycoplasma and other contaminants using PlasmoTest (InvivoGen, San Diego, CA).”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > METHODS > Patient derived melanoma cell culture
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“CD58 KO also impacted NK-mediated killing (Fig. 5g), which may have implications for NK cell-based therapies in tumors with loss of antigen presentation.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > DISCUSSION
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In the paper
“This procedure partially corrects for the bias of sample size and effect size in regulatory coefficients, and enables direct comparison of the empirical p values across targets.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > METHODS > Computational model for Perturb-CITE-Seq analysis
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Our experiments and analysis show that loss of CD58 confers immune evasion to a similar extent as loss of MHC Class I expression itself (through B2M KO), but through an independent path, and without impacting the expression of antigen presentation genes and proteins”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > DISCUSSION
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In the paper
“Including these covariates improved the model fit quality (residuals approach mean zero, independent and identically distributed; Extended Data Fig. 6b,c).”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > A computational framework for analysis of Perturb-CITE-Seq
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Some of the genes down-regulated by IFNγ pathway perturbations, such as CXCL10 and CXCL11, are genes whose downregulation was previously associated with immune evasion, suggesting that these do not represent a salient mechanisms of immune evasion.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > DISCUSSION
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“A full EM approach is not guaranteed to converge to a global minimum in a high-dimensional linear regression problem with noisy and missing data36.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > METHODS > Computational model for Perturb-CITE-Seq analysis
What the sources say
- Not checked yetcites [36] Loh, P.-L. & Wainwright, M. J. High-dimensional regression with noisy and missing data: provable guarantees with nonconvexity. Ann. Stat. 40, 1637–1664 (2012). source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“consistent with our previously reported patient and pre-clinical data, where we demonstrate that upregulation of MYC and CDK4/6 (and their transcriptional targets) was associated with increased resistance to immunotherapy, and CDK4/6 inhibitors reduced resistance in human and pre-clinical melanoma models9.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > RESULTS > Perturb-CITE-Seq identifies immune evasion programs/modules
What the sources say
- Not checked yetcites [9] Jerby-Arnon, L. et al. A cancer cell program promotes T cell exclusion and resistance to checkpoint blockade. Cell 175, 984–997 (2018). source
boosteddirect- Asserted: passes — The authors put it forward as true.
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In the paper
“All experiments were performed in triplicates in each of at least two independent experiments.”
- Also stated in: § Extended Data · plain
“All experiments were performed in triplicates in each of at least two independent experiments.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Extended Data
plain- Asserted: passes — The authors put it forward as true.
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- Also stated in: § Extended Data · plain
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In the paper
“Screen reproducibility across triplicates.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Extended Data
plainn = 3- Asserted: passes — The authors put it forward as true.
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In the paper
“Notably, the CD58/CD2 axis is a potent co-stimulatory pathway in CD8+ T cells that lack expression of CD28 (CD8+CD28- T cells)29, which are common in the tumor-microenvironment and peripheral blood of solid tumor patients30, and were the predominant T cells in our Perturb-CITE-Seq screen”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > DISCUSSION
What the sources say
- Not checked yetcites [29] Leitner, J., Herndler-Brandstetter, D., Zlabinger, G. J., Grubeck-Loebenstein, B. & Steinberger, P. CD58/CD2 is the primary costimulatory pathway in human CD28–CD8+ T cells. J. Immunol. 195, 477–487 (2015). source
- Not checked yetcites [30] Strioga, M., Pasukoniene, V. & Characiejus, D. CD8+CD28– and CD8+CD57+ T cells and their role in health and disease. Immunology 134, 17–32 (2011). source
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“We recover the landscape of resistance mechanisms to immunotherapies and, guided by our high-dimensional data, validate a novel mechanism of immune resistance.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > DISCUSSION
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“In contrast, other genes whose perturbation enhanced immune evasion in our screen (e.g., CD58, CD59) appear to reflect distinct mechanism, both because their expression was not impaired by IFNγ signaling defects, and because the molecular phenotype following their perturbation is distinct.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > DISCUSSION
hedgeddirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Loss or downregulation of CD58 does not interfere with antigen presentation or JAK/STAT-signaling per se, but reduces T cell co-stimulation while simultaneously promoting increased co-inhibitory signaling via PD-L1, and therefore overall confers resistance to T cell mediated killing.”
§ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion > Extended Data
plaindirect- Asserted: passes — The authors put it forward as true.
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- Rests on an assumption: The patient-derived melanoma-TIL co-culture with IFNγ pretreatment models T cell-mediated immune selection in human melanoma.
The paper relies on this without support.
Genetic signals account for only a minority of ICI resistance cases.
“However, genetic signals only account for a minority of cases.”
The paper relies on this without support.
The role of CD58 in cancer is poorly understood.
“The role of CD58 in cancer is poorly understood.”
The paper relies on this without support.
The patient-derived melanoma-TIL co-culture with IFNγ pretreatment models T cell-mediated immune selection in human melanoma.
“Surviving target cells on distinct plates containing all conditions as triplicates were counted to quantify target cell killing to verify accurate immune selection pressure as previously determined in the miniaturized co-culture experiments (above).”
Claims other papers make about this one
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In the citing paper
“Three CITE-seq datasets have protein and RNA counts that are downloadable separately6,9.”
From scPerturb: harmonized single-cell perturbation data (2024) · cites this paper as [6]
In the citing paper
“Protein, RNA and ATAC readouts for CRISPRi perturbation of MYC are all available for K562 cells6,20,42.”
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“ECCITE-seq [15] and Perturb-CITE-seq [16] are two paradigmatic cases that entail in tandem detection of transcripts, proteins, and sgRNAs.”
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Citations
Cites
Scikit-learn: Machine Learning in Python
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PD-1 and PD-L1 Immune Checkpoint Blockade to Treat Breast Cancer
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Self-citationSingle-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma
Patel, A. P., Tirosh, I., Trombetta, J. J., Shalek, A. K., Gillespie, S. M., Wakimoto, H., Cahill, D. P., Nahed, B. V., Curry, W. T., Martuza, R. L., et al. (2014) · Science · doi:10.1126/science.1254257 · Cited by 5,063
Self-citationThe future of immune checkpoint therapy
Sharma, P., & Allison, J. P. (2015) · Science · doi:10.1126/science.aaa8172 · Cited by 4,878
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Doench, J. G., Fusi, N., Sullender, M., Hegde, M., Vaimberg, E. W., Donovan, K. F., Smith, I., Tothova, Z., Wilen, C., Orchard, R., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3437 · Cited by 4,637
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de Sande, B. V., Lee, J. S., Mutasa-Gottgens, E., Naughton, B. J., Bacon, W., Manning, J. R., Wang, Y., Pollard, J. R., Mendez, M., Hill, J., et al. (2023) · Nature Reviews Drug Discovery · doi:10.1038/s41573-023-00688-4 · Cited by 462
CRISPR in cancer biology and therapy
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Metadata
- Authors
- Frangieh, C. J., Melms, J. C., Thakore, P. I., Geiger-Schuller, K. R., Ho, P., Luoma, A. M., Cleary, B., Jerby-Arnon, L., Malu, S., Cuoco, M. S., Zhao, M., Ager, C. R., Rogava, M., Hovey, L., Rotem, A., Bernatchez, C., Wucherpfennig, K. W., Johnson, B. E., Rozenblatt-Rosen, O., Schadendorf, D., Regev, A., & Izar, B.
- Affiliations
- Broad Institute (US)
- Columbia University Irving Medical Center (US)
- Dana-Farber Cancer Institute (US)
- Immunitas Therapeutics (United States) (US)
- Columbia University (US)
- The University of Texas MD Anderson Cancer Center (US)
- Essen University Hospital (DE)
- Corresponding author
- Regev, Aviv
- Izar, Benjamin
- ORCID
- Venue
- Nature Genetics
- Published
- 2021-03
- Volume
- 53
- Issue
- 3
- Pages
- 332-341
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC8376399
- OpenAlex
- W3134444564
- Cited by
- 276
- References
- 47
- Citations by year
- 2026: 54 · 2025: 66 · 2024: 58 · 2023: 44 · 2022: 35 · 2021: 19
- FWCI
- 14.21
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nature Genetics (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- Funders
- Burroughs Wellcome Fund
- U.S. Department of Health & Human Services | NIH | National Cancer Institute (K08CA222663, U54CA225088, P30CA013696)
- Topics
- Health Sciences › Medicine › Oncology › Cancer Immunotherapy and Biomarkers
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Immunology and Microbiology › Immunology › Immunotherapy and Immune Responses
- Keywords
- tumor immune evasion, immune checkpoint inhibitor resistance, melanoma, tumor-infiltrating lymphocytes, CD58, interferon-gamma signaling, JAK/STAT signaling, antigen presentation, MHC expression, single-cell transcriptomics, single-cell proteomics, patient-derived tumor models
- MeSH terms
- Immune Checkpoint Inhibitors, Epitopes, Humans, Interferon-gamma, Melanoma, Lymphocytes, Tumor-Infiltrating, Sequence Analysis, RNA, Coculture Techniques, CD58 Antigens, Drug Resistance, Neoplasm, Tumor Escape, Computational Biology, Gene Knockout Techniques, Single-Cell Analysis, CRISPR-Cas Systems
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
A language model drew the claims from the paper on 2026-10-04, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-04 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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