Andrea Y. Gu, Tet Woo Lee, Aziza Khan, Xuenan Zhang, Francis W. Hunter, Dean C. Singleton, Stephen M. F. Jamieson
Mutations in the oncogene NRAS that induce constitutive RAS-GTPase activity lead to unchecked cell proliferation and migration through downstream activation of the mitogen-activated protein kinase (MAPK) and phosphoinositide 3-kinase (PI3K) signalling pathways [1]. These mutations occur in approximately 20% of melanomas and very rarely coexist with BRAF V600 mutations. NRAS-mutant melanoma is associated with poor survival [2] and represents an unmet clinical need, with no effective therapies available following immunotherapy failure.
Identification of contextual essential genes that exert stronger fitness effects on NRAS-mutant melanoma cells presents an opportunity for the discovery of targeted therapies. In this study, we employed CRISPR-Cas9-mediated whole-genome dropout screens to identify genetic dependencies in NRAS-mutant melanoma. Typically, melanoma cell lines are cultured under ambient (∼20%) O2 conditions, despite O2 concentrations of < 8% at the epidermal-dermal junction where melanocytes reside, resulting in adaptations in gene and protein expression [3]. Therefore, for our screens, we used a panel of early-passage New Zealand Melanoma (NZM) cell lines that were established and cultured under physiological (5%) O2 conditions [4].
Six NRAS-mutant and seven NRAS-wildtype (five BRAF-mutant, two BRAF/NRAS/NF1-wildtype) NZM cell lines (Supplementary Table S1) were transduced in multiple replicates with the Brunello single guide RNA (sgRNA) library at a multiplicity of infection of approximately 0.3 and screened at 5% O2 for up to 35 days (Supplementary Methods and Materials). All NZM lines were cultured for transduction at fewer than 10 passages from derivation. The representation of the sgRNA libraries was assessed to evaluate transducibility, with any cell lines exhibiting poor sgRNA representation (< 80% of sgRNAs detected with ≥1 count) excluded from further analyses (Supplementary Table S2). Moderate to high representation was observed in nine of the 13 NZM cell lines, whereas four cell lines were excluded due to < 80% of sgRNAs being detected (Figure 1A). Reduced sgRNA representation was accompanied by dropout of non-targeting control (NTC) sgRNAs (Figure 1A), greater read count inequality (Supplementary Figure S1, Supplementary Table S2) and reduced correlation with the Brunello library plasmids and between individual cell line replicates (Supplementary Figure S2), suggesting stochastic evolution rather than knockout-induced fitness effects.
We used BAGEL2 to estimate gene essentiality relative to reference sets of common essential and nonessential genes. Typically, tissue-agnostic gene sets are used for this purpose [5], but we established a combined essential gene set incorporating both tissue-agnostic and melanoma-sp
{"title":"Whole-genome CRISPR-Cas9 knockout screens identify SHOC2 as a genetic dependency in NRAS-mutant melanoma","authors":"Andrea Y. Gu, Tet Woo Lee, Aziza Khan, Xuenan Zhang, Francis W. Hunter, Dean C. Singleton, Stephen M. F. Jamieson","doi":"10.1002/cac2.70013","DOIUrl":"10.1002/cac2.70013","url":null,"abstract":"<p>Mutations in the oncogene <i>NRAS</i> that induce constitutive RAS-GTPase activity lead to unchecked cell proliferation and migration through downstream activation of the mitogen-activated protein kinase (MAPK) and phosphoinositide 3-kinase (PI3K) signalling pathways [<span>1</span>]. These mutations occur in approximately 20% of melanomas and very rarely coexist with <i>BRAF</i> V600 mutations. <i>NRAS</i>-mutant melanoma is associated with poor survival [<span>2</span>] and represents an unmet clinical need, with no effective therapies available following immunotherapy failure.</p><p>Identification of contextual essential genes that exert stronger fitness effects on <i>NRAS</i>-mutant melanoma cells presents an opportunity for the discovery of targeted therapies. In this study, we employed CRISPR-Cas9-mediated whole-genome dropout screens to identify genetic dependencies in <i>NRAS</i>-mutant melanoma. Typically, melanoma cell lines are cultured under ambient (∼20%) O<sub>2</sub> conditions, despite O<sub>2</sub> concentrations of < 8% at the epidermal-dermal junction where melanocytes reside, resulting in adaptations in gene and protein expression [<span>3</span>]. Therefore, for our screens, we used a panel of early-passage New Zealand Melanoma (NZM) cell lines that were established and cultured under physiological (5%) O<sub>2</sub> conditions [<span>4</span>].</p><p>Six <i>NRAS</i>-mutant and seven <i>NRAS</i>-wildtype (five <i>BRAF</i>-mutant, two <i>BRAF</i>/<i>NRAS</i>/<i>NF1</i>-wildtype) NZM cell lines (Supplementary Table S1) were transduced in multiple replicates with the Brunello single guide RNA (sgRNA) library at a multiplicity of infection of approximately 0.3 and screened at 5% O<sub>2</sub> for up to 35 days (Supplementary Methods and Materials). All NZM lines were cultured for transduction at fewer than 10 passages from derivation. The representation of the sgRNA libraries was assessed to evaluate transducibility, with any cell lines exhibiting poor sgRNA representation (< 80% of sgRNAs detected with ≥1 count) excluded from further analyses (Supplementary Table S2). Moderate to high representation was observed in nine of the 13 NZM cell lines, whereas four cell lines were excluded due to < 80% of sgRNAs being detected (Figure 1A). Reduced sgRNA representation was accompanied by dropout of non-targeting control (NTC) sgRNAs (Figure 1A), greater read count inequality (Supplementary Figure S1, Supplementary Table S2) and reduced correlation with the Brunello library plasmids and between individual cell line replicates (Supplementary Figure S2), suggesting stochastic evolution rather than knockout-induced fitness effects.</p><p>We used BAGEL2 to estimate gene essentiality relative to reference sets of common essential and nonessential genes. Typically, tissue-agnostic gene sets are used for this purpose [<span>5</span>], but we established a combined essential gene set incorporating both tissue-agnostic and melanoma-sp","PeriodicalId":9495,"journal":{"name":"Cancer Communications","volume":"45 6","pages":"709-713"},"PeriodicalIF":20.1,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cac2.70013","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143646894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Florian Henning Geyer, Alina Ritter, Seneca Kinn-Gurzo, Tobias Faehling, Jing Li, Armin Jarosch, Carine Ngo, Endrit Vinca, Karim Aljakouch, Azhar Orynbek, Shunya Ohmura, Thomas Kirchner, Roland Imle, Laura Romero-Pérez, Juan Díaz-Martín, Stefanie Bertram, Enrique de Álava, Clémence Henon, Sophie Postel-Vilnay, Ana Banito, Martin Sill, Yvonne Versleijen-Jonkers, Benjamin Friedrich Berthold Mayer, Martin Ebinger, Monika Sparber-Sauer, Sabine Stegmaier, Daniel Baumhoer, Wolfgang Hartmann, Jeroen Krijgsveld, David Horst, Olivier Delattre, Patrick Joseph Grohar, Thomas Georg Phillip Grünewald, Florencia Cidre-Aranaz
<p>Desmoplastic small round cell tumor (DSRCT) is an aggressive cancer that predominantly affects adolescents and young adults, typically developing at sites lined by mesothelium [<span>1, 2</span>]. DSRCT is genetically defined by a chromosomal translocation that fuses the N-terminus of EWS RNA binding protein 1 (<i>EWSR1</i>) to the C-terminus of Wilms tumor protein (<i>WT1)</i>, forming EWSR1::WT1 [<span>3</span>]. This fusion encodes a potent transcription factor and is the only known driver of oncogenic transformation in DSRCT [<span>4</span>]. The lack of a comprehensive understanding of DSRCT biology parallels its dismal survival rate (5%-20%) [<span>1</span>]. These challenges are exacerbated by the absence of clinical trials, the limited systematic collection and analysis of DSRCT biomaterial [<span>1</span>], and the notable lack of specific diagnostic markers, necessitating resource-intensive molecular testing for an accurate diagnosis.</p><p>Here we first focused on identifying promising candidates for validation as single, fast, and reliable diagnostic DSRCT markers. For this, we performed differential gene expression (DEG) analysis on datasets comprising patient samples from 32 DSRCT and 20 morphological mimics, identifying 23 genes overexpressed in DSRCT (log<sub>2</sub> fold change (log<sub>2</sub>FC) > 2.5; adjusted <i>P</i>-value (<i>Padj)</i> < 0.01; Figure 1A, Supplementary Figure S1A). Secondly, we analyzed EWSR1::WT1 binding sites derived from chromatin immunoprecipitation followed by sequencing (ChIP-seq) data [<span>5</span>] obtained from the JN-DSRCT-1 cell line, identifying 2,065 genomic loci likely regulated by EWSR1::WT1 (Figure 1A). Third, we established JN-DSRCT-1 and SK-DSRCT2 cell lines expressing doxycycline (DOX)-inducible short hairpin RNA (shRNA)-mediated EWSR1::WT1 knockdown (KD) (Supplementary Figure S1B). Differential protein expression (DEP) analysis of these cells identified 104 proteins consistently regulated across both cell lines (log<sub>2</sub>FC > 1.0 and <i>Padj</i> < 0.01; Figure 1A, Supplementary Table S1). The intersection of these analyses revealed calcium voltage-gated channel auxiliary subunit alpha2delta 2 (CACNA2D2) and IQ motif containing G (IQCG) as potential DSRCT biomarkers (Figure 1A). <i>CACNA2D2</i> was selected for validation due to its significantly higher expression in DSRCTs compared to <i>IQCG</i> (<i>P</i> < 0.001; Figure 1A). Indeed, DSRCT exhibited the highest expression of <i>CACNA2D2</i> among all studied morphological mimics and normal tissues (<i>P <</i> 0.001; Supplementary Figures S1C-D). Further ChIP-seq data and motif analyses of EWSR1::WT1 binding coordinates and histone marks in JN-DSRCT-1 and four DSRCT patient samples [<span>5, 6</span>] suggested a direct regulatory role of EWSR1::WT1 through an enhancer interaction at the <i>CACNA2D2</i> locus (Figure 1B). Notably, KD of EWSR1::WT1 in JN-DSRCT-1 resulted in a loss of the EWSR1::WT1 signal and H
{"title":"Comprehensive DSRCT multi-omics analyses unveil CACNA2D2 as a diagnostic hallmark and super-enhancer-driven EWSR1::WT1 signature gene","authors":"Florian Henning Geyer, Alina Ritter, Seneca Kinn-Gurzo, Tobias Faehling, Jing Li, Armin Jarosch, Carine Ngo, Endrit Vinca, Karim Aljakouch, Azhar Orynbek, Shunya Ohmura, Thomas Kirchner, Roland Imle, Laura Romero-Pérez, Juan Díaz-Martín, Stefanie Bertram, Enrique de Álava, Clémence Henon, Sophie Postel-Vilnay, Ana Banito, Martin Sill, Yvonne Versleijen-Jonkers, Benjamin Friedrich Berthold Mayer, Martin Ebinger, Monika Sparber-Sauer, Sabine Stegmaier, Daniel Baumhoer, Wolfgang Hartmann, Jeroen Krijgsveld, David Horst, Olivier Delattre, Patrick Joseph Grohar, Thomas Georg Phillip Grünewald, Florencia Cidre-Aranaz","doi":"10.1002/cac2.70015","DOIUrl":"10.1002/cac2.70015","url":null,"abstract":"<p>Desmoplastic small round cell tumor (DSRCT) is an aggressive cancer that predominantly affects adolescents and young adults, typically developing at sites lined by mesothelium [<span>1, 2</span>]. DSRCT is genetically defined by a chromosomal translocation that fuses the N-terminus of EWS RNA binding protein 1 (<i>EWSR1</i>) to the C-terminus of Wilms tumor protein (<i>WT1)</i>, forming EWSR1::WT1 [<span>3</span>]. This fusion encodes a potent transcription factor and is the only known driver of oncogenic transformation in DSRCT [<span>4</span>]. The lack of a comprehensive understanding of DSRCT biology parallels its dismal survival rate (5%-20%) [<span>1</span>]. These challenges are exacerbated by the absence of clinical trials, the limited systematic collection and analysis of DSRCT biomaterial [<span>1</span>], and the notable lack of specific diagnostic markers, necessitating resource-intensive molecular testing for an accurate diagnosis.</p><p>Here we first focused on identifying promising candidates for validation as single, fast, and reliable diagnostic DSRCT markers. For this, we performed differential gene expression (DEG) analysis on datasets comprising patient samples from 32 DSRCT and 20 morphological mimics, identifying 23 genes overexpressed in DSRCT (log<sub>2</sub> fold change (log<sub>2</sub>FC) > 2.5; adjusted <i>P</i>-value (<i>Padj)</i> < 0.01; Figure 1A, Supplementary Figure S1A). Secondly, we analyzed EWSR1::WT1 binding sites derived from chromatin immunoprecipitation followed by sequencing (ChIP-seq) data [<span>5</span>] obtained from the JN-DSRCT-1 cell line, identifying 2,065 genomic loci likely regulated by EWSR1::WT1 (Figure 1A). Third, we established JN-DSRCT-1 and SK-DSRCT2 cell lines expressing doxycycline (DOX)-inducible short hairpin RNA (shRNA)-mediated EWSR1::WT1 knockdown (KD) (Supplementary Figure S1B). Differential protein expression (DEP) analysis of these cells identified 104 proteins consistently regulated across both cell lines (log<sub>2</sub>FC > 1.0 and <i>Padj</i> < 0.01; Figure 1A, Supplementary Table S1). The intersection of these analyses revealed calcium voltage-gated channel auxiliary subunit alpha2delta 2 (CACNA2D2) and IQ motif containing G (IQCG) as potential DSRCT biomarkers (Figure 1A). <i>CACNA2D2</i> was selected for validation due to its significantly higher expression in DSRCTs compared to <i>IQCG</i> (<i>P</i> < 0.001; Figure 1A). Indeed, DSRCT exhibited the highest expression of <i>CACNA2D2</i> among all studied morphological mimics and normal tissues (<i>P <</i> 0.001; Supplementary Figures S1C-D). Further ChIP-seq data and motif analyses of EWSR1::WT1 binding coordinates and histone marks in JN-DSRCT-1 and four DSRCT patient samples [<span>5, 6</span>] suggested a direct regulatory role of EWSR1::WT1 through an enhancer interaction at the <i>CACNA2D2</i> locus (Figure 1B). Notably, KD of EWSR1::WT1 in JN-DSRCT-1 resulted in a loss of the EWSR1::WT1 signal and H","PeriodicalId":9495,"journal":{"name":"Cancer Communications","volume":"45 6","pages":"702-708"},"PeriodicalIF":20.1,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cac2.70015","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}