A multiplexed in vivo gene knockout approach to identify cancer drivers in small cell lung cancer [RNAseq]
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE198634 | GEO | 2023/01/09
REPOSITORIES: GEO
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Project description:We generated a model of lentivirus-initiated mouse small cell lung cancer (SCLC) combined with CRISPR/Cas9 knockout and barcoding. We analyzed tumor suppressive functions of 39 gene candidates using these in vivo CRISPR screening approaches and found Tsc1 to be one of the top tumor suppressor genes in SCLC.
2023-01-09 | GSE198636 | GEO
Project description:We generated a model of lentivirus-initiated mouse small cell lung cancer (SCLC) combined with CRISPR/Cas9 knockout and barcoding. We analyzed tumor suppressive functions of 39 gene candidates using these in vivo CRISPR screening approaches and found Tsc1 to be one of the top tumor suppressor genes in SCLC.
2023-01-09 | GSE198635 | GEO
Project description:Approximately 15% of all lung cancer cases are small cell lung cancer (SCLC), which originates from neuroendocrine cells lining the airways (bronchi) of the lung. SCLC is known for its aggressive nature and swift growth, resulting in a five-year survival rate of around 6%. Understanding the genetic pathways that drive tumor development remains an ongoing challenge. In our study, we employed an in vivo multiplexed approach, known as Tuba-seq, to investigate the impact of the functional loss of 18 putative tumor suppressors. Our screening unveiled Pten and Keap1 as top candidates; knocking out either one promoted both tumor initiation and progression. We identified the Keap1/Cul3/Nrf2 pathway as a pivotal regulator for SCLC development, particularly in regulating the susceptibility of SCLC to ferroptosis. Our work not only established an in vivo multiplexed approach for assessing the role of tumor suppressors in SCLC but also uncovers a previously unappreciated role of Keap1 in SCLC.
2024-01-26 | GSE239440 | GEO
Project description:Approximately 15% of all lung cancer cases are small cell lung cancer (SCLC), which originates from neuroendocrine cells lining the airways (bronchi) of the lung. SCLC is known for its aggressive nature and swift growth, resulting in a five-year survival rate of around 6%. Understanding the genetic pathways that drive tumor development remains an ongoing challenge. In our study, we employed an in vivo multiplexed approach, known as Tuba-seq, to investigate the impact of the functional loss of 18 putative tumor suppressors. Our screening unveiled Pten and Keap1 as top candidates; knocking out either one promoted both tumor initiation and progression. We identified the Keap1/Cul3/Nrf2 pathway as a pivotal regulator for SCLC development, particularly in regulating the susceptibility of SCLC to ferroptosis. Our work not only established an in vivo multiplexed approach for assessing the role of tumor suppressors in SCLC but also uncovers a previously unappreciated role of Keap1 in SCLC.
2024-01-26 | GSE239436 | GEO
Project description:Small cell lung cancer (SCLC) is a highly aggressive subtype of lung cancer that remains among the most lethal of solid tumor malignancies. Recent genomic sequencing studies have identified many recurrently mutated genes in human SCLC tumors. However, the functional roles of most of these genes remain to be validated. Here, we adapt the CRISPR-Cas9 system to a well-established murine model of SCLC to rapidly model loss-of-function mutations in candidate genes identified from SCLC sequencing studies. We show that loss of the gene p107 significantly accelerates tumor progression. Notably, compared with loss of the closely related gene p130, p107 loss results in fewer but larger tumors, as well as earlier metastatic spread. In addition, we observe differences in proliferation and apoptosis, as well as altered distribution of initiated tumors in the lung, resulting from loss of p107 or p130. Collectively, these data demonstrate the feasibility of using the CRISPR-Cas9 system to model loss of candidate tumor suppressor genes in SCLC, and we anticipate that this approach will greatly facilitate efforts to investigate mechanisms driving tumor progression in this deadly disease.
2019-12-19 | GSE139444 | GEO
Project description:Small cell lung cancer (SCLC) is the most aggressive lung cancer entity with an extremely limited therapeutic outcome. Most patients are diagnosed at an extensive stage. However, the molecular mechanisms driving SCLC invasion and metastasis remain largely elusive. We used an autochthonous SCLC mouse model and matched primary and metastatic SCLC patient samples to investigate the molecular characteristics of tumor metastasis. We demonstrate that tumor cell invasion and liver metastasis in SCLC are triggered by an Angiopoietin-2/Integrin beta-1-dependent pathway in tumor cells, mediated by focal adhesion kinase-Src kinase signaling. Strikingly, CRISPR-Cas9 knock out of Integrin beta-1 or blocking Integrin beta-1 signaling by an anti-Angiopoietin-2 treatment abrogates liver metastasis formation in vivo. Interestingly, analysis of a unique collection of matched primary and metastatic SCLC patient samples confirmed a strong increase of Integrin beta-1 in liver metastasis in comparison to the primary tumor. We further show that Angiopoietin-2 blockade combined with anti-VEGFR and PD-1-targeted treatment displays synergistic treatment effects in SCLC. Together, our data demonstrate a fundamental role of Angiopoietin-2/Integrin beta-1 signaling in SCLC cells for tumor cell invasion and liver metastasis and provide a new effective treatment strategy for patients with SCLC.
2024-03-28 | GSE262409 | GEO
Project description:The tuberous sclerosis complex (TSC) family of tumor suppressors, TSC1 and TSC2, function together in an evolutionarily conserved protein complex that is a point of convergence for major cell signaling pathways that regulate mTOR complex 1 (mTORC1). Mutation or aberrant inhibition of the TSC complex is common in various human tumor syndromes and cancers. The discovery of novel therapeutic strategies to selectively target cells with functional loss of this complex is therefore of substantial clinical relevance to TSC and sporadic cancers. We developed a CRISPR-based method to generate homogenous mutant Drosophila cell lines. By combining TSC1 and TSC2 mutant cell lines with RNAi screens against all kinases and phosphatases, we identified synthetic interactions with TSC1 and TSC2. Knockdown of three candidate genes (mRNA-cap, Pitslre and CycT; orthologs of RNGTT, CDK11 and CCNT1 in humans) reduced the population growth rate of both Drosophila TSC1 and TSC2 mutant cells but not that of wild-type cells. Moreover, knockdown of all three genes displayed similar selective effects in mammalian TSC2-deficient cell lines, including human tumor-derived cells, illustrating the power of this cross species screening strategy to identify potential drug targets.
2018-10-24 | PXD002670 | Pride
Project description:Small-cell lung cancer (SCLC) is the most fatal form of lung cancer. Intra-tumoral heterogeneity, marked by neuroendocrine (NE) and non-neuroendocrine (non-NE) cell states, defines SCLC, but the drivers of SCLC plasticity are poorly understood. To map the landscape of SCLC tumor microenvironment (TME), we apply spatially resolved transcriptomics and quantitative mass spectrometry-based proteomics to metastatic SCLC tumors obtained via rapid autopsy. The phenotype and overall composition of non-malignant cells in the tumor microenvironment (TME) exhibits substantial variability, closely mirroring the tumor phenotype, suggesting TME-driven reprogramming of NE cell states. We identify cancer-associated fibroblasts (CAF) as a crucial element of SCLC TME heterogeneity, contributing to immune exclusion, and predicting an exceptionally poor prognosis. Together, our work provides the first comprehensive map of SCLC tumor and TME ecosystems, emphasizing their pivotal role in SCLCs adaptable nature, opening possibilities for re-programming the intercellular communications that shape SCLC tumor states.
2024-05-15 | PXD052033 | Pride
Project description:Small cell lung cancer (SCLC) is a disease characterized by aggressive clinical behavior and lack of effective therapy. Due to its high tendency of early dissemination, only a third of patients have limited-stage disease at the time of diagnosis. SCLC is thought to derive from neuroendocrine cells of the lung. Although several molecular abnormalities in SCLC have been described, there are relatively few studies on epigenetic alterations in this type of tumor. Here, we have used methylation profiling with the methylated CpG island recovery assay (MIRA) in combination with microarrays and conducted the first genome-scale analysis of methylation changes that occur in primary SCLC and SCLC cell lines. Among hundreds of tumor-specifically methylated genes, we identified 73 gene targets that are methylated in more than 77% of primary SCLC tumors, most of which have never been linked to aberrant methylation in tumors. These targets have excellent potential for development of biomarkers for early detection of SCLC. SCLC cell lines had an ~3-fold greater number of hypermethylated genes than primary tumors. Gene ontology analysis indicated a significant enrichment of methylated genes functioning as transcription factors and in processes of neuronal differentiation. Motif analysis of tumor-specific methylated regions identified enrichment of binding sites for several neural cell fate-specifying transcription factors including NEUROD1, HAND1, ZNF423 and REST. We hypothesize that functional inactivation of their corresponding binding sites by DNA methylation can lead to an escape route for early progenitor cells towards the malignant state and may contribute to the origin of SCLC. Comparison between healthy and SCLC tumor DNA methylation profiles
2012-01-26 | E-GEOD-35341 | biostudies-arrayexpress
Project description:Small cell lung cancer (SCLC) is a more aggressive and deadlier form of lung cancer with limited effective therapies currently available. By utilizing a genome-wide CRISPR-Cas9 dropout screen, we have identified the Paired box protein 9 (PAX9) as an essential factor for the cell viability of SCLC-A type, which accounts for approximately 70% of all SCLC. PAX9 is transcriptionally driven by the BAP1/ASXL3/BRD4 epigenetic axis and is overexpressed in human malignant SCLC tumor samples. Genome-wide studies have revealed that PAX9 occupies distal enhancer elements and represses gene expression by restricting enhancer activity. Genetic depletion of PAX9 leads to a dramatic induction of a primed-active enhancer transition, resulting in an increased expression of a large number of neural differentiation and tumor-suppressive genes in multiple SCLC cell lines. Mechanistically, PAX9 interacts and co-functions with the Nucleosome Remodeling and Deacetylase (NuRD) complex at enhancers and they repress the nearby gene expression, which could be rescued by pharmacological HDAC inhibition. Overall, this study provides mechanistic insight into the oncogenic function of the PAX9/NuRD complex epigenetic axis in human SCLC and suggests that re-activation of the primed enhancers may have therapeutic efficacy in treating SCLC-A type cancers expressing high levels of PAX9.
2021-08-03 | GSE164247 | GEO