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Genome-Scale Identification of SARS-CoV-2 and Pan-coronavirus Host Factor Networks

Schneider, William M; Luna, Joseph M; Hoffmann, H-Heinrich; Sánchez-Rivera, Francisco J; Leal, Andrew A; Ashbrook, Alison W; Le Pen, Jérémie; Ricardo-Lax, Inna; Michailidis, Eleftherios; Peace, Avery; Stenzel, Ansgar F; Lowe, Scott W; MacDonald, Margaret R; Rice, Charles M; Poirier, John T
The coronavirus disease 2019 (COVID-19) pandemic has claimed the lives of over one million people worldwide. The causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a member of the Coronaviridae family of viruses that can cause respiratory infections of varying severity. The cellular host factors and pathways co-opted during SARS-CoV-2 and related coronavirus life cycles remain ill defined. To address this gap, we performed genome-scale CRISPR knockout screens during infection by SARS-CoV-2 and three seasonal coronaviruses (HCoV-OC43, HCoV-NL63, and HCoV-229E). These screens uncovered host factors and pathways with pan-coronavirus and virus-specific functional roles, including major dependency on glycosaminoglycan biosynthesis, sterol regulatory element-binding protein (SREBP) signaling, bone morphogenetic protein (BMP) signaling, and glycosylphosphatidylinositol biosynthesis, as well as a requirement for several poorly characterized proteins. We identified an absolute requirement for the VMP1, TMEM41, and TMEM64 (VTT) domain-containing protein transmembrane protein 41B (TMEM41B) for infection by SARS-CoV-2 and three seasonal coronaviruses. This human coronavirus host factor compendium represents a rich resource to develop new therapeutic strategies for acute COVID-19 and potential future coronavirus pandemics.
PMID: 33382968
ISSN: 1097-4172
CID: 4762492

TMEM41B Is a Pan-flavivirus Host Factor

Hoffmann, H-Heinrich; Schneider, William M; Rozen-Gagnon, Kathryn; Miles, Linde A; Schuster, Felix; Razooky, Brandon; Jacobson, Eliana; Wu, Xianfang; Yi, Soon; Rudin, Charles M; MacDonald, Margaret R; McMullan, Laura K; Poirier, John T; Rice, Charles M
Flaviviruses pose a constant threat to human health. These RNA viruses are transmitted by the bite of infected mosquitoes and ticks and regularly cause outbreaks. To identify host factors required for flavivirus infection, we performed full-genome loss of function CRISPR-Cas9 screens. Based on these results, we focused our efforts on characterizing the roles that TMEM41B and VMP1 play in the virus replication cycle. Our mechanistic studies on TMEM41B revealed that all members of the Flaviviridae family that we tested require TMEM41B. We tested 12 additional virus families and found that SARS-CoV-2 of the Coronaviridae also required TMEM41B for infection. Remarkably, single nucleotide polymorphisms present at nearly 20% in East Asian populations reduce flavivirus infection. Based on our mechanistic studies, we propose that TMEM41B is recruited to flavivirus RNA replication complexes to facilitate membrane curvature, which creates a protected environment for viral genome replication.
PMID: 33338421
ISSN: 1097-4172
CID: 4728282

Direct genome editing of patient-derived xenografts using CRISPR-Cas9 enables rapid in vivo functional genomics

Hulton, Christopher H; Costa, Emily A; Shah, Nisargbhai S; Quintanal-Villalonga, Alvaro; Heller, Glenn; de Stanchina, Elisa; Rudin, Charles M; Poirier, John T
Patient-derived xenografts are high fidelity in vivo tumor models that accurately reflect many key aspects of human cancer. In contrast to either cancer cell lines or genetically engineered mouse models, the utility of PDXs has been limited by the inability to perform targeted genome editing of these tumors. To address this limitation, we have developed methods for CRISPR-Cas9 editing of PDXs using a tightly regulated, inducible Cas9 vector that does not require in vitro culture for selection of transduced cells. We demonstrate the utility of this platform in PDXs (1) to analyze genetic dependencies by targeted gene disruption and (2) to analyze mechanisms of acquired drug resistance by site-specific gene editing using templated homology-directed repair. This flexible system has broad application to other explant models and substantially augments the utility of PDXs as genetically programmable models of human cancer.
PMID: 33345196
ISSN: 2662-1347
CID: 4724672

Chemosensitive Relapse in Small Cell Lung Cancer Proceeds through an EZH2-SLFN11 Axis

Gardner, Eric E; Lok, Benjamin H; Schneeberger, Valentina E; Desmeules, Patrice; Miles, Linde A; Arnold, Paige K; Ni, Andy; Khodos, Inna; de Stanchina, Elisa; Nguyen, Thuyen; Sage, Julien; Campbell, John E; Ribich, Scott; Rekhtman, Natasha; Dowlati, Afshin; Massion, Pierre P; Rudin, Charles M; Poirier, John T
Small cell lung cancer is initially highly responsive to cisplatin and etoposide but in almost every case becomes rapidly chemoresistant, leading to death within 1 year. We modeled acquired chemoresistance in vivo using a series of patient-derived xenografts to generate paired chemosensitive and chemoresistant cancers. Multiple chemoresistant models demonstrated suppression of SLFN11, a factor implicated in DNA-damage repair deficiency. In vivo silencing of SLFN11 was associated with marked deposition of H3K27me3, a histone modification placed by EZH2, within the gene body of SLFN11, inducing local chromatin condensation and gene silencing. Inclusion of an EZH2 inhibitor with standard cytotoxic therapies prevented emergence of acquired resistance and augmented chemotherapeutic efficacy in both chemosensitive and chemoresistant models of small cell lung cancer.
PMID: 28196596
ISSN: 1878-3686
CID: 3958312

Functional interrogation of a SARS-CoV-2 host protein interactome identifies unique and shared coronavirus host factors

Hoffmann, H-Heinrich; Sánchez-Rivera, Francisco J; Schneider, William M; Luna, Joseph M; Soto-Feliciano, Yadira M; Ashbrook, Alison W; Le Pen, Jérémie; Leal, Andrew A; Ricardo-Lax, Inna; Michailidis, Eleftherios; Hao, Yuan; Stenzel, Ansgar F; Peace, Avery; Zuber, Johannes; Allis, C David; Lowe, Scott W; MacDonald, Margaret R; Poirier, John T; Rice, Charles M
The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has devastated the global economy and claimed more than 1.7 million lives, presenting an urgent global health crisis. To identify host factors required for infection by SARS-CoV-2 and seasonal coronaviruses, we designed a focused high-coverage CRISPR-Cas9 library targeting 332 members of a recently published SARS-CoV-2 protein interactome. We leveraged the compact nature of this library to systematically screen SARS-CoV-2 at two physiologically relevant temperatures along with three related coronaviruses (human coronavirus 229E [HCoV-229E], HCoV-NL63, and HCoV-OC43), allowing us to probe this interactome at a much higher resolution than genome-scale studies. This approach yielded several insights, including potential virus-specific differences in Rab GTPase requirements and glycosylphosphatidylinositol (GPI) anchor biosynthesis, as well as identification of multiple pan-coronavirus factors involved in cholesterol homeostasis. This coronavirus essentiality catalog could inform ongoing drug development efforts aimed at intercepting and treating coronavirus disease 2019 (COVID-19) and help prepare for future coronavirus outbreaks.
PMID: 33357464
ISSN: 1934-6069
CID: 4728252

Molecular subtypes of small cell lung cancer: a synthesis of human and mouse model data

Rudin, Charles M; Poirier, John T; Byers, Lauren Averett; Dive, Caroline; Dowlati, Afshin; George, Julie; Heymach, John V; Johnson, Jane E; Lehman, Jonathan M; MacPherson, David; Massion, Pierre P; Minna, John D; Oliver, Trudy G; Quaranta, Vito; Sage, Julien; Thomas, Roman K; Vakoc, Christopher R; Gazdar, Adi F
Small cell lung cancer (SCLC) is an exceptionally lethal malignancy for which more effective therapies are urgently needed. Several lines of evidence, from SCLC primary human tumours, patient-derived xenografts, cancer cell lines and genetically engineered mouse models, appear to be converging on a new model of SCLC subtypes defined by differential expression of four key transcription regulators: achaete-scute homologue 1 (ASCL1; also known as ASH1), neurogenic differentiation factor 1 (NeuroD1), yes-associated protein 1 (YAP1) and POU class 2 homeobox 3 (POU2F3). In this Perspectives article, we review and synthesize these recent lines of evidence and propose a working nomenclature for SCLC subtypes defined by relative expression of these four factors. Defining the unique therapeutic vulnerabilities of these subtypes of SCLC should help to focus and accelerate therapeutic research, leading to rationally targeted approaches that may ultimately improve clinical outcomes for patients with this disease.
PMID: 30926931
ISSN: 1474-1768
CID: 3958452

New approaches to small cell lung cancer therapy : from the laboratory to the clinic

Poirier, John T; George, Julie; Owonikoko, Taofeek K; Berns, Anton; Brambilla, Elisabeth; Byers, Lauren Averett; Carbone, David; Chen, Huanhuan Joyce; Christensen, Camilla L; Dive, Caroline; Farago, Anna F; Govindan, Ramaswamy; Hann, Christine; Hellmann, Matthew D; Horn, Leora; Johnson, Jane E; Ju, Young Seok; Kang, Sumin; Krasnow, Mark; Lee, James; Lee, Se-Hoon; Lehman, Jonathan; Lok, Benjamin; Lovly, Christine; MacPherson, David; McFadden, David; Minna, John; Oser, Matthew; Park, Keunchil; Park, Kwon-Sik; Pommier, Yves; Quaranta, Vito; Ready, Neal; Sage, Julien; Scagliotti, Giorgio; Sos, Martin L; Sutherland, Kate D; Travis, William D; Vakoc, Christopher R; Wait, Sarah J; Wistuba, Ignacio; Wong, Kwok Kin; Zhang, Hua; Daigneault, Jillian; Wiens, Jacinta; Rudin, Charles M; Oliver, Trudy G
Small cell lung cancer patient outcomes have not yet been significantly impacted by the revolution in precision oncology, primarily due to a paucity of genetic alterations in actionable driver oncogenes. Nevertheless, systemic therapies that include immunotherapy are beginning to show promise in the clinic. While these results are encouraging, many patients do not respond to or rapidly recur after current regimens, necessitating alternative or complementary therapeutic strategies. In this review, we discuss ongoing investigations into the pathobiology of this recalcitrant cancer and the therapeutic vulnerabilities that are exposed by the disease state. Included within this discussion is a snapshot of the current biomarker and clinical trial landscapes for small cell lung cancer. Finally, we identify key knowledge gaps that should be addressed in order to advance the field in pursuit of reduced small cell lung cancer mortality. This review largely summarizes work presented at the Third Biennial IASLC Small Cell Lung Cancer Meeting.
PMID: 32018053
ISSN: 1556-1380
CID: 4301362

DNA methylation in small cell lung cancer defines distinct disease subtypes and correlates with high expression of EZH2

Poirier, J T; Gardner, E E; Connis, N; Moreira, A L; de Stanchina, E; Hann, C L; Rudin, C M
Small cell lung cancer (SCLC) is an aggressive malignancy characterized by early metastasis, rapid development of resistance to chemotherapy and genetic instability. This study profiles DNA methylation in SCLC, patient-derived xenografts (PDX) and cell lines at single-nucleotide resolution. DNA methylation patterns of primary samples are distinct from those of cell lines, whereas PDX maintain a pattern closely consistent with primary samples. Clustering of DNA methylation and gene expression of primary SCLC revealed distinct disease subtypes among histologically indistinguishable primary patient samples with similar genetic alterations. SCLC is notable for dense clustering of high-level methylation in discrete promoter CpG islands, in a pattern clearly distinct from other lung cancers and strongly correlated with high expression of the E2F target and histone methyltransferase gene EZH2. Pharmacologic inhibition of EZH2 in a SCLC PDX markedly inhibited tumor growth.
PMID: 25746006
ISSN: 1476-5594
CID: 3958172

Genomic and transcriptomic analysis of a library of small cell lung cancer patient-derived xenografts

Caeser, Rebecca; Egger, Jacklynn V; Chavan, Shweta; Socci, Nicholas D; Jones, Caitlin Byrne; Kombak, Faruk Erdem; Asher, Marina; Roehrl, Michael H; Shah, Nisargbhai S; Allaj, Viola; Manoj, Parvathy; Tischfield, Sam E; Kulick, Amanda; Meneses, Maximiliano; Iacobuzio-Donahue, Christine A; Lai, W Victoria; Bhanot, Umeshkumar; Baine, Marina K; Rekhtman, Natasha; Hollmann, Travis J; de Stanchina, Elisa; Poirier, John T; Rudin, Charles M; Sen, Triparna
Access to clinically relevant small cell lung cancer (SCLC) tissue is limited because surgical resection is rare in metastatic SCLC. Patient-derived xenografts (PDX) and circulating tumor cell-derived xenografts (CDX) have emerged as valuable tools to characterize SCLC. Here, we present a resource of 46 extensively annotated PDX/CDX models derived from 33 patients with SCLC. We perform multi-omic analyses, using targeted tumor next-generation sequencing, RNA-sequencing, and immunohistochemistry to deconvolute the mutational landscapes, global expression profiles, and molecular subtypes of these SCLC models. SCLC subtypes characterized by transcriptional regulators, ASCL1, NEUROD1 and POU2F3 are confirmed in this cohort. A subset of SCLC clinical specimens, including matched PDX/CDX and clinical specimen pairs, confirm that the primary features and genomic and proteomic landscapes of the tumors of origin are preserved in the derivative PDX models. This resource provides a powerful system to study SCLC biology.
PMID: 35440124
ISSN: 2041-1723
CID: 5202132

Radioimmunotherapy Targeting Delta-like Ligand 3 in Small Cell Lung Cancer exhibits antitumor efficacy with low toxicity

Tully, Kathryn M; Tendler, Salomon; Carter, Lukas M; Sharma, Sai Kiran; Samuels, Zachary V; Mandleywala, Komal; Korsen, Joshua A; Delos Reyes, Avelyn Mae; Piersigilli, Alessandra; Travis, William D; Sen, Triparna; Pillarsetty, Nagavarakishore; Poirier, John T; Rudin, Charles M; Lewis, Jason S
PURPOSE/OBJECTIVE:Small cell lung cancer is an exceptionally lethal form of lung cancer with limited treatment options. Delta-like ligand 3 (DLL3) is an attractive therapeutic target as surface expression is almost exclusive to tumor cells. EXPERIMENTAL DESIGN/METHODS:Lu]Lu-DTPA-CHX-A"-SC16 binds to DLL3 on SCLC cells and delivers targeted radiotherapy while minimizing radiation to healthy tissue. RESULTS:Lu]Lu-DTPA-CHX-A"-SC16.
PMID: 35046060
ISSN: 1557-3265
CID: 5131612