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Synergistic targeting and resistance to PARP inhibition in DNA damage repair-deficient pancreatic cancer

Gout, Johann; Perkhofer, Lukas; Morawe, Mareen; Arnold, Frank; Ihle, Michaela; Biber, Stephanie; Lange, Sebastian; Roger, Elodie; Kraus, Johann M; Stifter, Katja; Hahn, Stephan A; Zamperone, Andrea; Engleitner, Thomas; Müller, Martin; Walter, Karolin; Rodriguez-Aznar, Eva; Sainz, Bruno; Hermann, Patrick C; Hessmann, Elisabeth; Müller, Sebastian; Azoitei, Ninel; Lechel, André; Liebau, Stefan; Wagner, Martin; Simeone, Diane M; Kestler, Hans A; Seufferlein, Thomas; Wiesmüller, Lisa; Rad, Roland; Frappart, Pierre-Olivier; Kleger, Alexander
OBJECTIVE:(ATM) is the most frequently mutated DNA damage response gene, involved in homologous recombination (HR), in pancreatic ductal adenocarcinoma (PDAC). DESIGN/METHODS:Combinational synergy screening was performed to endeavour a genotype-tailored targeted therapy. RESULTS:Synergy was found on inhibition of PARP, ATR and DNA-PKcs (PAD) leading to synthetic lethality in ATM-deficient murine and human PDAC. Mechanistically, PAD-induced PARP trapping, replication fork stalling and mitosis defects leading to P53-mediated apoptosis. Most importantly, chemical inhibition of ATM sensitises human PDAC cells toward PAD with long-term tumour control in vivo. Finally, we anticipated and elucidated PARP inhibitor resistance within the ATM-null background via whole exome sequencing. Arising cells were aneuploid, underwent epithelial-mesenchymal-transition and acquired multidrug resistance (MDR) due to upregulation of drug transporters and a bypass within the DNA repair machinery. These functional observations were mirrored in copy number variations affecting a region on chromosome 5 comprising several of the upregulated MDR genes. Using these findings, we ultimately propose alternative strategies to overcome the resistance. CONCLUSION/CONCLUSIONS:Analysis of the molecular susceptibilities triggered by ATM deficiency in PDAC allow elaboration of an efficient mutation-specific combinational therapeutic approach that can be also implemented in a genotype-independent manner by ATM inhibition.
PMCID:7948173
PMID: 32873698
ISSN: 1468-3288
CID: 4835152

ATDC binds to KEAP1 to drive NRF2-mediated tumorigenesis and chemoresistance in pancreatic cancer

Purohit, Vinee; Wang, Lidong; Yang, Huibin; Li, Jiufeng; Ney, Gina M; Gumkowski, Erica R; Vaidya, Akash J; Wang, Annie; Bhardwaj, Amit; Zhao, Ende; Dolgalev, Igor; Zamperone, Andrea; Abel, Ethan V; Magliano, Marina Pasca Di; Crawford, Howard C; Diolaiti, Daniel; Papagiannakopoulos, Thales Y; Lyssiotis, Costas A; Simeone, Diane M
Pancreatic ductal adenocarcinoma is a lethal disease characterized by late diagnosis, propensity for early metastasis and resistance to chemotherapy. Little is known about the mechanisms that drive innate therapeutic resistance in pancreatic cancer. The ataxia-telangiectasia group D-associated gene (ATDC) is overexpressed in pancreatic cancer and promotes tumor growth and metastasis. Our study reveals that increased ATDC levels protect cancer cells from reactive oxygen species (ROS) via stabilization of nuclear factor erythroid 2-related factor 2 (NRF2). Mechanistically, ATDC binds to Kelch-like ECH-associated protein 1 (KEAP1), the principal regulator of NRF2 degradation, and thereby prevents degradation of NRF2 resulting in activation of a NRF2-dependent transcriptional program, reduced intracellular ROS and enhanced chemoresistance. Our findings define a novel role of ATDC in regulating redox balance and chemotherapeutic resistance by modulating NRF2 activity.
PMID: 33446568
ISSN: 1549-5477
CID: 4747272

Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer

Dreyer, Stephan B; Upstill-Goddard, Rosie; Paulus-Hock, Viola; Paris, Clara; Lampraki, Eirini-Maria; Dray, Eloise; Serrels, Bryan; Caligiuri, Giuseppina; Rebus, Selma; Plenker, Dennis; Galluzzo, Zachary; Brunton, Holly; Cunningham, Richard; Tesson, Mathias; Nourse, Craig; Bailey, Ulla-Maja; Jones, Marc; Moran-Jones, Kim; Wright, Derek W; Duthie, Fraser; Oien, Karin; Evers, Lisa; McKay, Colin J; McGregor, Grant A; Gulati, Aditi; Brough, Rachel; Bajrami, Ilirjana; Pettitt, Stephan; Dziubinski, Michele L; Candido, Juliana; Balkwill, Frances; Barry, Simon T; Grützmann, Robert; Rahib, Lola; Johns, Amber; Pajic, Marina; Froeling, Fieke E M; Beer, Phillip; Musgrove, Elizabeth A; Petersen, Gloria M; Ashworth, Alan; Frame, Margaret C; Crawford, Howard C; Simeone, Diane M; Lord, Chris; Mukhopadhyay, Debabrata; Pilarsky, Christian; Tuveson, David A; Cooke, Susanna L; Jamieson, Nigel B; Morton, Jennifer P; Sansom, Owen J; Bailey, Peter J; Biankin, Andrew V; Chang, David K
BACKGROUND & AIMS/OBJECTIVE:Continuing recalcitrance to therapy cements pancreatic cancer (PC) as the most lethal malignancy, which is set to become the second leading cause of cancer death in our society. The study aim was to investigate the association between DNA damage response (DDR), replication stress, and novel therapeutic response in PC to develop a biomarker-driven therapeutic strategy targeting DDR and replication stress in PC. METHODS:We interrogated the transcriptome, genome, proteome, and functional characteristics of 61 novel PC patient-derived cell lines to define novel therapeutic strategies targeting DDR and replication stress. Validation was done in patient-derived xenografts and human PC organoids. RESULTS:Patient-derived cell lines faithfully recapitulate the epithelial component of pancreatic tumors, including previously described molecular subtypes. Biomarkers of DDR deficiency, including a novel signature of homologous recombination deficiency, cosegregates with response to platinum (P < .001) and PARP inhibitor therapy (P < .001) in vitro and in vivo. We generated a novel signature of replication stress that predicts response to ATR (P < .018) and WEE1 inhibitor (P < .029) treatment in both cell lines and human PC organoids. Replication stress was enriched in the squamous subtype of PC (P < .001) but was not associated with DDR deficiency. CONCLUSIONS:Replication stress and DDR deficiency are independent of each other, creating opportunities for therapy in DDR-proficient PC and after platinum therapy.
PMID: 33039466
ISSN: 1528-0012
CID: 4722552

Author Correction: Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas

Moncada, Reuben; Barkley, Dalia; Wagner, Florian; Chiodin, Marta; Devlin, Joseph C; Baron, Maayan; Hajdu, Cristina H; Simeone, Diane M; Yanai, Itai
A Correction to this paper has been published: https://doi.org/10.1038/s41587-019-0392-8.
PMID: 33230294
ISSN: 1546-1696
CID: 4680492

Extracellular Vesicle and Particle Biomarkers Define Multiple Human Cancers

Hoshino, Ayuko; Kim, Han Sang; Bojmar, Linda; Gyan, Kofi Ennu; Cioffi, Michele; Hernandez, Jonathan; Zambirinis, Constantinos P; Rodrigues, Gonçalo; Molina, Henrik; Heissel, Søren; Mark, Milica Tesic; Steiner, Loïc; Benito-Martin, Alberto; Lucotti, Serena; Di Giannatale, Angela; Offer, Katharine; Nakajima, Miho; Williams, Caitlin; Nogués, Laura; Pelissier Vatter, Fanny A; Hashimoto, Ayako; Davies, Alexander E; Freitas, Daniela; Kenific, Candia M; Ararso, Yonathan; Buehring, Weston; Lauritzen, Pernille; Ogitani, Yusuke; Sugiura, Kei; Takahashi, Naoko; Alečković, Maša; Bailey, Kayleen A; Jolissant, Joshua S; Wang, Huajuan; Harris, Ashton; Schaeffer, L Miles; García-Santos, Guillermo; Posner, Zoe; Balachandran, Vinod P; Khakoo, Yasmin; Raju, G Praveen; Scherz, Avigdor; Sagi, Irit; Scherz-Shouval, Ruth; Yarden, Yosef; Oren, Moshe; Malladi, Mahathi; Petriccione, Mary; De Braganca, Kevin C; Donzelli, Maria; Fischer, Cheryl; Vitolano, Stephanie; Wright, Geraldine P; Ganshaw, Lee; Marrano, Mariel; Ahmed, Amina; DeStefano, Joe; Danzer, Enrico; Roehrl, Michael H A; Lacayo, Norman J; Vincent, Theresa C; Weiser, Martin R; Brady, Mary S; Meyers, Paul A; Wexler, Leonard H; Ambati, Srikanth R; Chou, Alexander J; Slotkin, Emily K; Modak, Shakeel; Roberts, Stephen S; Basu, Ellen M; Diolaiti, Daniel; Krantz, Benjamin A; Cardoso, Fatima; Simpson, Amber L; Berger, Michael; Rudin, Charles M; Simeone, Diane M; Jain, Maneesh; Ghajar, Cyrus M; Batra, Surinder K; Stanger, Ben Z; Bui, Jack; Brown, Kristy A; Rajasekhar, Vinagolu K; Healey, John H; de Sousa, Maria; Kramer, Kim; Sheth, Sujit; Baisch, Jeanine; Pascual, Virginia; Heaton, Todd E; La Quaglia, Michael P; Pisapia, David J; Schwartz, Robert; Zhang, Haiying; Liu, Yuan; Shukla, Arti; Blavier, Laurence; DeClerck, Yves A; LaBarge, Mark; Bissell, Mina J; Caffrey, Thomas C; Grandgenett, Paul M; Hollingsworth, Michael A; Bromberg, Jacqueline; Costa-Silva, Bruno; Peinado, Hector; Kang, Yibin; Garcia, Benjamin A; O'Reilly, Eileen M; Kelsen, David; Trippett, Tanya M; Jones, David R; Matei, Irina R; Jarnagin, William R; Lyden, David
There is an unmet clinical need for improved tissue and liquid biopsy tools for cancer detection. We investigated the proteomic profile of extracellular vesicles and particles (EVPs) in 426 human samples from tissue explants (TEs), plasma, and other bodily fluids. Among traditional exosome markers, CD9, HSPA8, ALIX, and HSP90AB1 represent pan-EVP markers, while ACTB, MSN, and RAP1B are novel pan-EVP markers. To confirm that EVPs are ideal diagnostic tools, we analyzed proteomes of TE- (n = 151) and plasma-derived (n = 120) EVPs. Comparison of TE EVPs identified proteins (e.g., VCAN, TNC, and THBS2) that distinguish tumors from normal tissues with 90% sensitivity/94% specificity. Machine-learning classification of plasma-derived EVP cargo, including immunoglobulins, revealed 95% sensitivity/90% specificity in detecting cancer. Finally, we defined a panel of tumor-type-specific EVP proteins in TEs and plasma, which can classify tumors of unknown primary origin. Thus, EVP proteins can serve as reliable biomarkers for cancer detection and determining cancer type.
PMID: 32795414
ISSN: 1097-4172
CID: 4565512

Vitamin D receptor activation and photodynamic priming enable durable low-dose chemotherapy

Anbil, Sriram; Pigula, Michael; Huang, Huang-Chiao; Mallidi, Srivalleesha; Broekgaarden, Mans; Baglo, Yan; De Silva, Pushpamali; Simeone, Diane M; Mino-Kenudson, Mari; Maytin, Edward V; Rizvi, Imran; Hasan, Tayyaba
Cancer patients often confront the decision of whether to continue high dose chemotherapy at the expense of cumulative toxicities. Reducing the dose of chemotherapy regimens while preserving efficacy is sorely needed to preserve the performance status of these vulnerable patients, yet has not been prioritized. Here, we introduce a dual pronged approach to modulate the microenvironment of desmoplastic pancreatic tumors and enable significant dose de-escalation of the FDA-approved chemotherapeutic nanoliposomal irinotecan (nal-IRI) without compromising tumor control. We demonstrate that light-based photodynamic priming (PDP) coupled with vitamin D3 receptor (VDR) activation within fibroblasts increases intratumoral nal-IRI accumulation and suppresses pro-tumorigenic CXCL12/CXCR7 crosstalk. Combined photodynamic and biochemical modulation of the tumor microenvironment enables a 75% dose reduction of nal-IRI while maintaining treatment efficacy, resulting in improved tolerability. Modifying the disease landscape to increase the susceptibility of cancer, via preferentially modulating fibroblasts, represents a promising and relatively underexplored strategy to enable dose de-escalation. The approach presented here, using a combination of three clinically available therapies with non-overlapping toxicities, can be rapidly translated with minimal modification to treatment workflow, and challenges the notion that significant improvements in chemotherapy efficacy can only be achieved at the expense of increased toxicity.
PMID: 32220968
ISSN: 1538-8514
CID: 4371172

HNF4A and GATA6 Loss Reveals Therapeutically Actionable Subtypes in Pancreatic Cancer

Brunton, Holly; Caligiuri, Giuseppina; Cunningham, Richard; Upstill-Goddard, Rosie; Bailey, Ulla-Maja; Garner, Ian M; Nourse, Craig; Dreyer, Stephan; Jones, Marc; Moran-Jones, Kim; Wright, Derek W; Paulus-Hock, Viola; Nixon, Colin; Thomson, Gemma; Jamieson, Nigel B; McGregor, Grant A; Evers, Lisa; McKay, Colin J; Gulati, Aditi; Brough, Rachel; Bajrami, Ilirjana; Pettitt, Stephen J; Dziubinski, Michele L; Barry, Simon T; Grützmann, Robert; Brown, Robert; Curry, Edward; Pajic, Marina; Musgrove, Elizabeth A; Petersen, Gloria M; Shanks, Emma; Ashworth, Alan; Crawford, Howard C; Simeone, Diane M; Froeling, Fieke E M; Lord, Christopher J; Mukhopadhyay, Debabrata; Pilarsky, Christian; Grimmond, Sean E; Morton, Jennifer P; Sansom, Owen J; Chang, David K; Bailey, Peter J; Biankin, Andrew V
Pancreatic ductal adenocarcinoma (PDAC) can be divided into transcriptomic subtypes with two broad lineages referred to as classical (pancreatic) and squamous. We find that these two subtypes are driven by distinct metabolic phenotypes. Loss of genes that drive endodermal lineage specification, HNF4A and GATA6, switch metabolic profiles from classical (pancreatic) to predominantly squamous, with glycogen synthase kinase 3 beta (GSK3β) a key regulator of glycolysis. Pharmacological inhibition of GSK3β results in selective sensitivity in the squamous subtype; however, a subset of these squamous patient-derived cell lines (PDCLs) acquires rapid drug tolerance. Using chromatin accessibility maps, we demonstrate that the squamous subtype can be further classified using chromatin accessibility to predict responsiveness and tolerance to GSK3β inhibitors. Our findings demonstrate that distinct patterns of chromatin accessibility can be used to identify patient subgroups that are indistinguishable by gene expression profiles, highlighting the utility of chromatin-based biomarkers for patient selection in the treatment of PDAC.
PMID: 32402285
ISSN: 2211-1247
CID: 4438132

Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas

Moncada, Reuben; Barkley, Dalia; Wagner, Florian; Chiodin, Marta; Devlin, Joseph C; Baron, Maayan; Hajdu, Cristina H; Simeone, Diane M; Yanai, Itai
Single-cell RNA sequencing (scRNA-seq) enables the systematic identification of cell populations in a tissue, but characterizing their spatial organization remains challenging. We combine a microarray-based spatial transcriptomics method that reveals spatial patterns of gene expression using an array of spots, each capturing the transcriptomes of multiple adjacent cells, with scRNA-Seq generated from the same sample. To annotate the precise cellular composition of distinct tissue regions, we introduce a method for multimodal intersection analysis. Applying multimodal intersection analysis to primary pancreatic tumors, we find that subpopulations of ductal cells, macrophages, dendritic cells and cancer cells have spatially restricted enrichments, as well as distinct coenrichments with other cell types. Furthermore, we identify colocalization of inflammatory fibroblasts and cancer cells expressing a stress-response gene module. Our approach for mapping the architecture of scRNA-seq-defined subpopulations can be applied to reveal the interactions inherent to complex tissues.
PMID: 31932730
ISSN: 1546-1696
CID: 4263152

Management of patients with increased risk for familial pancreatic cancer: updated recommendations from the International Cancer of the Pancreas Screening (CAPS) Consortium

Goggins, Michael; Overbeek, Kasper Alexander; Brand, Randall; Syngal, Sapna; Del Chiaro, Marco; Bartsch, Detlef K; Bassi, Claudio; Carrato, Alfredo; Farrell, James; Fishman, Elliot; Fockens, Paul; Gress, Thomas M; van Hooft, Jeanin E; Hruban, R H; Kastrinos, Fay; Klein, Allison; Lennon, Anne Marie; Lucas, Aimee; Park, Walter; Rustgi, Anil; Simeone, Diane; Stoffel, Elena; Vasen, Hans F A; Cahen, Djuna L; Canto, Marcia Irene; Bruno, Marco
BACKGROUND AND AIM/OBJECTIVE:The International Cancer of the Pancreas Screening Consortium met in 2018 to update its consensus recommendations for the management of individuals with increased risk of pancreatic cancer based on family history or germline mutation status (high-risk individuals). METHODS:A modified Delphi approach was employed to reach consensus among a multidisciplinary group of experts who voted on consensus statements. Consensus was considered reached if ≥75% agreed or disagreed. RESULTS:mutation carriers with one affected first-degree relative are now considered eligible for surveillance. Experts agreed that preferred surveillance tests are endoscopic ultrasound and MRI/magnetic retrograde cholangiopancreatography, but no consensus was reached on how to alternate these modalities. Annual surveillance is recommended in the absence of concerning lesions. Main areas of disagreement included if and how surveillance should be performed for hereditary pancreatitis, and the management of indeterminate lesions. CONCLUSIONS:Pancreatic surveillance is recommended for selected high-risk individuals to detect early pancreatic cancer and its high-grade precursors, but should be performed in a research setting by multidisciplinary teams in centres with appropriate expertise. Until more evidence supporting these recommendations is available, the benefits, risks and costs of surveillance of pancreatic surveillance need additional evaluation.
PMID: 31672839
ISSN: 1468-3288
CID: 4163432

Tyme-88-Panc Part 2: A randomized phase II/III of SM-88 with MPS as third-line in metastatic PDAC [Meeting Abstract]

Pant, S; Chawla, S P; Chung, V; Del, Priore G; Kim, D W; Noel, M S; Oberstein, P E; Ocean, A J; Philip, P A; Picozzi, V J; Simeone, D M; Wang-Gillam, A
Background: Patients with metastatic pancreatic cancer who have progressed on two prior lines of therapy have a poor prognosis with an overall survival in the range of 2-2.5 months. (Manax, et al. J Clin Oncol 37, 2019 suppl 4; abstr 226). There is currently no standard of care for these patients that has demonstrated improved outcomes. SM-88 (D,Lalpha- metyrosine; racemetyrosine [USAN]) is a proprietary dysfunctional tyrosine derivative and is the backbone of SM-88 used with MPS (Methoxsalen 10mg, Phenytoin 50mg and Sirolimus 0.5mg; all administered daily). SM-88 monotherapy was relatively well tolerated, with improvement in survival in select patients with heavily pretreated PDAC who achieved stable disease on therapy (HR 0.08, p = 0.02). Circulating tumor cells (CTC's) were prognostic and decreased on therapy with SM-88 potentially identifying a subgroup of PDAC that may be most likely to benefit from therapy (Noel et al. Annal Oncol V30, Suppl 4, 2019). Preliminary radiomic analysis of the largest metastases at baseline suggested the same benefits including a correlation with baseline CTCs, changes in CTCs on therapy and OS (Ocean et al, Annal Oncol, V30, Suppl 5, 2019). Here, we describe a randomized, open-label, phase 2/3 trial evaluating the efficacy of SM-88 + MPS vs physician's choice treatment as third line therapy for patients with metastatic PDAC.
Method(s): This is a multi-center Phase 3 study of patients >=18 years with metastatic PDAC that progressed after 2nd lines of chemotherapy (gemcitabine [gem] and 5-fluorouracil [5-FU] based) with an ECOG <2. Randomization will be 1:1 with 250 patients being stratified by site, ECOG, and choice of chemotherapy. SM-88 will be administered at a dose of 460mg twice daily (920 mg/day). Primary end point is Overall Survival (OS). Secondary end points include progression free survival, response rate, duration of response, pharmacokinetics, safety and CTCs
EMBASE:630960562
ISSN: 1527-7755
CID: 4326252