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Clinical and genomic characterisation of mismatch repair deficient pancreatic adenocarcinoma

Grant, Robert C; Denroche, Robert; Jang, Gun Ho; Nowak, Klaudia M; Zhang, Amy; Borgida, Ayelet; Holter, Spring; Topham, James T; Wilson, Julie; Dodd, Anna; Jang, Raymond; Prince, Rebecca; Karasinska, Joanna M; Schaeffer, David F; Wang, Yifan; Zogopoulos, George; Berry, Scott; Simeone, Diane; Renouf, Daniel J; Notta, Faiyaz; O'Kane, Grainne; Knox, Jennifer; Fischer, Sandra; Gallinger, Steven
OBJECTIVE:To describe the clinical, pathological and genomic characteristics of pancreatic cancer with DNA mismatch repair deficiency (MMRD) and proficiency (MMRP). DESIGN/METHODS:We identified patients with MMRD and MMRP pancreatic cancer in a clinical cohort (N=1213, 519 with genetic testing, 53 with immunohistochemistry (IHC)) and a genomic cohort (N=288 with whole-genome sequencing (WGS)). RESULTS:. MMRD tumours were significantly more likely to have a basal-like transcriptional programme and elevated transcriptional markers of immunogenicity. CONCLUSIONS:MMRD pancreatic cancers have distinct clinical, pathological and genomic profiles. Patients with MMRD pancreatic cancer should be considered for basket trials targeting enhanced immunogenicity or the unique genomic drivers in these malignancies.
PMID: 32933947
ISSN: 1468-3288
CID: 5010412

A pan-cancer organoid platform for precision medicine

Larsen, Brian M; Kannan, Madhavi; Langer, Lee F; Leibowitz, Benjamin D; Bentaieb, Aicha; Cancino, Andrea; Dolgalev, Igor; Drummond, Bridgette E; Dry, Jonathan R; Ho, Chi-Sing; Khullar, Gaurav; Krantz, Benjamin A; Mapes, Brandon; McKinnon, Kelly E; Metti, Jessica; Perera, Jason F; Rand, Tim A; Sanchez-Freire, Veronica; Shaxted, Jenna M; Stein, Michelle M; Streit, Michael A; Tan, Yi-Hung Carol; Zhang, Yilin; Zhao, Ende; Venkataraman, Jagadish; Stumpe, Martin C; Borgia, Jeffrey A; Masood, Ashiq; Catenacci, Daniel V T; Mathews, Jeremy V; Gursel, Demirkan B; Wei, Jian-Jun; Welling, Theodore H; Simeone, Diane M; White, Kevin P; Khan, Aly A; Igartua, Catherine; Salahudeen, Ameen A
Patient-derived tumor organoids (TOs) are emerging as high-fidelity models to study cancer biology and develop novel precision medicine therapeutics. However, utilizing TOs for systems-biology-based approaches has been limited by a lack of scalable and reproducible methods to develop and profile these models. We describe a robust pan-cancer TO platform with chemically defined media optimized on cultures acquired from over 1,000 patients. Crucially, we demonstrate tumor genetic and transcriptomic concordance utilizing this approach and further optimize defined minimal media for organoid initiation and propagation. Additionally, we demonstrate a neural-network-based high-throughput approach for label-free, light-microscopy-based drug assays capable of predicting patient-specific heterogeneity in drug responses with applicability across solid cancers. The pan-cancer platform, molecular data, and neural-network-based drug assay serve as resources to accelerate the broad implementation of organoid models in precision medicine research and personalized therapeutic profiling programs.
PMID: 34320344
ISSN: 2211-1247
CID: 4949752

Cancer surveillance awareness and practice among families at increased risk for pancreatic adenocarcinoma

Everett, Jessica N; Burgos, Gabriela; Chun, Jennifer; Baptiste, Ariele; Khanna, Lauren G; Oberstein, Paul E; Simeone, Diane M
BACKGROUND:Early detection of pancreatic ductal adenocarcinoma (PDAC) is an important goal for improving survival. Individuals who meet published guidelines for surveillance may be underidentified, and family communication about risk represents a pathway to increasing participation in surveillance. We investigated the uptake of and barriers to surveillance in at-risk relatives of clinic patients. METHODS:We conducted a retrospective record review of patients with personal or family history of PDAC evaluated over 12 months. The first relative presenting to clinic (proband) reported surveillance status and reasons for nonparticipation for at-risk relatives. Descriptive analyses and Fisher's exact tests were conducted to evaluate differences in surveillance participation. RESULTS:Among 193 at-risk relatives, 21% were in surveillance. The primary reasons for nonparticipation were lack of awareness (36%) and lack of interest (24%). Neither the sex nor the cancer status of probands impacted surveillance. At-risk relatives with familial pancreatic cancer (FPC) who also carried relevant pathogenic germline variants (PGVs) were more likely to undergo surveillance than those with FPC or PGVs alone (P = .003). Among families with PGVs, 59% of relatives potentially eligible for surveillance had not completed genetic testing. CONCLUSION/CONCLUSIONS:PDAC surveillance is underutilized in high-risk families. Communication interventions to address informational needs and decisional support could improve outcomes.
PMID: 33721345
ISSN: 1097-0142
CID: 4823462

The biological underpinnings of therapeutic resistance in pancreatic cancer

Beatty, Gregory L; Werba, Gregor; Lyssiotis, Costas A; Simeone, Diane M
Pancreatic ductal adenocarcinoma (PDAC) is a leading cause of cancer-related mortality in the United States and has only recently achieved a 5-yr survival rate of 10%. This dismal prognosis reflects the remarkable capacity of PDAC to effectively adapt to and resist therapeutic intervention. In this review, we discuss recent advances in our understanding of the biological underpinnings of PDAC and their implications as targetable vulnerabilities in this highly lethal disease.
PMID: 34117095
ISSN: 1549-5477
CID: 4916382

Impact of changing guidelines on genetic testing and surveillance recommendations in a contemporary cohort of breast cancer survivors with family history of pancreatic cancer

Wang, Annie; Everett, Jessica N; Chun, Jennifer; Cen, Cindy; Simeone, Diane M; Schnabel, Freya
Changing practice guidelines and recommendations have important implications for cancer survivors. This study investigated genetic testing patterns and outcomes and reported family history of pancreatic cancer (FHPC) in a large registry population of breast cancer (BC) patients. Variables including clinical and demographic characteristics, FHPC in a first or second-degree relative, and genetic testing outcomes were analyzed for BC patients diagnosed between 2010 and 2018 in the NYU Langone Health Breast Cancer Database. Among 3334 BC patients, 232 (7%) had a positive FHPC. BC patients with FHPC were 1.68 times more likely to have undergone genetic testing (p < 0.001), but 33% had testing for BRCA1/2 only and 44% had no genetic testing. Pathogenic germline variants (PGV) were identified in 15/129 (11.6%) BC patients with FHPC, and in 145/1315 (11.0%) BC patients without FHPC. Across both groups, updates in genetic testing criteria and recommendations could impact up to 80% of this cohort. Within a contemporary cohort of BC patients, 7% had a positive FHPC. The majority of these patients (56%) had no genetic testing, or incomplete testing by current standards, suggesting under-diagnosis of PC risk. This study supports recommendations for survivorship care that incorporate ongoing genetic risk assessment and counseling.
PMCID:8203798
PMID: 34127761
ISSN: 2045-2322
CID: 4924652

A novel target for combination immunotherapy in pancreatic cancer: IL-1β mediates immunosuppression in the tumour microenvironment

Winograd, Rafael; Simeone, Diane M; Bar-Sagi, Dafna
Immune checkpoint blockade (ICB) has demonstrated efficacy in multiple cancers, offering the potential of long-term disease control not achievable with cytotoxic or targeted therapies. However, the field has not yet achieved the crucial next steps - the expansion of the response rate and achievement of clinical efficacy in so-called "cold tumours". Mechanistic studies of tumour-type specific immunosuppressive pathways can reveal underlying biological hurdles to immunotherapy and offer new therapeutic insights. Our finding that tumour-derived IL-1β mediates immunosuppression in pancreatic cancer has precipitated a new clinical trial.
PMID: 33758330
ISSN: 1532-1827
CID: 4822682

Dominant role of CDKN2B/p15INK4B of 9p21.3 tumor suppressor hub in inhibition of cell-cycle and glycolysis

Xia, Yong; Liu, Yan; Yang, Chao; Simeone, Diane M; Sun, Tung-Tien; DeGraff, David J; Tang, Moon-Shong; Zhang, Yingkai; Wu, Xue-Ru
Human chromosome 9p21.3 is susceptible to inactivation in cell immortalization and diseases, such as cancer, coronary artery disease and type-2 diabetes. Although this locus encodes three cyclin-dependent kinase (CDK) inhibitors (p15INK4B, p14ARF and p16INK4A), our understanding of their functions and modes of action is limited to the latter two. Here, we show that in vitro p15INK4B is markedly stronger than p16INK4A in inhibiting pRb1 phosphorylation, E2F activity and cell-cycle progression. In mice, urothelial cells expressing oncogenic HRas and lacking p15INK4B, but not those expressing HRas and lacking p16INK4A, develop early-onset bladder tumors. The potency of CDKN2B/p15INK4B in tumor suppression relies on its strong binding via key N-terminal residues to and inhibition of CDK4/CDK6. p15INK4B also binds and inhibits enolase-1, a glycolytic enzyme upregulated in most cancer types. Our results highlight the dual inhibition of p15INK4B on cell proliferation, and unveil mechanisms whereby p15INK4B aberrations may underpin cancer and non-cancer conditions.
PMID: 33824349
ISSN: 2041-1723
CID: 4840932

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