1
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Lansbergen MF, Dings MPG, Manoukian P, Fariña A, Waasdorp C, Hooijer GKJ, Verheij J, Koster J, Zwijnenburg DA, Wilmink JW, Medema JP, Dijk F, van Laarhoven HWM, Bijlsma MF. Transcriptome-based classification to predict FOLFIRINOX response in a real-world metastatic pancreatic cancer cohort. Transl Res 2024; 273:137-147. [PMID: 39154856 DOI: 10.1016/j.trsl.2024.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 06/18/2024] [Accepted: 08/13/2024] [Indexed: 08/20/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is often diagnosed at metastatic stage and typically treated with fluorouracil, leucovorin, irinotecan and oxaliplatin (FOLFIRINOX). Few patients benefit from this treatment. Molecular subtypes are prognostic in particularly resectable PDAC and might predict treatment response. This study aims to correlate molecular subtypes in metastatic PDAC with FOLFIRINOX responses using real-world data, providing assistance in counselling patients. We collected 131 RNA-sequenced metastatic biopsies and applied a network-based meta-analysis using published PDAC classifiers. Subsequent survival analysis was performed using the most suitable classifier. For validation, we developed an immunohistochemistry (IHC) classifier using GATA6 and keratin-17 (KRT17), and applied it to 86 formalin-fixed paraffin-embedded samples of advanced PDAC. Lastly, GATA6 knockdown models were generated in PDAC organoids and cell lines. We showed that the PurIST classifier was the most suitable classifier. With this classifier, classical tumors had longer PFS and OS than basal-like tumors (PFS: 216 vs. 78 days, p = 0.0002; OS: 251 vs. 195 days, p = 0.049). The validation cohort showed a similar trend. Importantly, IHC GATA6low patients had significantly shorter survival with FOLFIRINOX (323 vs. 746 days, p = 0.006), but no difference in non-treated patients (61 vs. 54 days, p = 0.925). This suggests that GATA6 H-score predicts therapy response. GATA6 knockdown models did not lead to increased FOLFIRINOX responsiveness. These data suggest a predictive role for subtyping (transcriptomic and GATA6 IHC), though no direct causal relationship was found between GATA6 expression and chemoresistance. GATA6 immunohistochemistry should be seamlessly added to current diagnostics and integrated into upcoming clinical trials.
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Affiliation(s)
- Marjolein F Lansbergen
- Amsterdam UMC, location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Amsterdam UMC, location University of Amsterdam, Medical Oncology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Mark P G Dings
- Amsterdam UMC, location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands; Oncode Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Paul Manoukian
- Amsterdam UMC, location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Arantza Fariña
- Cancer Center Amsterdam, Amsterdam, the Netherlands; Amsterdam UMC, location University of Amsterdam, Pathology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Cynthia Waasdorp
- Amsterdam UMC, location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Gerrit K J Hooijer
- Cancer Center Amsterdam, Amsterdam, the Netherlands; Amsterdam UMC, location University of Amsterdam, Pathology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Joanne Verheij
- Cancer Center Amsterdam, Amsterdam, the Netherlands; Amsterdam UMC, location University of Amsterdam, Pathology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Jan Koster
- Amsterdam UMC, location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Danny A Zwijnenburg
- Amsterdam UMC, location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Johanna W Wilmink
- Amsterdam UMC, location University of Amsterdam, Medical Oncology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Jan Paul Medema
- Amsterdam UMC, location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands; Oncode Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Frederike Dijk
- Cancer Center Amsterdam, Amsterdam, the Netherlands; Amsterdam UMC, location University of Amsterdam, Pathology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Hanneke W M van Laarhoven
- Amsterdam UMC, location University of Amsterdam, Medical Oncology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Maarten F Bijlsma
- Amsterdam UMC, location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands; Oncode Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands.
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2
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Sevrin T, Imoto H, Robertson S, Rauch N, Dyn'ko U, Koubova K, Wynne K, Kolch W, Rukhlenko OS, Kholodenko BN. Cell-specific models reveal conformation-specific RAF inhibitor combinations that synergistically inhibit ERK signaling in pancreatic cancer cells. Cell Rep 2024; 43:114710. [PMID: 39240715 DOI: 10.1016/j.celrep.2024.114710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 07/16/2024] [Accepted: 08/20/2024] [Indexed: 09/08/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) presents significant challenges for targeted clinical interventions due to prevalent KRAS mutations, rendering PDAC resistant to RAF and MEK inhibitors (RAFi and MEKi). In addition, responses to targeted therapies vary between patients. Here, we explored the differential sensitivities of PDAC cell lines to RAFi and MEKi and developed an isogenic pair comprising the most sensitive and resistant PDAC cells. To simulate patient- or tumor-specific variations, we constructed cell-line-specific mechanistic models based on protein expression profiling and differential properties of KRAS mutants. These models predicted synergy between two RAFi with different conformation specificity (type I½ and type II RAFi) in inhibiting phospho-ERK (ppERK) and reducing PDAC cell viability. This synergy was experimentally validated across all four studied PDAC cell lines. Our findings underscore the need for combination approaches to inhibit the ERK pathway in PDAC.
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Affiliation(s)
- Thomas Sevrin
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Hiroaki Imoto
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Sarah Robertson
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Nora Rauch
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Uscinnia Dyn'ko
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Katerina Koubova
- Systems Biology Ireland, University College Dublin, Dublin, Ireland; Department of Histology and Embryology, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech Republic
| | - Kieran Wynne
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Walter Kolch
- Systems Biology Ireland, University College Dublin, Dublin, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland; School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | | | - Boris N Kholodenko
- Systems Biology Ireland, University College Dublin, Dublin, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland; School of Medicine and Medical Science, University College Dublin, Dublin, Ireland; Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA.
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3
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de Back TR, van Hooff SR, Sommeijer DW, Vermeulen L. Transcriptomic subtyping of gastrointestinal malignancies. Trends Cancer 2024; 10:842-856. [PMID: 39019673 DOI: 10.1016/j.trecan.2024.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/19/2024]
Abstract
Gastrointestinal (GI) cancers are highly heterogeneous at multiple levels. Tumor heterogeneity can be captured by molecular profiling, such as genetic, epigenetic, proteomic, and transcriptomic classification. Transcriptomic subtyping has the advantage of combining genetic and epigenetic information, cancer cell-intrinsic properties, and the tumor microenvironment (TME). Unsupervised transcriptomic subtyping systems of different GI malignancies have gained interest because they reveal shared biological features across cancers and bear prognostic and predictive value. Importantly, transcriptomic subtypes accurately reflect complex phenotypic states varying not only per tumor region, but also throughout disease progression, with consequences for clinical management. Here, we discuss methodologies of transcriptomic subtyping, proposed taxonomies for GI malignancies, and the challenges posed to clinical implementation, highlighting opportunities for future transcriptomic profiling efforts to optimize clinical impact.
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Affiliation(s)
- Tim R de Back
- Cancer Center Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands; Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Sander R van Hooff
- Cancer Center Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands; Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Dirkje W Sommeijer
- Flevohospital, Department of Internal Medicine, Hospitaalweg 1, 1315 RA, Almere, The Netherlands
| | - Louis Vermeulen
- Cancer Center Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands; Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
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4
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Vallés‐Martí A, de Goeij‐de Haas RR, Henneman AA, Piersma SR, Pham TV, Knol JC, Verheij J, Dijk F, Halfwerk H, Giovannetti E, Jiménez CR, Bijlsma MF. Kinase activities in pancreatic ductal adenocarcinoma with prognostic and therapeutic avenues. Mol Oncol 2024; 18:2020-2041. [PMID: 38650175 PMCID: PMC11306541 DOI: 10.1002/1878-0261.13625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 12/12/2023] [Accepted: 02/21/2024] [Indexed: 04/25/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with a limited number of known driver mutations but considerable cancer cell heterogeneity. Phosphoproteomics provides a direct read-out of aberrant signaling and the resultant clinically relevant phenotype. Mass spectrometry (MS)-based proteomics and phosphoproteomics were applied to 42 PDAC tumors. Data encompassed over 19 936 phosphoserine or phosphothreonine (pS/T; in 5412 phosphoproteins) and 1208 phosphotyrosine (pY; in 501 phosphoproteins) sites and a total of 3756 proteins. Proteome data identified three distinct subtypes with tumor intrinsic and stromal features. Subsequently, three phospho-subtypes were apparent: two tumor intrinsic (Phos1/2) and one stromal (Phos3), resembling known PDAC molecular subtypes. Kinase activity was analyzed by the Integrative iNferred Kinase Activity (INKA) scoring. Phospho-subtypes displayed differential phosphorylation signals and kinase activity, such as FGR and GSK3 activation in Phos1, SRC kinase family and EPHA2 in Phos2, and EGFR, INSR, MET, ABL1, HIPK1, JAK, and PRKCD in Phos3. Kinase activity analysis of an external PDAC cohort supported our findings and underscored the importance of PI3K/AKT and ERK pathways, among others. Interestingly, unfavorable patient prognosis correlated with higher RTK, PAK2, STK10, and CDK7 activity and high proliferation, whereas long survival was associated with MYLK and PTK6 activity, which was previously unknown. Subtype-associated activity profiles can guide therapeutic combination approaches in tumor and stroma-enriched tissues, and emphasize the critical role of parallel signaling pathways. In addition, kinase activity profiling identifies potential disease markers with prognostic significance.
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Affiliation(s)
- Andrea Vallés‐Martí
- Department of Medical Oncology, Amsterdam University Medical CenterVU UniversityAmsterdamThe Netherlands
- OncoProteomics LaboratoryCancer Center AmsterdamThe Netherlands
- Cancer BiologyCancer Center AmsterdamThe Netherlands
- Pharmacology LaboratoryCancer Center AmsterdamThe Netherlands
| | - Richard R. de Goeij‐de Haas
- Department of Medical Oncology, Amsterdam University Medical CenterVU UniversityAmsterdamThe Netherlands
- OncoProteomics LaboratoryCancer Center AmsterdamThe Netherlands
| | - Alex A. Henneman
- Department of Medical Oncology, Amsterdam University Medical CenterVU UniversityAmsterdamThe Netherlands
- OncoProteomics LaboratoryCancer Center AmsterdamThe Netherlands
| | - Sander R. Piersma
- Department of Medical Oncology, Amsterdam University Medical CenterVU UniversityAmsterdamThe Netherlands
- OncoProteomics LaboratoryCancer Center AmsterdamThe Netherlands
| | - Thang V. Pham
- Department of Medical Oncology, Amsterdam University Medical CenterVU UniversityAmsterdamThe Netherlands
- OncoProteomics LaboratoryCancer Center AmsterdamThe Netherlands
| | - Jaco C. Knol
- Department of Medical Oncology, Amsterdam University Medical CenterVU UniversityAmsterdamThe Netherlands
- OncoProteomics LaboratoryCancer Center AmsterdamThe Netherlands
| | - Joanne Verheij
- Department of PathologyAmsterdam University Medical CenterThe Netherlands
| | - Frederike Dijk
- Department of PathologyAmsterdam University Medical CenterThe Netherlands
| | - Hans Halfwerk
- Department of PathologyAmsterdam University Medical CenterThe Netherlands
| | - Elisa Giovannetti
- Department of Medical Oncology, Amsterdam University Medical CenterVU UniversityAmsterdamThe Netherlands
- Pharmacology LaboratoryCancer Center AmsterdamThe Netherlands
- Cancer Pharmacology Lab, AIRC Start‐Up UnitFondazione Pisana per la ScienzaSan Giuliano TermeItaly
| | - Connie R. Jiménez
- Department of Medical Oncology, Amsterdam University Medical CenterVU UniversityAmsterdamThe Netherlands
- OncoProteomics LaboratoryCancer Center AmsterdamThe Netherlands
| | - Maarten F. Bijlsma
- Cancer BiologyCancer Center AmsterdamThe Netherlands
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam University Medical CenterUniversity of AmsterdamThe Netherlands
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5
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Brown BA, Myers PJ, Adair SJ, Pitarresi JR, Sah-Teli SK, Campbell LA, Hart WS, Barbeau MC, Leong K, Seyler N, Kane W, Lee KE, Stelow E, Jones M, Simon MC, Koivunen P, Bauer TW, Stanger BZ, Lazzara MJ. A Histone Methylation-MAPK Signaling Axis Drives Durable Epithelial-Mesenchymal Transition in Hypoxic Pancreatic Cancer. Cancer Res 2024; 84:1764-1780. [PMID: 38471099 DOI: 10.1158/0008-5472.can-22-2945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/10/2023] [Accepted: 03/01/2024] [Indexed: 03/14/2024]
Abstract
The tumor microenvironment in pancreatic ductal adenocarcinoma (PDAC) plays a key role in tumor progression and response to therapy. The dense PDAC stroma causes hypovascularity, which leads to hypoxia. Here, we showed that hypoxia drives long-lasting epithelial-mesenchymal transition (EMT) in PDAC primarily through a positive-feedback histone methylation-MAPK signaling axis. Transformed cells preferentially underwent EMT in hypoxic tumor regions in multiple model systems. Hypoxia drove a cell autonomous EMT in PDAC cells, which, unlike EMT in response to growth factors, could last for weeks. Furthermore, hypoxia reduced histone demethylase KDM2A activity, suppressed PP2 family phosphatase expression, and activated MAPKs to post-translationally stabilize histone methyltransferase NSD2, leading to an H3K36me2-dependent EMT in which hypoxia-inducible factors played only a supporting role. Hypoxia-driven EMT could be antagonized in vivo by combinations of MAPK inhibitors. Collectively, these results suggest that hypoxia promotes durable EMT in PDAC by inducing a histone methylation-MAPK axis that can be effectively targeted with multidrug therapies, providing a potential strategy for overcoming chemoresistance. SIGNIFICANCE Integrated regulation of histone methylation and MAPK signaling by the low-oxygen environment of pancreatic cancer drives long-lasting EMT that promotes chemoresistance and shortens patient survival and that can be pharmacologically inhibited. See related commentary by Wirth and Schneider, p. 1739.
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Affiliation(s)
- Brooke A Brown
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia
| | - Paul J Myers
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia
| | - Sara J Adair
- Department of Surgery, University of Virginia, Charlottesville, Virginia
| | - Jason R Pitarresi
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Shiv K Sah-Teli
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Logan A Campbell
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia
| | - William S Hart
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia
| | | | - Kelsey Leong
- Engineering Science, University of Virginia, Charlottesville, Virginia
| | - Nicholas Seyler
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia
| | - William Kane
- Department of Surgery, University of Virginia, Charlottesville, Virginia
| | - Kyoung Eun Lee
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan
| | - Edward Stelow
- Department of Pathology, University of Virginia, Charlottesville, Virginia
| | - Marieke Jones
- Claude Moore Health Sciences Library, University of Virginia, Charlottesville, Virginia
| | - M Celeste Simon
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Peppi Koivunen
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Todd W Bauer
- Department of Surgery, University of Virginia, Charlottesville, Virginia
| | - Ben Z Stanger
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Matthew J Lazzara
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia
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6
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Bootsma S, Dings MPG, Kesselaar J, Helderman RFCPA, van Megesen K, Constantinides A, Moreno LF, Stelloo E, Scutigliani EM, Bokan B, Torang A, van Hooff SR, Zwijnenburg DA, Wouters VM, van de Vlasakker VCJ, Galanos LJK, Nijman LE, Logiantara A, Veenstra VL, Schlingemann S, van Piggelen S, van der Wel N, Krawczyk PM, Platteeuw JJ, Tuynman JB, de Hingh IH, Klomp JPG, Oubrie A, Snaebjornsson P, Medema JP, Oei AL, Kranenburg O, Elbers CC, Lenos KJ, Vermeulen L, Bijlsma MF. Exploiting a subtype-specific mitochondrial vulnerability for successful treatment of colorectal peritoneal metastases. Cell Rep Med 2024; 5:101523. [PMID: 38670098 PMCID: PMC11148637 DOI: 10.1016/j.xcrm.2024.101523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 11/22/2023] [Accepted: 04/02/2024] [Indexed: 04/28/2024]
Abstract
Peritoneal metastases (PMs) from colorectal cancer (CRC) respond poorly to treatment and are associated with unfavorable prognosis. For example, the addition of hyperthermic intraperitoneal chemotherapy (HIPEC) to cytoreductive surgery in resectable patients shows limited benefit, and novel treatments are urgently needed. The majority of CRC-PMs represent the CMS4 molecular subtype of CRC, and here we queried the vulnerabilities of this subtype in pharmacogenomic databases to identify novel therapies. This reveals the copper ionophore elesclomol (ES) as highly effective against CRC-PMs. ES exhibits rapid cytotoxicity against CMS4 cells by targeting mitochondria. We find that a markedly reduced mitochondrial content in CMS4 cells explains their vulnerability to ES. ES demonstrates efficacy in preclinical models of PMs, including CRC-PMs and ovarian cancer organoids, mouse models, and a HIPEC rat model of PMs. The above proposes ES as a promising candidate for the local treatment of CRC-PMs, with broader implications for other PM-prone cancers.
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Affiliation(s)
- Sanne Bootsma
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, the Netherlands
| | - Mark P G Dings
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, the Netherlands
| | - Job Kesselaar
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, the Netherlands
| | - Roxan F C P A Helderman
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands; Amsterdam UMC Location University of Amsterdam, Department of Radiation Oncology, Amsterdam, the Netherlands
| | - Kyah van Megesen
- Laboratory of Translational Oncology, UMC Utrecht Cancer Center, Utrecht, the Netherlands
| | | | - Leandro Ferreira Moreno
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands
| | - Ellen Stelloo
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Enzo M Scutigliani
- Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands; Amsterdam UMC Location University of Amsterdam, Department of Medical Biology, Amsterdam, the Netherlands
| | - Bella Bokan
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands; Amsterdam UMC Location University of Amsterdam, Department of Radiation Oncology, Amsterdam, the Netherlands
| | - Arezo Torang
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands
| | - Sander R van Hooff
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands
| | - Danny A Zwijnenburg
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands
| | - Valérie M Wouters
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands
| | | | | | - Lisanne E Nijman
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands
| | - Adrian Logiantara
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands
| | - Veronique L Veenstra
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands
| | - Sophie Schlingemann
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands
| | - Sterre van Piggelen
- Laboratory of Translational Oncology, UMC Utrecht Cancer Center, Utrecht, the Netherlands
| | - Nicole van der Wel
- Amsterdam UMC Location University of Amsterdam, Electron Microscopy Center, Amsterdam, the Netherlands
| | - Przemek M Krawczyk
- Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands; Amsterdam UMC Location University of Amsterdam, Department of Medical Biology, Amsterdam, the Netherlands
| | | | - Jurriaan B Tuynman
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Surgery, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, the Netherlands
| | - Ignace H de Hingh
- Department of Surgery, Catharina Hospital, Eindhoven, the Netherlands; GROW - School for Oncology and Developmental Biology, Maastricht University, Maastricht, the Netherlands
| | | | | | - Petur Snaebjornsson
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jan Paul Medema
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands
| | - Arlene L Oei
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands; Amsterdam UMC Location University of Amsterdam, Department of Radiation Oncology, Amsterdam, the Netherlands
| | - Onno Kranenburg
- Laboratory of Translational Oncology, UMC Utrecht Cancer Center, Utrecht, the Netherlands
| | - Clara C Elbers
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands
| | - Kristiaan J Lenos
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands
| | - Louis Vermeulen
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, the Netherlands
| | - Maarten F Bijlsma
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands.
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7
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D'Amico S, Kirillov V, Petrenko O, Reich NC. STAT3 is a genetic modifier of TGF-beta induced EMT in KRAS mutant pancreatic cancer. eLife 2024; 13:RP92559. [PMID: 38573819 PMCID: PMC10994661 DOI: 10.7554/elife.92559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024] Open
Abstract
Oncogenic mutations in KRAS are among the most common in cancer. Classical models suggest that loss of epithelial characteristics and the acquisition of mesenchymal traits are associated with cancer aggressiveness and therapy resistance. However, the mechanistic link between these phenotypes and mutant KRAS biology remains to be established. Here, we identify STAT3 as a genetic modifier of TGF-beta-induced epithelial to mesenchymal transition. Gene expression profiling of pancreatic cancer cells identifies more than 200 genes commonly regulated by STAT3 and oncogenic KRAS. Functional classification of the STAT3-responsive program reveals its major role in tumor maintenance and epithelial homeostasis. The signatures of STAT3-activated cell states can be projected onto human KRAS mutant tumors, suggesting that they faithfully reflect characteristics of human disease. These observations have implications for therapeutic intervention and tumor aggressiveness.
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Affiliation(s)
- Stephen D'Amico
- Department of Microbiology and Immunology, Stony Brook UniversityStony BrookUnited States
| | - Varvara Kirillov
- Department of Microbiology and Immunology, Stony Brook UniversityStony BrookUnited States
| | - Oleksi Petrenko
- Department of Microbiology and Immunology, Stony Brook UniversityStony BrookUnited States
| | - Nancy C Reich
- Department of Microbiology and Immunology, Stony Brook UniversityStony BrookUnited States
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8
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Kim J, Lee TS, Lee MH, Cho IR, Ryu JK, Kim YT, Lee SH, Paik WH. Pancreatic Cancer Treatment Targeting the HGF/c-MET Pathway: The MEK Inhibitor Trametinib. Cancers (Basel) 2024; 16:1056. [PMID: 38473413 DOI: 10.3390/cancers16051056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/26/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
Pancreatic cancer is characterized by fibrosis/desmoplasia in the tumor microenvironment, which is primarily mediated by pancreatic stellate cells and cancer-associated fibroblasts. HGF/c-MET signaling, which is instrumental in embryonic development and wound healing, is also implicated for its mitogenic and motogenic properties. In pancreatic cancer, this pathway, along with its downstream signaling pathways, is associated with disease progression, prognosis, metastasis, chemoresistance, and other tumor-related factors. Other features of the microenvironment in pancreatic cancer with the HGF/c-MET pathway include hypoxia, angiogenesis, metastasis, and the urokinase plasminogen activator positive feed-forward loop. All these attributes critically influence the initiation, progression, and metastasis of pancreatic cancer. Therefore, targeting the HGF/c-MET signaling pathway appears promising for the development of innovative drugs for pancreatic cancer treatment. One of the primary downstream effects of c-MET activation is the MAPK/ERK (Ras, Ras/Raf/MEK/ERK) signaling cascade, and MEK (Mitogen-activated protein kinase kinase) inhibitors have demonstrated therapeutic value in RAS-mutant melanoma and lung cancer. Trametinib is a selective MEK1 and MEK2 inhibitor, and it has evolved as a pivotal therapeutic agent targeting the MAPK/ERK pathway in various malignancies, including BRAF-mutated melanoma, non-small cell lung cancer and thyroid cancer. The drug's effectiveness increases when combined with agents like BRAF inhibitors. However, resistance remains a challenge, necessitating ongoing research to counteract the resistance mechanisms. This review offers an in-depth exploration of the HGF/c-MET signaling pathway, trametinib's mechanism, clinical applications, combination strategies, and future directions in the context of pancreatic cancer.
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Affiliation(s)
- Junyeol Kim
- Department of Internal Medicine, Liver Research Institute, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Tae Seung Lee
- Department of Internal Medicine, Liver Research Institute, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Myeong Hwan Lee
- Department of Internal Medicine, Liver Research Institute, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - In Rae Cho
- Department of Internal Medicine, Liver Research Institute, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Ji Kon Ryu
- Department of Internal Medicine, Liver Research Institute, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Yong-Tae Kim
- Department of Internal Medicine, Liver Research Institute, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Sang Hyub Lee
- Department of Internal Medicine, Liver Research Institute, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Woo Hyun Paik
- Department of Internal Medicine, Liver Research Institute, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
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9
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Riviere D, Aarntzen E, van Geenen E, Chang D, de Geus-Oei LF, Brosens L, van Laarhoven K, Gotthardt M, Hermans J. Qualitative flow metabolic phenotype of pancreatic cancer. A new prognostic biomarker? HPB (Oxford) 2024; 26:389-399. [PMID: 38114400 DOI: 10.1016/j.hpb.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/26/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023]
Abstract
BACKGROUND Retrospective analysis to investigate the relationship between the flow-metabolic phenotype and overall survival (OS) of pancreatic ductal adenocarcinoma (PDAC) and its potential clinical utility. METHODS Patients with histopathologically proven PDAC between 2005 and 2014 using tumor attenuation on routine pre-operative CECT as a surrogate for the vascularity and [18F]FDG-uptake as a surrogate for metabolic activity on [18F]FDG-PET. RESULTS In total, 93 patients (50 male, 43 female, median age 63) were included. Hypoattenuating PDAC with high [18F]FDG-uptake has the poorest prognosis (median OS 7 ± 1 months), compared to hypoattenuating PDAC with low [18F]FDG-uptake (median OS 11 ± 3 months; p = 0.176), iso- or hyperattenuating PDAC with high [18F]FDG-uptake (median OS 15 ± 5 months; p = 0.004) and iso- or hyperattenuating PDAC with low [18F]FDG-uptake (median OS 23 ± 4 months; p = 0.035). In multivariate analysis, surgery combined with tumor differentiation, tumor stage, systemic therapy and flow metabolic phenotype remained independent predictors for overall survival. DISCUSSION The novel qualitative flow-metabolic phenotype of PDAC using a combination of CECT and [18F]FDG-PET features, predicted significantly worse survival for hypoattenuating-high uptake pancreatic cancers compared to the other phenotypes.
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Affiliation(s)
- Deniece Riviere
- Department of Medical Imaging, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Erik Aarntzen
- Department of Medical Imaging, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Erwin van Geenen
- Department of Gastroenterology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - David Chang
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Bearsden, Glasgow, Scotland, United Kingdom; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, Scotland, United Kingdom
| | - Lioe-Fee de Geus-Oei
- Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Lodewijk Brosens
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Kees van Laarhoven
- Department of Surgery, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Martin Gotthardt
- Department of Medical Imaging, Radboud University Medical Center, Nijmegen, the Netherlands
| | - John Hermans
- Department of Medical Imaging, Radboud University Medical Center, Nijmegen, the Netherlands.
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10
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Heiling HM, Rashid NU, Li Q, Peng XL, Yeh JJ, Ibrahim JG. Efficient computation of high-dimensional penalized generalized linear mixed models by latent factor modeling of the random effects. Biometrics 2024; 80:ujae016. [PMID: 38497825 PMCID: PMC10946237 DOI: 10.1093/biomtc/ujae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 11/22/2023] [Accepted: 02/16/2024] [Indexed: 03/19/2024]
Abstract
Modern biomedical datasets are increasingly high-dimensional and exhibit complex correlation structures. Generalized linear mixed models (GLMMs) have long been employed to account for such dependencies. However, proper specification of the fixed and random effects in GLMMs is increasingly difficult in high dimensions, and computational complexity grows with increasing dimension of the random effects. We present a novel reformulation of the GLMM using a factor model decomposition of the random effects, enabling scalable computation of GLMMs in high dimensions by reducing the latent space from a large number of random effects to a smaller set of latent factors. We also extend our prior work to estimate model parameters using a modified Monte Carlo Expectation Conditional Minimization algorithm, allowing us to perform variable selection on both the fixed and random effects simultaneously. We show through simulation that through this factor model decomposition, our method can fit high-dimensional penalized GLMMs faster than comparable methods and more easily scale to larger dimensions not previously seen in existing approaches.
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Affiliation(s)
- Hillary M Heiling
- Department of Biostatistics, University of North Carolina Chapel Hill, Chapel Hill, NC 27599, United States
| | - Naim U Rashid
- Department of Biostatistics, University of North Carolina Chapel Hill, Chapel Hill, NC 27599, United States
| | - Quefeng Li
- Department of Biostatistics, University of North Carolina Chapel Hill, Chapel Hill, NC 27599, United States
| | - Xianlu L Peng
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Jen Jen Yeh
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- Department of Surgery, University of North Carolina Chapel Hill, Chapel Hill, NC 27599, United States
- Department of Pharmacology, University of North Carolina Chapel Hill, Chapel Hill, NC 27599, United States
| | - Joseph G Ibrahim
- Department of Biostatistics, University of North Carolina Chapel Hill, Chapel Hill, NC 27599, United States
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11
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van Goor IW, Schouten TJ, Verburg DN, Besselink MG, Bonsing BA, Bosscha K, Brosens LA, Busch OR, Cirkel GA, van Dam RM, Festen S, Koerkamp BG, van der Harst E, de Hingh IH, Intven MP, Kazemier G, Los M, Meijer GJ, de Meijer VE, Nieuwenhuijs VB, Roos D, Schreinemakers JM, Stommel MW, Verdonk RC, van Santvoort HC, Daamen LA, Molenaar IQ. Predicting Long-term Disease-free Survival After Resection of Pancreatic Ductal Adenocarcinoma: A Nationwide Cohort Study. Ann Surg 2024; 279:132-137. [PMID: 37450706 PMCID: PMC10727199 DOI: 10.1097/sla.0000000000006004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
OBJECTIVE To develop a prediction model for long-term (≥5 years) disease-free survival (DFS) after the resection of pancreatic ductal adenocarcinoma (PDAC). BACKGROUND Despite high recurrence rates, ~10% of patients have long-term DFS after PDAC resection. A model to predict long-term DFS may aid individualized prognostication and shared decision-making. METHODS This nationwide cohort study included all consecutive patients who underwent PDAC resection in the Netherlands (2014-2016). The best-performing prognostic model was selected by Cox-proportional hazard analysis and Akaike's Information Criterion, presented by hazard ratios (HRs) with 95% confidence intervals (CIs). Internal validation was performed, and discrimination and calibration indices were assessed. RESULTS In all, 836 patients with a median follow-up of 67 months (interquartile range 51-79) were analyzed. Long-term DFS was seen in 118 patients (14%). Factors predictive of long-term DFS were low preoperative carbohydrate antigen 19-9 (logarithmic; HR 1.21; 95% CI 1.10-1.32), no vascular resection (HR 1.33; 95% CI 1.12-1.58), T1 or T2 tumor stage (HR 1.52; 95% CI 1.14-2.04, and HR 1.17; 95% CI 0.98-1.39, respectively), well/moderate tumor differentiation (HR 1.44; 95% CI 1.22-1.68), absence of perineural and lymphovascular invasion (HR 1.42; 95% CI 1.11-1.81 and HR 1.14; 95% CI 0.96-1.36, respectively), N0 or N1 nodal status (HR 1.92; 95% CI 1.54-2.40, and HR 1.33; 95% CI 1.11-1.60, respectively), R0 resection margin status (HR 1.25; 95% CI 1.07-1.46), no major complications (HR 1.14; 95% CI 0.97-1.35) and adjuvant chemotherapy (HR 1.74; 95% CI 1.47-2.06). Moderate performance (concordance index 0.68) with adequate calibration (slope 0.99) was achieved. CONCLUSIONS The developed prediction model, readily available at www.pancreascalculator.com, can be used to estimate the probability of long-term DFS after resection of pancreatic ductal adenocarcinoma.
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Affiliation(s)
- Iris W.J.M. van Goor
- Department of Surgery, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & St. Antonius Hospital Nieuwegein, Utrecht, the Netherlands
- Department of Radiation Oncology, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center, Utrecht, the Netherlands
| | - Thijs J. Schouten
- Department of Surgery, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & St. Antonius Hospital Nieuwegein, Utrecht, the Netherlands
| | - Daphne N. Verburg
- Department of Surgery, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & St. Antonius Hospital Nieuwegein, Utrecht, the Netherlands
| | - Marc G. Besselink
- Department of Surgery, Amsterdam UMC, location University of Amsterdam, Amsterdam, the Netherlands
- Cancer Center Amsterdam, the Netherlands
| | - Bert A. Bonsing
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | - Koop Bosscha
- Department of Surgery, Jeroen Bosch Hospital, Den Bosch, the Netherlands
| | - Lodewijk A.A. Brosens
- Department of Pathology, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & St. Antonius Hospital Nieuwegein, Utrecht, the Netherlands
| | - Olivier R. Busch
- Department of Surgery, Amsterdam UMC, location University of Amsterdam, Amsterdam, the Netherlands
- Cancer Center Amsterdam, the Netherlands
| | - Geert A. Cirkel
- Department of Medical Oncology, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & Meander Medical Center Amersfoort, Utrecht, the Netherlands
| | | | | | - Bas Groot Koerkamp
- Department of Surgery, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | | | | | - Martijn P.W. Intven
- Department of Radiation Oncology, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center, Utrecht, the Netherlands
| | - Geert Kazemier
- Cancer Center Amsterdam, the Netherlands
- Department of Surgery, Amsterdam UMC, location Vrije Universiteit, Amsterdam, the Netherlands
| | - Maartje Los
- Department of Medical Oncology, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & St. Antonius Hospital Nieuwegein, Utrecht, the Netherlands
| | - Gert J. Meijer
- Department of Radiation Oncology, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center, Utrecht, the Netherlands
| | - Vincent E. de Meijer
- Department of Surgery, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Daphne Roos
- Department of Surgery, Renier de Graaf Gasthuis, Delft, the Netherlands
| | | | - Martijn W.J. Stommel
- Department of Surgery, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Robert C. Verdonk
- Department of Gastroenterology, Regional Academic Cancer Center Utrecht, Utrecht, the Netherlands
| | - Hjalmar C. van Santvoort
- Department of Surgery, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & St. Antonius Hospital Nieuwegein, Utrecht, the Netherlands
| | - Lois A. Daamen
- Department of Surgery, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & St. Antonius Hospital Nieuwegein, Utrecht, the Netherlands
- Imaging Division, University Medical Centre Utrecht, Utrecht University, Utrecht, the Netherlands
| | - I. Quintus Molenaar
- Department of Surgery, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & St. Antonius Hospital Nieuwegein, Utrecht, the Netherlands
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12
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Maurin M, Ranjouri M, Megino-Luque C, Newberg JY, Du D, Martin K, Miner RE, Prater MS, Wee DKB, Centeno B, Pruett-Miller SM, Stewart P, Fleming JB, Yu X, Bravo-Cordero JJ, Guccione E, Black MA, Mann KM. RBFOX2 deregulation promotes pancreatic cancer progression and metastasis through alternative splicing. Nat Commun 2023; 14:8444. [PMID: 38114498 PMCID: PMC10730836 DOI: 10.1038/s41467-023-44126-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 11/30/2023] [Indexed: 12/21/2023] Open
Abstract
RNA splicing is an important biological process associated with cancer initiation and progression. However, the contribution of alternative splicing to pancreatic cancer (PDAC) development is not well understood. Here, we identify an enrichment of RNA binding proteins (RBPs) involved in splicing regulation linked to PDAC progression from a forward genetic screen using Sleeping Beauty insertional mutagenesis in a mouse model of pancreatic cancer. We demonstrate downregulation of RBFOX2, an RBP of the FOX family, promotes pancreatic cancer progression and liver metastasis. Specifically, we show RBFOX2 regulates exon splicing events in transcripts encoding proteins involved in cytoskeletal remodeling programs. These exons are differentially spliced in PDAC patients, with enhanced exon skipping in the classical subtype for several RBFOX2 targets. RBFOX2 mediated splicing of ABI1, encoding the Abelson-interactor 1 adapter protein, controls the abundance and localization of ABI1 protein isoforms in pancreatic cancer cells and promotes the relocalization of ABI1 from the cytoplasm to the periphery of migrating cells. Using splice-switching antisense oligonucleotides (AONs) we demonstrate the ABI1 ∆Ex9 isoform enhances cell migration. Together, our data identify a role for RBFOX2 in promoting PDAC progression through alternative splicing regulation.
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Affiliation(s)
- Michelle Maurin
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | | | - Cristina Megino-Luque
- Division of Hematology and Oncology, Department of Medicine, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Justin Y Newberg
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Dongliang Du
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Katelyn Martin
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Robert E Miner
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Mollie S Prater
- Department of Cell and Molecular Biology and Center for Advanced Genome Engineering (CAGE), St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Dave Keng Boon Wee
- Institute for Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Republic of Singapore
| | - Barbara Centeno
- Department of Anatomic Pathology, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology and Center for Advanced Genome Engineering (CAGE), St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Paul Stewart
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Jason B Fleming
- Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Xiaoqing Yu
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Jose Javier Bravo-Cordero
- Division of Hematology and Oncology, Department of Medicine, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ernesto Guccione
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Therapeutics Discovery, Department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Michael A Black
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Karen M Mann
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL, 33612, USA.
- Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, FL, 33612, USA.
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13
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Utami AM, Halfwerk JBG, de Boer OJ, Mackaaij C, Pabittei DR, van der Horst CMAM, Meijer-Jorna LB, van der Wal AC. Relative expression of hormone receptors by endothelial and smooth muscle cells in proliferative and non-proliferative areas of congenital arteriovenous malformations. Eur J Med Res 2023; 28:449. [PMID: 37864259 PMCID: PMC10588228 DOI: 10.1186/s40001-023-01436-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 10/07/2023] [Indexed: 10/22/2023] Open
Abstract
BACKGROUND Episodic growth due to microvascular proliferations (MVP) has been reported in congenital arteriovenous malformations (AVM), which are normally quiescent lesions composed of mature malformed vessels. Since AVM also may worsen under conditions of hormonal dysregulation, we hypothesized that hormonal influences may stimulate this process of vasoproliferative growth through potential interactions with hormone receptors (HR). METHODS 13 Cases of AVM tissue with histologically documented vasoproliferative growth were analyzed quantitatively for the presence and tissue localization of estrogen receptor (ER), progesterone receptor (PGR), growth hormone receptor (GHR) and follicle-stimulating hormone receptor (FSHR) in relation to resident cells of interest (endothelial cells (EC), smooth muscle cells (SMC) and mast cells (MC)) by applying multiplex immunohistochemistry (IHC) staining. Expression patterns in lesions with MVP and mature vessels were quantified and compared. Available fresh frozen tissues of 3 AVM samples were used to confirm the presence of HR using Reverse-Transcriptase quantitative Polymerase Chain Reaction (RT-qPCR). RESULTS All four HR studied were expressed in all cases within EC and SMC in areas of MVP and mature vessels, but not in normal skin tissue. ER, GHR, and FSHR showed more expression in EC of MVP and in SMC of mature vessels. RT-qPCR confirmed presence of all 4 HR in both areas. CONCLUSION Expression of ER, PGR, GHR, and FSHR in vasoproliferative areas of congenital AVM could explain onset of sudden symptomatic growth, as has observed in a subpopulation of patients. These findings may have implications for eventual anti-hormonal targeted therapy in the lesions involved.
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Affiliation(s)
- A M Utami
- Department of Pathology, Amsterdam University Medical Center-Location AMC, University of Amsterdam, Amsterdam, The Netherlands.
- Department of Anatomical Pathology, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia.
| | - J B G Halfwerk
- Department of Pathology, Amsterdam University Medical Center-Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - O J de Boer
- Department of Pathology, Amsterdam University Medical Center-Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - C Mackaaij
- Department of Anatomy, University Medical Center Utrecht, Utrecht, The Netherlands
| | - D R Pabittei
- Department of Physiology, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia
| | - C M A M van der Horst
- Department of Plastic Surgery, Amsterdam University Medical Center-Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - L B Meijer-Jorna
- Symbiant Pathology Expert Center, NWZ- Noordwest Ziekenhuisgroep, Alkmaar, The Netherlands
| | - A C van der Wal
- Department of Pathology, Amsterdam University Medical Center-Location AMC, University of Amsterdam, Amsterdam, The Netherlands
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14
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Li J, D’Amico S, Kirillov V, Petrenko O, Reich NC. Oncogenic dependency plays a dominant role in the immune response to cancer. Proc Natl Acad Sci U S A 2023; 120:e2308635120. [PMID: 37782788 PMCID: PMC10576078 DOI: 10.1073/pnas.2308635120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/01/2023] [Indexed: 10/04/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest human malignancies. Advanced PDAC is considered incurable. Nearly 90% of pancreatic cancers are caused by oncogenic KRAS mutations. The mechanisms of primary or acquired resistance to KRAS inhibition are currently unknown. Here, we propose that oncogenic dependency, rather than KRAS mutation per se, plays a dominant role in the immune response to cancer, including late-stage PDAC. Classifying tumor samples according to KRAS activity scores allows accurate prediction of tumor immune composition and therapy response. Dual RAS/MAPK pathway blockade combining KRAS and MEK inhibitors is more effective than the selective KRAS inhibitor alone in attenuating MAPK activation and unblocking the influx of T cells into the tumor. Lowering KRAS activity in established tumors promotes immune infiltration, but with a limited antitumor effect, whereas combining KRAS/MEK inhibition with immune checkpoint blockade achieves durable regression in preclinical models. The results are directly applicable to stratifying human PDAC based on KRAS dependency values and immune cell composition to improve therapeutic design.
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Affiliation(s)
- Jinyu Li
- Department of Pathology, Stony Brook University, Stony Brook, NY11794
| | - Stephen D’Amico
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY11794
| | - Varvara Kirillov
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY11794
| | - Oleksi Petrenko
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY11794
| | - Nancy C. Reich
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY11794
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15
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D’Amico S, Kirillov V, Petrenko O, Reich NC. STAT3 is a genetic modifier of TGF-beta induced EMT in KRAS mutant pancreatic cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.01.555946. [PMID: 37732258 PMCID: PMC10508731 DOI: 10.1101/2023.09.01.555946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Oncogenic mutations in KRAS are among the most common in cancer. Classical models suggest that loss of epithelial characteristics and the acquisition of mesenchymal traits are associated with cancer aggressiveness and therapy resistance. However, the mechanistic link between these phenotypes and mutant KRAS biology remains to be established. Here we identify STAT3 as a genetic modifier of TGF-beta-induced epithelial to mesenchymal transition. Gene expression profiling of pancreatic cancer cells identifies more than 200 genes commonly regulated by STAT3 and oncogenic KRAS. Functional classification of STAT3 responsive program reveals its major role in tumor maintenance and epithelial homeostasis. The signatures of STAT3-activated cell states can be projected onto human KRAS mutant tumors, suggesting that they faithfully reflect characteristics of human disease. These observations have implications for therapeutic intervention and tumor aggressiveness.
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Affiliation(s)
- Stephen D’Amico
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Varvara Kirillov
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Oleksi Petrenko
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Nancy C. Reich
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY 11794, USA
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16
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Vallés-Martí A, Mantini G, Manoukian P, Waasdorp C, Sarasqueta AF, de Goeij-de Haas RR, Henneman AA, Piersma SR, Pham TV, Knol JC, Giovannetti E, Bijlsma MF, Jiménez CR. Phosphoproteomics guides effective low-dose drug combinations against pancreatic ductal adenocarcinoma. Cell Rep 2023; 42:112581. [PMID: 37269289 DOI: 10.1016/j.celrep.2023.112581] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 04/04/2023] [Accepted: 05/16/2023] [Indexed: 06/05/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with a limited set of known driver mutations but considerable cancer cell heterogeneity. Phosphoproteomics provides a readout of aberrant signaling and has the potential to identify new targets and guide treatment decisions. Using two-step sequential phosphopeptide enrichment, we generate a comprehensive phosphoproteome and proteome of nine PDAC cell lines, encompassing more than 20,000 phosphosites on 5,763 phospho-proteins, including 316 protein kinases. By using integrative inferred kinase activity (INKA) scoring, we identify multiple (parallel) activated kinases that are subsequently matched to kinase inhibitors. Compared with high-dose single-drug treatments, INKA-tailored low-dose 3-drug combinations against multiple targets demonstrate superior efficacy against PDAC cell lines, organoid cultures, and patient-derived xenografts. Overall, this approach is particularly more effective against the aggressive mesenchymal PDAC model compared with the epithelial model in both preclinical settings and may contribute to improved treatment outcomes in PDAC patients.
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Affiliation(s)
- Andrea Vallés-Martí
- Amsterdam University Medical Center, VU University, Department of Medical Oncology, Amsterdam, the Netherlands; Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands; Cancer Center Amsterdam, Pharmacology Laboratory, Amsterdam, the Netherlands
| | - Giulia Mantini
- Amsterdam University Medical Center, VU University, Department of Medical Oncology, Amsterdam, the Netherlands; Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, the Netherlands; Cancer Center Amsterdam, Pharmacology Laboratory, Amsterdam, the Netherlands; Cancer Pharmacology Lab, AIRC Start-Up Unit, Fondazione Pisana per la Scienza, San Giuliano Terme, Pisa, Italy
| | - Paul Manoukian
- Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands; Amsterdam University Medical Center, University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands
| | - Cynthia Waasdorp
- Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands; Amsterdam University Medical Center, University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands
| | | | - Richard R de Goeij-de Haas
- Amsterdam University Medical Center, VU University, Department of Medical Oncology, Amsterdam, the Netherlands; Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, the Netherlands
| | - Alex A Henneman
- Amsterdam University Medical Center, VU University, Department of Medical Oncology, Amsterdam, the Netherlands; Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, the Netherlands
| | - Sander R Piersma
- Amsterdam University Medical Center, VU University, Department of Medical Oncology, Amsterdam, the Netherlands; Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, the Netherlands
| | - Thang V Pham
- Amsterdam University Medical Center, VU University, Department of Medical Oncology, Amsterdam, the Netherlands; Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, the Netherlands
| | - Jaco C Knol
- Amsterdam University Medical Center, VU University, Department of Medical Oncology, Amsterdam, the Netherlands; Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, the Netherlands
| | - Elisa Giovannetti
- Amsterdam University Medical Center, VU University, Department of Medical Oncology, Amsterdam, the Netherlands; Cancer Center Amsterdam, Pharmacology Laboratory, Amsterdam, the Netherlands; Cancer Pharmacology Lab, AIRC Start-Up Unit, Fondazione Pisana per la Scienza, San Giuliano Terme, Pisa, Italy
| | - Maarten F Bijlsma
- Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands; Amsterdam University Medical Center, University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands
| | - Connie R Jiménez
- Amsterdam University Medical Center, VU University, Department of Medical Oncology, Amsterdam, the Netherlands; Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, the Netherlands.
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17
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Bärthel S, Falcomatà C, Rad R, Theis FJ, Saur D. Single-cell profiling to explore pancreatic cancer heterogeneity, plasticity and response to therapy. NATURE CANCER 2023; 4:454-467. [PMID: 36959420 DOI: 10.1038/s43018-023-00526-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 02/08/2023] [Indexed: 03/25/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer entity characterized by a heterogeneous genetic landscape and an immunosuppressive tumor microenvironment. Recent advances in high-resolution single-cell sequencing and spatial transcriptomics technologies have enabled an in-depth characterization of both malignant and host cell types and increased our understanding of the heterogeneity and plasticity of PDAC in the steady state and under therapeutic perturbation. In this Review we outline single-cell analyses in PDAC, discuss their implications on our understanding of the disease and present future perspectives of multimodal approaches to elucidate its biology and response to therapy at the single-cell level.
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Affiliation(s)
- Stefanie Bärthel
- Division of Translational Cancer Research, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
- Institute of Experimental Cancer Therapy, Klinikum Rechts der Isar, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Chiara Falcomatà
- Division of Translational Cancer Research, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
- Institute of Experimental Cancer Therapy, Klinikum Rechts der Isar, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Roland Rad
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- German Cancer Consortium Partner Site Munich, Munich, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- School of Computation, Information and Technology (CIT), Technische Universität München, Munich, Germany
| | - Dieter Saur
- Division of Translational Cancer Research, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany.
- Institute of Experimental Cancer Therapy, Klinikum Rechts der Isar, School of Medicine, Technische Universität München, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany.
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18
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Bootsma S, Bijlsma MF, Vermeulen L. The molecular biology of peritoneal metastatic disease. EMBO Mol Med 2023; 15:e15914. [PMID: 36700339 PMCID: PMC9994485 DOI: 10.15252/emmm.202215914] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 01/27/2023] Open
Abstract
Peritoneal metastases are a common form of tumor cell dissemination in gastrointestinal malignancies. Peritoneal metastatic disease (PMD) is associated with severe morbidity and resistance to currently employed therapies. Given the distinct route of dissemination compared with distant organ metastases, and the unique microenvironment of the peritoneal cavity, specific tumor cell characteristics are needed for the development of PMD. In this review, we provide an overview of the known histopathological, genomic, and transcriptomic features of PMD. We find that cancers representing the mesenchymal subtype are strongly associated with PMD in various malignancies. Furthermore, we discuss the peritoneal niche in which the metastatic cancer cells reside, including the critical role of the peritoneal immune system. Altogether, we show that PMD should be regarded as a distinct disease entity, that requires tailored treatment strategies.
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Affiliation(s)
- Sanne Bootsma
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular MedicineAmsterdam UMC, Location University of AmsterdamAmsterdamThe Netherlands
- Cancer Center Amsterdam, Cancer BiologyAmsterdamThe Netherlands
- Amsterdam Gastroenterology Endocrinology MetabolismAmsterdamThe Netherlands
- Oncode InstituteAmsterdamThe Netherlands
| | - Maarten F Bijlsma
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular MedicineAmsterdam UMC, Location University of AmsterdamAmsterdamThe Netherlands
- Cancer Center Amsterdam, Cancer BiologyAmsterdamThe Netherlands
- Amsterdam Gastroenterology Endocrinology MetabolismAmsterdamThe Netherlands
- Oncode InstituteAmsterdamThe Netherlands
| | - Louis Vermeulen
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular MedicineAmsterdam UMC, Location University of AmsterdamAmsterdamThe Netherlands
- Cancer Center Amsterdam, Cancer BiologyAmsterdamThe Netherlands
- Amsterdam Gastroenterology Endocrinology MetabolismAmsterdamThe Netherlands
- Oncode InstituteAmsterdamThe Netherlands
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19
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Lansbergen MF, Khelil M, Etten-Jamaludin FSV, Bijlsma MF, van Laarhoven HWM. Poor-prognosis molecular subtypes in adenocarcinomas of pancreato-biliary and gynecological origin: A systematic review. Crit Rev Oncol Hematol 2023; 185:103982. [PMID: 37004743 DOI: 10.1016/j.critrevonc.2023.103982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 04/03/2023] Open
Abstract
Pancreato-biliary and gynecological adenocarcinomas need better tools to predict clinical outcome. Potential prognostic mesenchymal(-like) transcriptome-based subtypes have been identified in these cancers. In this systematic review, we include studies into molecular subtyping and summarize biological and clinical features of the subtypes within and across sites of origin, searching for suggestions to improve classification and prognostication. PubMed and Embase were searched for original research articles describing potential mesenchymal(-like) mRNA-based subtypes in pancreato-biliary or gynecological adenocarcinomas. Studies limited to supervised clustering were excluded. Fourty-four studies, discussing cholangiocarcinomas, gallbladder, ampullary, pancreatic, ovarian, and endometrial adenocarcinomas were included. There was overlap in molecular and clinical features in mesenchymal(-like) subtypes across all adenocarcinomas. Approaches including microdissection were more likely to identify prognosis-associating subtypes. To conclude, molecular subtypes in pancreato-biliary and gynecological adenocarcinomas share biological and clinical characteristics. Furthermore, separation of stromal and epithelial signals should be applied in future studies into biliary and gynecological adenocarcinomas.
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Affiliation(s)
- Marjolein F Lansbergen
- Amsterdam UMC location University of Amsterdam, Medical Oncology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Amsterdam UMC location University of Amsterdam, Center for Experimental Molecular Medicine, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, the Netherlands.
| | - Maryam Khelil
- University of Amsterdam, Spui 21, 1012 WX Amsterdam, the Netherlands
| | - Faridi S van Etten-Jamaludin
- Amsterdam UMC location University of Amsterdam, Research Support Medical Library, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Maarten F Bijlsma
- Amsterdam UMC location University of Amsterdam, Center for Experimental Molecular Medicine, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, the Netherlands; Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands
| | - Hanneke W M van Laarhoven
- Amsterdam UMC location University of Amsterdam, Medical Oncology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, the Netherlands
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20
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Dings MPG, Manoukian P, Waasdorp C, Quik JSE, Strijker M, Lodestijn SC, van Neerven SM, Moreno LF, de Oliveira RL, Bonsing BA, Bruno MJ, Busch OR, Doukas M, van Eijck CH, Mohammad NH, de Hingh IH, Molenaar QI, Besselink MG, Vermeulen L, Medema JP, van Laarhoven HWM, Bijlsma MF. Serum levels of iCAF-derived osteoglycin predict favorable outcome in pancreatic cancer. Int J Cancer 2023; 152:511-523. [PMID: 36069222 PMCID: PMC10087204 DOI: 10.1002/ijc.34276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/29/2022] [Accepted: 08/18/2022] [Indexed: 02/01/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is characterized by abundant stroma, the main cellular constituents of which are cancer-associated fibroblasts (CAFs). Stroma-targeting agents have been proposed to improve the poor outcome of current treatments. However, clinical trials using these agents showed disappointing results. Heterogeneity in the PDAC CAF population was recently delineated demonstrating that both tumor-promoting and tumor-suppressive activities co-exist in the stroma. Here, we aimed to identify biomarkers for the CAF population that contribute to a favorable outcome. RNA-sequencing reads from patient-derived xenografts (PDXs) were mapped to the human and mouse genome to allocate the expression of genes to the tumor or stroma. Survival meta-analysis for stromal genes was performed and applied to human protein atlas data to identify circulating biomarkers. The candidate protein was perturbed in co-cultures and assessed in existing and novel single-cell gene expression analysis from control, pancreatitis, pancreatitis-recovered and PDAC mouse models. Serum levels of the candidate biomarker were measured in two independent cohorts totaling 148 PDAC patients and related them to overall survival. Osteoglycin (OGN) was identified as a candidate serum prognostic marker. Single-cell analysis indicated that Ogn is derived from a subgroup of inflammatory CAFs. Ogn-expressing fibroblasts are distinct from resident healthy pancreatic stellate cells and arise during pancreatitis. Serum OGN levels were prognostic for favorable overall survival in two independent PDAC cohorts (HR = 0.47, P = .042 and HR = 0.53, P = .006). Altogether, we conclude that high circulating OGN levels inform on a previously unrecognized subgroup of CAFs and predict favorable outcomes in resectable PDAC.
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Affiliation(s)
- Mark P G Dings
- Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Paul Manoukian
- Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Cynthia Waasdorp
- Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Judith S E Quik
- Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Marin Strijker
- Department of Surgery, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Sophie C Lodestijn
- Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Sanne M van Neerven
- Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Leandro F Moreno
- Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Rodrigo Leite de Oliveira
- Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands.,CRISPR Expertise Center, Cancer Center Amsterdam, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Bert A Bonsing
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Marco J Bruno
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Olivier R Busch
- Department of Surgery, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Michael Doukas
- Department of Pathology, Erasmus MC-University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Casper H van Eijck
- Department of Surgery, Erasmus MC-University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Nadia Haj Mohammad
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Ignace H de Hingh
- Department of Surgery, Catharina Hospital, Eindhoven, The Netherlands
| | - Quintus I Molenaar
- Department of Surgery, Regional Academic Cancer Center Utrecht, University Medical Center Utrecht and St Antonius Hospital, Nieuwegein, The Netherlands
| | - Marc G Besselink
- Department of Surgery, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Louis Vermeulen
- Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Jan Paul Medema
- Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Hanneke W M van Laarhoven
- Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands.,Department of Medical Oncology, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Maarten F Bijlsma
- Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
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21
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An Immunogenic Cell Death-Related Gene Signature Reflects Immune Landscape and Predicts Prognosis in Melanoma Independently of BRAF V600E Status. BIOMED RESEARCH INTERNATIONAL 2023; 2023:1189022. [PMID: 36704723 PMCID: PMC9871414 DOI: 10.1155/2023/1189022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/26/2022] [Accepted: 12/29/2022] [Indexed: 01/18/2023]
Abstract
Immunogenic cell death (ICD) is a type of regulated cell death that can activate adaptive immune response, and its ability to reshape the tumor microenvironment via multiple mechanisms may contribute to immunotherapy. The treatment options for patients with skin cutaneous melanoma (SKCM) vary based on BRAF V600E statuses. However, all standard treatments include immunotherapy. Therefore, it is critical to identify ICD-associated signatures that can help classify patients according to benefits from ICD immunotherapy. In this study, data on melanoma samples with BRAF V600E mutation (BRAF V600E-mutant melanoma) and melanoma samples with wild-type BRAF V600E alleles (BRAF V600E WT melanoma) were collected from The Cancer Genome Atlas (TCGA) database. The ICD-related (ICD-high and ICD-low) subgroups of patients with BRAF V600E WT melanoma were established via consensus clustering. The analyses of survival, differentially expressed genes (DEGs), functional annotation, and immune landscape were performed in these two subgroups. Results showed that ICD-high subgroup was correlated with a positive overall survival (OS) and active tumor immune landscape. A model comprising seven prognosis ICD-related gene biomarkers was developed. Survival analysis and receiver operating characteristic (ROC) curve evaluation in both cohorts with BRAF V600E WT and BRAF V600E-mutant melanoma showed an accurate prognostic estimation of ICD-related risk signature. There was a correlation between immune cell infiltration and immunotherapy response and risk score. Thus, the ICD risk signature was closely associated with the tumor's immune microenvironment. Our results may provide insights to further individualize and improve precision therapeutic decision-making in BRAF V600E-mutant and WT melanoma.
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22
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LaPlante EL, Liu D, Petrosyan V, Yao Q, Milosavljevic A. XDec-CHI reveals immunosuppressive interactions in pancreatic ductal adenocarcinoma. iScience 2022; 25:105249. [PMID: 36274954 PMCID: PMC9579012 DOI: 10.1016/j.isci.2022.105249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 07/27/2022] [Accepted: 09/26/2022] [Indexed: 11/21/2022] Open
Abstract
Most cancers harbor a diverse collection of cell types including a typically heterogeneous cancer cell fraction. To reconstruct cell-intrinsic and heterotypic interactions driving tumor progression, we combine the XDec deconvolution method with cell-type-specific gene expression correlation analysis into the XDec-CHI method. XDec-CHI identifies intra- and inter-cellular pathways using correlation and places them in the context of specific tumor subtypes, as defined by the state of constituent cancer cells. We make the method web-accessible for analysis of publicly accessible pancreatic ductal adenocarcinoma, breast, head and neck, glioblastoma, and glioma tumors. We apply the method to TCGA and ICGC datasets to identify immune-suppressive interactions within PDAC tumors that are relevant for immunotherapies targeting PD-L1. Subtype-specific interactions derived from correlative analyses validated in co-culture experiments suggest PDAC subtypes have distinct therapeutic weaknesses, with Basal-like and MSLN-high Classical B tumors most likely to respond to therapies targeting PD-L1.
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Affiliation(s)
- Emily L. LaPlante
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dongliang Liu
- Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX, USA
| | - Varduhi Petrosyan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qizhi Yao
- Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX, USA
- Center for Translational Research on Inflammatory Diseases (CTRID), Michael E. DeBakey VA Medical Center, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Aleksandar Milosavljevic
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
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23
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Suurmeijer JA, Soer EC, Dings MPG, Kim Y, Strijker M, Bonsing BA, Brosens LAA, Busch OR, Groen JV, Halfwerk JB, Slooff RAE, van Laarhoven HWM, Molenaar IQ, Offerhaus GJA, Morreau H, van de Vijver MJ, Fariña Sarasqueta A, Verheij J, Besselink MG, Bijlsma MF, Dijk F. Impact of classical and basal-like molecular subtypes on overall survival in resected pancreatic cancer in the SPACIOUS-2 multicentre study. Br J Surg 2022; 109:1150-1155. [PMID: 35979597 PMCID: PMC10364758 DOI: 10.1093/bjs/znac272] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/30/2022] [Accepted: 07/15/2022] [Indexed: 08/02/2023]
Abstract
BACKGROUND The recently identified classical and basal-like molecular subtypes of pancreatic cancer impact on overall survival (OS). However, the added value of routine subtyping in both clinical practice and randomized trials is still unclear, as most studies do not consider clinicopathological parameters. This study examined the clinical prognostic value of molecular subtyping in patients with resected pancreatic cancer. METHODS Subtypes were determined on fresh-frozen resected pancreatic cancer samples from three Dutch centres using the Purity Independent Subtyping of Tumours classification. Patient, treatment, and histopathological variables were compared between subtypes. The prognostic value of subtyping in (simulated) pre- and postoperative settings was assessed using Kaplan-Meier and Cox regression analyses. RESULTS Of 199 patients with resected pancreatic cancer, 164 (82.4 per cent) were classified as the classical and 35 (17.6 per cent) as the basal-like subtype. Patients with a basal-like subtype had worse OS (11 versus 16 months (HR 1.49, 95 per cent c.i. 1.03 to 2.15; P = 0.035)) than patients with a classical subtype. In multivariable Cox regression analysis, including only clinical variables, the basal-like subtype was a statistically significant predictor for poor OS (HR 1.61, 95 per cent c.i. 1.11 to 2.34; P = 0.013). When histopathological variables were added to this model, the prognostic value of subtyping decreased (HR 1.49, 95 per cent c.i. 1.01 to 2.19; P = 0.045). CONCLUSION The basal-like subtype was associated with worse OS in patients with resected pancreatic cancer. Adding molecular classification to inform on tumor biology may be used in patient stratification.
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Affiliation(s)
- J Annelie Suurmeijer
- *Correspondence to: Frederike Dijk, Department of Pathology, Amsterdam UMC, University of Amsterdam, Cancer Center Amsterdam, Meibergdreef 9 (AMC hospital), 1105 AZ Amsterdam, The Netherlands (e-mail: ); Marc Gerard Besselink, Department of Surgery, Amsterdam UMC, University of Amsterdam, Cancer Center Amsterdam, De Boelelaan 1117 (VUMC Hospital, ZH-7F), 1081 HV Amsterdam, The Netherlands (e-mail: )
| | - Eline C Soer
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Department of Pathology, Amsterdam UMC, location University of Amsterdam, Amsterdam, The Netherlands
| | - Mark P G Dings
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam UMC, location University of Amsterdam, Amsterdam, The Netherlands
| | - Yongsoo Kim
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Department of Pathology, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Marin Strijker
- Department of Surgery, Amsterdam UMC, location University of Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Bert A Bonsing
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Lodewijk A A Brosens
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
- Faculty of Medicine, Utrecht University, Utrecht, The Netherlands
| | - Olivier R Busch
- Department of Surgery, Amsterdam UMC, location University of Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Jesse V Groen
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Johannes B Halfwerk
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Department of Pathology, Amsterdam UMC, location University of Amsterdam, Amsterdam, The Netherlands
| | - Robbert A E Slooff
- Department of Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Hanneke W M van Laarhoven
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Department of Medical Oncology, Amsterdam UMC, location University of Amsterdam, Amsterdam, The Netherlands
| | - I Quintus Molenaar
- Regional Academic Cancer Center Utrecht, Department of Hepato-Pancreato-Biliary Surgery, St. Antonius Hospital Nieuwegein & University Medical Center Utrecht, Utrecht, The Netherlands
| | - G Johan A Offerhaus
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
- Faculty of Medicine, Utrecht University, Utrecht, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marc J van de Vijver
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Department of Pathology, Amsterdam UMC, location University of Amsterdam, Amsterdam, The Netherlands
| | - Arantza Fariña Sarasqueta
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Department of Pathology, Amsterdam UMC, location University of Amsterdam, Amsterdam, The Netherlands
| | - Joanne Verheij
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Department of Pathology, Amsterdam UMC, location University of Amsterdam, Amsterdam, The Netherlands
| | - Marc G Besselink
- *Correspondence to: Frederike Dijk, Department of Pathology, Amsterdam UMC, University of Amsterdam, Cancer Center Amsterdam, Meibergdreef 9 (AMC hospital), 1105 AZ Amsterdam, The Netherlands (e-mail: ); Marc Gerard Besselink, Department of Surgery, Amsterdam UMC, University of Amsterdam, Cancer Center Amsterdam, De Boelelaan 1117 (VUMC Hospital, ZH-7F), 1081 HV Amsterdam, The Netherlands (e-mail: )
| | - Maarten F Bijlsma
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam UMC, location University of Amsterdam, Amsterdam, The Netherlands
| | - Frederike Dijk
- *Correspondence to: Frederike Dijk, Department of Pathology, Amsterdam UMC, University of Amsterdam, Cancer Center Amsterdam, Meibergdreef 9 (AMC hospital), 1105 AZ Amsterdam, The Netherlands (e-mail: ); Marc Gerard Besselink, Department of Surgery, Amsterdam UMC, University of Amsterdam, Cancer Center Amsterdam, De Boelelaan 1117 (VUMC Hospital, ZH-7F), 1081 HV Amsterdam, The Netherlands (e-mail: )
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24
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Chijimatsu R, Kobayashi S, Takeda Y, Kitakaze M, Tatekawa S, Arao Y, Nakayama M, Tachibana N, Saito T, Ennishi D, Tomida S, Sasaki K, Yamada D, Tomimaru Y, Takahashi H, Okuzaki D, Motooka D, Ohshiro T, Taniguchi M, Suzuki Y, Ogawa K, Mori M, Doki Y, Eguchi H, Ishii H. Establishment of a reference single-cell RNA sequencing dataset for human pancreatic adenocarcinoma. iScience 2022; 25:104659. [PMID: 35847558 PMCID: PMC9283889 DOI: 10.1016/j.isci.2022.104659] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/14/2022] [Accepted: 06/17/2022] [Indexed: 11/28/2022] Open
Abstract
Single-cell RNA sequencing (scRNAseq) has been used to assess the intra-tumor heterogeneity and microenvironment of pancreatic ductal adenocarcinoma (PDAC). However, previous knowledge is not fully universalized. Here, we built a single cell atlas of PDAC from six datasets containing over 70 samples and >130,000 cells, and demonstrated its application to the reanalysis of the previous bulk transcriptomic cohorts and inferring cell-cell communications. The cell decomposition of bulk transcriptomics using scRNAseq data showed the cellular heterogeneity of PDAC; moreover, high levels of tumor cells and fibroblasts were indicative of poor-prognosis. Refined tumor subtypes signature indicated the tumor cell dynamics in intra-tumor and their specific regulatory network. We further identified functionally distinct tumor clusters that had close interaction with fibroblast subtypes via different signaling pathways dependent on subtypes. Our analysis provided a reference dataset for PDAC and showed its utility in research on the microenvironment of intra-tumor heterogeneity.
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Affiliation(s)
- Ryota Chijimatsu
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan
- Center for Comprehensive Genomic Medicine, Okayama University Hospital, Shikata-cho, Kita-ku, Okayama 700-8558, Japan
| | - Shogo Kobayashi
- Department of Gastroenterology, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan
| | - Yu Takeda
- Department of Gastroenterology, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan
| | - Masatoshi Kitakaze
- Department of Gastroenterology, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan
| | - Shotaro Tatekawa
- Department of Radiation Oncology, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan
| | - Yasuko Arao
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan
| | - Mika Nakayama
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan
| | - Naohiro Tachibana
- Department of Orthopaedic Surgery, Section of Sensory and Motor System Medicine, Graduate School of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Taku Saito
- Department of Orthopaedic Surgery, Section of Sensory and Motor System Medicine, Graduate School of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Daisuke Ennishi
- Center for Comprehensive Genomic Medicine, Okayama University Hospital, Shikata-cho, Kita-ku, Okayama 700-8558, Japan
| | - Shuta Tomida
- Center for Comprehensive Genomic Medicine, Okayama University Hospital, Shikata-cho, Kita-ku, Okayama 700-8558, Japan
| | - Kazuki Sasaki
- Department of Gastroenterology, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan
| | - Daisaku Yamada
- Department of Gastroenterology, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan
| | - Yoshito Tomimaru
- Department of Gastroenterology, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan
| | - Hidenori Takahashi
- Department of Gastroenterology, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Takahito Ohshiro
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Osaka, Ibaraki 567-0047, Japan
| | - Masateru Taniguchi
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Osaka, Ibaraki 567-0047, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa-shi, Chiba 272-8562, Japan
| | - Kazuhiko Ogawa
- Department of Radiation Oncology, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan
| | - Masaki Mori
- Department of Gastroenterology, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan
- Tokai University Graduate School of Medicine, Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Yuichiro Doki
- Department of Gastroenterology, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan
| | - Hidetoshi Eguchi
- Department of Gastroenterology, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan
| | - Hideshi Ishii
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan
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25
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Park J, Barahona‐Torres N, Jang S, Mok KY, Kim HJ, Han S, Cho K, Zhou X, Fu AKY, Ip NY, Seo J, Choi M, Jeong H, Hwang D, Lee DY, Byun MS, Yi D, Han JW, Mook‐Jung I, Hardy J. Multi-Omics-Based Autophagy-Related Untypical Subtypes in Patients with Cerebral Amyloid Pathology. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2201212. [PMID: 35694866 PMCID: PMC9376815 DOI: 10.1002/advs.202201212] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/26/2022] [Indexed: 05/05/2023]
Abstract
Recent multi-omics analyses paved the way for a comprehensive understanding of pathological processes. However, only few studies have explored Alzheimer's disease (AD) despite the possibility of biological subtypes within these patients. For this study, unsupervised classification of four datasets (genetics, miRNA transcriptomics, proteomics, and blood-based biomarkers) using Multi-Omics Factor Analysis+ (MOFA+), along with systems-biological approaches following various downstream analyses are performed. New subgroups within 170 patients with cerebral amyloid pathology (Aβ+) are revealed and the features of them are identified based on the top-rated targets constructing multi-omics factors of both whole (M-TPAD) and immune-focused models (M-IPAD). The authors explored the characteristics of subtypes and possible key-drivers for AD pathogenesis. Further in-depth studies showed that these subtypes are associated with longitudinal brain changes and autophagy pathways are main contributors. The significance of autophagy or clustering tendency is validated in peripheral blood mononuclear cells (PBMCs; n = 120 including 30 Aβ- and 90 Aβ+), induced pluripotent stem cell-derived human brain organoids/microglia (n = 12 including 5 Aβ-, 5 Aβ+, and CRISPR-Cas9 apolipoprotein isogenic lines), and human brain transcriptome (n = 78). Collectively, this study provides a strategy for precision medicine therapy and drug development for AD using integrative multi-omics analysis and network modelling.
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Affiliation(s)
- Jong‐Chan Park
- Department of Neurodegenerative DiseaseUCL Queen Square Institute of NeurologyUniversity College LondonLondonWC1N 3BGUK
- Department of Biochemistry and Biomedical SciencesCollege of MedicineSeoul National UniversitySeoul03080Republic of Korea
- Neuroscience Research InstituteMedical Research CenterCollege of MedicineSeoul National UniversitySeoul03080Republic of Korea
- SNU Korea Dementia Research CenterCollege of MedicineSeoul National UniversitySeoul03080Republic of Korea
| | - Natalia Barahona‐Torres
- Department of Neurodegenerative DiseaseUCL Queen Square Institute of NeurologyUniversity College LondonLondonWC1N 3BGUK
| | - So‐Yeong Jang
- Department of Bio and Brain EngineeringKorea Advanced Institute of Science and TechnologyDaejeon34141Republic of Korea
| | - Kin Y. Mok
- Department of Neurodegenerative DiseaseUCL Queen Square Institute of NeurologyUniversity College LondonLondonWC1N 3BGUK
| | - Haeng Jun Kim
- Department of Biochemistry and Biomedical SciencesCollege of MedicineSeoul National UniversitySeoul03080Republic of Korea
- SNU Korea Dementia Research CenterCollege of MedicineSeoul National UniversitySeoul03080Republic of Korea
| | - Sun‐Ho Han
- Department of Biochemistry and Biomedical SciencesCollege of MedicineSeoul National UniversitySeoul03080Republic of Korea
- Neuroscience Research InstituteMedical Research CenterCollege of MedicineSeoul National UniversitySeoul03080Republic of Korea
- SNU Korea Dementia Research CenterCollege of MedicineSeoul National UniversitySeoul03080Republic of Korea
| | - Kwang‐Hyun Cho
- Department of Bio and Brain EngineeringKorea Advanced Institute of Science and TechnologyDaejeon34141Republic of Korea
| | - Xiaopu Zhou
- Division of Life ScienceState Key Laboratory of Molecular NeuroscienceMolecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water Bay, KowloonHong Kong999077China
- Hong Kong Center for Neurodegenerative DiseasesHong Kong Science ParkHong Kong999077China
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhen‐Hong Kong Institute of Brain ScienceShenzhenGuangdong518057China
| | - Amy K. Y. Fu
- Division of Life ScienceState Key Laboratory of Molecular NeuroscienceMolecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water Bay, KowloonHong Kong999077China
- Hong Kong Center for Neurodegenerative DiseasesHong Kong Science ParkHong Kong999077China
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhen‐Hong Kong Institute of Brain ScienceShenzhenGuangdong518057China
| | - Nancy Y. Ip
- Division of Life ScienceState Key Laboratory of Molecular NeuroscienceMolecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water Bay, KowloonHong Kong999077China
- Hong Kong Center for Neurodegenerative DiseasesHong Kong Science ParkHong Kong999077China
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhen‐Hong Kong Institute of Brain ScienceShenzhenGuangdong518057China
| | - Jieun Seo
- Department of Laboratory MedicineSeverance HospitalYonsei University College of MedicineSeoul03722Republic of Korea
| | - Murim Choi
- Department of Biochemistry and Biomedical SciencesCollege of MedicineSeoul National UniversitySeoul03080Republic of Korea
| | - Hyobin Jeong
- European Molecular Biology LaboratoryGenome Biology UnitHeidelberg69117Germany
| | - Daehee Hwang
- Department of Biological SciencesSeoul National UniversitySeoul08826Republic of Korea
| | - Dong Young Lee
- Institute of Human Behavioral MedicineMedical Research CenterSeoul National UniversitySeoul03080Republic of Korea
- Department of PsychiatryCollege of medicineSeoul National UniversitySeoul03080Republic of Korea
- Department of NeuropsychiatrySeoul National University HospitalSeoul03080Republic of Korea
| | - Min Soo Byun
- Department of PsychiatryPusan National University Yangsan HospitalYangsan50612Republic of Korea
| | - Dahyun Yi
- Biomedical Research InstituteSeoul National University HospitalSeoul03082Republic of Korea
| | - Jong Won Han
- Department of Biochemistry and Biomedical SciencesCollege of MedicineSeoul National UniversitySeoul03080Republic of Korea
| | - Inhee Mook‐Jung
- Department of Biochemistry and Biomedical SciencesCollege of MedicineSeoul National UniversitySeoul03080Republic of Korea
- Neuroscience Research InstituteMedical Research CenterCollege of MedicineSeoul National UniversitySeoul03080Republic of Korea
- SNU Korea Dementia Research CenterCollege of MedicineSeoul National UniversitySeoul03080Republic of Korea
| | - John Hardy
- Department of Neurodegenerative DiseaseUCL Queen Square Institute of NeurologyUniversity College LondonLondonWC1N 3BGUK
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26
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Pijnappel EN, Suurmeijer JA, Koerkamp BG, Kos M, Siveke JT, Salvia R, Ghaneh P, van Eijck CHJ, van Etten-Jamaludin FS, Abrams R, Brasiuniene B, Büchler MW, Casadei R, van Laethem JL, Berlin J, Boku N, Conroy T, Golcher H, Sinn M, Neoptolemos JP, van Tienhoven G, Besselink MG, Wilmink JW, van Laarhoven HWM. Consensus Statement on Mandatory Measurements for Pancreatic Cancer Trials for Patients With Resectable or Borderline Resectable Disease (COMM-PACT-RB): A Systematic Review and Delphi Consensus Statement. JAMA Oncol 2022; 8:929-937. [PMID: 35446336 DOI: 10.1001/jamaoncol.2022.0168] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Importance Pancreatic cancer is the third most common cause of cancer death; however, randomized clinical trials (RCTs) of survival in patients with resectable pancreatic cancer lack mandatory measures for reporting baseline and prognostic factors, which hampers comparisons between outcome measures. Objective To develop a consensus on baseline and prognostic factors to be used as mandatory measurements in RCTs of resectable and borderline resectable pancreatic cancer. Evidence Review We performed a systematic literature search of the Cochrane Central Register of Controlled Trials (CENTRAL), PubMed, and Embase for RCTs on resectable and borderline resectable pancreatic cancer with overall survival as the primary outcome. We produced a systematic summary of all baseline and prognostic factors identified in the RCTs. A Delphi panel that included 13 experts was surveyed to reach a consensus on mandatory and recommended baseline and prognostic factors. Findings The 42 RCTs that met inclusion criteria reported a total of 60 baseline and 19 prognostic factors. After 2 Delphi rounds, agreement was reached on 50 mandatory baseline and 20 mandatory prognostic factors for future RCTs, with a distinction between studies of neoadjuvant vs adjuvant treatment. Conclusion and Relevance This findings of this systematic review and international expert consensus have produced this Consensus Statement on Mandatory Measurements in Pancreatic Cancer Trials for Resectable and Borderline Resectable Disease (COMM-PACT-RB). The baseline and prognostic factors comprising the mandatory measures will facilitate better comparison across RCTs and eventually will enable improved clinical practice among patients with resectable and borderline resectable pancreatic cancer.
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Affiliation(s)
- Esther N Pijnappel
- Department of Medical Oncology, Cancer Center, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - J Annelie Suurmeijer
- Department of Surgery, Cancer Center, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Bas Groot Koerkamp
- Department of Surgery, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Milan Kos
- Department of Medical Oncology, Cancer Center, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Jens T Siveke
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Medicine Essen, Essen, Germany
- Division of Solid Tumor Translational Oncology, German Cancer Consortium and German Cancer Research Center, Heidelberg, Germany
| | | | - Paula Ghaneh
- Department of Molecular and Clinical Cancer Medicine University of Liverpool, Liverpool, UK
| | | | | | - Ross Abrams
- Sharett Institute of Oncology, Hadassah Medical Center, Jerusalem, Israel
| | - Birute Brasiuniene
- Department of Medical Oncology, National Cancer Institute, Faculty of Medicine, Vilnius University, Lithuania
| | - Markus W Büchler
- Department of General Surgery, University of Heidelberg, Heidelberg, Germany
| | | | - Jean-Luc van Laethem
- Department of Gastroenterology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Jordan Berlin
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee, US
| | - Narikazu Boku
- Division of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Thierry Conroy
- Department of Medical Oncology, Institut de Cancérologie de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Henriette Golcher
- Department of Surgery, University Hospital Erlangen, Erlangen, Germany
| | - Marianne Sinn
- Charite-Universitatsmedizin Berlin, CONKO study group, Berlin, Germany
- University Medical Center of Hamburg-Eppendorf, Hamburg, Germany
| | - John P Neoptolemos
- Department of General Surgery, University of Heidelberg, Heidelberg, Germany
| | - Geertjan van Tienhoven
- Department of Radiation Oncology, Cancer Center, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Marc G Besselink
- Department of Surgery, Cancer Center, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Johanna W Wilmink
- Department of Medical Oncology, Cancer Center, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Hanneke W M van Laarhoven
- Department of Medical Oncology, Cancer Center, Amsterdam University Medical Centers, Amsterdam, the Netherlands
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27
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Selective multi-kinase inhibition sensitizes mesenchymal pancreatic cancer to immune checkpoint blockade by remodeling the tumor microenvironment. NATURE CANCER 2022; 3:318-336. [PMID: 35122074 PMCID: PMC7612546 DOI: 10.1038/s43018-021-00326-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 12/13/2021] [Indexed: 12/14/2022]
Abstract
KRAS-mutant pancreatic ductal adenocarcinoma (PDAC) is highly immunosuppressive and resistant to targeted and immunotherapies. Among the different PDAC subtypes, basal-like mesenchymal PDAC, which is driven by allelic imbalance, increased gene dosage and subsequent high expression levels of oncogenic KRAS, shows the most aggressive phenotype and strongest therapy resistance. In the present study, we performed a systematic high-throughput combination drug screen and identified a synergistic interaction between the MEK inhibitor trametinib and the multi-kinase inhibitor nintedanib, which targets KRAS-directed oncogenic signaling in mesenchymal PDAC. This combination treatment induces cell-cycle arrest and cell death, and initiates a context-dependent remodeling of the immunosuppressive cancer cell secretome. Using a combination of single-cell RNA-sequencing, CRISPR screens and immunophenotyping, we show that this combination therapy promotes intratumor infiltration of cytotoxic and effector T cells, which sensitizes mesenchymal PDAC to PD-L1 immune checkpoint inhibition. Overall, our results open new avenues to target this aggressive and therapy-refractory mesenchymal PDAC subtype.
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28
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Krauß L, Urban BC, Hastreiter S, Schneider C, Wenzel P, Hassan Z, Wirth M, Lankes K, Terrasi A, Klement C, Cernilogar FM, Öllinger R, de Andrade Krätzig N, Engleitner T, Schmid RM, Steiger K, Rad R, Krämer OH, Reichert M, Schotta G, Saur D, Schneider G. HDAC2 Facilitates Pancreatic Cancer Metastasis. Cancer Res 2022; 82:695-707. [PMID: 34903606 PMCID: PMC9359718 DOI: 10.1158/0008-5472.can-20-3209] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 09/17/2021] [Accepted: 12/02/2021] [Indexed: 01/07/2023]
Abstract
The mortality of patients with pancreatic ductal adenocarcinoma (PDAC) is strongly associated with metastasis, a multistep process that is incompletely understood in this disease. Although genetic drivers of PDAC metastasis have not been defined, transcriptional and epigenetic rewiring can contribute to the metastatic process. The epigenetic eraser histone deacetylase 2 (HDAC2) has been connected to less differentiated PDAC, but the function of HDAC2 in PDAC has not been comprehensively evaluated. Using genetically defined models, we show that HDAC2 is a cellular fitness factor that controls cell cycle in vitro and metastasis in vivo, particularly in undifferentiated, mesenchymal PDAC cells. Unbiased expression profiling detected a core set of HDAC2-regulated genes. HDAC2 controlled expression of several prosurvival receptor tyrosine kinases connected to mesenchymal PDAC, including PDGFRα, PDGFRβ, and EGFR. The HDAC2-maintained program disabled the tumor-suppressive arm of the TGFβ pathway, explaining impaired metastasis formation of HDAC2-deficient PDAC. These data identify HDAC2 as a tractable player in the PDAC metastatic cascade. The complexity of the function of epigenetic regulators like HDAC2 implicates that an increased understanding of these proteins is needed for implementation of effective epigenetic therapies. SIGNIFICANCE HDAC2 has a context-specific role in undifferentiated PDAC and the capacity to disseminate systemically, implicating HDAC2 as targetable protein to prevent metastasis.
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Affiliation(s)
- Lukas Krauß
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
| | - Bettina C. Urban
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
| | - Sieglinde Hastreiter
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
| | - Carolin Schneider
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
| | - Patrick Wenzel
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
| | - Zonera Hassan
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
| | - Matthias Wirth
- Department of Hematology, Oncology and Tumor Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, German
| | - Katharina Lankes
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
| | - Andrea Terrasi
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
| | - Christine Klement
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
- Institute of Molecular Oncology and Functional Genomics, Technical University Munich, München, Germany
| | - Filippo M. Cernilogar
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, Technical University Munich, München, Germany
| | - Niklas de Andrade Krätzig
- Institute of Molecular Oncology and Functional Genomics, Technical University Munich, München, Germany
| | - Thomas Engleitner
- Institute of Molecular Oncology and Functional Genomics, Technical University Munich, München, Germany
| | - Roland M. Schmid
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
| | - Katja Steiger
- Institute of Pathology, Technische Universität München, München, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, Technical University Munich, München, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Oliver H. Krämer
- Department of Toxicology, University of Mainz Medical Center, Mainz, Germany
| | - Maximilian Reichert
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Gunnar Schotta
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
- Center for Integrated Protein Science Munich, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
| | - Dieter Saur
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Institute for Translational Cancer Research and Experimental Cancer Therapy, Technical University Munich, München, Germany
| | - Günter Schneider
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
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29
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Rodriguez E, Boelaars K, Brown K, Madunić K, van Ee T, Dijk F, Verheij J, Li RJE, Schetters STT, Meijer LL, Le Large TYS, Driehuis E, Clevers H, Bruijns SCM, O'Toole T, van Vliet SJ, Bijlsma MF, Wuhrer M, Kazemier G, Giovannetti E, Garcia-Vallejo JJ, van Kooyk Y. Analysis of the glyco-code in pancreatic ductal adenocarcinoma identifies glycan-mediated immune regulatory circuits. Commun Biol 2022; 5:41. [PMID: 35017635 PMCID: PMC8752754 DOI: 10.1038/s42003-021-02934-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 11/30/2021] [Indexed: 12/12/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) remains one of the most aggressive malignancies with a 5-year survival rate of only 9%. Despite the fact that changes in glycosylation patterns during tumour progression have been reported, no systematic approach has been conducted to evaluate its potential for patient stratification. By analysing publicly available transcriptomic data of patient samples and cell lines, we identified here two specific glycan profiles in PDAC that correlated with progression, clinical outcome and epithelial to mesenchymal transition (EMT) status. These different glycan profiles, confirmed by glycomics, can be distinguished by the expression of O-glycan fucosylated structures, present only in epithelial cells and regulated by the expression of GALNT3. Moreover, these fucosylated glycans can serve as ligands for DC-SIGN positive tumour-associated macrophages, modulating their activation and inducing the production of IL-10. Our results show mechanisms by which the glyco-code contributes to the tolerogenic microenvironment in PDAC. Rodriguez et al. present a transcriptomic analysis of glycosylation associated gene profiles, including bulk patient sequencing, sc-RNA seq, cell lines and organoids, to examine glycosylation in PDAC. They find 2 specific glycan profiles correlating with progression, clinical outcome and EMT, and conclude that the glyco-code contributes to the tolerogenic microenvironment in PDAC.
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Affiliation(s)
- Ernesto Rodriguez
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Kelly Boelaars
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Kari Brown
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Katarina Madunić
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, Leiden, The Netherlands
| | - Thomas van Ee
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Frederike Dijk
- Amsterdam UMC, Academic Medical Center Amsterdam, University of Amsterdam, Department of Pathology, Cancer Center Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Joanne Verheij
- Amsterdam UMC, Academic Medical Center Amsterdam, University of Amsterdam, Department of Pathology, Cancer Center Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - R J Eveline Li
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Sjoerd T T Schetters
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Laura L Meijer
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Surgery, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Tessa Y S Le Large
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Surgery, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Else Driehuis
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and UMC Utrecht, Utrecht, The Netherlands
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and UMC Utrecht, Utrecht, The Netherlands
| | - Sven C M Bruijns
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Tom O'Toole
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Sandra J van Vliet
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Maarten F Bijlsma
- Amsterdam UMC, University of Amsterdam, LEXOR, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.,Oncode Institute, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, Leiden, The Netherlands
| | - Geert Kazemier
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Surgery, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Elisa Giovannetti
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands.,Cancer Pharmacology Lab, AIRC Start-Up Unit, Fondazione Pisana per la Scienza, Pisa, Italy
| | - Juan J Garcia-Vallejo
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Yvette van Kooyk
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, De Boelelaan 1117, Amsterdam, The Netherlands.
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30
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Ju J, Wismans LV, Mustafa DAM, Reinders MJT, van Eijck CHJ, Stubbs AP, Li Y. Robust deep learning model for prognostic stratification of pancreatic ductal adenocarcinoma patients. iScience 2021; 24:103415. [PMID: 34901786 PMCID: PMC8637475 DOI: 10.1016/j.isci.2021.103415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/27/2021] [Accepted: 11/05/2021] [Indexed: 02/07/2023] Open
Abstract
A major challenge for treating patients with pancreatic ductal adenocarcinoma (PDAC) is the unpredictability of their prognoses due to high heterogeneity. We present Multi-Omics DEep Learning for Prognosis-correlated subtyping (MODEL-P) to identify PDAC subtypes and to predict prognoses of new patients. MODEL-P was trained on autoencoder integrated multi-omics of 146 patients with PDAC together with their survival outcome. Using MODEL-P, we identified two PDAC subtypes with distinct survival outcomes (median survival 10.1 and 22.7 months, respectively, log rank p = 1 × 10−6), which correspond to DNA damage repair and immune response. We rigorously validated MODEL-P by stratifying patients in five independent datasets into these two survival groups and achieved significant survival difference, which is superior to current practice and other subtyping schemas. We believe the subtype-specific signatures would facilitate PDAC pathogenesis discovery, and MODEL-P can provide clinicians the prognoses information in the treatment decision-making to better gauge the benefits versus the risks. We developed DL-based MODEL-P to identify prognosis-correlated PDAC subtypes The identified subtypes related to DNA damage repair and immune response processes MODEL-P stratified patients from independent datasets into distinct survival groups MODEL-P could be used in clinics to aid treatment decision-making
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Affiliation(s)
- Jie Ju
- Department of Pathology & Clinical Bioinformatics, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Leonoor V Wismans
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Dana A M Mustafa
- Department of Pathology & Clinical Bioinformatics, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Marcel J T Reinders
- The Delft Bioinformatics Lab, Delft University of Technology, Rotterdam, the Netherlands
| | - Casper H J van Eijck
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Andrew P Stubbs
- Department of Pathology & Clinical Bioinformatics, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Yunlei Li
- Department of Pathology & Clinical Bioinformatics, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
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31
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Ewers KM, Patil S, Kopp W, Thomale J, Quilitz T, Magerhans A, Wang X, Hessmann E, Dobbelstein M. HSP90 Inhibition Synergizes with Cisplatin to Eliminate Basal-like Pancreatic Ductal Adenocarcinoma Cells. Cancers (Basel) 2021; 13:cancers13246163. [PMID: 34944784 PMCID: PMC8699576 DOI: 10.3390/cancers13246163] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/30/2021] [Accepted: 12/03/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Pancreatic cancer is currently difficult to treat, but the drug cisplatin represents one of the most important therapeutic options. We find that cells derived from this cancer fall into two classes regarding their sensitivity towards cisplatin, and we observe that cells with high expression levels of GATA6 and microRNA 200 are mostly sensitive. However, those cells that respond poorly to cisplatin can be sensitized by drugs that inhibit HSP90, a protein that helps other proteins to fold properly. This was also found in a mouse model of pancreatic cancer. Our results suggest that the combination of cisplatin with HSP90-inhibitory drugs might improve the treatment of pancreatic cancer. Abstract To improve the treatment of pancreatic ductal adenocarcinoma (PDAC), a promising strategy consists of personalized chemotherapy based on gene expression profiles. Investigating a panel of PDAC-derived human cell lines, we found that their sensitivities towards cisplatin fall in two distinct classes. The platinum-sensitive class is characterized by the expression of GATA6, miRNA-200a, and miRNA-200b, which might be developable as predictive biomarkers. In the case of resistant PDAC cells, we identified a synergism of cisplatin with HSP90 inhibitors. Mechanistic explanations of this synergy include the degradation of Fanconi anemia pathway factors upon HSP90 inhibition. Treatment with the drug combination resulted in increased DNA damage and chromosome fragmentation, as we have reported previously for ovarian cancer cells. On top of this, HSP90 inhibition also enhanced the accumulation of DNA-bound platinum. We next investigated an orthotopic syngeneic animal model consisting of tumors arising from KPC cells (LSL-KrasG12D/+; LSL-Trp53R172H/+; Pdx-1-Cre, C57/BL6 genetic background). Here again, when treating established tumors, the combination of cisplatin with the HSP90 inhibitor onalespib was highly effective and almost completely prevented further tumor growth. We propose that the combination of platinum drugs and HSP90 inhibitors might be worth testing in the clinics for the treatment of cisplatin-resistant PDACs.
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Affiliation(s)
- Katharina M. Ewers
- Institute of Molecular Oncology, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany; (K.M.E.); (T.Q.); (A.M.)
- Clinical Research Unit 5002, KFO5002, University Medical Center Göttingen, 37075 Göttingen, Germany; (S.P.); (W.K.); (E.H.)
| | - Shilpa Patil
- Clinical Research Unit 5002, KFO5002, University Medical Center Göttingen, 37075 Göttingen, Germany; (S.P.); (W.K.); (E.H.)
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Waltraut Kopp
- Clinical Research Unit 5002, KFO5002, University Medical Center Göttingen, 37075 Göttingen, Germany; (S.P.); (W.K.); (E.H.)
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Jürgen Thomale
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen Medical School, 45141 Essen, Germany;
| | - Tabea Quilitz
- Institute of Molecular Oncology, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany; (K.M.E.); (T.Q.); (A.M.)
- Clinical Research Unit 5002, KFO5002, University Medical Center Göttingen, 37075 Göttingen, Germany; (S.P.); (W.K.); (E.H.)
| | - Anna Magerhans
- Institute of Molecular Oncology, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany; (K.M.E.); (T.Q.); (A.M.)
- Clinical Research Unit 5002, KFO5002, University Medical Center Göttingen, 37075 Göttingen, Germany; (S.P.); (W.K.); (E.H.)
| | - Xin Wang
- Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China;
| | - Elisabeth Hessmann
- Clinical Research Unit 5002, KFO5002, University Medical Center Göttingen, 37075 Göttingen, Germany; (S.P.); (W.K.); (E.H.)
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Matthias Dobbelstein
- Institute of Molecular Oncology, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany; (K.M.E.); (T.Q.); (A.M.)
- Clinical Research Unit 5002, KFO5002, University Medical Center Göttingen, 37075 Göttingen, Germany; (S.P.); (W.K.); (E.H.)
- Correspondence:
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32
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Xu Z, Hu K, Bailey P, Springfeld C, Roth S, Kurilov R, Brors B, Gress T, Buchholz M, An J, Wei K, Peccerella T, Büchler MW, Hackert T, Neoptolemos JP. Clinical Impact of Molecular Subtyping of Pancreatic Cancer. Front Cell Dev Biol 2021; 9:743908. [PMID: 34805152 PMCID: PMC8603393 DOI: 10.3389/fcell.2021.743908] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/17/2021] [Indexed: 12/12/2022] Open
Abstract
Pancreatic ductal adenocarcinoma is a highly lethal malignancy, which has now become the seventh most common cause of cancer death in the world, with the highest mortality rates in Europe and North America. In the past 30 years, there has been some progress in 5-year survival (rates increasing from 2.5 to 10%), but this is still extremely poor compared to all other common cancer types. Targeted therapies for advanced pancreatic cancer based on actionable mutations have been disappointing, with only 3–5% showing even a short clinical benefit. There is, however, a molecular diversity beyond mutations in genes responsible for producing classical canonical signaling pathways. Pancreatic cancer is almost unique in promoting an excess production of other components of the stroma, resulting in a complex tumor microenvironment that contributes to tumor development, progression, and response to treatment. Various transcriptional subtypes have also been described. Most notably, there is a strong alignment between the Classical/Pancreatic progenitor and Quasi-mesenchymal/Basal-like/Squamous subtype signatures of Moffit, Collinson, Bailey, Puleo, and Chan-Seng-Yue, which have potential clinical impact. Sequencing of epithelial cell populations enriched by laser capture microscopy combined with single-cell RNA sequencing has revealed the potential genomic evolution of pancreatic cancer as being a consequence of a gene expression continuum from mixed Basal-like and Classical cell populations within the same tumor, linked to allelic imbalances in mutant KRAS, with metastatic tumors being more copy number-unstable compared to primary tumors. The Basal-like subtype appears more chemoresistant with reduced survival compared to the Classical subtype. Chemotherapy and/or chemoradiation will also enrich the Basal-like subtype. Squamous/Basal-like programs facilitate immune infiltration compared with the Classical-like programs. The immune infiltrates associated with Basal and Classical type cells are distinct, potentially opening the door to differential strategies. Single-cell and spatial transcriptomics will now allow single cell profiling of tumor and resident immune cell populations that may further advance subtyping. Multiple clinical trials have been launched based on transcriptomic response signatures and molecular subtyping including COMPASS, Precision Promise, ESPAC6/7, PREDICT-PACA, and PASS1. We review several approaches to explore the clinical relevance of molecular profiling to provide optimal bench-to-beside translation with clinical impact.
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Affiliation(s)
- Zhou Xu
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany.,Section of Surgical Research, Heidelberg University Hospital, Heidelberg, Germany
| | - Kai Hu
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany.,Section of Surgical Research, Heidelberg University Hospital, Heidelberg, Germany
| | - Peter Bailey
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany.,Section of Surgical Research, Heidelberg University Hospital, Heidelberg, Germany.,Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Christoph Springfeld
- Department of Medical Oncology, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Susanne Roth
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Roma Kurilov
- Division of Applied Bioinformatics, German Cancer Research Center, Heidelberg, Germany
| | - Benedikt Brors
- Department of Medical Oncology, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany.,Division of Applied Bioinformatics, German Cancer Research Center, Heidelberg, Germany
| | - Thomas Gress
- Department of Gastroenterology and Endocrinology, Philipps University of Marburg, Marburg, Germany
| | - Malte Buchholz
- Department of Gastroenterology and Endocrinology, Philipps University of Marburg, Marburg, Germany
| | - Jingyu An
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany.,Section of Surgical Research, Heidelberg University Hospital, Heidelberg, Germany
| | - Kongyuan Wei
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany.,Section of Surgical Research, Heidelberg University Hospital, Heidelberg, Germany
| | - Teresa Peccerella
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany.,Section of Surgical Research, Heidelberg University Hospital, Heidelberg, Germany
| | - Markus W Büchler
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Thilo Hackert
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - John P Neoptolemos
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany.,Section of Surgical Research, Heidelberg University Hospital, Heidelberg, Germany
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33
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Andrade Barbosa B, van Asten SD, Oh JW, Farina-Sarasqueta A, Verheij J, Dijk F, van Laarhoven HWM, Ylstra B, Garcia Vallejo JJ, van de Wiel MA, Kim Y. Bayesian log-normal deconvolution for enhanced in silico microdissection of bulk gene expression data. Nat Commun 2021; 12:6106. [PMID: 34671028 PMCID: PMC8528834 DOI: 10.1038/s41467-021-26328-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 09/27/2021] [Indexed: 01/29/2023] Open
Abstract
Deconvolution of bulk gene expression profiles into the cellular components is pivotal to portraying tissue's complex cellular make-up, such as the tumor microenvironment. However, the inherently variable nature of gene expression requires a comprehensive statistical model and reliable prior knowledge of individual cell types that can be obtained from single-cell RNA sequencing. We introduce BLADE (Bayesian Log-normAl Deconvolution), a unified Bayesian framework to estimate both cellular composition and gene expression profiles for each cell type. Unlike previous comprehensive statistical approaches, BLADE can handle > 20 types of cells due to the efficient variational inference. Throughout an intensive evaluation with > 700 simulated and real datasets, BLADE demonstrated enhanced robustness against gene expression variability and better completeness than conventional methods, in particular, to reconstruct gene expression profiles of each cell type. In summary, BLADE is a powerful tool to unravel heterogeneous cellular activity in complex biological systems from standard bulk gene expression data.
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Affiliation(s)
- Bárbara Andrade Barbosa
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Saskia D van Asten
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Department of Molecular Cell Biology & Immunology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Infection and Immunity Institute, Amsterdam, the Netherlands
| | - Ji Won Oh
- Department of Anatomy, School of Medicine, Kyungpook National University, Daegu, South Korea
- Bio-Medical Research Institute, Kyungpook National University Hospital, Daegu, South Korea
| | | | - Joanne Verheij
- Department of Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Frederike Dijk
- Department of Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Hanneke W M van Laarhoven
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Bauke Ylstra
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Juan J Garcia Vallejo
- Department of Molecular Cell Biology & Immunology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Infection and Immunity Institute, Amsterdam, the Netherlands
| | - Mark A van de Wiel
- Department of Epidemiology and Data Science, Amsterdam Public Health research institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.
| | - Yongsoo Kim
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.
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34
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Gutiérrez ML, Muñoz-Bellvís L, Orfao A. Genomic Heterogeneity of Pancreatic Ductal Adenocarcinoma and Its Clinical Impact. Cancers (Basel) 2021; 13:4451. [PMID: 34503261 PMCID: PMC8430663 DOI: 10.3390/cancers13174451] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 02/07/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the leading causes of cancer death due to limited advances in recent years in early diagnosis and personalized therapy capable of overcoming tumor resistance to chemotherapy. In the last decades, significant advances have been achieved in the identification of recurrent genetic and molecular alterations of PDAC including those involving the KRAS, CDKN2A, SMAD4, and TP53 driver genes. Despite these common genetic traits, PDAC are highly heterogeneous tumors at both the inter- and intra-tumoral genomic level, which might contribute to distinct tumor behavior and response to therapy, with variable patient outcomes. Despite this, genetic and genomic data on PDAC has had a limited impact on the clinical management of patients. Integration of genomic data for classification of PDAC into clinically defined entities-i.e., classical vs. squamous subtypes of PDAC-leading to different treatment approaches has the potential for significantly improving patient outcomes. In this review, we summarize current knowledge about the most relevant genomic subtypes of PDAC including the impact of distinct patterns of intra-tumoral genomic heterogeneity on the classification and clinical and therapeutic management of PDAC.
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Affiliation(s)
- María Laura Gutiérrez
- Department of Medicine and Cytometry Service (NUCLEUS), Universidad de Salamanca, 37007 Salamanca, Spain;
- Cancer Research Center (IBMCC-CSIC/USAL), 37007 Salamanca, Spain;
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain
- Biomedical Research Networking Centre Consortium-CIBER-CIBERONC, 28029 Madrid, Spain
| | - Luis Muñoz-Bellvís
- Cancer Research Center (IBMCC-CSIC/USAL), 37007 Salamanca, Spain;
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain
- Biomedical Research Networking Centre Consortium-CIBER-CIBERONC, 28029 Madrid, Spain
- Service of General and Gastrointestinal Surgery, University Hospital of Salamanca, 37007 Salamanca, Spain
| | - Alberto Orfao
- Department of Medicine and Cytometry Service (NUCLEUS), Universidad de Salamanca, 37007 Salamanca, Spain;
- Cancer Research Center (IBMCC-CSIC/USAL), 37007 Salamanca, Spain;
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain
- Biomedical Research Networking Centre Consortium-CIBER-CIBERONC, 28029 Madrid, Spain
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35
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Hessmann E, Schneider G. New Insights Into Pancreatic Cancer: Notes from a Virtual Meeting. Gastroenterology 2021; 161:785-791. [PMID: 34089734 DOI: 10.1053/j.gastro.2021.04.082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 04/20/2021] [Accepted: 04/20/2021] [Indexed: 12/28/2022]
Abstract
Pancreatic ductal adenocarcinoma remains a major challenge in cancer medicine. Given the increase in incidence and mortality, interdisciplinary research is necessary to translate basic knowledge into therapeutic strategies improving the outcome of patients. On the 4th and 5th of February 2021, three German pancreatic cancer research centers, the Clinical Research Unit 5002 from Göttingen, the Collaborative Research Center 1321 from Munich, and Clinical Research Unit 325 from Marburg organized the 1st Virtual Göttingen-Munich-Marburg Pancreatic Cancer Meeting in order to foster scientific exchange. This report summarizes current research and proceedings presented during that meeting.
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Affiliation(s)
- Elisabeth Hessmann
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Göttingen, Göttingen, Germany.
| | - Günter Schneider
- Medical Clinic and Policlinic II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.
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Adam RS, Blomberg I, Ten Hoorn S, Bijlsma MF, Vermeulen L. The recurring features of molecular subtypes in distinct gastrointestinal malignancies-A systematic review. Crit Rev Oncol Hematol 2021; 164:103428. [PMID: 34284100 DOI: 10.1016/j.critrevonc.2021.103428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 07/13/2021] [Accepted: 07/16/2021] [Indexed: 12/26/2022] Open
Abstract
In colorectal cancer (CRC), pancreatic ductal adenocarcinoma (PDAC) and gastric cancer (GC) multiple studies of inter-tumor heterogeneity have identified molecular subtypes, which correlate with clinical features. Our aim was to investigate the attributes of molecular subtypes across three different gastrointestinal cancer types. We performed a systematic search for publications on molecular subtypes or classifications in PDAC and GC and compared the described subtypes with the established consensus molecular subtypes of CRC. Examining the characteristics of subtypes across CRC, PDAC and GC resulted in four categories of subtypes. We describe uniting and distinguishing features within a mesenchymal, an epithelial, an immunogenic and a metabolic and digestive subtype category. We conclude that molecular subtypes of CRC, PDAC and GC display relevant overlap in molecular features and clinical outcomes. This finding encourages quantitative studies on subtypes across different cancer types and could lead to a paradigm shift in future treatment strategies.
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Affiliation(s)
- Ronja S Adam
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands; Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
| | - Ilse Blomberg
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands; Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
| | - Sanne Ten Hoorn
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands; Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
| | - Maarten F Bijlsma
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands; Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
| | - Louis Vermeulen
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands; Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands.
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37
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Li R, He Y, Zhang H, Wang J, Liu X, Liu H, Wu H, Liang Z. Identification and Validation of Immune Molecular Subtypes in Pancreatic Ductal Adenocarcinoma: Implications for Prognosis and Immunotherapy. Front Immunol 2021; 12:690056. [PMID: 34335594 PMCID: PMC8320597 DOI: 10.3389/fimmu.2021.690056] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/29/2021] [Indexed: 12/27/2022] Open
Abstract
Background Pancreatic ductal adenocarcinoma (PDAC) remains treatment refractory. Immunotherapy has achieved success in the treatment of multiple malignancies. However, the efficacy of immunotherapy in PDAC is limited by a lack of promising biomarkers. In this research, we aimed to identify robust immune molecular subtypes of PDAC to facilitate prognosis prediction and patient selection for immunotherapy. Methods A training cohort of 149 PDAC samples from The Cancer Genome Atlas (TCGA) with mRNA expression data was analyzed. By means of non-negative matrix factorization (NMF), we virtually dissected the immune-related signals from bulk gene expression data. Detailed immunogenomic and survival analyses of the immune molecular subtypes were conducted to determine their biological and clinical relevance. Validation was performed in five independent datasets on a total of 615 samples. Results Approximately 31% of PDAC samples (46/149) had higher immune cell infiltration, more active immune cytolytic activity, higher activation of the interferon pathway, a higher tumor mutational burden (TMB), and fewer copy number alterations (CNAs) than the other samples (all P < 0.001). This new molecular subtype was named Immune Class, which served as an independent favorable prognostic factor for overall survival (hazard ratio, 0.56; 95% confidence interval, 0.33-0.97). Immune Class in cooperation with previously reported tumor and stroma classifications had a cumulative effect on PDAC prognostic stratification. Moreover, programmed cell death-1 (PD-1) inhibitors showed potential efficacy for Immune Class (P = 0.04). The robustness of our immune molecular subtypes was further verified in the validation cohort. Conclusions By capturing immune-related signals in the PDAC tumor microenvironment, we reveal a novel molecular subtype, Immune Class. Immune Class serves as an independent favorable prognostic factor for overall survival in PDAC patients.
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Affiliation(s)
- Ruiyu Li
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Disease, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yangzhige He
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Hui Zhang
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Disease, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jing Wang
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Disease, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiaoding Liu
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Disease, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hangqi Liu
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Disease, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Huanwen Wu
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Disease, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zhiyong Liang
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Disease, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Poh AR, Ernst M. Tumor-Associated Macrophages in Pancreatic Ductal Adenocarcinoma: Therapeutic Opportunities and Clinical Challenges. Cancers (Basel) 2021; 13:cancers13122860. [PMID: 34201127 PMCID: PMC8226457 DOI: 10.3390/cancers13122860] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/03/2021] [Accepted: 06/06/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Macrophages are a major component of the pancreatic tumor microenvironment, and their increased abundance is associated with poor patient survival. Given the multi-faceted role of macrophages in promoting pancreatic tumor development and progression, these cells represent promising targets for anti-cancer therapy. Abstract Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignant disease with a 5-year survival rate of less than 10%. Macrophages are one of the earliest infiltrating cells in the pancreatic tumor microenvironment, and are associated with an increased risk of disease progression, recurrence, metastasis, and shorter overall survival. Pre-clinical studies have demonstrated an unequivocal role of macrophages in PDAC by contributing to chronic inflammation, cancer cell stemness, desmoplasia, immune suppression, angiogenesis, invasion, metastasis, and drug resistance. Several macrophage-targeting therapies have also been investigated in pre-clinical models, and include macrophage depletion, inhibiting macrophage recruitment, and macrophage reprogramming. However, the effectiveness of these drugs in pre-clinical models has not always translated into clinical trials. In this review, we discuss the molecular mechanisms that underpin macrophage heterogeneity within the pancreatic tumor microenvironment, and examine the contribution of macrophages at various stages of PDAC progression. We also provide a comprehensive update of macrophage-targeting therapies that are currently undergoing clinical evaluation, and discuss clinical challenges associated with these treatment modalities in human PDAC patients.
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Beirith I, Renz BW, Mudusetti S, Ring NS, Kolorz J, Koch D, Bazhin AV, Berger M, Wang J, Angele MK, D’Haese JG, Guba MO, Niess H, Andrassy J, Werner J, Ilmer M. Identification of the Neurokinin-1 Receptor as Targetable Stratification Factor for Drug Repurposing in Pancreatic Cancer. Cancers (Basel) 2021; 13:cancers13112703. [PMID: 34070805 PMCID: PMC8198055 DOI: 10.3390/cancers13112703] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 12/22/2022] Open
Abstract
The SP/NK1R-complex plays an important role in tumor proliferation. Targeting of the neurokinin-1 receptor in previous studies with its antagonist aprepitant (AP) resulted in anti-tumoral effects in colorectal cancer and hepatoblastoma. However, there is still a lack of knowledge regarding its effects on pancreatic cancer. Therefore, we treated human pancreatic ductal adenocarcinoma (PDAC) cell lines (Capan-1, DanG, HuP-T3, Panc-1, and MIA PaCa-2) and their cancer stem cell-like cells (CSCs) with AP and analyzed functional effects by MTT-, colony, and sphere formation assays, respectively; moreover, we monitored downstream mechanisms by flow cytometry. NK1R inhibition resulted in dose-dependent growth reduction in both CSCs and non-CSCs without induction of apoptosis in most PDAC cell lines. More importantly, we identified striking AP dependent cell cycle arrest in all parental cells. Furthermore, gene expression and the importance of key genes in PDAC tumorigenesis were analyzed combining RT-qPCR in eight PDAC cell lines with publicly available datasets (TCGA, GEO, CCLE). Surprisingly, we found a better overall survival in patients with high NK1R levels, while at the same time, NK1R was significantly decreased in PDAC tissue compared to normal tissue. Interestingly, there is currently no differentiation between the isoforms of NK1R (truncated and full; NK1R-tr and -fl) in any of the indicated public transcriptomic records, although many publications already emphasize on important regulatory differences between the two isoforms of NK1R in many cancer entities. In conclusion, analysis of splice variants might potentially lead to a stratification of PDAC patients for NK1R-directed therapies. Furthermore, we presume PDAC patients with high expressions of NK1R-tr might benefit from treatment with AP to improve chemoresistance. Therefore, analysis of splice variants might potentially lead to a stratification of PDAC patients for NK1R-directed therapies.
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Affiliation(s)
- Iris Beirith
- Department of General, Visceral and Transplantation Surgery, University Hospital, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; (I.B.); (B.W.R.); (S.M.); (N.S.R.); (D.K.); (A.V.B.); (J.W.); (M.K.A.); (J.G.D.); (M.O.G.); (H.N.); (J.A.); (J.W.)
| | - Bernhard W. Renz
- Department of General, Visceral and Transplantation Surgery, University Hospital, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; (I.B.); (B.W.R.); (S.M.); (N.S.R.); (D.K.); (A.V.B.); (J.W.); (M.K.A.); (J.G.D.); (M.O.G.); (H.N.); (J.A.); (J.W.)
- German Center for Translations Cancer Research (DKTK), Partner Site Munich, 80336 Munich, Germany
| | - Shristee Mudusetti
- Department of General, Visceral and Transplantation Surgery, University Hospital, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; (I.B.); (B.W.R.); (S.M.); (N.S.R.); (D.K.); (A.V.B.); (J.W.); (M.K.A.); (J.G.D.); (M.O.G.); (H.N.); (J.A.); (J.W.)
| | - Natalja Sergejewna Ring
- Department of General, Visceral and Transplantation Surgery, University Hospital, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; (I.B.); (B.W.R.); (S.M.); (N.S.R.); (D.K.); (A.V.B.); (J.W.); (M.K.A.); (J.G.D.); (M.O.G.); (H.N.); (J.A.); (J.W.)
| | - Julian Kolorz
- Department of Pediatric Surgery, Research Laboratories, von Hauner Children’s Hospital, Ludwig-Maximilians-University Munich, 80337 Munich, Germany; (J.K.); (M.B.)
| | - Dominik Koch
- Department of General, Visceral and Transplantation Surgery, University Hospital, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; (I.B.); (B.W.R.); (S.M.); (N.S.R.); (D.K.); (A.V.B.); (J.W.); (M.K.A.); (J.G.D.); (M.O.G.); (H.N.); (J.A.); (J.W.)
| | - Alexandr V. Bazhin
- Department of General, Visceral and Transplantation Surgery, University Hospital, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; (I.B.); (B.W.R.); (S.M.); (N.S.R.); (D.K.); (A.V.B.); (J.W.); (M.K.A.); (J.G.D.); (M.O.G.); (H.N.); (J.A.); (J.W.)
- German Center for Translations Cancer Research (DKTK), Partner Site Munich, 80336 Munich, Germany
| | - Michael Berger
- Department of Pediatric Surgery, Research Laboratories, von Hauner Children’s Hospital, Ludwig-Maximilians-University Munich, 80337 Munich, Germany; (J.K.); (M.B.)
- Department of General, Abdominal and Transplant Surgery, Essen University Hospital, 45417 Essen, Germany
| | - Jing Wang
- Department of General, Visceral and Transplantation Surgery, University Hospital, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; (I.B.); (B.W.R.); (S.M.); (N.S.R.); (D.K.); (A.V.B.); (J.W.); (M.K.A.); (J.G.D.); (M.O.G.); (H.N.); (J.A.); (J.W.)
- Department of General Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230036, China
| | - Martin K. Angele
- Department of General, Visceral and Transplantation Surgery, University Hospital, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; (I.B.); (B.W.R.); (S.M.); (N.S.R.); (D.K.); (A.V.B.); (J.W.); (M.K.A.); (J.G.D.); (M.O.G.); (H.N.); (J.A.); (J.W.)
| | - Jan G. D’Haese
- Department of General, Visceral and Transplantation Surgery, University Hospital, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; (I.B.); (B.W.R.); (S.M.); (N.S.R.); (D.K.); (A.V.B.); (J.W.); (M.K.A.); (J.G.D.); (M.O.G.); (H.N.); (J.A.); (J.W.)
| | - Markus O. Guba
- Department of General, Visceral and Transplantation Surgery, University Hospital, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; (I.B.); (B.W.R.); (S.M.); (N.S.R.); (D.K.); (A.V.B.); (J.W.); (M.K.A.); (J.G.D.); (M.O.G.); (H.N.); (J.A.); (J.W.)
| | - Hanno Niess
- Department of General, Visceral and Transplantation Surgery, University Hospital, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; (I.B.); (B.W.R.); (S.M.); (N.S.R.); (D.K.); (A.V.B.); (J.W.); (M.K.A.); (J.G.D.); (M.O.G.); (H.N.); (J.A.); (J.W.)
| | - Joachim Andrassy
- Department of General, Visceral and Transplantation Surgery, University Hospital, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; (I.B.); (B.W.R.); (S.M.); (N.S.R.); (D.K.); (A.V.B.); (J.W.); (M.K.A.); (J.G.D.); (M.O.G.); (H.N.); (J.A.); (J.W.)
| | - Jens Werner
- Department of General, Visceral and Transplantation Surgery, University Hospital, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; (I.B.); (B.W.R.); (S.M.); (N.S.R.); (D.K.); (A.V.B.); (J.W.); (M.K.A.); (J.G.D.); (M.O.G.); (H.N.); (J.A.); (J.W.)
- German Center for Translations Cancer Research (DKTK), Partner Site Munich, 80336 Munich, Germany
| | - Matthias Ilmer
- Department of General, Visceral and Transplantation Surgery, University Hospital, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; (I.B.); (B.W.R.); (S.M.); (N.S.R.); (D.K.); (A.V.B.); (J.W.); (M.K.A.); (J.G.D.); (M.O.G.); (H.N.); (J.A.); (J.W.)
- German Center for Translations Cancer Research (DKTK), Partner Site Munich, 80336 Munich, Germany
- Correspondence: ; Tel.: +49-089-4400-711218
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Singh HM, Leber MF, Bossow S, Engeland CE, Dessila J, Grossardt C, Zaoui K, Bell JC, Jäger D, von Kalle C, Ungerechts G. MicroRNA-sensitive oncolytic measles virus for chemovirotherapy of pancreatic cancer. MOLECULAR THERAPY-ONCOLYTICS 2021; 21:340-355. [PMID: 34141871 PMCID: PMC8182383 DOI: 10.1016/j.omto.2021.04.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 04/28/2021] [Indexed: 02/07/2023]
Abstract
Advanced pancreatic cancer is characterized by few treatment options and poor outcomes. Oncolytic virotherapy and chemotherapy involve complementary pharmacodynamics and could synergize to improve therapeutic efficacy. Likewise, multimodality treatment may cause additional toxicity, and new agents have to be safe. Balancing both aims, we generated an oncolytic measles virus for 5-fluorouracil-based chemovirotherapy of pancreatic cancer with enhanced tumor specificity through microRNA-regulated vector tropism. The resulting vector encodes a bacterial prodrug convertase, cytosine deaminase-uracil phosphoribosyl transferase, and carries synthetic miR-148a target sites in the viral F gene. Combination of the armed and targeted virus with 5-fluorocytosine, a prodrug of 5-fluorouracil, resulted in cytotoxicity toward both infected and bystander pancreatic cancer cells. In pancreatic cancer xenografts, a single intratumoral injection of the virus induced robust in vivo expression of prodrug convertase. Based on intratumoral transgene expression kinetics, we devised a chemovirotherapy regimen to assess treatment efficacy. Concerted multimodality treatment with intratumoral virus and systemic prodrug administration delayed tumor growth and prolonged survival of xenograft-bearing mice. Our results demonstrate that 5-fluorouracil-based chemovirotherapy with microRNA-sensitive measles virus is an effective strategy against pancreatic cancer at a favorable therapeutic index that warrants future clinical translation.
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Affiliation(s)
- Hans Martin Singh
- Clinical Cooperation Unit Virotherapy, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.,Department of Medical Oncology, National Center for Tumor Diseases (NCT) and Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Mathias Felix Leber
- Clinical Cooperation Unit Virotherapy, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.,Department of Medical Oncology, National Center for Tumor Diseases (NCT) and Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany.,Cancer Therapeutics Program, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ONT, Canada
| | - Sascha Bossow
- Clinical Cooperation Unit Virotherapy, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Christine E Engeland
- Clinical Cooperation Unit Virotherapy, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.,Department of Medical Oncology, National Center for Tumor Diseases (NCT) and Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany.,Clinical Cooperation Unit Virotherapy, Research Group Mechanisms of Oncolytic Immunotherapy, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.,Faculty of Health/School of Medicine, Institute of Virology and Microbiology, Witten/Herdecke University, Stockumer Straße 10, 58453 Witten, Germany
| | - Jan Dessila
- Clinical Cooperation Unit Virotherapy, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Christian Grossardt
- Clinical Cooperation Unit Virotherapy, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Karim Zaoui
- Clinical Cooperation Unit Virotherapy, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.,Department of Otorhinolaryngology and Head and Neck Surgery, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany
| | - John C Bell
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ONT, Canada
| | - Dirk Jäger
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) and Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Christof von Kalle
- Berlin Institute of Health and Charité Universitätsmedizin, Anna-Louisa-Karsch-Straße 2, 10178 Berlin, Germany.,Sidra Medical and Research Center, Al Luqta Street, Education City, North Campus, P.O. Box 26999, Doha, Qatar
| | - Guy Ungerechts
- Clinical Cooperation Unit Virotherapy, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.,Department of Medical Oncology, National Center for Tumor Diseases (NCT) and Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany.,Cancer Therapeutics Program, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ONT, Canada
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Gao R, Bai S, Henderson YC, Lin Y, Schalck A, Yan Y, Kumar T, Hu M, Sei E, Davis A, Wang F, Shaitelman SF, Wang JR, Chen K, Moulder S, Lai SY, Navin NE. Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes. Nat Biotechnol 2021; 39:599-608. [PMID: 33462507 PMCID: PMC8122019 DOI: 10.1038/s41587-020-00795-2] [Citation(s) in RCA: 293] [Impact Index Per Article: 97.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 12/10/2020] [Indexed: 01/29/2023]
Abstract
Single-cell transcriptomic analysis is widely used to study human tumors. However, it remains challenging to distinguish normal cell types in the tumor microenvironment from malignant cells and to resolve clonal substructure within the tumor. To address these challenges, we developed an integrative Bayesian segmentation approach called copy number karyotyping of aneuploid tumors (CopyKAT) to estimate genomic copy number profiles at an average genomic resolution of 5 Mb from read depth in high-throughput single-cell RNA sequencing (scRNA-seq) data. We applied CopyKAT to analyze 46,501 single cells from 21 tumors, including triple-negative breast cancer, pancreatic ductal adenocarcinoma, anaplastic thyroid cancer, invasive ductal carcinoma and glioblastoma, to accurately (98%) distinguish cancer cells from normal cell types. In three breast tumors, CopyKAT resolved clonal subpopulations that differed in the expression of cancer genes, such as KRAS, and signatures, including epithelial-to-mesenchymal transition, DNA repair, apoptosis and hypoxia. These data show that CopyKAT can aid in the analysis of scRNA-seq data in a variety of solid human tumors.
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Affiliation(s)
- Ruli Gao
- The Center for Bioinformatics and Computational Biology, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA 77030,Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 77030
| | - Shanshan Bai
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 77030,Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 77030
| | - Ying C. Henderson
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 77030
| | - Yiyun Lin
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 77030,The University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA 77030
| | - Aislyn Schalck
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 77030,The University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA 77030
| | - Yun Yan
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 77030,The University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA 77030
| | - Tapsi Kumar
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 77030,The University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA 77030
| | - Min Hu
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 77030
| | - Emi Sei
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 77030
| | - Alexander Davis
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 77030,The University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA 77030
| | - Fang Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston TX, USA 77030
| | - Simona F. Shaitelman
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 77030
| | - Jennifer Rui Wang
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 77030
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston TX, USA 77030
| | - Stacy Moulder
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 77030
| | - Stephen Y. Lai
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 77030,The University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA 77030,Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 77030,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 77030
| | - Nicholas E. Navin
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 77030,The University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA 77030,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston TX, USA 77030,Correspondence:
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Molecular and Metabolic Subtypes Correspondence for Pancreatic Ductal Adenocarcinoma Classification. J Clin Med 2020; 9:jcm9124128. [PMID: 33371431 PMCID: PMC7767410 DOI: 10.3390/jcm9124128] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/14/2020] [Accepted: 12/17/2020] [Indexed: 12/13/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC), the most common form of pancreatic cancer, is an extremely lethal disease due to late diagnosis, aggressiveness and lack of effective therapies. Considering its intrinsic heterogeneity, patient stratification models based on transcriptomic and genomic signatures, with partially overlapping subgroups, have been established. Besides molecular alterations, PDAC tumours show a strong desmoplastic response, resulting in profound metabolic reprogramming involving increased glucose and amino acid consumption, as well as lipid scavenging and biosynthesis. Interestingly, recent works have also revealed the existence of metabolic subtypes with differential prognosis within PDAC, which correlated to defined molecular subclasses in patients: lipogenic subtype correlated with a classical/progenitor signature, while glycolytic tumours associated with the highly aggressive basal/squamous profile. Bioinformatic analyses have demonstrated that the representative genes of each metabolic subtype are up-regulated in PDAC samples and predict patient survival. This suggests a relationship between the genetic signature, metabolic profile, and aggressiveness of the tumour. Considering all this, defining metabolic subtypes represents a clear opportunity for patient stratification considering tumour functional behaviour independently of their mutational background.
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Liu D, Steins A, Klaassen R, van der Zalm AP, Bennink RJ, van Tienhoven G, Besselink MG, Bijlsma MF, van Laarhoven HWM. Soluble Compounds Released by Hypoxic Stroma Confer Invasive Properties to Pancreatic Ductal Adenocarcinoma. Biomedicines 2020; 8:biomedicines8110444. [PMID: 33105540 PMCID: PMC7690284 DOI: 10.3390/biomedicines8110444] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/17/2020] [Accepted: 10/20/2020] [Indexed: 02/07/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is characterized by abundant stroma and a hypoxic microenvironment. Pancreatic stellate cells (PSC) are activated by hypoxia and promote excessive desmoplasia, further contributing to the development of hypoxia. We aimed to explore how hypoxia and stroma interact to contribute to invasive growth in PDAC. [18F]HX4 PET/CT was found to be a feasible non-invasive method to assess tumor hypoxia in 42 patients and correlated with HIF1α immunohistochemistry in matched surgical specimens. [18F]HX4 uptake and HIF1α were strong prognostic markers for overall survival. Co-culture and medium transfer experiments demonstrated that hypoxic PSCs and their supernatant induce upregulation of mesenchymal markers in tumor cells, and that hypoxia-induced stromal factors drive invasive growth in hypoxic PDACs. Through stepwise selection, stromal MMP10 was identified as the most likely candidate responsible for this. In conclusion, hypoxia-activated PSCs promote the invasiveness of PDAC through paracrine signaling. The identification of PSC-derived MMP10 may provide a lead to develop novel stroma-targeting therapies.
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Affiliation(s)
- Dajia Liu
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, UMC, University of Amsterdam, Cancer Center Amsterdam, 1105 AZ Amsterdam, The Netherlands; (D.L.); (A.S.); (R.K.); (A.P.v.d.Z.)
- Department of Medical Oncology, Amsterdam UMC, University of Amsterdam, Cancer Center Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Anne Steins
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, UMC, University of Amsterdam, Cancer Center Amsterdam, 1105 AZ Amsterdam, The Netherlands; (D.L.); (A.S.); (R.K.); (A.P.v.d.Z.)
- Department of Medical Oncology, Amsterdam UMC, University of Amsterdam, Cancer Center Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Remy Klaassen
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, UMC, University of Amsterdam, Cancer Center Amsterdam, 1105 AZ Amsterdam, The Netherlands; (D.L.); (A.S.); (R.K.); (A.P.v.d.Z.)
- Department of Medical Oncology, Amsterdam UMC, University of Amsterdam, Cancer Center Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Amber P. van der Zalm
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, UMC, University of Amsterdam, Cancer Center Amsterdam, 1105 AZ Amsterdam, The Netherlands; (D.L.); (A.S.); (R.K.); (A.P.v.d.Z.)
- Department of Medical Oncology, Amsterdam UMC, University of Amsterdam, Cancer Center Amsterdam, 1105 AZ Amsterdam, The Netherlands;
- Oncode Institute, 1105 AZ Amsterdam, The Netherlands
| | - Roel J. Bennink
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, University of Amsterdam, Cancer Center Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Geertjan van Tienhoven
- Department of Radiation Oncology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Marc G. Besselink
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Maarten F. Bijlsma
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, UMC, University of Amsterdam, Cancer Center Amsterdam, 1105 AZ Amsterdam, The Netherlands; (D.L.); (A.S.); (R.K.); (A.P.v.d.Z.)
- Oncode Institute, 1105 AZ Amsterdam, The Netherlands
- Correspondence: ; Tel.: +31-(0)20-5664824
| | - Hanneke W. M. van Laarhoven
- Department of Medical Oncology, Amsterdam UMC, University of Amsterdam, Cancer Center Amsterdam, 1105 AZ Amsterdam, The Netherlands;
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CCAAT/Enhancer-Binding Protein Delta (C/EBPδ): A Previously Unrecognized Tumor Suppressor that Limits the Oncogenic Potential of Pancreatic Ductal Adenocarcinoma Cells. Cancers (Basel) 2020; 12:cancers12092546. [PMID: 32906832 PMCID: PMC7564797 DOI: 10.3390/cancers12092546] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/01/2020] [Accepted: 09/03/2020] [Indexed: 12/17/2022] Open
Abstract
Simple Summary Here we show that a protein called C/EBPδ is present in healthy pancreas tissue but almost absent in pancreas tumors. Patients with less C/EBPδ in their tumors had the most metastases and the worst survival chances, showing that C/EBPδ has tumor-suppressive properties in pancreatic cancer. In this study, we reactivated C/EBPδ in pancreatic cancer cells in vitro and observed a reduction in cell proliferation in a 2-dimentional and 3-dimensional space. This implies that tumor cells grow slower when C/EBPδ is activated and they are likely also less capable to escape the primary tumor in order to form metastases. Conversely, when we deleted C/EBPδ in pancreatic cancer cells, we observed accelerated growth. We suggest that reactivating C/EBPδ can suppress tumor growth and formation of metastases, thereby improving patient survival. Abstract CCAAT/enhancer-binding protein δ (C/EBPδ) is a transcription factor involved in growth arrest and differentiation, which has consequently been suggested to harbor tumor suppressive activities. However, C/EBPδ over-expression correlates with poor prognosis in glioblastoma and promotes genomic instability in cervical cancer, hinting at an oncogenic role of C/EBPδ in these contexts. Here, we explore the role of C/EBPδ in pancreatic cancer. We determined C/EBPδ expression in biopsies from pancreatic cancer patients using public gene-expression datasets and in-house tissue microarrays. We found that C/EBPδ is highly expressed in healthy pancreatic ductal cells but lost in pancreatic ductal adenocarcinoma. Furthermore, loss of C/EBPδ correlated with increased lymph node involvement and shorter overall survival in pancreatic ductal adenocarcinoma patients. In accordance with this, in vitro experiments showed reduced clonogenic capacity and proliferation of pancreatic ductal adenocarcinoma cells following C/EBPδ re-expression, concurrent with decreased sphere formation capacity in soft agar assays. We thus report a previously unrecognized but important tumor suppressor role of C/EBPδ in pancreatic ductal adenocarcinoma. This is of particular interest since only few tumor suppressors have been identified in the context of pancreatic cancer. Moreover, our findings suggest that restoration of C/EBPδ activity could hold therapeutic value in pancreatic ductal adenocarcinoma, although the latter claim needs to be substantiated in future studies.
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Le Large TY, Mantini G, Meijer LL, Pham TV, Funel N, van Grieken NC, Kok B, Knol J, van Laarhoven HW, Piersma SR, Jimenez CR, Kazemier G, Giovannetti E, Bijlsma MF. Microdissected pancreatic cancer proteomes reveal tumor heterogeneity and therapeutic targets. JCI Insight 2020; 5:138290. [PMID: 32634123 PMCID: PMC7455080 DOI: 10.1172/jci.insight.138290] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/24/2020] [Indexed: 12/12/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is characterized by a relative paucity of cancer cells that are surrounded by an abundance of nontumor cells and extracellular matrix, known as stroma. The interaction between stroma and cancer cells contributes to poor outcome, but how proteins from these individual compartments drive aggressive tumor behavior is not known. Here, we report the proteomic analysis of laser-capture microdissected (LCM) PDAC samples. We isolated stroma, tumor, and bulk samples from a cohort with long- and short-term survivors. Compartment-specific proteins were measured by mass spectrometry, yielding what we believe to be the largest PDAC proteome landscape to date. These analyses revealed that, in bulk analysis, tumor-derived proteins were typically masked and that LCM was required to reveal biology and prognostic markers. We validated tumor CALB2 and stromal COL11A1 expression as compartment-specific prognostic markers. We identified and functionally addressed the contributions of the tumor cell receptor EPHA2 to tumor cell viability and motility, underscoring the value of compartment-specific protein analysis in PDAC.
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Affiliation(s)
- Tessa Y.S. Le Large
- Department of Surgery and
- Department of Medical Oncology, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
- Laboratory for Experimental Oncology and Radiobiology, Amsterdam University Medical Centers, University of Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
- OncoProteomics Laboratory, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Giulia Mantini
- Department of Medical Oncology, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
- OncoProteomics Laboratory, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
- Cancer Pharmacology Lab, Fondazione Pisana per la Scienza, Pisa, Italy
| | - Laura L. Meijer
- Department of Surgery and
- Department of Medical Oncology, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Thang V. Pham
- Department of Medical Oncology, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
- OncoProteomics Laboratory, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Niccola Funel
- Unit of Anatomic Pathology II, Azienda Ospedaliera Universitaria Pisana, Pisa, Italy
| | | | | | - Jaco Knol
- Department of Medical Oncology, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
- OncoProteomics Laboratory, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Hanneke W.M. van Laarhoven
- Department of Medical Oncology, Amsterdam University Medical Centers, University of Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Sander R. Piersma
- Department of Medical Oncology, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
- OncoProteomics Laboratory, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Connie R. Jimenez
- Department of Medical Oncology, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
- OncoProteomics Laboratory, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
| | | | - Elisa Giovannetti
- Department of Medical Oncology, Amsterdam University Medical Centers, Free University Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
- Cancer Pharmacology Lab, Fondazione Pisana per la Scienza, Pisa, Italy
| | - Maarten F. Bijlsma
- Laboratory for Experimental Oncology and Radiobiology, Amsterdam University Medical Centers, University of Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
- Oncode Institute, Amsterdam, Netherlands
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Juiz N, Elkaoutari A, Bigonnet M, Gayet O, Roques J, Nicolle R, Iovanna J, Dusetti N. Basal-like and classical cells coexist in pancreatic cancer revealed by single-cell analysis on biopsy-derived pancreatic cancer organoids from the classical subtype. FASEB J 2020; 34:12214-12228. [PMID: 32686876 DOI: 10.1096/fj.202000363rr] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/16/2020] [Accepted: 06/30/2020] [Indexed: 12/22/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is composed of stromal, immune, and cancerous epithelial cells. Transcriptomic analysis of the epithelial compartment allows classification into different phenotypic subtypes as classical and basal-like. However, little is known about the intra-tumor heterogeneity particularly in the epithelial compartment. Growing evidences suggest that this phenotypic segregation is not so precise and different cancerous cell types may coexist in a single tumor. To test this hypothesis, we performed single-cell transcriptomic analyses using combinational barcoding exclusively on epithelial cells from six different classical PDAC patients obtained by Endoscopic Ultrasound (EUS) with Fine Needle Aspiration (FNA). To purify the epithelial compartment, PDAC were grown as biopsy-derived pancreatic cancer organoids. Single-cell transcriptomic analysis allowed the identification of four main cell clusters present in different proportions in all tumors. Remarkably, although all these tumors were classified as classical, one cluster present in all corresponded to a basal-like phenotype. These results reveal an unanticipated high heterogeneity of pancreatic cancers and demonstrate that basal-like cells, which have a highly aggressive phenotype, are more widespread than expected.
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Affiliation(s)
- Natalia Juiz
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - Abdessamad Elkaoutari
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - Martin Bigonnet
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - Odile Gayet
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - Julie Roques
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - Rémy Nicolle
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre le Cancer, Paris, France
| | - Juan Iovanna
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France.,Institut Paoli-Calmettes, Marseille, France
| | - Nelson Dusetti
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
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Steins A, van Mackelenbergh MG, van der Zalm AP, Klaassen R, Serrels B, Goris SG, Kocher HM, Waasdorp C, de Jong JH, Tekin C, Besselink MG, Busch OR, van de Vijver MJ, Verheij J, Dijk F, van Tienhoven G, Wilmink JW, Medema JP, van Laarhoven HWM, Bijlsma MF. High-grade mesenchymal pancreatic ductal adenocarcinoma drives stromal deactivation through CSF-1. EMBO Rep 2020; 21:e48780. [PMID: 32173982 PMCID: PMC7202203 DOI: 10.15252/embr.201948780] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 02/11/2020] [Accepted: 02/18/2020] [Indexed: 01/05/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is characterized by an abundance of stroma. Multiple molecular classification efforts have identified a mesenchymal tumor subtype that is consistently characterized by high-grade growth and poor clinical outcome. The relation between PDAC stroma and tumor subtypes is still unclear. Here, we aimed to identify how PDAC cells instruct the main cellular component of stroma, the pancreatic stellate cells (PSCs). We found in primary tissue that high-grade PDAC had reduced collagen deposition compared to low-grade PDAC. Xenografts and organotypic co-cultures established from mesenchymal-like PDAC cells featured reduced collagen and activated PSC content. Medium transfer experiments using a large set of PDAC cell lines revealed that mesenchymal-like PDAC cells consistently downregulated ACTA2 and COL1A1 expression in PSCs and reduced proliferation. We identified colony-stimulating factor 1 as the mesenchymal PDAC-derived ligand that deactivates PSCs, and inhibition of its receptor CSF1R was able to counteract this effect. In conclusion, high-grade PDAC features stroma that is low in collagen and activated PSC content, and targeting CSF1R offers direct options to maintain a tumor-restricting microenvironment.
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Affiliation(s)
- Anne Steins
- Laboratory for Experimental Oncology and RadiobiologyCenter for Experimental and Molecular MedicineCancer Center AmsterdamAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Department of Medical OncologyCancer Center AmsterdamAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Madelaine G van Mackelenbergh
- Laboratory for Experimental Oncology and RadiobiologyCenter for Experimental and Molecular MedicineCancer Center AmsterdamAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Department of Medical OncologyCancer Center AmsterdamAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Amber P van der Zalm
- Laboratory for Experimental Oncology and RadiobiologyCenter for Experimental and Molecular MedicineCancer Center AmsterdamAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Department of Medical OncologyCancer Center AmsterdamAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Remy Klaassen
- Laboratory for Experimental Oncology and RadiobiologyCenter for Experimental and Molecular MedicineCancer Center AmsterdamAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Department of Medical OncologyCancer Center AmsterdamAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Bryan Serrels
- Wolfson Wohl Cancer Research CentreGlasgow Precision Oncology LaboratoryUniversity of GlasgowGlasgowUK
| | - Sandrine G Goris
- Laboratory for Experimental Oncology and RadiobiologyCenter for Experimental and Molecular MedicineCancer Center AmsterdamAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Department of Medical OncologyCancer Center AmsterdamAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Hemant M Kocher
- Centre for Tumor BiologyBarts Cancer InstituteQueen Mary University of LondonLondonUK
| | - Cynthia Waasdorp
- Laboratory for Experimental Oncology and RadiobiologyCenter for Experimental and Molecular MedicineCancer Center AmsterdamAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Joan H de Jong
- Laboratory for Experimental Oncology and RadiobiologyCenter for Experimental and Molecular MedicineCancer Center AmsterdamAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Cansu Tekin
- Laboratory for Experimental Oncology and RadiobiologyCenter for Experimental and Molecular MedicineCancer Center AmsterdamAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Marc G Besselink
- Department of SurgeryCancer Center AmsterdamAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Olivier R Busch
- Department of SurgeryCancer Center AmsterdamAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Marc J van de Vijver
- Department of PathologyAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Joanne Verheij
- Department of PathologyAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Frederike Dijk
- Department of PathologyAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Geertjan van Tienhoven
- Department of Radiation OncologyAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Johanna W Wilmink
- Department of Medical OncologyCancer Center AmsterdamAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Jan Paul Medema
- Laboratory for Experimental Oncology and RadiobiologyCenter for Experimental and Molecular MedicineCancer Center AmsterdamAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Hanneke WM van Laarhoven
- Department of Medical OncologyCancer Center AmsterdamAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Maarten F Bijlsma
- Laboratory for Experimental Oncology and RadiobiologyCenter for Experimental and Molecular MedicineCancer Center AmsterdamAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
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