1
|
Shukla A, Kalayarasan R, Sai Krishna P, Pottakkat B. Remnant pancreatic carcinoma: The current status. World J Clin Oncol 2025; 16:107039. [DOI: 10.5306/wjco.v16.i5.107039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2025] [Revised: 03/31/2025] [Accepted: 04/11/2025] [Indexed: 05/19/2025] Open
Abstract
Pancreatic carcinoma is one of the most lethal malignancies and has a dismal prognosis. However, advances in diagnostic modalities and better multidisciplinary management have contributed to improved survival in these patients. Of late, various recurrence patterns have been observed; the most common of them being distant metastasis followed by the pancreatic bed and lymph node recurrence. Recurrence in the remnant pancreas is on the rise due to improved survival in patients who previously underwent surgery for pancreatic cancer. Total remnant pancreatectomy is an appealing option in resectable remnant pancreatic carcinoma without distant metastasis. It is an entity showing an increasing incidence and demanding further in-depth studies to elucidate the exact pathological mechanism and to establish appropriate management protocols.
Collapse
Affiliation(s)
- Ankit Shukla
- Department of Surgery, Dr Rajendra Prasad Government Medical College, Tanda 176001, India
| | - Raja Kalayarasan
- Department of Surgical Gastroenterology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry 605006, India
| | - Pothugunta Sai Krishna
- Department of Surgical Gastroenterology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry 605006, India
| | - Biju Pottakkat
- Department of Surgical Gastroenterology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry 605006, India
| |
Collapse
|
2
|
Gofrit ON, Gofrit B, Popovtzer A, Sosna J, Goldberg SN. The Clonal Trajectory of Liver and Lung Metastases in Pancreatic Ductal Adenocarcinoma. Cancer Rep (Hoboken) 2025; 8:e70228. [PMID: 40348585 PMCID: PMC12063064 DOI: 10.1002/cnr2.70228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2024] [Revised: 04/16/2025] [Accepted: 04/29/2025] [Indexed: 05/14/2025] Open
Abstract
BACKGROUND Metastatic spread can follow either the linear route-dissemination of fully malignant cells from the primary tumor, or the parallel route-dissemination of immature tumor cells and independent maturation to metastases in target organs. The linear/parallel ratio (LPR) is a model that uses metastases diameter comparisons to decipher dissemination route. LPR of +1 suggests pure linear and -1 pure parallel spread. AIMS To examine the metastases trajectory in pancreatic duct adenocarcinoma (PDAC). METHODS AND RESULTS A total of 133 patients with PDAC, including 97 patients (72.9%) with synchronous and 36 (27.1%) with metachronous metastases with a total of 1054 lung and 2898 liver metastases, were evaluated. We found that metastatic spread to both liver and lungs is almost exclusively via the linear route (lungs median LPR + 1, interquartile range [IQR] 0.97,1. Liver median LPR + 0.98, IQR 0.83,1). Calculated from the primary diagnosis, overall survival (OS) of patients with metachronous metastases was significantly better compared to patients with synchronous disease (14 months, IQR 10,26, vs. 7 months, IQR 6,9, p < 0.0001). However, calculated from the time of metastases diagnosis, OS of both groups was similar (4 months, IQR 3,8, vs. 7 months, IQR 6,9, p = 0.235). CONCLUSION These two observations suggest that metastatic spread of PDAC is almost exclusively via the linear route, that is, directly from the primary tumor. Therefore, liver or lung metastases are already present in most patients with PDAC at the time of initial diagnosis. This suggests that local treatment in patients with seemingly localized disease does not decrease their risk of developing metastases and that systemic treatment must follow.
Collapse
Affiliation(s)
- Ofer N. Gofrit
- Department of UrologyHadassah Medical Center, Faculty of Medicine, Hebrew University of JerusalemJerusalemIsrael
| | - Ben Gofrit
- School of Engineering and Computer Science, Hebrew University of JerusalemJerusalemIsrael
| | - Aron Popovtzer
- Department of OncologyHadassah Medical Center, Faculty of Medicine, Hebrew University of JerusalemJerusalemIsrael
| | - Jacob Sosna
- Department of RadiologyHadassah Medical Center, Faculty of Medicine, Hebrew University of JerusalemJerusalemIsrael
| | - S. Nahum Goldberg
- Department of RadiologyHadassah Medical Center, Faculty of Medicine, Hebrew University of JerusalemJerusalemIsrael
| |
Collapse
|
3
|
Pei G, Min J, Rajapakshe KI, Branchi V, Liu Y, Selvanesan BC, Thege F, Sadeghian D, Zhang D, Cho KS, Chu Y, Dai E, Han G, Li M, Yee C, Takahashi K, Garg B, Tiriac H, Bernard V, Semaan A, Grem JL, Caffrey TC, Burks JK, Lowy AM, Aguirre AJ, Grandgenett PM, Hollingsworth MA, Guerrero PA, Wang L, Maitra A. Spatial mapping of transcriptomic plasticity in metastatic pancreatic cancer. Nature 2025:10.1038/s41586-025-08927-x. [PMID: 40269162 DOI: 10.1038/s41586-025-08927-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/20/2025] [Indexed: 04/25/2025]
Abstract
Patients with treatment-refractory pancreatic cancer often succumb to systemic metastases1-3; however, the transcriptomic heterogeneity that underlies therapeutic recalcitrance remains understudied, particularly in a spatial context. Here we construct high-resolution maps of lineage states, clonal architecture and the tumour microenvironment (TME) using spatially resolved transcriptomics from 55 samples of primary tumour and metastases (liver, lung and peritoneum) collected from rapid autopsies of 13 people. We observe discernible transcriptomic shifts in cancer-cell lineage states as tumours transition from primary sites to organ-specific metastases, with the most pronounced intra-patient distinctions between liver and lung. Phylogenetic trees constructed from inferred copy number variations in primary and metastatic loci in each patient highlight diverse patient-specific evolutionary trajectories and clonal dissemination. We show that multiple tumour lineage states co-exist in each tissue, including concurrent metastatic foci in the same organ. Agnostic to tissue site, lineage states correlate with distinct TME features, such as the spatial proximity of TGFB1-expressing myofibroblastic cancer-associated fibroblasts (myCAFs) to aggressive 'basal-like' cancer cells, but not to cells in the 'classical' or 'intermediate' states. These findings were validated through orthogonal and cross-species analyses using mouse tissues and patient-derived organoids. Notably, basal-like cancer cells aligned with myCAFs correlate with plasma-cell exclusion from the tumour milieu, and neighbouring cell analyses suggest that CXCR4-CXCL12 signalling is the underlying basis for observed immune exclusion. Collectively, our findings underscore the profound transcriptomic heterogeneity and microenvironmental dynamics that characterize treatment-refractory pancreatic cancer.
Collapse
Affiliation(s)
- Guangsheng Pei
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jimin Min
- Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kimal I Rajapakshe
- Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vittorio Branchi
- Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yunhe Liu
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Benson Chellakkan Selvanesan
- Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fredrik Thege
- Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dorsay Sadeghian
- Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Daiwei Zhang
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Kyung Serk Cho
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yanshuo Chu
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Enyu Dai
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Guangchun Han
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mingyao Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Cassian Yee
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Immunology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kazuki Takahashi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Bharti Garg
- Department of Surgery, Division of Surgical Oncology, Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Herve Tiriac
- Department of Surgery, Division of Surgical Oncology, Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Vincent Bernard
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexander Semaan
- Department of Surgery, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Jean L Grem
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Thomas C Caffrey
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Jared K Burks
- Department of Leukemia and Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew M Lowy
- Department of Surgery, Division of Surgical Oncology, Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Andrew J Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Paul M Grandgenett
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Michael A Hollingsworth
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Paola A Guerrero
- Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linghua Wang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA.
- James P. Allison Institute, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Institute for Data Science in Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Anirban Maitra
- Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| |
Collapse
|
4
|
Dawalibi A, Bakir M, Mohammad KS. The genetic architecture of bone metastases: unveiling the role of epigenetic and genetic modifications in drug resistance. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2025; 8:19. [PMID: 40342734 PMCID: PMC12059479 DOI: 10.20517/cdr.2025.28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2025] [Revised: 03/26/2025] [Accepted: 04/17/2025] [Indexed: 05/11/2025]
Abstract
Bone metastases represent frequent and severe complications in various cancers, notably impacting prognosis and quality of life. This review article delves into the genetic and epigenetic mechanisms underpinning drug resistance in bone metastases, a key challenge in effective cancer treatment. The development of drug resistance in cancer can manifest as either intrinsic or acquired, with genetic heterogeneity playing a pivotal role. Intrinsic resistance is often due to pre-existing mutations, while acquired resistance evolves through genetic and epigenetic alterations during treatment. These alterations include mutations in driver genes like TP53 and RB1, epigenetic modifications such as DNA methylation and histone changes, and pathway alterations, notably involving RANK-RANKL signaling and the PI3K/AKT/mTOR cascade. Recent studies underline the significance of the tumor microenvironment in fostering drug resistance, with components such as cancer-associated fibroblasts and hypoxia playing crucial roles. The interactions between metastatic cancer cells and the bone microenvironment facilitate survival and the proliferation of drug-resistant clones. This review highlights the necessity of understanding these complex interactions to develop targeted therapies that can overcome resistance and improve treatment outcomes. Current therapeutic strategies and future directions are discussed, emphasizing the integration of genomic profiling and targeted interventions in managing bone metastases. The evolving landscape of genetic research, including the application of next-generation sequencing and CRISPR technology, offers promising avenues for novel and more effective therapeutic strategies. This comprehensive exploration aims to provide insights into the molecular intricacies of drug resistance in bone metastases, paving the way for improved clinical management and patient care.
Collapse
Affiliation(s)
- Ahmad Dawalibi
- Department of Anatomy, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Mohamad Bakir
- Department of Medicine, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Khalid S. Mohammad
- Department of Anatomy, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| |
Collapse
|
5
|
Naxerova K. Evolutionary paths towards metastasis. Nat Rev Cancer 2025:10.1038/s41568-025-00814-x. [PMID: 40263543 DOI: 10.1038/s41568-025-00814-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/18/2025] [Indexed: 04/24/2025]
Abstract
The evolution of metastasis in humans is considerably less well understood than the biology of early carcinogenesis. For over a century, clinicians and scientists have been debating whether metastatic potential is the intrinsic property of a cancer, pre-determined by the molecular characteristics of the tumour founder cell, or whether metastatic capacity evolves in a stepwise fashion as the tumour grows, akin to the multistage accumulation of oncogenic alterations that give rise to the first cancer cell. In this Perspective, I examine how genetic analyses of primary tumours and matched metastases can distinguish between these two competing metastasis evolution models, with particular emphasis on the utility of metastatic randomness - a quantitative measure that reflects whether metastases arise from a random selection of primary tumour subclones or whether they are enriched for descendants of privileged lineages that have acquired pro-metastatic traits. Probable metastasis evolution trajectories in tumours with high and low baseline metastatic capacity are discussed, along with the role of seeding rates and selection at different metastatic host sites. Finally, I argue that trailblazing insights into human metastasis biology are immediately possible if we make a concerted effort to apply existing experimental and theoretical tools to the right patient cohorts.
Collapse
Affiliation(s)
- Kamila Naxerova
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
6
|
Liaki V, Rosas-Perez B, Guerra C. Unlocking the Genetic Secrets of Pancreatic Cancer: KRAS Allelic Imbalances in Tumor Evolution. Cancers (Basel) 2025; 17:1226. [PMID: 40227826 PMCID: PMC11987834 DOI: 10.3390/cancers17071226] [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: 01/05/2025] [Revised: 03/13/2025] [Accepted: 03/31/2025] [Indexed: 04/15/2025] Open
Abstract
Pancreatic Ductal Adenocarcinoma (PDAC) belongs to the types of cancer with the highest lethality. It is also remarkably chemoresistant to the few available cytotoxic therapeutic options. PDAC is characterized by limited mutational heterogeneity of the known driver genes, KRAS, CDKN2A, TP53, and SMAD4, observed in both early-stage and advanced tumors. In this review, we summarize the two proposed models of genetic evolution of pancreatic cancer. The gradual or stepwise accumulated mutations model has been widely studied. On the contrary, less evidence exists on the more recent simultaneous model, according to which rapid tumor evolution is driven by the concurrent accumulation of genetic alterations. In both models, oncogenic KRAS mutations are the main initiating event. Here, we analyze the emerging topic of KRAS allelic imbalances and how it arises during tumor evolution, as it is often detected in advanced and metastatic PDAC. We also summarize recent evidence on how it affects tumor biology, metastasis, and response to therapy. To this extent, we highlight the necessity to include studies of KRAS allelic frequencies in the design of future therapeutic strategies against pancreatic cancer.
Collapse
Affiliation(s)
- Vasiliki Liaki
- Molecular Oncology Program, Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain; (B.R.-P.); (C.G.)
| | - Blanca Rosas-Perez
- Molecular Oncology Program, Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain; (B.R.-P.); (C.G.)
| | - Carmen Guerra
- Molecular Oncology Program, Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain; (B.R.-P.); (C.G.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| |
Collapse
|
7
|
Ramesh RPG, Yasmin H, Ponnachan P, Al-Ramadi B, Kishore U, Joseph AM. Phenotypic heterogeneity and tumor immune microenvironment directed therapeutic strategies in pancreatic ductal adenocarcinoma. Front Immunol 2025; 16:1573522. [PMID: 40230862 PMCID: PMC11994623 DOI: 10.3389/fimmu.2025.1573522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2025] [Accepted: 03/04/2025] [Indexed: 04/16/2025] Open
Abstract
Pancreatic cancer is an aggressive tumor with high metastatic potential which leads to decreased survival rate and resistance to chemotherapy and immunotherapy. Nearly 90% of pancreatic cancer comprises pancreatic ductal adenocarcinoma (PDAC). About 80% of diagnoses takes place at the advanced metastatic stage when it is unresectable, which renders chemotherapy regimens ineffective. There is also a dearth of specific biomarkers for early-stage detection. Advances in next generation sequencing and single cell profiling have identified molecular alterations and signatures that play a role in PDAC progression and subtype plasticity. Most chemotherapy regimens have shown only modest survival benefits, and therefore, translational approaches for immunotherapies and combination therapies are urgently required. In this review, we have examined the immunosuppressive and dense stromal network of tumor immune microenvironment with various metabolic and transcriptional changes that underlie the pro-tumorigenic properties in PDAC in terms of phenotypic heterogeneity, plasticity and subtype co-existence. Moreover, the stromal heterogeneity as well as genetic and epigenetic changes that impact PDAC development is discussed. We also review the PDAC interaction with sequestered cellular and humoral components present in the tumor immune microenvironment that modify the outcome of chemotherapy and radiation therapy. Finally, we discuss different therapeutic interventions targeting the tumor immune microenvironment aimed at better prognosis and improved survival in PDAC.
Collapse
Affiliation(s)
- Remya P. G. Ramesh
- Department of Veterinary Medicine, UAE University, Al Ain, United Arab Emirates
| | - Hadida Yasmin
- Immunology and Cell Biology Laboratory, Department of Zoology, Cooch Behar Panchanan Barma University, Cooch Behar, West Bengal, India
| | - Pretty Ponnachan
- Department of Veterinary Medicine, UAE University, Al Ain, United Arab Emirates
| | - Basel Al-Ramadi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Uday Kishore
- Department of Veterinary Medicine, UAE University, Al Ain, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Ann Mary Joseph
- Department of Veterinary Medicine, UAE University, Al Ain, United Arab Emirates
| |
Collapse
|
8
|
Lo EKW, Idrizi A, Tryggvadottir R, Zhou W, Hou W, Ji H, Cahan P, Feinberg AP. DNA methylation memory of pancreatic acinar-ductal metaplasia transition state altering Kras-downstream PI3K and Rho GTPase signaling in the absence of Kras mutation. Genome Med 2025; 17:32. [PMID: 40156071 PMCID: PMC11951614 DOI: 10.1186/s13073-025-01452-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Accepted: 03/10/2025] [Indexed: 04/01/2025] Open
Abstract
BACKGROUND A critical area of recent cancer research is the emergence of transition states between normal and cancer that exhibit increased cell plasticity which underlies tumor cell heterogeneity. Pancreatic ductal adenocarcinoma (PDAC) can arise from the combination of a transition state termed acinar-to-ductal metaplasia (ADM) and a gain-of-function mutation in the proto-oncogene KRAS. During ADM, digestive enzyme-producing acinar cells acquire a transient ductal epithelium-like phenotype while maintaining their geographical acinar organization. One route of ADM initiation is the overexpression of the Krüppel-like factor 4 gene (KLF4) in the absence of oncogenic driver mutations. Here, we asked to what extent cells acquire and retain an epigenetic memory of the ADM transition state in the absence of oncogene mutation. METHODS We profiled the DNA methylome and transcriptome of KLF4-induced ADM in transgenic mice at various timepoints during and after recovery from ADM. We validated the identified DNA methylation and transcriptomic signatures in the widely used caerulein model of inducible pancreatitis. RESULTS We identified differential DNA methylation at Kras-downstream PI3K and Rho/Rac/Cdc42 GTPase pathway genes during ADM, as well as a corresponding gene expression increase in these pathways. Importantly, differential methylation persisted after gene expression returned to normal. Caerulein exposure, which induces widespread digestive system changes in addition to ADM, showed similar changes in DNA methylation in ADM cells. Regions of differential methylation were enriched for motifs of KLF and AP-1 family transcription factors, as were those of human pancreatic intraepithelial neoplasia (PanIN) samples, demonstrating the relevance of this epigenetic transition state memory in human carcinogenesis. Finally, single-cell spatial transcriptomics revealed that these ADM transition cells were enriched for PI3K pathway and AP1 family members. CONCLUSIONS Our comprehensive study of DNA methylation in the acinar-ductal metaplasia transition state links epigenetic memory to cancer-related cell plasticity even in the absence of oncogenic mutation.
Collapse
Affiliation(s)
- Emily K W Lo
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, 720 Rutland Avenue, Baltimore, MD, 21205, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, 1830 E. Monument Street, Baltimore, MD, USA
| | - Adrian Idrizi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, 1830 E. Monument Street, Baltimore, MD, USA
| | - Rakel Tryggvadottir
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, 1830 E. Monument Street, Baltimore, MD, USA
| | - Weiqiang Zhou
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Wenpin Hou
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Patrick Cahan
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, 720 Rutland Avenue, Baltimore, MD, 21205, USA.
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Andrew P Feinberg
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, 720 Rutland Avenue, Baltimore, MD, 21205, USA.
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Medicine, Johns Hopkins University School of Medicine, 1830 E. Monument Street, Baltimore, MD, USA.
| |
Collapse
|
9
|
Mullen KM, Hong J, Attiyeh MA, Hayashi A, Sakamoto H, Kohutek ZA, McIntyre CA, Zhang H, Makohon-Moore AP, Zucker A, Wood LD, Myers MA, Arnold BJ, Zaccaria S, Chou JF, Capanu M, Socci ND, Raphael BJ, Iacobuzio-Donahue CA. The Evolutionary Forest of Pancreatic Cancer. Cancer Discov 2025; 15:329-345. [PMID: 39378050 PMCID: PMC11803399 DOI: 10.1158/2159-8290.cd-23-1541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 08/06/2024] [Accepted: 10/04/2024] [Indexed: 02/08/2025]
Abstract
SIGNIFICANCE Although the pancreatic cancer genome has been described, it has not been explored with respect to stages of diagnosis or treatment bottlenecks. We now describe and quantify the genomic features of PDAC in the context of evolutionary metrics and in doing so have identified a novel prognostic biomarker.
Collapse
Affiliation(s)
- Katelyn M. Mullen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jungeui Hong
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc A. Attiyeh
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Akimasa Hayashi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hitomi Sakamoto
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zachary A. Kohutek
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Caitlin A. McIntyre
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Haochen Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Amanda Zucker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Laura D. Wood
- Division of Gastrointestinal Pathology, Department of Pathology, Johns Hopkins Hospital, Baltimore, Maryland
| | - Matthew A. Myers
- Department of Computer Science, Princeton University, Princeton, New Jersey
| | - Brian J. Arnold
- Department of Computer Science, Princeton University, Princeton, New Jersey
| | - Simone Zaccaria
- Department of Computer Science, Princeton University, Princeton, New Jersey
| | - Joanne F. Chou
- Biostatistics and Epidemiology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marinela Capanu
- Biostatistics and Epidemiology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nicholas D. Socci
- Bioinformatics Core, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Christine A. Iacobuzio-Donahue
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
- The David M. Rubenstein Center for Pancreatic Cancer Research, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| |
Collapse
|
10
|
Yao L, Qin W, Hu L, Shi T, Yu Yang J, Li Q, Nie H, Li J, Wang X, Zhu L, Liu D, Zhang Y, Jiang S, Zhang Z, Yang X, Li D, Zhang X. Reciprocal tumor-platelet interaction through the EPHB1-EFNB1 axis in the liver metastatic niche promotes metastatic tumor outgrowth in pancreatic ductal adenocarcinoma. Cancer Commun (Lond) 2025; 45:143-166. [PMID: 39648610 PMCID: PMC11833672 DOI: 10.1002/cac2.12637] [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: 04/02/2024] [Revised: 11/08/2024] [Accepted: 11/27/2024] [Indexed: 12/10/2024] Open
Abstract
BACKGROUND The interaction between the metastatic microenvironment and tumor cells plays an important role in metastatic tumor formation. Platelets play pivotal roles in hematogenous cancer metastasis through tumor cell-platelet interaction in blood vessels. Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy distinguished by its notable tendency to metastasize to the liver. However, the role of platelet in the liver metastatic niche of PDAC remains elusive. This study aimed to elucidate the role of platelets and their interactions with tumor cells in the liver metastatic niche of PDAC. METHODS An mCherry niche-labeling system was established to identify cells in the liver metastatic niche of PDAC. Platelet depletion in a liver metastasis mouse model was used to observe the function of platelets in PDAC liver metastasis. Gain-of-function and loss-of-function of erythropoietin-producing hepatocellular receptor B1 (Ephb1), tumor cell-platelet adhesion, recombinant protein, and tryptophan hydroxylase 1 (Tph1)-knockout mice were used to study the crosstalk between platelets and tumor cells in the liver metastatic niche. RESULTS The mCherry metastatic niche-labeling system revealed the presence of activated platelets in the liver metastatic niche of PDAC patients. Platelet depletion decreased liver metastatic tumor growth in mice. Mechanistically, tumor cell-expressed EPHB1 and platelet-expressed Ephrin B1 (EFNB1) mediated contact-dependent activation of platelets via reverse signaling-mediated AKT signaling activation, and in turn, activated platelet-released 5-HT, further enhancing tumor growth. CONCLUSION We revealed the crosstalk between platelets and tumor cells in the liver metastatic niche of PDAC. Reciprocal tumor-platelet interaction mediated by the EPHB1-EFNB1 reverse signaling promoted metastatic PDAC outgrowth via 5-HT in the liver. Interfering the tumor-platelet interaction by targeting the EPHB1-EFNB1 axis may represent a promising therapeutic intervention for PDAC liver metastasis.
Collapse
Affiliation(s)
- Lin‐Li Yao
- State Key Laboratory of Systems Medicine for CancerShanghai Cancer InstituteRen Ji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiP. R. China
| | - Wei‐Ting Qin
- Department of Radiation OncologyRen Ji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiP. R. China
| | - Li‐Peng Hu
- State Key Laboratory of Systems Medicine for CancerShanghai Cancer InstituteRen Ji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiP. R. China
| | - Tie‐Zhu Shi
- Department of UrologyShanghai General HospitalShanghai Jiao Tong UniversityShanghaiP. R. China
| | - Jian Yu Yang
- Department of Biliary‐Pancreatic SurgeryRen Ji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiP. R. China
| | - Qing Li
- State Key Laboratory of Systems Medicine for CancerShanghai Cancer InstituteRen Ji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiP. R. China
| | - Hui‐Zhen Nie
- State Key Laboratory of Systems Medicine for CancerShanghai Cancer InstituteRen Ji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiP. R. China
| | - Jun Li
- State Key Laboratory of Systems Medicine for CancerShanghai Cancer InstituteRen Ji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiP. R. China
| | - Xu Wang
- State Key Laboratory of Systems Medicine for CancerShanghai Cancer InstituteRen Ji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiP. R. China
| | - Lei Zhu
- State Key Laboratory of Systems Medicine for CancerShanghai Cancer InstituteRen Ji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiP. R. China
| | - De‐Jun Liu
- Department of Biliary‐Pancreatic SurgeryRen Ji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiP. R. China
| | - Yan‐Li Zhang
- State Key Laboratory of Systems Medicine for CancerShanghai Cancer InstituteRen Ji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiP. R. China
| | - Shu‐Heng Jiang
- State Key Laboratory of Systems Medicine for CancerShanghai Cancer InstituteRen Ji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiP. R. China
| | - Zhi‐Gang Zhang
- State Key Laboratory of Systems Medicine for CancerShanghai Cancer InstituteRen Ji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiP. R. China
| | - Xiao‐Mei Yang
- State Key Laboratory of Systems Medicine for CancerShanghai Cancer InstituteRen Ji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiP. R. China
| | - Dong‐Xue Li
- State Key Laboratory of Systems Medicine for CancerShanghai Cancer InstituteRen Ji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiP. R. China
| | - Xue‐Li Zhang
- State Key Laboratory of Systems Medicine for CancerShanghai Cancer InstituteRen Ji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiP. R. China
| |
Collapse
|
11
|
Oyon D, Lopez-Pascual A, Castello-Uribe B, Uriarte I, Orsi G, Llorente S, Elurbide J, Adan-Villaescusa E, Valbuena-Goiricelaya E, Irigaray-Miramon A, Latasa MU, Martinez-Perez LA, Bonetti LR, Prosper F, Ponz-Sarvise M, Vicent S, Pineda-Lucena A, Ruiz-Clavijo D, Sangro B, Larracoechea UA, Tian TV, Casadei-Gardini A, Amat I, Arechederra M, Berasain C, Urman JM, Avila MA, Fernandez-Barrena MG. Targeting of the G9a, DNMT1 and UHRF1 epigenetic complex as an effective strategy against pancreatic ductal adenocarcinoma. J Exp Clin Cancer Res 2025; 44:13. [PMID: 39810240 PMCID: PMC11734372 DOI: 10.1186/s13046-024-03268-5] [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: 09/28/2024] [Accepted: 12/24/2024] [Indexed: 01/16/2025] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with limited treatment options and a poor prognosis. The critical role of epigenetic alterations such as changes in DNA methylation, histones modifications, and chromatin remodeling, in pancreatic tumors progression is becoming increasingly recognized. Moreover, in PDAC these aberrant epigenetic mechanisms can also limit therapy efficacy. This study aimed to investigate the expression and prognostic significance of a key epigenetic complex encompassing DNA methyltransferase-1 (DNMT1), the histone methyltransferase G9a, and the scaffold protein UHRF1 in PDAC. We also evaluated the therapeutic potential of an innovative inhibitor targeting these epigenetic effectors. METHODS Immunohistochemical analysis of DNMT1, G9a, and UHRF1 expression was conducted in human PDAC tissue samples. Staining was semi-quantitatively scored, and overexpression was defined as moderate to strong positivity. The prognostic impact was assessed by correlating protein expression with patient survival. The antitumoral effects of the dual DNMT1-G9a inhibitor CM272 were tested in PDAC cell lines, followed by transcriptomic analyses to identify underlying mechanisms. The in vivo antitumoral efficacy of CM272 was evaluated in PDAC xenograft and syngeneic mouse models, both alone and in combination with anti-PD1 immunotherapy. RESULTS DNMT1, G9a, and UHRF1 were significantly overexpressed in PDAC cells and stroma compared to normal pancreatic tissues. Simultaneous overexpression of the three proteins was associated with significantly reduced survival in resected PDAC patients. CM272 exhibited potent antiproliferative activity in PDAC cell lines, inducing apoptosis and altering key metabolic and cell cycle-related genes. CM272 also enhanced chemotherapy sensitivity and significantly inhibited tumor growth in vivo without detectable toxicity. Combination of CM272 with anti-PD1 therapy further improved antitumor responses and immune cell infiltration, particularly CD4 + and CD8 + T cells. CONCLUSIONS The combined overexpression of DNMT1, G9a, and UHRF1 in PDAC is a strong predictor of poor prognosis. CM272, by targeting this epigenetic complex, shows promising therapeutic potential by inducing apoptosis, reprogramming metabolic pathways, and enhancing immune responses. The combination of CM272 with immunotherapy offers a novel, effective treatment strategy for PDAC.
Collapse
Affiliation(s)
- Daniel Oyon
- Department of Gastroenterology, Galdakao-Usansolo Hospital, Galdakao, Spain
- Biobizkaia Health Research Institute, Bizkaia, Spain
| | - Amaya Lopez-Pascual
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research, IdiSNA, Pamplona, Spain
| | - Borja Castello-Uribe
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
| | - Iker Uriarte
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Giulia Orsi
- Oncology Department, University Hospital of Modena, Modena, Italy
- Department of Oncology, IRCCS San Raffaele Scientific Institute Hospital, Vita-Salute San Raffaele University, Milan, Italy
| | - Sofia Llorente
- Preclinical and Translational Research Program, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Jasmin Elurbide
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Elena Adan-Villaescusa
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
| | | | - Ainara Irigaray-Miramon
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
| | - Maria Ujue Latasa
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
| | - Luz A Martinez-Perez
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
- Universidad de Guadalajara Centro Universitario de Ciencias de La Salud, Guadalajara, Mexico
| | - Luca Reggiani Bonetti
- Department of Medical and Surgical Sciences for Children and Adults, Division of Pathology University-Hospital of Modena and Reggio Emilia, Modena, Italy
| | - Felipe Prosper
- Navarra Institute for Health Research, IdiSNA, Pamplona, Spain
- Hemato-Oncology Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
- CIBERonc, Instituto de Salud Carlos III, Madrid, Spain
| | - Mariano Ponz-Sarvise
- Navarra Institute for Health Research, IdiSNA, Pamplona, Spain
- CIBERonc, Instituto de Salud Carlos III, Madrid, Spain
- Departments of Oncology and Immunology, Clinica Universidad de Navarra, Pamplona, Spain
| | - Silvestre Vicent
- Navarra Institute for Health Research, IdiSNA, Pamplona, Spain
- CIBERonc, Instituto de Salud Carlos III, Madrid, Spain
- Oncogenes and Effector Targets Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
| | | | - David Ruiz-Clavijo
- Department of Gastroenterology and Hepatology, Navarra University Hospital Complex, Pamplona, Spain
| | - Bruno Sangro
- Navarra Institute for Health Research, IdiSNA, Pamplona, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Hepatology Unit, Clínica Universidad de Navarra, CCUN, Pamplona, Spain
| | - Urko Aguirre Larracoechea
- Research Unit, Osakidetza Basque Health Service, Barrualde-Galdakao Integrated Health Organisation, Galdakao-Usansolo Hospital, Galdakao, Spain
| | - Tian V Tian
- Preclinical and Translational Research Program, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Andrea Casadei-Gardini
- Oncology Department, University Hospital of Modena, Modena, Italy
- Department of Oncology, IRCCS San Raffaele Scientific Institute Hospital, Vita-Salute San Raffaele University, Milan, Italy
| | - Irene Amat
- Navarra Institute for Health Research, IdiSNA, Pamplona, Spain
- Department of Pathology, Navarra University Hospital Complex, Pamplona, Spain
| | - Maria Arechederra
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research, IdiSNA, Pamplona, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Berasain
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Jesus M Urman
- Navarra Institute for Health Research, IdiSNA, Pamplona, Spain
- Department of Gastroenterology and Hepatology, Navarra University Hospital Complex, Pamplona, Spain
| | - Matias A Avila
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research, IdiSNA, Pamplona, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Maite G Fernandez-Barrena
- Hepatology Laboratory, Solid Tumors Program, CIMA, CCUN, University of Navarra, Pamplona, Spain.
- Navarra Institute for Health Research, IdiSNA, Pamplona, Spain.
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain.
| |
Collapse
|
12
|
Ying H, Kimmelman AC, Bardeesy N, Kalluri R, Maitra A, DePinho RA. Genetics and biology of pancreatic ductal adenocarcinoma. Genes Dev 2025; 39:36-63. [PMID: 39510840 PMCID: PMC11789498 DOI: 10.1101/gad.351863.124] [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: 11/15/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) poses a grim prognosis for patients. Recent multidisciplinary research efforts have provided critical insights into its genetics and tumor biology, creating the foundation for rational development of targeted and immune therapies. Here, we review the PDAC genomic landscape and the role of specific oncogenic events in tumor initiation and progression, as well as their contributions to shaping its tumor biology. We further summarize and synthesize breakthroughs in single-cell and metabolic profiling technologies that have illuminated the complex cellular composition and heterotypic interactions of the PDAC tumor microenvironment, with an emphasis on metabolic cross-talk across cancer and stromal cells that sustains anabolic growth and suppresses tumor immunity. These conceptual advances have generated novel immunotherapy regimens, particularly cancer vaccines, which are now in clinical testing. We also highlight the advent of KRAS targeted therapy, a milestone advance that has transformed treatment paradigms and offers a platform for combined immunotherapy and targeted strategies. This review provides a perspective summarizing current scientific and therapeutic challenges as well as practice-changing opportunities for the PDAC field at this major inflection point.
Collapse
Affiliation(s)
- Haoqiang Ying
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA;
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, University of Texas Health Science Center, Houston, Texas 77030, USA
| | - Alec C Kimmelman
- Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, New York 10016, USA
- Department of Radiation Oncology, New York University Grossman School of Medicine, New York, New York 10016, USA
| | - Nabeel Bardeesy
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts 02114, USA
- The Cancer Program, Broad Institute, Cambridge, Massachusetts 02142, USA
| | - Raghu Kalluri
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, University of Texas Health Science Center, Houston, Texas 77030, USA
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Department of Bioengineering, Rice University, Houston, Texas 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Anirban Maitra
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, University of Texas Health Science Center, Houston, Texas 77030, USA
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Sheikh Ahmed Pancreatic Cancer Research Center, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Ronald A DePinho
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, University of Texas Health Science Center, Houston, Texas 77030, USA;
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| |
Collapse
|
13
|
Laisné M, Lupien M, Vallot C. Epigenomic heterogeneity as a source of tumour evolution. Nat Rev Cancer 2025; 25:7-26. [PMID: 39414948 DOI: 10.1038/s41568-024-00757-9] [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] [Accepted: 09/16/2024] [Indexed: 10/18/2024]
Abstract
In the past decade, remarkable progress in cancer medicine has been achieved by the development of treatments that target DNA sequence variants. However, a purely genetic approach to treatment selection is hampered by the fact that diverse cell states can emerge from the same genotype. In multicellular organisms, cell-state heterogeneity is driven by epigenetic processes that regulate DNA-based functions such as transcription; disruption of these processes is a hallmark of cancer that enables the emergence of defective cell states. Advances in single-cell technologies have unlocked our ability to quantify the epigenomic heterogeneity of tumours and understand its mechanisms, thereby transforming our appreciation of how epigenomic changes drive cancer evolution. This Review explores the idea that epigenomic heterogeneity and plasticity act as a reservoir of cell states and therefore as a source of tumour evolution. Best practices to quantify epigenomic heterogeneity and explore its various causes and consequences are discussed, including epigenomic reprogramming, stochastic changes and lasting memory. The design of new therapeutic approaches to restrict epigenomic heterogeneity, with the long-term objective of limiting cancer development and progression, is also addressed.
Collapse
Affiliation(s)
- Marthe Laisné
- CNRS UMR3244, Institut Curie, PSL University, Paris, France
- Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontorio, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontorio, Canada.
- Ontario Institute for Cancer Research, Toronto, Ontorio, Canada.
| | - Céline Vallot
- CNRS UMR3244, Institut Curie, PSL University, Paris, France.
- Translational Research Department, Institut Curie, PSL University, Paris, France.
- Single Cell Initiative, Institut Curie, PSL University, Paris, France.
| |
Collapse
|
14
|
Roszkowska M. Multilevel Mechanisms of Cancer Drug Resistance. Int J Mol Sci 2024; 25:12402. [PMID: 39596466 PMCID: PMC11594576 DOI: 10.3390/ijms252212402] [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: 11/04/2024] [Revised: 11/14/2024] [Accepted: 11/17/2024] [Indexed: 11/28/2024] Open
Abstract
Cancer drug resistance represents one of the most significant challenges in oncology and manifests through multiple interconnected molecular and cellular mechanisms. Objective: To provide a comprehensive analysis of multilevel processes driving treatment resistance by integrating recent advances in understanding genetic, epigenetic, and microenvironmental factors. This is a systematic review of the recent literature focusing on the mechanisms of cancer drug resistance, including genomic studies, clinical trials, and experimental research. Key findings include the following: (1) Up to 63% of somatic mutations can be heterogeneous within individual tumors, contributing to resistance development; (2) cancer stem cells demonstrate enhanced DNA repair capacity and altered metabolic profiles; (3) the tumor microenvironment, including cancer-associated fibroblasts and immune cell populations, plays a crucial role in promoting resistance; and (4) selective pressure from radiotherapy drives the emergence of radioresistant phenotypes through multiple adaptive mechanisms. Understanding the complex interplay between various resistance mechanisms is essential for developing effective treatment strategies. Future therapeutic approaches should focus on combination strategies that target multiple resistance pathways simultaneously, guided by specific biomarkers.
Collapse
Affiliation(s)
- Malgorzata Roszkowska
- Department of Clinical Neuropsychology, Collegium Medicum, Nicolaus Copernicus University, 85-067 Bydgoszcz, Poland
| |
Collapse
|
15
|
Zhao Y, Qin C, Lin C, Li Z, Zhao B, Li T, Zhang X, Wang W. Pancreatic ductal adenocarcinoma cells reshape the immune microenvironment: Molecular mechanisms and therapeutic targets. Biochim Biophys Acta Rev Cancer 2024; 1879:189183. [PMID: 39303859 DOI: 10.1016/j.bbcan.2024.189183] [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: 06/09/2024] [Revised: 08/23/2024] [Accepted: 09/13/2024] [Indexed: 09/22/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a digestive system malignancy characterized by challenging early detection, limited treatment alternatives, and generally poor prognosis. Although there have been significant advancements in immunotherapy for hematological malignancies and various solid tumors in recent decades, with impressive outcomes in recent preclinical and clinical trials, the effectiveness of these therapies in treating PDAC continues to be modest. The unique immunological microenvironment of PDAC, especially the abnormal distribution, complex composition, and variable activation states of tumor-infiltrating immune cells, greatly restricts the effectiveness of immunotherapy. Undoubtedly, integrating data from both preclinical models and human studies helps accelerate the identification of reliable molecules and pathways responsive to targeted biological therapies and immunotherapies, thereby continuously optimizing therapeutic combinations. In this review, we delve deeply into how PDAC cells regulate the immune microenvironment through complex signaling networks, affecting the quantity and functional status of immune cells to promote immune escape and tumor progression. Furthermore, we explore the multi-modal immunotherapeutic strategies currently under development, emphasizing the transformation of the immunosuppressive environment into an anti-tumor milieu by targeting specific molecular and cellular pathways, providing insights for the development of novel treatment strategies.
Collapse
Affiliation(s)
- Yutong Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China
| | - Cheng Qin
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China
| | - Chen Lin
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China
| | - Zeru Li
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China
| | - Bangbo Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China
| | - Tianyu Li
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China
| | - Xiangyu Zhang
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China
| | - Weibin Wang
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China.
| |
Collapse
|
16
|
Lo EKW, Idrizi A, Tryggvadottir R, Zhou W, Hou W, Ji H, Cahan P, Feinberg AP. DNA methylation memory of pancreatic acinar-ductal metaplasia transition state altering Kras-downstream PI3K and Rho GTPase signaling in the absence of Kras mutation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.26.620414. [PMID: 39553977 PMCID: PMC11565792 DOI: 10.1101/2024.10.26.620414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
Abstract
A critical area of recent cancer research is the emergence of transition states between normal and cancer that exhibit increased cell plasticity which underlies tumor cell heterogeneity. Pancreatic ductal adenocarcinoma (PDAC) can arise from the combination of a transition state termed acinar-to-ductal metaplasia (ADM) and a gain-of-function mutation in the proto-oncogene KRAS . During ADM, digestive enzyme-producing acinar cells acquire a transient ductal epithelium-like phenotype while maintaining their geographical acinar organization. One route of ADM initiation is the overexpression of the Krüppel-like factor 4 gene ( KLF4 ) in the absence of oncogenic driver mutations. Here, we asked to what extent cells acquire and retain an epigenetic memory of the ADM transition state in the absence of oncogene mutation. We identified differential DNA methylation at Kras-downstream PI3K and Rho / Rac / Cdc42 GTPase pathway genes during ADM, as well as a corresponding gene expression increase in these pathways. Importantly, differential methylation persisted after gene expression returned to normal. Caerulein exposure, which induces widespread digestive system changes in addition to ADM, showed similar changes in DNA methylation in ADM cells. Regions of differential methylation were enriched for motifs of KLF and AP-1 family transcription factors, as were those of human pancreatic intraepithelial neoplasia (PanIN) samples, demonstrating the relevance of this epigenetic transition state memory in human carcinogenesis. Finally, single-cell spatial transcriptomics revealed that these ADM transition cells were enriched for PI3K pathway and AP1 family members, linking epigenetic memory to cancer cell plasticity even in the absence of oncogene mutation.
Collapse
|
17
|
Liu Z, Chen J, Ren Y, Liu S, Ba Y, Zuo A, Luo P, Cheng Q, Xu H, Han X. Multi-stage mechanisms of tumor metastasis and therapeutic strategies. Signal Transduct Target Ther 2024; 9:270. [PMID: 39389953 PMCID: PMC11467208 DOI: 10.1038/s41392-024-01955-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 07/18/2024] [Accepted: 08/24/2024] [Indexed: 10/12/2024] Open
Abstract
The cascade of metastasis in tumor cells, exhibiting organ-specific tendencies, may occur at numerous phases of the disease and progress under intense evolutionary pressures. Organ-specific metastasis relies on the formation of pre-metastatic niche (PMN), with diverse cell types and complex cell interactions contributing to this concept, adding a new dimension to the traditional metastasis cascade. Prior to metastatic dissemination, as orchestrators of PMN formation, primary tumor-derived extracellular vesicles prepare a fertile microenvironment for the settlement and colonization of circulating tumor cells at distant secondary sites, significantly impacting cancer progression and outcomes. Obviously, solely intervening in cancer metastatic sites passively after macrometastasis is often insufficient. Early prediction of metastasis and holistic, macro-level control represent the future directions in cancer therapy. This review emphasizes the dynamic and intricate systematic alterations that occur as cancer progresses, illustrates the immunological landscape of organ-specific PMN creation, and deepens understanding of treatment modalities pertinent to metastasis, thereby identifying some prognostic and predictive biomarkers favorable to early predict the occurrence of metastasis and design appropriate treatment combinations.
Collapse
Affiliation(s)
- Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Interventional Institute of Zhengzhou University, Zhengzhou, Henan, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan, China
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jingqi Chen
- Department of Clinical Medicine, Zhengzhou University, Zhengzhou, Henan, China
| | - Yuqing Ren
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Shutong Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yuhao Ba
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Anning Zuo
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Peng Luo
- The Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Hui Xu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
- Interventional Institute of Zhengzhou University, Zhengzhou, Henan, China.
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan, China.
| |
Collapse
|
18
|
Xie G, Zhang L, Usman OH, Kumar S, Modak C, Patel D, Kavanaugh M, Mallory X, Wang YJ, Irianto J. Phenotypic, Genomic, and Transcriptomic Heterogeneity in a Pancreatic Cancer Cell Line. Pancreas 2024; 53:e748-e759. [PMID: 38710020 PMCID: PMC11384550 DOI: 10.1097/mpa.0000000000002371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
OBJECTIVE To evaluate the suitability of the MIA PaCa-2 cell line for studying pancreatic cancer intratumor heterogeneity, we aim to further characterize the nature of MIA PaCa-2 cells' phenotypic, genomic, and transcriptomic heterogeneity. MATERIALS AND METHODS MIA PaCa-2 single-cell clones were established through flow cytometry. For the phenotypic study, we quantified the cellular morphology, proliferation rate, migration potential, and drug sensitivity of the clones. The chromosome copy number and transcriptomic profiles were quantified using SNPa and RNA-seq, respectively. RESULTS Four MIA PaCa-2 clones showed distinctive phenotypes, with differences in cellular morphology, proliferation rate, migration potential, and drug sensitivity. We also observed a degree of genomic variations between these clones in form of chromosome copy number alterations and single nucleotide variations, suggesting the genomic heterogeneity of the population, and the intrinsic genomic instability of MIA PaCa-2 cells. Lastly, transcriptomic analysis of the clones also revealed gene expression profile differences between the clones, including the uniquely regulated ITGAV , which dictates the morphology of MIA PaCa-2 clones. CONCLUSIONS MIA PaCa-2 is comprised of cells with distinctive phenotypes, heterogeneous genomes, and differential transcriptomic profiles, suggesting its suitability as a model to study the underlying mechanisms behind pancreatic cancer heterogeneity.
Collapse
Affiliation(s)
- Gengqiang Xie
- From the Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL
| | - Liting Zhang
- Department of Computer Science, Florida State University, Tallahassee, FL
| | - Olalekan H Usman
- From the Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL
| | - Sampath Kumar
- From the Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL
| | - Chaity Modak
- From the Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL
| | - Dhenu Patel
- From the Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL
| | - Megan Kavanaugh
- From the Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL
| | - Xian Mallory
- Department of Computer Science, Florida State University, Tallahassee, FL
| | - Yue Julia Wang
- From the Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL
| | - Jerome Irianto
- From the Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL
| |
Collapse
|
19
|
Sivanand S, Gultekin Y, Winter PS, Vermeulen SY, Tchourine KM, Abbott KL, Danai LV, Gourgue F, Do BT, Crowder K, Kunchok T, Lau AN, Darnell AM, Jefferson A, Morita S, Duda DG, Aguirre AJ, Wolpin BM, Henning N, Spanoudaki V, Maiorino L, Irvine DJ, Yilmaz OH, Lewis CA, Vitkup D, Shalek AK, Vander Heiden MG. Cancer tissue of origin constrains the growth and metabolism of metastases. Nat Metab 2024; 6:1668-1681. [PMID: 39160333 PMCID: PMC11450831 DOI: 10.1038/s42255-024-01105-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 07/09/2024] [Indexed: 08/21/2024]
Abstract
Metastases arise from subsets of cancer cells that disseminate from the primary tumour1,2. The ability of cancer cells to thrive in a new tissue site is influenced by genetic and epigenetic changes that are important for disease initiation and progression, but these factors alone do not predict if and where cancers metastasize3,4. Specific cancer types metastasize to consistent subsets of tissues, suggesting that primary tumour-associated factors influence where cancers can grow. We find primary and metastatic pancreatic tumours have metabolic similarities and that the tumour-initiating capacity and proliferation of both primary-derived and metastasis-derived cells is favoured in the primary site relative to the metastatic site. Moreover, propagating cells as tumours in the lung or the liver does not enhance their relative ability to form large tumours in those sites, change their preference to grow in the primary site, nor stably alter aspects of their metabolism relative to primary tumours. Primary liver and lung cancer cells also exhibit a preference to grow in their primary site relative to metastatic sites. These data suggest cancer tissue of origin influences both primary and metastatic tumour metabolism and may impact where cancer cells can metastasize.
Collapse
Affiliation(s)
- Sharanya Sivanand
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yetis Gultekin
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter S Winter
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sidney Y Vermeulen
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Keene L Abbott
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Laura V Danai
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Florian Gourgue
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brian T Do
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kayla Crowder
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Tenzin Kunchok
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Allison N Lau
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alicia M Darnell
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alexandria Jefferson
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Satoru Morita
- Edwin L Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Dan G Duda
- Edwin L Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Andrew J Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicole Henning
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Preclinical Imaging and Testing Facility, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Virginia Spanoudaki
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Preclinical Imaging and Testing Facility, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Laura Maiorino
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Darrell J Irvine
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Ragon Institute of MGH, MITnd Harvard, Cambridge, MA, USA
| | - Omer H Yilmaz
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital and Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Caroline A Lewis
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Dennis Vitkup
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
- Department of Biomedical Informatics, Columbia University Medical Center, New York, NY, USA
| | - Alex K Shalek
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of MGH, MITnd Harvard, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
20
|
Yao G, Zhu Y, Liu C, Man Y, Liu K, Zhang Q, Tan Y, Duan Q, Chen D, Du Z, Fan Y. Comparative analysis of the mutational landscape and evolutionary patterns of pancreatic ductal adenocarcinoma metastases in the liver or peritoneum. Heliyon 2024; 10:e35428. [PMID: 39170579 PMCID: PMC11336646 DOI: 10.1016/j.heliyon.2024.e35428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 07/02/2024] [Accepted: 07/29/2024] [Indexed: 08/23/2024] Open
Abstract
Background Pancreatic ductal adenocarcinoma (PDAC) often presents with liver or peritoneal metastases at diagnosis. Despite similar treatment approaches, patient outcomes vary between these metastatic sites. To improve targeted therapies for metastatic PDAC, a comprehensive analysis of the genetic profiles and evolutionary patterns at these distinct metastatic locations is essential. Methods We performed whole exome sequencing on 44 tissue samples from 27 PDAC patients, including primary tumours and matched liver or peritoneal metastases. We analysed somatic mutation profiles, signatures, and affected pathways for each group, and examined clonal evolution using subclonal architectures and phylogenetic trees. Results KRAS mutations remained the predominant driver alteration, with a prevalence of 89 % across all tumours. Notably, we observed site-specific differences in mutation frequencies, with KRAS alterations detected in 77.8 % (7/9) of peritoneal metastases and 87.5 % (7/8) of liver metastases. TP53 mutations exhibited a similar pattern, occurring in 55.6 % (5/9) of peritoneal and 37.5 % (3/8) of liver metastases. Intriguingly, we identified site-specific alterations in DNA repair pathway genes, including ATM and BRCA1, with distinct mutational profiles in liver versus peritoneal metastases. Furthermore, liver metastases demonstrated a significantly higher tumor mutational burden (TMB) compared to peritoneal metastases (median [IQR]: 2.14 [1.77-2.71] vs. 1.29 [1.21-1.69] mutations/Mb; P = 0.048). Conclusions In conclusion, metastasis of pancreatic cancer may be influenced by variables other than KRAS mutations, such as TP53. PDAC peritoneal and liver metastases may differ in potential therapeutic biomarkers. Further inquiry is needed on the biological mechanisms underlying metastasis and the treatment of diverse metastases.
Collapse
Affiliation(s)
- Guoliang Yao
- Department of General Surgery, The First Affiliated Hospital of Henan University of Science and Technology, 636 Guanlin Road, Luoyang, China
| | - Yanfeng Zhu
- Department of Nursing, Huashan Hospital, Fudan University, No.12 Middle Urumqi Road, Shangha, China
| | - Chunhui Liu
- Department of General Surgery, The First Affiliated Hospital of Henan University of Science and Technology, 636 Guanlin Road, Luoyang, China
| | - Yanwen Man
- Department of General Surgery, The First Affiliated Hospital of Henan University of Science and Technology, 636 Guanlin Road, Luoyang, China
| | - Kefeng Liu
- Department of General Surgery, The First Affiliated Hospital of Henan University of Science and Technology, 636 Guanlin Road, Luoyang, China
| | - Qin Zhang
- Jiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd., The State Key Laboratory of Neurology and Oncology Drug Development, China
| | - Yuan Tan
- Jiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd., The State Key Laboratory of Neurology and Oncology Drug Development, China
| | - Qianqian Duan
- Jiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd., The State Key Laboratory of Neurology and Oncology Drug Development, China
| | - Dongsheng Chen
- Jiangsu Simcere Diagnostics Co., Ltd., Nanjing Simcere Medical Laboratory Science Co., Ltd., The State Key Laboratory of Neurology and Oncology Drug Development, China
| | - Zunguo Du
- Department of Pathology, Huashan Hospital, Fudan University, No.12 Middle Urumqi Road, Shanghai, China
| | - Yonggang Fan
- Department of General Surgery, The First Affiliated Hospital of Henan University of Science and Technology, 636 Guanlin Road, Luoyang, China
| |
Collapse
|
21
|
Kiri S, Ryba T. Cancer, metastasis, and the epigenome. Mol Cancer 2024; 23:154. [PMID: 39095874 PMCID: PMC11295362 DOI: 10.1186/s12943-024-02069-w] [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: 04/30/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024] Open
Abstract
Cancer is the second leading cause of death worldwide and disease burden is expected to increase globally throughout the next several decades, with the majority of cancer-related deaths occurring in metastatic disease. Cancers exhibit known hallmarks that endow them with increased survival and proliferative capacities, frequently as a result of de-stabilizing mutations. However, the genomic features that resolve metastatic clones from primary tumors are not yet well-characterized, as no mutational landscape has been identified as predictive of metastasis. Further, many cancers exhibit no known mutation signature. This suggests a larger role for non-mutational genome re-organization in promoting cancer evolution and dissemination. In this review, we highlight current critical needs for understanding cell state transitions and clonal selection advantages for metastatic cancer cells. We examine links between epigenetic states, genome structure, and misregulation of tumor suppressors and oncogenes, and discuss how recent technologies for understanding domain-scale regulation have been leveraged for a more complete picture of oncogenic and metastatic potential.
Collapse
Affiliation(s)
- Saurav Kiri
- College of Medicine, University of Central Florida, 6850 Lake Nona Blvd., Orlando, 32827, Florida, USA.
| | - Tyrone Ryba
- Department of Natural Sciences, New College of Florida, 5800 Bay Shore Rd., Sarasota, 34243, Florida, USA.
| |
Collapse
|
22
|
Chen B, Yang Y, Wang X, Yang W, Lu Y, Wang D, Zhuo E, Tang Y, Su J, Tang G, Shao S, Gu K. mRNA vaccine development and applications: A special focus on tumors (Review). Int J Oncol 2024; 65:81. [PMID: 38994758 PMCID: PMC11251742 DOI: 10.3892/ijo.2024.5669] [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: 01/14/2024] [Accepted: 05/20/2024] [Indexed: 07/13/2024] Open
Abstract
Cancer is characterized by unlimited proliferation and metastasis, and traditional therapeutic strategies usually result in the acquisition of drug resistance, thus highlighting the need for more personalized treatment. mRNA vaccines transfer the gene sequences of exogenous target antigens into human cells through transcription and translation to stimulate the body to produce specific immune responses against the encoded proteins, so as to enable the body to obtain immune protection against said antigens; this approach may be adopted for personalized cancer therapy. Since the recent coronavirus pandemic, the development of mRNA vaccines has seen substantial progress and widespread adoption. In the present review, the development of mRNA vaccines, their mechanisms of action, factors influencing their function and the current clinical applications of the vaccine are discussed. A focus is placed on the application of mRNA vaccines in cancer, with the aim of highlighting unique advances and the remaining challenges of this novel and promising therapeutic approach.
Collapse
Affiliation(s)
- Bangjie Chen
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Yipin Yang
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Xinyi Wang
- Department of Radiation Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Wenzhi Yang
- First Clinical Medical College, Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - You Lu
- First Clinical Medical College, Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Daoyue Wang
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Enba Zhuo
- Department of Anesthesiology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Yanchao Tang
- Department of Anesthesiology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Junhong Su
- Department of Rehabilitation, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Guozheng Tang
- Department of Orthopedics, Lu'an Hospital of Anhui Medical University, Lu'an, Anhui 237008, P.R. China
| | - Song Shao
- Department of Orthopedics, Lu'an Hospital of Anhui Medical University, Lu'an, Anhui 237008, P.R. China
| | - Kangsheng Gu
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| |
Collapse
|
23
|
Ban GI, Puviindran V, Xiang Y, Nadesan P, Tang J, Ou J, Guardino N, Nakagawa M, Browne M, Wallace A, Ishikawa K, Shimada E, Martin JT, Diao Y, Kirsch DG, Alman BA. The COMPASS complex maintains the metastatic capacity imparted by a subpopulation of cells in UPS. iScience 2024; 27:110187. [PMID: 38989451 PMCID: PMC11233968 DOI: 10.1016/j.isci.2024.110187] [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: 01/01/2024] [Revised: 04/20/2024] [Accepted: 06/03/2024] [Indexed: 07/12/2024] Open
Abstract
Intratumoral heterogeneity is common in cancer, particularly in sarcomas like undifferentiated pleomorphic sarcoma (UPS), where individual cells demonstrate a high degree of cytogenic diversity. Previous studies showed that a small subset of cells within UPS, known as the metastatic clone (MC), as responsible for metastasis. Using a CRISPR-based genomic screen in-vivo, we identified the COMPASS complex member Setd1a as a key regulator maintaining the metastatic phenotype of the MC in murine UPS. Depletion of Setd1a inhibited metastasis development in the MC. Transcriptome and chromatin sequencing revealed COMPASS complex target genes in UPS, such as Cxcl10, downregulated in the MC. Deleting Cxcl10 in non-MC cells increased their metastatic potential. Treating mice with human UPS xenografts with a COMPASS complex inhibitor suppressed metastasis without affecting tumor growth in the primary tumor. Our data identified an epigenetic program in a subpopulation of sarcoma cells that maintains metastatic potential.
Collapse
Affiliation(s)
- Ga I. Ban
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Vijitha Puviindran
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Yu Xiang
- Department of Cell Biology and Duke Regeneration Center, Duke University School of Medicine, Durham, NC, USA
| | - Puvi Nadesan
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Jackie Tang
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Jianhong Ou
- Department of Cell Biology and Duke Regeneration Center, Duke University School of Medicine, Durham, NC, USA
| | - Nicholas Guardino
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Makoto Nakagawa
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - MaKenna Browne
- Department of Cell Biology and Duke Regeneration Center, Duke University School of Medicine, Durham, NC, USA
| | - Asjah Wallace
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Koji Ishikawa
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Eijiro Shimada
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - John T. Martin
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Yarui Diao
- Department of Cell Biology and Duke Regeneration Center, Duke University School of Medicine, Durham, NC, USA
| | - David G. Kirsch
- Department of Radiation Oncology, Duke University School of Medicine, Durham, NC, USA
- The Princes Margaret Cancer Centre, Department of Radiation Oncology, University Health Network and the University of Toronto, Toronto, ON, Canada
| | - Benjamin A. Alman
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
| |
Collapse
|
24
|
Kinny-Köster B, Ahmad Y, Pflüger MJ, Habib JR, Fujikura K, Hutchings D, Cameron JL, Shubert CR, Lafaro KJ, Burkhart RA, Burns WR, Javed AA, Yu J, Hruban RH, Wood LD, Thompson ED, He J. Clinical Relevance of Cancerization of Ducts in Resected Pancreatic Ductal Adenocarcinoma. Pancreas 2024; 53:e528-e536. [PMID: 38888841 DOI: 10.1097/mpa.0000000000002326] [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] [Indexed: 06/20/2024]
Abstract
OBJECTIVES Although prevalent in 50%-90% of pancreatic ductal adenocarcinomas, the clinical relevance of "cancerization of ducts" (COD) remains unknown. METHODS Pathologists retrospectively reviewed slides classifying prevalence of COD. Histopathological parameters, location of first recurrence, recurrence-free survival (RFS), and overall survival (OS) were collected from the institutional pancreatectomy registry. RESULTS Among 311 pancreatic ductal adenocarcinomas, COD was present in 216 (69.5%) and more prevalent in the cohort that underwent upfront surgery (75.3% vs 63.1%, P = 0.019). Furthermore, COD was associated with female gender (P = 0.040), advanced T stage (P = 0.007), perineural invasion (P = 0.014), lymphovascular invasion (P = 0.025), and R1 margin (P = 0.009), but not N stage (P = 0.401) or tumor differentiation (P = 0.717). In multivariable regression, COD was associated with less liver recurrence (odds ratio, 0.44; P < 0.005). This association was driven by the cohort of patients who had received preoperative treatment (odds ratio, 0.18; P < 0.001). COD was not predictive for RFS or OS. CONCLUSIONS Cancerization of ducts was not associated with RFS or OS. Currently underrecognized, standardized implementation into histopathological reports may have merit, and further mechanistic scientific experiments need to illuminate its clinical and biologic impact.
Collapse
Affiliation(s)
- Benedict Kinny-Köster
- From the Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Yembur Ahmad
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Michael J Pflüger
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Joseph R Habib
- From the Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Kohei Fujikura
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Danielle Hutchings
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - John L Cameron
- From the Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Christopher R Shubert
- From the Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Kelly J Lafaro
- From the Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Richard A Burkhart
- From the Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | - William R Burns
- From the Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Ammar A Javed
- From the Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jun Yu
- From the Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Ralph H Hruban
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Laura D Wood
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Elizabeth D Thompson
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jin He
- From the Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| |
Collapse
|
25
|
Maurer HC, Garcia-Curiel A, Holmstrom SR, Castillo C, Palermo CF, Sastra SA, Andren A, Zhang L, Le Large TYS, Sagalovskiy I, Ross DR, Wong W, Shaw K, Genkinger J, Manji GA, Iuga AC, Schmid RM, Johnson K, Badgley MA, Lyssiotis CA, Shah Y, Califano A, Olive KP. Ras-dependent activation of BMAL2 regulates hypoxic metabolism in pancreatic cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.19.533333. [PMID: 36993718 PMCID: PMC10055246 DOI: 10.1101/2023.03.19.533333] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
To identify drivers of malignancy in human pancreatic ductal adenocarcinoma (PDAC), we performed regulatory network analysis on a large collection of expression profiles from laser capture microdissected samples of PDAC and benign precursors. We discovered that BMAL2 plays a role in the initiation, progression, post resection survival, and KRAS activity in PDAC. Functional analysis of BMAL2 target genes led us to hypothesize that it plays a role in regulating the response to hypoxia, a critical but poorly understood feature of PDAC physiology. Knockout of BMAL2 in multiple human PDAC cell lines revealed effects on viability and invasion, particularly under hypoxic conditions. Loss of BMAL2 also affected glycolysis and other metabolic processes. We found that BMAL2 directly regulates hypoxia-responsive target genes. We also found that BMAL2 is necessary for the stabilization of HIF1A upon exposure to hypoxia, but destabilizes HIF2A under hypoxia. These data demonstrate that BMAL2 is a master transcriptional regulator of hypoxia responses in PDAC and may serve as a long-sought molecular switch that distinguishes HIF1A- and HIF2A-dependent modes of hypoxic metabolism.
Collapse
Affiliation(s)
- H Carlo Maurer
- Department of Internal Medicine II, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Alvaro Garcia-Curiel
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- Columbia University Digestive and Liver Disease Research Center, Columbia University Irving Medical Center, New York, NY
| | - Sam R Holmstrom
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX
| | - Cristina Castillo
- Department of Molecular & Integrative Physiology and Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI
- University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI
| | - Carmine F Palermo
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- Columbia University Digestive and Liver Disease Research Center, Columbia University Irving Medical Center, New York, NY
| | - Steven A Sastra
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- Columbia University Digestive and Liver Disease Research Center, Columbia University Irving Medical Center, New York, NY
| | - Anthony Andren
- Department of Molecular & Integrative Physiology and Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI
- University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI
| | - Li Zhang
- Department of Molecular & Integrative Physiology and Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI
- University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI
| | - Tessa Y S Le Large
- Department of Surgery, Amsterdam UMC, Location Vrije Universiteit, Amsterdam, Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
| | - Irina Sagalovskiy
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Daniel R Ross
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- Columbia University Digestive and Liver Disease Research Center, Columbia University Irving Medical Center, New York, NY
| | - Winston Wong
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Kaitlin Shaw
- Division of GI/Endocrine Surgery, Department of Surgery, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Jeanine Genkinger
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY
| | - Gulam A Manji
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Alina C Iuga
- Department of Pathology, Columbia University Irving Medical Center, New York, NY
| | - Roland M Schmid
- Department of Internal Medicine II, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | | | - Michael A Badgley
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- Columbia University Digestive and Liver Disease Research Center, Columbia University Irving Medical Center, New York, NY
| | - Costas A Lyssiotis
- Department of Molecular & Integrative Physiology and Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI
- University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI
| | - Yatrik Shah
- Department of Molecular & Integrative Physiology and Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI
- University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI
| | - Andrea Califano
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- Darwin Therapeutics, New York, NY
- Chan Zuckerberg Biohub, New York, NY
| | - Kenneth P Olive
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- Columbia University Digestive and Liver Disease Research Center, Columbia University Irving Medical Center, New York, NY
| |
Collapse
|
26
|
Geukens T, Maetens M, Hooper JE, Oesterreich S, Lee AV, Miller L, Atkinson JM, Rosenzweig M, Puhalla S, Thorne H, Devereux L, Bowtell D, Loi S, Bacon ER, Ihle K, Song M, Rodriguez‐Rodriguez L, Welm AL, Gauchay L, Murali R, Chanda P, Karacay A, Naceur‐Lombardelli C, Bridger H, Swanton C, Jamal‐Hanjani M, Kollath L, True L, Morrissey C, Chambers M, Chinnaiyan AM, Wilson A, Mehra R, Reichert Z, Carey LA, Perou CM, Kelly E, Maeda D, Goto A, Kulka J, Székely B, Szasz AM, Tőkés A, Van Den Bogaert W, Floris G, Desmedt C. Research autopsy programmes in oncology: shared experience from 14 centres across the world. J Pathol 2024; 263:150-165. [PMID: 38551513 PMCID: PMC11497336 DOI: 10.1002/path.6271] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/22/2023] [Accepted: 02/09/2024] [Indexed: 05/12/2024]
Abstract
While there is a great clinical need to understand the biology of metastatic cancer in order to treat it more effectively, research is hampered by limited sample availability. Research autopsy programmes can crucially advance the field through synchronous, extensive, and high-volume sample collection. However, it remains an underused strategy in translational research. Via an extensive questionnaire, we collected information on the study design, enrolment strategy, study conduct, sample and data management, and challenges and opportunities of research autopsy programmes in oncology worldwide. Fourteen programmes participated in this study. Eight programmes operated 24 h/7 days, resulting in a lower median postmortem interval (time between death and start of the autopsy, 4 h) compared with those operating during working hours (9 h). Most programmes (n = 10) succeeded in collecting all samples within a median of 12 h after death. A large number of tumour sites were sampled during each autopsy (median 15.5 per patient). The median number of samples collected per patient was 58, including different processing methods for tumour samples but also non-tumour tissues and liquid biopsies. Unique biological insights derived from these samples included metastatic progression, treatment resistance, disease heterogeneity, tumour dormancy, interactions with the tumour micro-environment, and tumour representation in liquid biopsies. Tumour patient-derived xenograft (PDX) or organoid (PDO) models were additionally established, allowing for drug discovery and treatment sensitivity assays. Apart from the opportunities and achievements, we also present the challenges related with postmortem sample collections and strategies to overcome them, based on the shared experience of these 14 programmes. Through this work, we hope to increase the transparency of postmortem tissue donation, to encourage and aid the creation of new programmes, and to foster collaborations on these unique sample collections. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Collapse
Affiliation(s)
- Tatjana Geukens
- Laboratory for Translational Breast Cancer Research, Department of OncologyKU LeuvenLeuvenBelgium
| | - Marion Maetens
- Laboratory for Translational Breast Cancer Research, Department of OncologyKU LeuvenLeuvenBelgium
| | - Jody E Hooper
- Stanford University School of MedicinePalo AltoCAUSA
| | - Steffi Oesterreich
- University of Pittsburgh UPMC Hillman Cancer Center, and Magee Womens Research InstitutePittsburghPAUSA
| | - Adrian V Lee
- University of Pittsburgh UPMC Hillman Cancer Center, and Magee Womens Research InstitutePittsburghPAUSA
| | - Lori Miller
- University of Pittsburgh UPMC Hillman Cancer Center, and Magee Womens Research InstitutePittsburghPAUSA
| | - Jenny M Atkinson
- University of Pittsburgh UPMC Hillman Cancer Center, and Magee Womens Research InstitutePittsburghPAUSA
| | - Margaret Rosenzweig
- University of Pittsburgh UPMC Hillman Cancer Center, and Magee Womens Research InstitutePittsburghPAUSA
| | - Shannon Puhalla
- University of Pittsburgh UPMC Hillman Cancer Center, and Magee Womens Research InstitutePittsburghPAUSA
| | - Heather Thorne
- Peter MacCallum Cancer CentreMelbourneAustralia
- Sir Peter MacCallum Department of OncologyThe University of MelbourneParkvilleAustralia
| | - Lisa Devereux
- Peter MacCallum Cancer CentreMelbourneAustralia
- Sir Peter MacCallum Department of OncologyThe University of MelbourneParkvilleAustralia
| | | | - Sherene Loi
- Peter MacCallum Cancer CentreMelbourneAustralia
- Sir Peter MacCallum Department of OncologyThe University of MelbourneParkvilleAustralia
| | - Eliza R Bacon
- Center for Precision MedicineCity of Hope National Medical CenterDuarteCAUSA
| | - Kena Ihle
- Center for Precision MedicineCity of Hope National Medical CenterDuarteCAUSA
| | - Mihae Song
- Center for Precision MedicineCity of Hope National Medical CenterDuarteCAUSA
| | | | - Alana L Welm
- University of Utah Huntsman Cancer InstituteSalt Lake CityUTUSA
| | - Lisa Gauchay
- University of Utah Huntsman Cancer InstituteSalt Lake CityUTUSA
| | | | | | - Ali Karacay
- Memorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | | | - Hayley Bridger
- Cancer Research UK, and UCL Cancer Trials CentreUniversity College LondonLondonUK
| | - Charles Swanton
- Cancer Evolution and Genome Instability LaboratoryThe Francis Crick InstituteLondonUK
- Cancer Research UK Lung Cancer Centre of ExcellenceUCL Cancer InstituteLondonUK
- Department of Medical OncologyUniversity College London HospitalsLondonUK
| | - Mariam Jamal‐Hanjani
- Cancer Research UK Lung Cancer Centre of ExcellenceUCL Cancer InstituteLondonUK
- Department of Medical OncologyUniversity College London HospitalsLondonUK
- Cancer Metastasis LaboratoryUniversity College London Cancer InstituteLondonUK
| | | | | | | | | | | | | | | | | | - Lisa A Carey
- University of North Carolina, Lineberger Comprehensive Cancer CenterChapel HillNCUSA
| | - Charles M Perou
- University of North Carolina, Lineberger Comprehensive Cancer CenterChapel HillNCUSA
| | - Erin Kelly
- University of North Carolina, Lineberger Comprehensive Cancer CenterChapel HillNCUSA
| | - Daichi Maeda
- Department of Molecular and Cellular Pathology, Graduate School of Medical SciencesKanazawa UniversityKanazawaJapan
| | - Akiteru Goto
- Department of Cellular and Organ Pathology, Graduate School of MedicineAkita UniversityAkitaJapan
| | - Janina Kulka
- Department of Pathology, Forensic and Insurance MedicineSemmelweis UniversityBudapestHungary
| | - Borbála Székely
- Department of Pathology, Forensic and Insurance MedicineSemmelweis UniversityBudapestHungary
- National Institute of OncologyBudapestHungary
| | - A Marcell Szasz
- Division of Oncology, Department of Internal Medicine and OncologySemmelweis UniversityBudapestHungary
| | - Anna‐Mária Tőkés
- Department of Pathology, Forensic and Insurance MedicineSemmelweis UniversityBudapestHungary
| | | | - Giuseppe Floris
- Department of PathologyUniversity Hospitals LeuvenLeuvenBelgium
| | - Christine Desmedt
- Laboratory for Translational Breast Cancer Research, Department of OncologyKU LeuvenLeuvenBelgium
| |
Collapse
|
27
|
Thakur C, Qiu Y, Pawar A, Chen F. Epigenetic regulation of breast cancer metastasis. Cancer Metastasis Rev 2024; 43:597-619. [PMID: 37857941 DOI: 10.1007/s10555-023-10146-7] [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: 07/22/2023] [Accepted: 10/02/2023] [Indexed: 10/21/2023]
Abstract
Breast cancer is the most frequently diagnosed malignancy and the second leading cause of cancer-related mortality among women worldwide. Recurrent metastasis is associated with poor patient outcomes and poses a significant challenge in breast cancer therapies. Cancer cells adapting to a new tissue microenvironment is the key event in distant metastasis development, where the disseminating tumor cells are likely to acquire genetic and epigenetic alterations during the process of metastatic colonization. Despite several decades of research in this field, the exact mechanisms governing metastasis are not fully understood. However, emerging body of evidence indicates that in addition to genetic changes, epigenetic reprogramming of cancer cells and the metastatic niche are paramount toward successful metastasis. Here, we review and discuss the latest knowledge about the salient attributes of metastasis and epigenetic regulation in breast cancer and crucial research domains that need further investigation.
Collapse
Affiliation(s)
- Chitra Thakur
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, Lauterbur Drive, Stony Brook, NY, 11794, USA.
| | - Yiran Qiu
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, Lauterbur Drive, Stony Brook, NY, 11794, USA
| | - Aashna Pawar
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, Lauterbur Drive, Stony Brook, NY, 11794, USA
| | - Fei Chen
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, Lauterbur Drive, Stony Brook, NY, 11794, USA.
| |
Collapse
|
28
|
Ferrer CM, Cho HM, Boon R, Bernasocchi T, Wong LP, Cetinbas M, Haggerty ER, Mitsiades I, Wojtkiewicz GR, McLoughlin DE, Aboushousha R, Abdelhamid H, Kugel S, Rheinbay E, Sadreyev R, Juric D, Janssen-Heininger YMW, Mostoslavsky R. The glutathione S-transferase Gstt1 drives survival and dissemination in metastases. Nat Cell Biol 2024; 26:975-990. [PMID: 38862786 DOI: 10.1038/s41556-024-01426-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 04/18/2024] [Indexed: 06/13/2024]
Abstract
Identifying the adaptive mechanisms of metastatic cancer cells remains an elusive question in the treatment of metastatic disease, particularly in pancreatic cancer (pancreatic adenocarcinoma, PDA). A loss-of-function shRNA targeted screen in metastatic-derived cells identified Gstt1, a member of the glutathione S-transferase superfamily, as uniquely required for dissemination and metastasis, but dispensable for primary tumour growth. Gstt1 is expressed in latent disseminated tumour cells (DTCs), is retained within a subpopulation of slow-cycling cells within existing metastases, and its inhibition leads to complete regression of macrometastatic tumours. This distinct Gstt1high population is highly metastatic and retains slow-cycling phenotypes, epithelial-mesenchymal transition features and DTC characteristics compared to the Gstt1low population. Mechanistic studies indicate that in this subset of cancer cells, Gstt1 maintains metastases by binding and glutathione-modifying intracellular fibronectin, in turn promoting its secretion and deposition into the metastatic microenvironment. We identified Gstt1 as a mediator of metastasis, highlighting the importance of heterogeneity and its influence on the metastatic tumour microenvironment.
Collapse
Affiliation(s)
- Christina M Ferrer
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA.
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- University of Maryland School of Medicine and the Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA.
| | - Hyo Min Cho
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ruben Boon
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Galapagos NV, 2800 Mechelen, Belgium
| | - Tiziano Bernasocchi
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lai Ping Wong
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Murat Cetinbas
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Elizabeth R Haggerty
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Irene Mitsiades
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | | | - Daniel E McLoughlin
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Termeer Center for Targeted Therapies, Massachusetts General Hospital, Boston, MA, USA
| | - Reem Aboushousha
- University of Vermont Larner College of Medicine, Burlington, VT, USA
| | - Hend Abdelhamid
- University of Vermont Larner College of Medicine, Burlington, VT, USA
| | - Sita Kugel
- Fred Hutchison Cancer Research Center, Seattle, WA, USA
| | - Esther Rheinbay
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Dejan Juric
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Termeer Center for Targeted Therapies, Massachusetts General Hospital, Boston, MA, USA
| | | | - Raul Mostoslavsky
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA.
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| |
Collapse
|
29
|
Myers MA, Arnold BJ, Bansal V, Balaban M, Mullen KM, Zaccaria S, Raphael BJ. HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data. Genome Biol 2024; 25:130. [PMID: 38773520 PMCID: PMC11110434 DOI: 10.1186/s13059-024-03267-x] [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: 07/13/2023] [Accepted: 05/03/2024] [Indexed: 05/24/2024] Open
Abstract
Bulk DNA sequencing of multiple samples from the same tumor is becoming common, yet most methods to infer copy-number aberrations (CNAs) from this data analyze individual samples independently. We introduce HATCHet2, an algorithm to identify haplotype- and clone-specific CNAs simultaneously from multiple bulk samples. HATCHet2 extends the earlier HATCHet method by improving identification of focal CNAs and introducing a novel statistic, the minor haplotype B-allele frequency (mhBAF), that enables identification of mirrored-subclonal CNAs. We demonstrate HATCHet2's improved accuracy using simulations and a single-cell sequencing dataset. HATCHet2 analysis of 10 prostate cancer patients reveals previously unreported mirrored-subclonal CNAs affecting cancer genes.
Collapse
Affiliation(s)
- Matthew A Myers
- Department of Computer Science, Princeton University, Princeton, USA
| | - Brian J Arnold
- Center for Statistics and Machine Learning, Princeton University, Princeton, USA
| | - Vineet Bansal
- Princeton Research Computing, Princeton University, Princeton, NJ, USA
| | - Metin Balaban
- Department of Computer Science, Princeton University, Princeton, USA
| | - Katelyn M Mullen
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simone Zaccaria
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK.
| | | |
Collapse
|
30
|
Ross AB, Gorhe D, Kim JK, Hodapp S, DeVine L, Chan KM, Chio IIC, Jovanovic M, Ayres Pereira M. Systematic analysis of proteome turnover in an organoid model of pancreatic cancer by dSILO. CELL REPORTS METHODS 2024; 4:100760. [PMID: 38677284 PMCID: PMC11133751 DOI: 10.1016/j.crmeth.2024.100760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/26/2024] [Accepted: 03/25/2024] [Indexed: 04/29/2024]
Abstract
The role of protein turnover in pancreatic ductal adenocarcinoma (PDA) metastasis has not been previously investigated. We introduce dynamic stable-isotope labeling of organoids (dSILO): a dynamic SILAC derivative that combines a pulse of isotopically labeled amino acids with isobaric tandem mass-tag (TMT) labeling to measure proteome-wide protein turnover rates in organoids. We applied it to a PDA model and discovered that metastatic organoids exhibit an accelerated global proteome turnover compared to primary tumor organoids. Globally, most turnover changes are not reflected at the level of protein abundance. Interestingly, the group of proteins that show the highest turnover increase in metastatic PDA compared to tumor is involved in mitochondrial respiration. This indicates that metastatic PDA may adopt alternative respiratory chain functionality that is controlled by the rate at which proteins are turned over. Collectively, our analysis of proteome turnover in PDA organoids offers insights into the mechanisms underlying PDA metastasis.
Collapse
Affiliation(s)
- Alison B Ross
- Department of Biological Sciences, Columbia University, New York City, NY 10027, USA
| | - Darvesh Gorhe
- Department of Biological Sciences, Columbia University, New York City, NY 10027, USA
| | - Jenny Kim Kim
- Department of Biological Sciences, Columbia University, New York City, NY 10027, USA
| | - Stefanie Hodapp
- Department of Biological Sciences, Columbia University, New York City, NY 10027, USA
| | - Lela DeVine
- Department of Biology, Barnard College, New York, NY 10027, USA; Institute for Cancer Genetics, Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Karina M Chan
- Institute for Cancer Genetics, Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Iok In Christine Chio
- Institute for Cancer Genetics, Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York City, NY 10027, USA.
| | - Marina Ayres Pereira
- Institute for Cancer Genetics, Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
| |
Collapse
|
31
|
Jamali M, Barar E, Shi J. Unveiling the Molecular Landscape of Pancreatic Ductal Adenocarcinoma: Insights into the Role of the COMPASS-like Complex. Int J Mol Sci 2024; 25:5069. [PMID: 38791111 PMCID: PMC11121229 DOI: 10.3390/ijms25105069] [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: 04/03/2024] [Revised: 05/02/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is poised to become the second leading cause of cancer-related death by 2030, necessitating innovative therapeutic strategies. Genetic and epigenetic alterations, including those involving the COMPASS-like complex genes, have emerged as critical drivers of PDAC progression. This review explores the genetic and epigenetic landscape of PDAC, focusing on the role of the COMPASS-like complex in regulating chromatin accessibility and gene expression. Specifically, we delve into the functions of key components such as KDM6A, KMT2D, KMT2C, KMT2A, and KMT2B, highlighting their significance as potential therapeutic targets. Furthermore, we discuss the implications of these findings for developing novel treatment modalities for PDAC.
Collapse
Affiliation(s)
- Marzieh Jamali
- Department of Pathology & Clinical Labs, Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Erfaneh Barar
- Liver and Pancreatobiliary Diseases Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran 1416634793, Iran
| | - Jiaqi Shi
- Department of Pathology & Clinical Labs, Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
32
|
Braxton AM, Kiemen AL, Grahn MP, Forjaz A, Parksong J, Mahesh Babu J, Lai J, Zheng L, Niknafs N, Jiang L, Cheng H, Song Q, Reichel R, Graham S, Damanakis AI, Fischer CG, Mou S, Metz C, Granger J, Liu XD, Bachmann N, Zhu Y, Liu Y, Almagro-Pérez C, Jiang AC, Yoo J, Kim B, Du S, Foster E, Hsu JY, Rivera PA, Chu LC, Liu F, Fishman EK, Yuille A, Roberts NJ, Thompson ED, Scharpf RB, Cornish TC, Jiao Y, Karchin R, Hruban RH, Wu PH, Wirtz D, Wood LD. 3D genomic mapping reveals multifocality of human pancreatic precancers. Nature 2024; 629:679-687. [PMID: 38693266 DOI: 10.1038/s41586-024-07359-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/26/2024] [Indexed: 05/03/2024]
Abstract
Pancreatic intraepithelial neoplasias (PanINs) are the most common precursors of pancreatic cancer, but their small size and inaccessibility in humans make them challenging to study1. Critically, the number, dimensions and connectivity of human PanINs remain largely unknown, precluding important insights into early cancer development. Here, we provide a microanatomical survey of human PanINs by analysing 46 large samples of grossly normal human pancreas with a machine-learning pipeline for quantitative 3D histological reconstruction at single-cell resolution. To elucidate genetic relationships between and within PanINs, we developed a workflow in which 3D modelling guides multi-region microdissection and targeted and whole-exome sequencing. From these samples, we calculated a mean burden of 13 PanINs per cm3 and extrapolated that the normal intact adult pancreas harbours hundreds of PanINs, almost all with oncogenic KRAS hotspot mutations. We found that most PanINs originate as independent clones with distinct somatic mutation profiles. Some spatially continuous PanINs were found to contain multiple KRAS mutations; computational and in situ analyses demonstrated that different KRAS mutations localize to distinct cell subpopulations within these neoplasms, indicating their polyclonal origins. The extensive multifocality and genetic heterogeneity of PanINs raises important questions about mechanisms that drive precancer initiation and confer differential progression risk in the human pancreas. This detailed 3D genomic mapping of molecular alterations in human PanINs provides an empirical foundation for early detection and rational interception of pancreatic cancer.
Collapse
Affiliation(s)
- Alicia M Braxton
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Comparative Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Ashley L Kiemen
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mia P Grahn
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - André Forjaz
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jeeun Parksong
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jaanvi Mahesh Babu
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jiaying Lai
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Lily Zheng
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA
- McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Noushin Niknafs
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Liping Jiang
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haixia Cheng
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qianqian Song
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rebecca Reichel
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sarah Graham
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alexander I Damanakis
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Catherine G Fischer
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Stephanie Mou
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Cameron Metz
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Julie Granger
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xiao-Ding Liu
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Niklas Bachmann
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yutong Zhu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - YunZhou Liu
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Cristina Almagro-Pérez
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Ann Chenyu Jiang
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jeonghyun Yoo
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Bridgette Kim
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Scott Du
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Eli Foster
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jocelyn Y Hsu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Paula Andreu Rivera
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Linda C Chu
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fengze Liu
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elliot K Fishman
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alan Yuille
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Nicholas J Roberts
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth D Thompson
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert B Scharpf
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Toby C Cornish
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Yuchen Jiao
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
- Institute of Cancer Research, Henan Academy of Innovations in Medical Science, Zhengzhou, China.
| | - Rachel Karchin
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Ralph H Hruban
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Pei-Hsun Wu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Denis Wirtz
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Laura D Wood
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
33
|
Brown NF, Murray ER, Cutmore LC, Howard P, Masterson L, Zammarchi F, Hartley JA, van Berkel PH, Marshall JF. Integrin-αvβ6 targeted peptide-toxin therapy in a novel αvβ6-expressing immunocompetent model of pancreatic cancer. Pancreatology 2024; 24:445-455. [PMID: 38519394 DOI: 10.1016/j.pan.2024.02.013] [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: 10/24/2023] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/24/2024]
Abstract
Previously we reported that a novel αvβ6-specific peptide-drug conjugate (SG3299) could eliminate established human pancreatic ductal adenocarcinoma (PDAC) xenografts. However the development of effective therapies for PDAC, which is an essential need, must show efficacy in relevant immunocompetent animals. Previously we reported that the KPC mouse transgenic PDAC model that closely recapitulates most stages of development of human PDAC, unlike in humans, failed to express αvβ6 on their tumours or metastases. In this study we have taken the KPC-derived PDAC line TB32043 and engineered a variant line (TB32043mb6S2) that expresses mouse integrin αvβ6. We report that orthotopic implantation of the αvβ6 over-expressing TB32043mb6S2 cells promotes shorter overall survival and increase in metastases. Moreover, systemic treatment of mice with established TB32043mb6S2 tumours in the pancreas with SG2399 lived significantly longer (p < 0.001; mean OS 48d) compared with PBS or control SG3511 (mean OS 25.5d and 26d, respectively). Thus SG3299 is confirmed as a promising candidate therapeutic for the therapy of PDAC.
Collapse
Affiliation(s)
- Nicholas F Brown
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Elizabeth R Murray
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Lauren C Cutmore
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Philip Howard
- Spirogen, QMB Innovation Centre, 42 New Road, London, E1 2AX, UK
| | - Luke Masterson
- Spirogen, QMB Innovation Centre, 42 New Road, London, E1 2AX, UK
| | - Francesca Zammarchi
- ADC Therapeutics (UK) Ltd, Translation & Innovation Hub Building, Imperial College White City Campus, 84 Wood Lane, London, W12 0BZ, UK
| | - John A Hartley
- Cancer Research UK Drug-DNA Interactions Research Group, University College London Cancer Institute, 72 Huntley Street, London, WC1E 6BT, UK
| | - Patrick H van Berkel
- ADC Therapeutics (UK) Ltd, Translation & Innovation Hub Building, Imperial College White City Campus, 84 Wood Lane, London, W12 0BZ, UK
| | - John F Marshall
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK.
| |
Collapse
|
34
|
Parreno V, Loubiere V, Schuettengruber B, Fritsch L, Rawal CC, Erokhin M, Győrffy B, Normanno D, Di Stefano M, Moreaux J, Butova NL, Chiolo I, Chetverina D, Martinez AM, Cavalli G. Transient loss of Polycomb components induces an epigenetic cancer fate. Nature 2024; 629:688-696. [PMID: 38658752 PMCID: PMC11096130 DOI: 10.1038/s41586-024-07328-w] [Citation(s) in RCA: 58] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/15/2024] [Indexed: 04/26/2024]
Abstract
Although cancer initiation and progression are generally associated with the accumulation of somatic mutations1,2, substantial epigenomic alterations underlie many aspects of tumorigenesis and cancer susceptibility3-6, suggesting that genetic mechanisms might not be the only drivers of malignant transformation7. However, whether purely non-genetic mechanisms are sufficient to initiate tumorigenesis irrespective of mutations has been unknown. Here, we show that a transient perturbation of transcriptional silencing mediated by Polycomb group proteins is sufficient to induce an irreversible switch to a cancer cell fate in Drosophila. This is linked to the irreversible derepression of genes that can drive tumorigenesis, including members of the JAK-STAT signalling pathway and zfh1, the fly homologue of the ZEB1 oncogene, whose aberrant activation is required for Polycomb perturbation-induced tumorigenesis. These data show that a reversible depletion of Polycomb proteins can induce cancer in the absence of driver mutations, suggesting that tumours can emerge through epigenetic dysregulation leading to inheritance of altered cell fates.
Collapse
Affiliation(s)
- V Parreno
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - V Loubiere
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - B Schuettengruber
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - L Fritsch
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - C C Rawal
- University of Southern California, Los Angeles, CA, USA
| | - M Erokhin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - B Győrffy
- Semmelweis University Department of Bioinformatics, Budapest, Hungary
- Department of Biophysics, Medical School, University of Pécs, Pécs, Hungary
| | - D Normanno
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - M Di Stefano
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - J Moreaux
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
- Department of Biological Hematology, CHU Montpellier, Montpellier, France
- UFR Medicine, University of Montpellier, Montpellier, France
| | - N L Butova
- University of Southern California, Los Angeles, CA, USA
| | - I Chiolo
- University of Southern California, Los Angeles, CA, USA
| | - D Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - A-M Martinez
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France.
| | - G Cavalli
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France.
| |
Collapse
|
35
|
Carrolo M, Miranda JAI, Vilhais G, Quintela A, Sousa MFE, Costa DA, Pinto FR. Metastatic organotropism: a brief overview. Front Oncol 2024; 14:1358786. [PMID: 38725618 PMCID: PMC11079203 DOI: 10.3389/fonc.2024.1358786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/12/2024] [Indexed: 05/12/2024] Open
Abstract
Organotropism has been known since 1889, yet this vital component of metastasis has predominantly stayed elusive. This mini-review gives an overview of the current understanding of the underlying mechanisms of organotropism and metastases development by focusing on the formation of the pre-metastatic niche, immune defenses against metastases, and genomic alterations associated with organotropism. The particular case of brain metastases is also addressed, as well as the impact of organotropism in cancer therapy. The limited comprehension of the factors behind organotropism underscores the necessity for efficient strategies and treatments to manage metastases.
Collapse
Affiliation(s)
| | - João A. I. Miranda
- BioISI – Institute for Biosystems and Integrative Sciences, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | | | - António Quintela
- Hematology and Oncology Department, CUF Oncologia, Lisbon, Portugal
| | | | - Diogo Alpuim Costa
- Hematology and Oncology Department, CUF Oncologia, Lisbon, Portugal
- Medical Oncology Department, Hospital de Cascais, Cascais, Portugal
- NOVA Medical School, Faculdade de Ciências Médicas, Lisbon, Portugal
| | - Francisco R. Pinto
- BioISI – Institute for Biosystems and Integrative Sciences, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| |
Collapse
|
36
|
Spadafora V, Pryce BR, Oles A, Talbert EE, Romeo M, Vaena S, Berto S, Ostrowski MC, Wang DJ, Guttridge DC. Optimization of a mouse model of pancreatic cancer to simulate the human phenotypes of metastasis and cachexia. BMC Cancer 2024; 24:414. [PMID: 38570770 PMCID: PMC10993462 DOI: 10.1186/s12885-024-12104-0] [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: 11/29/2023] [Accepted: 03/11/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) presents with a high mortality rate. Two important features of PDAC contribute to this poor outcome. The first is metastasis which occurs in ~ 80% of PDAC patients. The second is cachexia, which compromises treatment tolerance for patients and reduces their quality of life. Although various mouse models of PDAC exist, recapitulating both metastatic and cachectic features have been challenging. METHODS Here, we optimize an orthotopic mouse model of PDAC by altering several conditions, including the subcloning of parental murine PDAC cells, implantation site, number of transplanted cells, and age of recipient mice. We perform spatial profiling to compare primary and metastatic immune microenvironments and RNA sequencing to gain insight into the mechanisms of muscle wasting in PDAC-induced cachexia, comparing non-metastatic to metastatic conditions. RESULTS These modifications extend the time course of the disease and concurrently increase the rate of metastasis to approximately 70%. Furthermore, reliable cachexia endpoints are achieved in both PDAC mice with and without metastases, which is reminiscent of patients. We also find that cachectic muscles from PDAC mice with metastasis exhibit a similar transcriptional profile to muscles derived from mice and patients without metastasis. CONCLUSION Together, this model is likely to be advantageous in both advancing our understanding of the mechanism of PDAC cachexia, as well as in the evaluation of novel therapeutics.
Collapse
Affiliation(s)
- Victoria Spadafora
- Department of Pediatrics, Darby Children's Research Institute, 416, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC, 29425, USA
| | - Benjamin R Pryce
- Department of Pediatrics, Darby Children's Research Institute, 416, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC, 29425, USA
| | - Alexander Oles
- Department of Pediatrics, Darby Children's Research Institute, 416, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC, 29425, USA
| | - Erin E Talbert
- Department of Health and Human Physiology, and the Holden Comprehensive Cancer Center, University of Iowa, Iowa, 52242, USA
| | - Martin Romeo
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Silvia Vaena
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Stefano Berto
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Michael C Ostrowski
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - David J Wang
- Department of Pediatrics, Darby Children's Research Institute, 416, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC, 29425, USA.
| | - Denis C Guttridge
- Department of Pediatrics, Darby Children's Research Institute, 416, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC, 29425, USA.
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA.
| |
Collapse
|
37
|
Okuno K, Ikemura K, Okamoto R, Oki K, Watanabe A, Kuroda Y, Kidachi M, Fujino S, Nie Y, Higuchi T, Chuman M, Washio M, Sakuraya M, Niihara M, Kumagai K, Sangai T, Kumamoto Y, Naitoh T, Hiki N, Yamashita K. CAF-associated genes putatively representing distinct prognosis by in silico landscape of stromal components of colon cancer. PLoS One 2024; 19:e0299827. [PMID: 38557819 PMCID: PMC10984474 DOI: 10.1371/journal.pone.0299827] [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: 12/21/2023] [Accepted: 02/15/2024] [Indexed: 04/04/2024] Open
Abstract
Comprehensive understanding prognostic relevance of distinct tumor microenvironment (TME) remained elusive in colon cancer. In this study, we performed in silico analysis of the stromal components of primary colon cancer, with a focus on the markers of cancer-associated fibroblasts (CAF) and tumor-associated endothelia (TAE), as well as immunological infiltrates like tumor-associated myeloid cells (TAMC) and cytotoxic T lymphocytes (CTL). The relevant CAF-associated genes (CAFG)(representing R index = 0.9 or beyond with SPARC) were selected based on stroma specificity (cancer stroma/epithelia, cS/E = 10 or beyond) and expression amounts, which were largely exhibited negative prognostic impacts. CAFG were partially shared with TAE-associated genes (TAEG)(PLAT, ANXA1, and PTRF) and TAMC-associated genes (TAMCG)(NNMT), but not with CTL-associated genes (CTLG). Intriguingly, CAFG were prognostically subclassified in order of fibrosis (representing COL5A2, COL5A1, and COL12A1) followed by exclusive TAEG and TAMCG. Prognosis was independently stratified by CD8A, a CTL marker, in the context of low expression of the strongest negative prognostic CAFG, COL8A1. CTLG were comprehensively identified as IFNG, B2M, and TLR4, in the group of low S/E, representing good prognosis. Our current in silico analysis of the micro-dissected stromal gene signatures with prognostic relevance clarified comprehensive understanding of clinical features of the TME and provides deep insights of the landscape.
Collapse
Affiliation(s)
- Kota Okuno
- Division of Advanced Surgical Oncology, Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, Sagamihara, Japan
| | - Kyonosuke Ikemura
- Division of Advanced Surgical Oncology, Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, Sagamihara, Japan
| | - Riku Okamoto
- Division of Advanced Surgical Oncology, Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, Sagamihara, Japan
| | - Keiko Oki
- Division of Advanced Surgical Oncology, Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, Sagamihara, Japan
| | - Akiko Watanabe
- Division of Advanced Surgical Oncology, Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, Sagamihara, Japan
| | - Yu Kuroda
- Division of Advanced Surgical Oncology, Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, Sagamihara, Japan
| | - Mikiko Kidachi
- Division of Advanced Surgical Oncology, Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, Sagamihara, Japan
| | - Shiori Fujino
- Division of Advanced Surgical Oncology, Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, Sagamihara, Japan
| | - Yusuke Nie
- Division of Advanced Surgical Oncology, Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, Sagamihara, Japan
| | - Tadashi Higuchi
- Department of Upper Gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Motohiro Chuman
- Department of Upper Gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Marie Washio
- Department of Upper Gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Mikiko Sakuraya
- Department of Upper Gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Masahiro Niihara
- Department of Upper Gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Koshi Kumagai
- Department of Upper Gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Takafumi Sangai
- Department of Breast and Thyroid Surgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Yusuke Kumamoto
- Department of General-Pediatric-Hepatobiliary Pancreatic Surgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Takeshi Naitoh
- Department of Lower Gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Naoki Hiki
- Department of Upper Gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Keishi Yamashita
- Division of Advanced Surgical Oncology, Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, Sagamihara, Japan
| |
Collapse
|
38
|
Debernardi S, Liszka L, Ntala C, Steiger K, Esposito I, Carlotti E, Baker A, McDonald S, Graham T, Dmitrovic B, Feakins RM, Crnogorac‐Jurcevic T. Molecular characteristics of early-onset pancreatic ductal adenocarcinoma. Mol Oncol 2024; 18:677-690. [PMID: 38145461 PMCID: PMC10920080 DOI: 10.1002/1878-0261.13576] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/01/2023] [Accepted: 12/22/2023] [Indexed: 12/26/2023] Open
Abstract
The median age of patients with pancreatic ductal adenocarcinoma (PDAC) at diagnosis is 71 years; however, around 10% present with early-onset pancreatic cancer (EOPC), i.e., before age 50. The molecular mechanisms underlying such an early onset are unknown. We assessed the role of common PDAC drivers (KRAS, TP53, CDKN2A and SMAD4) and determined their mutational status and protein expression in 90 formalin-fixed, paraffin-embedded tissues, including multiple primary and matched metastases, from 37 EOPC patients. KRAS was mutated in 88% of patients; p53 was altered in 94%, and p16 and SMAD4 were lost in 86% and 71% of patients, respectively. Meta-synthesis showed a higher rate of p53 alterations in EOPC than in late-onset PDAC (94% vs. 69%, P = 0.0009) and significantly higher loss of SMAD4 (71% vs. 44%, P = 0.0025). The majority of EOPC patients accumulated aberrations in all four drivers; in addition, high tumour heterogeneity was observed across all tissues. The cumulative effect of an exceptionally high rate of alterations in all common PDAC driver genes combined with high tumour heterogeneity suggests an important mechanism underlying the early onset of PDAC.
Collapse
Affiliation(s)
- Silvana Debernardi
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer InstituteQueen Mary University of LondonUK
| | - Lukasz Liszka
- Department of Pathomorphology and Molecular DiagnosticsMedical University of SilesiaKatowicePoland
| | | | - Katja Steiger
- Institute of Pathology, School of Medicine and HealthTechnical University of MunichGermany
| | - Irene Esposito
- Institute of PathologyHeinrich‐Heine University and University Hospital of DusseldorfGermany
| | - Emanuela Carlotti
- Centre for Tumour Biology, Barts Cancer InstituteQueen Mary University of LondonUK
| | - Ann‐Marie Baker
- Centre for Tumour Biology, Barts Cancer InstituteQueen Mary University of LondonUK
| | - Stuart McDonald
- Centre for Tumour Biology, Barts Cancer InstituteQueen Mary University of LondonUK
| | - Trevor Graham
- Centre for Tumour Biology, Barts Cancer InstituteQueen Mary University of LondonUK
| | - Branko Dmitrovic
- Department of Pathology and Forensic MedicineClinical Hospital Center OsijekCroatia
| | - Roger M. Feakins
- Department of Cellular PathologyRoyal Free London NHS Foundation TrustUK
| | - Tatjana Crnogorac‐Jurcevic
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer InstituteQueen Mary University of LondonUK
| |
Collapse
|
39
|
Gu M, Ren B, Fang Y, Ren J, Liu X, Wang X, Zhou F, Xiao R, Luo X, You L, Zhao Y. Epigenetic regulation in cancer. MedComm (Beijing) 2024; 5:e495. [PMID: 38374872 PMCID: PMC10876210 DOI: 10.1002/mco2.495] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/21/2024] Open
Abstract
Epigenetic modifications are defined as heritable changes in gene activity that do not involve changes in the underlying DNA sequence. The oncogenic process is driven by the accumulation of alterations that impact genome's structure and function. Genetic mutations, which directly disrupt the DNA sequence, are complemented by epigenetic modifications that modulate gene expression, thereby facilitating the acquisition of malignant characteristics. Principals among these epigenetic changes are shifts in DNA methylation and histone mark patterns, which promote tumor development and metastasis. Notably, the reversible nature of epigenetic alterations, as opposed to the permanence of genetic changes, positions the epigenetic machinery as a prime target in the discovery of novel therapeutics. Our review delves into the complexities of epigenetic regulation, exploring its profound effects on tumor initiation, metastatic behavior, metabolic pathways, and the tumor microenvironment. We place a particular emphasis on the dysregulation at each level of epigenetic modulation, including but not limited to, the aberrations in enzymes responsible for DNA methylation and histone modification, subunit loss or fusions in chromatin remodeling complexes, and the disturbances in higher-order chromatin structure. Finally, we also evaluate therapeutic approaches that leverage the growing understanding of chromatin dysregulation, offering new avenues for cancer treatment.
Collapse
Affiliation(s)
- Minzhi Gu
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Bo Ren
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Yuan Fang
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Jie Ren
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Xiaohong Liu
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Xing Wang
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Feihan Zhou
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Ruiling Xiao
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Xiyuan Luo
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Lei You
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Yupei Zhao
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| |
Collapse
|
40
|
Dwivedi K, Rajpal A, Rajpal S, Kumar V, Agarwal M, Kumar N. XL 1R-Net: Explainable AI-driven improved L 1-regularized deep neural architecture for NSCLC biomarker identification. Comput Biol Chem 2024; 108:107990. [PMID: 38000327 DOI: 10.1016/j.compbiolchem.2023.107990] [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: 05/31/2023] [Revised: 10/29/2023] [Accepted: 11/21/2023] [Indexed: 11/26/2023]
Abstract
BACKGROUND AND OBJECTIVE Non-small cell lung cancer (NSCLC) exhibits intrinsic molecular heterogeneity, primarily driven by the mutation of specific biomarkers. Identification of these biomarkers would assist not only in distinguishing NSCLC into its major subtypes - Adenocarcinoma and Squamous Cell Carcinoma, but also in developing targeted therapy. Medical practitioners use one or more types of omic data to identify these biomarkers, copy number variation (CNV) being one such type. CNV provides a measure of genomic instability, which is considered a hallmark of carcinoma. However, the CNV data has not received much attention for biomarker identification. This paper aims to identify biomarkers for NSCLC using CNV data. METHODS An eXplainable AI (XAI)-driven L1-regularized deep learning architecture, XL1R-Net, is proposed that introduces a novel modification of the standard L1-regularized gradient descent algorithm to arrive at an improved deep neural classifier for NSCLC subtyping. Further, XAI-based feature identification has been used to leverage the trained classifier to uncover a set of twenty NCSLC-relevant biomarkers. RESULTS The identified biomarkers are evaluated based on their classification performance and clinical relevance. Using Multilayer Perceptron (MLP)-based model, a classification accuracy of 84.95% using 10-fold cross-validation is achieved. Moreover, the statistical significance test on the classification performance also revealed the superiority of the MLP model over the competitive machine learning models. Further, the publicly available Drug-Gene Interaction Database reveals twelve of the identified biomarkers as potentially druggable. The K-M Plotter tool was used to verify eighteen of the identified biomarkers with a high probability of predicting NSCLC patients' likelihood of survival. While nine of the identified biomarkers confirm the recent literature, five find mention in the OncoKB Gene List. CONCLUSION A set of seven novel biomarkers that have not been reported in the literature could be investigated for their potential contribution towards NSCLC therapy. Given NSCLC's genetic diversity, using only one omics data type may not adequately capture the tumor's complexity. Multiomics data and its integration with other sources will be examined in the future to better understand NSCLC heterogeneity.
Collapse
Affiliation(s)
- Kountay Dwivedi
- Department of Computer Science, University of Delhi, Delhi, India.
| | - Ankit Rajpal
- Department of Computer Science, University of Delhi, Delhi, India.
| | - Sheetal Rajpal
- Department of Computer Science, Dyal Singh College, Delhi, India.
| | - Virendra Kumar
- Department of Nuclear Magnetic Resonance, All India Institute of Medical Sciences, New Delhi, India.
| | - Manoj Agarwal
- Department of Computer Science, Hans Raj College, University of Delhi, Delhi, India.
| | - Naveen Kumar
- Department of Computer Science, University of Delhi, Delhi, India.
| |
Collapse
|
41
|
Orlacchio A, Muzyka S, Gonda TA. Epigenetic therapeutic strategies in pancreatic cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 383:1-40. [PMID: 38359967 DOI: 10.1016/bs.ircmb.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal solid malignancies, characterized by its aggressiveness and metastatic potential, with a 5-year survival rate of only 8-11%. Despite significant improvements in PDAC treatment and management, therapeutic alternatives are still limited. One of the main reasons is its high degree of intra- and inter-individual tumor heterogeneity which is established and maintained through a complex network of transcription factors and epigenetic regulators. Epigenetic drugs, have shown promising preclinical results in PDAC and are currently being evaluated in clinical trials both for their ability to sensitize cancer cells to cytotoxic drugs and to counteract the immunosuppressive characteristic of PDAC tumor microenvironment. In this review, we discuss the current status of epigenetic treatment strategies to overcome molecular and cellular PDAC heterogeneity in order to improve response to therapy.
Collapse
Affiliation(s)
- Arturo Orlacchio
- Division of Gastroenterology and Hepatology, New York University, New York, NY, United States
| | - Stephen Muzyka
- Division of Gastroenterology and Hepatology, New York University, New York, NY, United States
| | - Tamas A Gonda
- Division of Gastroenterology and Hepatology, New York University, New York, NY, United States.
| |
Collapse
|
42
|
Pascual G, Majem B, Benitah SA. Targeting lipid metabolism in cancer metastasis. Biochim Biophys Acta Rev Cancer 2024; 1879:189051. [PMID: 38101461 DOI: 10.1016/j.bbcan.2023.189051] [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: 08/06/2023] [Revised: 11/29/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
Abstract
This review delves into the most recent research on the metabolic adaptability of cancer cells and examines how their metabolic functions can impact their progression into metastatic forms. We emphasize the growing significance of lipid metabolism and dietary lipids within the tumor microenvironment, underscoring their influence on tumor progression. Additionally, we present an outline of the interplay between metabolic processes and the epigenome of cancer cells, underscoring the importance regarding the metastatic process. Lastly, we examine the potential of targeting metabolism as a therapeutic approach in combating cancer progression, shedding light on innovative drugs/targets currently undergoing preclinical evaluation.
Collapse
Affiliation(s)
- Gloria Pascual
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
| | - Blanca Majem
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Salvador Aznar Benitah
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
| |
Collapse
|
43
|
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: 20] [Impact Index Per Article: 10.0] [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.
Collapse
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.
| |
Collapse
|
44
|
Usman OH, Kumar S, Walker RR, Xie G, Sumajit HC, Jalil AR, Ramakrishnan S, Dooling LJ, Wang YJ, Irianto J. Differential modulation of cellular phenotype and drug sensitivity by extracellular matrix proteins in primary and metastatic pancreatic cancer cells. Mol Biol Cell 2023; 34:ar130. [PMID: 37903222 PMCID: PMC10848942 DOI: 10.1091/mbc.e23-02-0075] [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: 02/28/2023] [Revised: 09/06/2023] [Accepted: 10/10/2023] [Indexed: 11/01/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is reported to be the third highest cause of cancer-related deaths in the United States. PDAC is known for its high proportion of stroma, which accounts for 90% of the tumor mass. The stroma is made up of extracellular matrix (ECM) and nonmalignant cells such as inflammatory cells, cancer-associated fibroblasts, and lymphatic and blood vessels. Here, we decoupled the effects of the ECM on PDAC cell lines by culturing cells on surfaces coated with different ECM proteins. Our data show that the primary tumor-derived cell lines have different morphology depending on the ECM proteins on which they are cultured, while metastatic lesion-derived PDAC lines' morphology does not change with respect to the different ECM proteins. Similarly, ECM proteins modulate the proliferation rate and the gemcitabine sensitivity of the primary tumor PDAC cell lines, but not the metastatic PDAC lines. Lastly, transcriptomics analysis of the primary tumor PDAC cells cultured on different ECM proteins reveals the regulation of various pathways, such as cell cycle, cell-adhesion molecules, and focal adhesion, including the regulation of several integrin genes that are essential for ECM recognition.
Collapse
Affiliation(s)
- Olalekan H. Usman
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306
| | - Sampath Kumar
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306
| | - Reddick R. Walker
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306
| | - Gengqiang Xie
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306
| | - Hyeje C. Sumajit
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306
| | - AbdelAziz R. Jalil
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA 19104
| | - Subramanian Ramakrishnan
- Department of Chemical and Biomedical Engineering, Florida A&M University-Florida State University College of Engineering, Tallahassee, FL 32310
| | - Lawrence J. Dooling
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA 19104
| | - Yue Julia Wang
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306
| | - Jerome Irianto
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306
| |
Collapse
|
45
|
Tang X, Xiang L, Li Q, Shao Y, Wan L, Zhao D, Li X, Wu S, Wang H, Li D, Ding K. Molecular evolution in different subtypes of multifocal hepatocellular carcinoma. Hepatol Int 2023; 17:1429-1443. [PMID: 37273168 DOI: 10.1007/s12072-023-10551-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/07/2023] [Indexed: 06/06/2023]
Abstract
BACKGROUND Multifocal hepatocellular carcinoma (MF-HCC) accounts for > 40% of HCCs, exhibiting a poor prognosis than single primary HCCs. Characterizing molecular features including dynamic changes of mutational signature along with clonal evolution, intrahepatic metastatic timing, and genetic footprint in the preneoplastic stage underlying different subtypes of MF-HCC are important for understanding their molecular evolution and developing a precision management strategy. METHODS We conducted whole-exome sequencing in 74 tumor samples from spatially distinct regions in 35 resected lesions and adjacent noncancerous tissues from 11 patients, 15 histologically confirmed preneoplastic lesions, and six samples from peripheral blood mononuclear cells. A previously published MF-HCC cohort (n = 9) was included as an independent validation dataset. We combined well-established approaches to investigate tumor heterogeneity, intrahepatic metastatic timing, and molecular footprints in different subtypes of MF-HCCs. RESULTS We classified MF-HCCs patients into three subtypes, including intrahepatic metastasis, multicentric occurrence, and mixed intrahepatic metastasis and multicentric occurrence. The dynamic changes in mutational signatures between tumor subclonal expansions demonstrated varied etiologies (e.g., aristolochic acid exposure) underlying the clonal progression in different MF-HCC subtypes. Furthermore, the clonal evolution in intrahepatic metastasis exhibited an early metastatic seeding at 10-4-0.01 cm3 in primary tumor volume (below the limits of clinical detection), further validated in an independent cohort. In addition, mutational footprints in the preneoplastic lesions for multicentric occurrence patients revealed common preneoplastic arising clones, evidently being ancestors of different tumor lesions. CONCLUSION Our study comprehensively characterized the varied tumor clonal evolutionary history underlying different subtypes of MF-HCC and provided important implications for optimizing personalized clinical management for MF-HCC.
Collapse
Affiliation(s)
- Xia Tang
- Shanghai Pudong Hospital and Pudong Medical Center of Fudan University, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Lei Xiang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Qingshu Li
- Department of Pathology, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Yue Shao
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Li Wan
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Dachun Zhao
- Department of Pathology, Peking Union Medical College Hospital, Beijing, 100730, People's Republic of China
| | - Xiaoyuan Li
- Department of Oncology, Peking Union Medical College Hospital, Beijing, 100730, People's Republic of China
| | - Songfeng Wu
- Beijing Qinglian Biotech Co., Ltd, Beijing, 102206, People's Republic of China
| | - Haijian Wang
- Shanghai Pudong Hospital and Pudong Medical Center of Fudan University, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China.
| | - Dewei Li
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China.
- Hepatobiliary and Pancreatic Cancer Center, Chongqing University Cancer Hospital, Chongqing, 400030, People's Republic of China.
| | - Keyue Ding
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
| |
Collapse
|
46
|
Krauß L, Schneider C, Hessmann E, Saur D, Schneider G. Epigenetic control of pancreatic cancer metastasis. Cancer Metastasis Rev 2023; 42:1113-1131. [PMID: 37659057 PMCID: PMC10713713 DOI: 10.1007/s10555-023-10132-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/10/2023] [Indexed: 09/05/2023]
Abstract
Surgical resection, when combined with chemotherapy, has been shown to significantly improve the survival rate of patients with pancreatic ductal adenocarcinoma (PDAC). However, this treatment option is only feasible for a fraction of patients, as more than 50% of cases are diagnosed with metastasis. The multifaceted process of metastasis is still not fully understood, but recent data suggest that transcriptional and epigenetic plasticity play significant roles. Interfering with epigenetic reprogramming can potentially control the adaptive processes responsible for metastatic progression and therapy resistance, thereby enhancing treatment responses and preventing recurrence. This review will focus on the relevance of histone-modifying enzymes in pancreatic cancer, specifically on their impact on the metastatic cascade. Additionally, it will also provide a brief update on the current clinical developments in epigenetic therapies.
Collapse
Affiliation(s)
- Lukas Krauß
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany.
| | - Carolin Schneider
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Elisabeth Hessmann
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Göttingen, 37075, Göttingen, Germany
- Clinical Research Unit 5002, KFO5002, University Medical Center Göttingen, 37075, Göttingen, Germany
- CCC-N (Comprehensive Cancer Center Lower Saxony), 37075, Göttingen, Germany
| | - Dieter Saur
- Institute for Translational Cancer Research and Experimental Cancer Therapy, Technical University Munich, 81675, Munich, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
| | - Günter Schneider
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany.
- CCC-N (Comprehensive Cancer Center Lower Saxony), 37075, Göttingen, Germany.
| |
Collapse
|
47
|
Hongwei S, Xinzhong H, Huiqin X, Shuqin X, Ruonan W, Li L, Jianzhong C, Sijin L. Standard deviation of CT radiomic features among malignancies in each individual: prognostic ability in lung cancer patients. J Cancer Res Clin Oncol 2023; 149:7165-7173. [PMID: 36884114 DOI: 10.1007/s00432-023-04649-7] [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: 10/31/2022] [Accepted: 02/12/2023] [Indexed: 03/09/2023]
Abstract
PURPOSE It was reported that individual heterogeneity among malignancies (IHAM) might correlate well to the prognosis of lung cancer; however, seldom radiomic study is on this field. Standard deviation (SD) in statistics could scale average amount of variability of a variable; therefore, we used SD of CT feature (FeatureSD) among primary tumor and malignant lymph nodes (LNs) in an individual to represent IHAM, and its prognostic ability was explored. METHODS The enrolled patients who had accepted PET/CT scans were selected from our previous study (ClinicalTrials.gov, NCT03648151). The patients had primary tumor and at least one LN, and standardized uptake value of LN higher than 2.0 and 2.5 were enrolled as the cohort 1 (n = 94) and 2 (n = 88), respectively. FeatureSD from the combined or thin-section CT were calculated among primary tumor and malignant LNs in each patient, and were separately selected by the survival XGBoost method. Finally, their prognostic ability was compared to the significant patient characteristics identified by the Cox regression. RESULTS In the univariate and multi-variate Cox analysis, surgery, target therapy, and TNM stage were significantly against OS in the both cohorts. In the survival XGBoost analysis of the thin-section CT dataset, none FeatureSD could be repeatably ranked on the top list of the both cohorts. For the combined CT dataset, only one FeatureSD ranked in the top three of both cohorts, but the three significant factors in the Cox regression were not even on the list. Both in the cohort 1 and 2, C-index of the model composed of the three factors could be improved by integrating the continuous FeatureSD; furthermore, that of each factor was obviously lower than FeatureSD. CONCLUSION Standard deviation of CT features among malignant foci within an individual was a powerful prognostic factor in vivo for lung cancer patients.
Collapse
Affiliation(s)
- Si Hongwei
- Department of Nuclear Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, China.
- Department of Nuclear Medicine, The First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi Province, China.
| | - Hao Xinzhong
- Department of Nuclear Medicine, The First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi Province, China
| | - Xu Huiqin
- Department of Medical imaging, Shenzhen Second People's Hospital/the First Affiliated Hospital of Shenzhen University Health Science Center, 518035, Shenzhen, China
| | - Xue Shuqin
- Department of Nuclear Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, China
| | - Wang Ruonan
- Department of Nuclear Medicine, The First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi Province, China
| | - Li Li
- Department of Nuclear Medicine, The First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi Province, China
| | - Cao Jianzhong
- Department of Radiation Oncology, The Cancer Hospital of Shanxi Province, Taiyuan, 030013, Shanxi Province, China
| | - Li Sijin
- Department of Nuclear Medicine, The First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi Province, China
| |
Collapse
|
48
|
Lu S, Kim HS, Cao Y, Bedi K, Zhao L, Narayanan IV, Magnuson B, Gu Y, Yang J, Yi Z, Babaniamansour S, Shameon S, Xu C, Paulsen MT, Qiu P, Jeyarajan S, Ljungman M, Thomas D, Dou Y, Crawford H, di Magliano MP, Ge K, Yang B, Shi J. KMT2D links TGF-β signaling to noncanonical activin pathway and regulates pancreatic cancer cell plasticity. Int J Cancer 2023; 153:552-570. [PMID: 37140208 PMCID: PMC10330100 DOI: 10.1002/ijc.34528] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 03/02/2023] [Accepted: 03/13/2023] [Indexed: 05/05/2023]
Abstract
Although KMT2D, also known as MLL2, is known to play an essential role in development, differentiation, and tumor suppression, its role in pancreatic cancer development is not well understood. Here, we discovered a novel signaling axis mediated by KMT2D, which links TGF-β to the activin A pathway. We found that TGF-β upregulates a microRNA, miR-147b, which in turn leads to post-transcriptional silencing of KMT2D. Loss of KMT2D induces the expression and secretion of activin A, which activates a noncanonical p38 MAPK-mediated pathway to modulate cancer cell plasticity, promote a mesenchymal phenotype, and enhance tumor invasion and metastasis in mice. We observed a decreased KMT2D expression in human primary and metastatic pancreatic cancer. Furthermore, inhibition or knockdown of activin A reversed the protumoral role of KMT2D loss. These findings support a tumor-suppressive role of KMT2D in pancreatic cancer and identify miR-147b and activin A as novel therapeutic targets.
Collapse
Affiliation(s)
- Shuang Lu
- Department of Pathology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
- Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, PR China
| | - Hong Sun Kim
- Department of Pathology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yubo Cao
- Department of Pathology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Karan Bedi
- Department of Radiation Oncology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lili Zhao
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ishwarya Venkata Narayanan
- Department of Radiation Oncology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Brian Magnuson
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yumei Gu
- Department of Pathology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jing Yang
- Department of Pathology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zhujun Yi
- Department of Pathology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sepideh Babaniamansour
- Department of Pathology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sargis Shameon
- Department of Pathology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chang Xu
- Department of Pathology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michelle T. Paulsen
- Department of Radiation Oncology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ping Qiu
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sivakumar Jeyarajan
- Department of Pathology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mats Ljungman
- Department of Radiation Oncology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dafydd Thomas
- Department of Pathology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yali Dou
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | | | | | - Kai Ge
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, MD 20892, USA
| | - Bo Yang
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jiaqi Shi
- Department of Pathology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
49
|
Myers MA, Arnold BJ, Bansal V, Mullen KM, Zaccaria S, Raphael BJ. HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548855. [PMID: 37502835 PMCID: PMC10370020 DOI: 10.1101/2023.07.13.548855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Multi-region DNA sequencing of primary tumors and metastases from individual patients helps identify somatic aberrations driving cancer development. However, most methods to infer copy-number aberrations (CNAs) analyze individual samples. We introduce HATCHet2 to identify haplotype- and clone-specific CNAs simultaneously from multiple bulk samples. HATCHet2 introduces a novel statistic, the mirrored haplotype B-allele frequency (mhBAF), to identify mirrored-subclonal CNAs having different numbers of copies of parental haplotypes in different tumor clones. HATCHet2 also has high accuracy in identifying focal CNAs and extends the earlier HATCHet method in several directions. We demonstrate HATCHet2's improved accuracy using simulations and a single-cell sequencing dataset. HATCHet2 analysis of 50 prostate cancer samples from 10 patients reveals previously-unreported mirrored-subclonal CNAs affecting cancer genes.
Collapse
Affiliation(s)
- Matthew A. Myers
- Department of Computer Science, Princeton University, Princeton, USA
| | - Brian J. Arnold
- Center for Statistics and Machine Learning, Princeton University, Princeton, USA
| | - Vineet Bansal
- Princeton Research Computing, Princeton University, Princeton, NJ, USA
| | - Katelyn M. Mullen
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simone Zaccaria
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | | |
Collapse
|
50
|
Lilly AC, Astsaturov I, Golemis EA. Intrapancreatic fat, pancreatitis, and pancreatic cancer. Cell Mol Life Sci 2023; 80:206. [PMID: 37452870 PMCID: PMC10349727 DOI: 10.1007/s00018-023-04855-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023]
Abstract
Pancreatic cancer is typically detected at an advanced stage, and is refractory to most forms of treatment, contributing to poor survival outcomes. The incidence of pancreatic cancer is gradually increasing, linked to an aging population and increasing rates of obesity and pancreatitis, which are risk factors for this cancer. Sources of risk include adipokine signaling from fat cells throughout the body, elevated levels of intrapancreatic intrapancreatic adipocytes (IPAs), inflammatory signals arising from pancreas-infiltrating immune cells and a fibrotic environment induced by recurring cycles of pancreatic obstruction and acinar cell lysis. Once cancers become established, reorganization of pancreatic tissue typically excludes IPAs from the tumor microenvironment, which instead consists of cancer cells embedded in a specialized microenvironment derived from cancer-associated fibroblasts (CAFs). While cancer cell interactions with CAFs and immune cells have been the topic of much investigation, mechanistic studies of the source and function of IPAs in the pre-cancerous niche are much less developed. Intriguingly, an extensive review of studies addressing the accumulation and activity of IPAs in the pancreas reveals that unexpectedly diverse group of factors cause replacement of acinar tissue with IPAs, particularly in the mouse models that are essential tools for research into pancreatic cancer. Genes implicated in regulation of IPA accumulation include KRAS, MYC, TGF-β, periostin, HNF1, and regulators of ductal ciliation and ER stress, among others. These findings emphasize the importance of studying pancreas-damaging factors in the pre-cancerous environment, and have significant implications for the interpretation of data from mouse models for pancreatic cancer.
Collapse
Affiliation(s)
- Anna C Lilly
- Program in Cancer Signaling and Microenvironment, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA, 19111, USA
- Molecular & Cell Biology & Genetics (MCBG) Program, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Igor Astsaturov
- Program in Cancer Signaling and Microenvironment, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA, 19111, USA
- The Marvin & Concetta Greenberg Pancreatic Cancer Institute, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Erica A Golemis
- Program in Cancer Signaling and Microenvironment, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA, 19111, USA.
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA.
| |
Collapse
|