1
|
Park JK, Jeong HO, Kim H, Choi JH, Lee EM, Kim S, Jang J, Choi DWY, Lee SH, Kim KM, Jang KT, Lee KH, Lee KT, Lee MW, Lee JK, Lee S. Single-cell transcriptome analysis reveals subtype-specific clonal evolution and microenvironmental changes in liver metastasis of pancreatic adenocarcinoma and their clinical implications. Mol Cancer 2024; 23:87. [PMID: 38702773 PMCID: PMC11067162 DOI: 10.1186/s12943-024-02003-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 04/16/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Intratumoral heterogeneity (ITH) and tumor microenvironment (TME) of pancreatic ductal adenocarcinoma (PDAC) play important roles in tumor evolution and patient outcomes. However, the precise characterization of diverse cell populations and their crosstalk associated with PDAC progression and metastasis is still challenging. METHODS We performed single-cell RNA sequencing (scRNA-seq) of treatment-naïve primary PDAC samples with and without paired liver metastasis samples to understand the interplay between ITH and TME in the PDAC evolution and its clinical associations. RESULTS scRNA-seq analysis revealed that even a small proportion (22%) of basal-like malignant ductal cells could lead to poor chemotherapy response and patient survival and that epithelial-mesenchymal transition programs were largely subtype-specific. The clonal homogeneity significantly increased with more prevalent and pronounced copy number gains of oncogenes, such as KRAS and ETV1, and losses of tumor suppressor genes, such as SMAD2 and MAP2K4, along PDAC progression and metastasis. Moreover, diverse immune cell populations, including naïve SELLhi regulatory T cells (Tregs) and activated TIGIThi Tregs, contributed to shaping immunosuppressive TMEs of PDAC through cellular interactions with malignant ductal cells in PDAC evolution. Importantly, the proportion of basal-like ductal cells negatively correlated with that of immunoreactive cell populations, such as cytotoxic T cells, but positively correlated with that of immunosuppressive cell populations, such as Tregs. CONCLUSION We uncover that the proportion of basal-like subtype is a key determinant for chemotherapy response and patient outcome, and that PDAC clonally evolves with subtype-specific dosage changes of cancer-associated genes by forming immunosuppressive microenvironments in its progression and metastasis.
Collapse
Affiliation(s)
- Joo Kyung Park
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Sungkyunkwan University, Seoul, Republic of Korea
| | - Hyoung-Oh Jeong
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Hyemin Kim
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jin Ho Choi
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Eun Mi Lee
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Seunghoon Kim
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Jinho Jang
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - David Whee-Young Choi
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Se-Hoon Lee
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Sungkyunkwan University, Seoul, Republic of Korea
| | - Kyoung Mee Kim
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kee-Taek Jang
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kwang Hyuck Lee
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyu Taek Lee
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Min Woo Lee
- Department of Radiology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
| | - Jong Kyun Lee
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
| | - Semin Lee
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.
| |
Collapse
|
2
|
Ali HR, West RB. Spatial Biology of Breast Cancer. Cold Spring Harb Perspect Med 2024; 14:a041335. [PMID: 38110242 PMCID: PMC11065165 DOI: 10.1101/cshperspect.a041335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Spatial findings have shaped on our understanding of breast cancer. In this review, we discuss how spatial methods, including spatial transcriptomics and proteomics and the resultant understanding of spatial relationships, have contributed to concepts regarding cancer progression and treatment. In addition to discussing traditional approaches, we examine how emerging multiplex imaging technologies have contributed to the field and how they might influence future research.
Collapse
Affiliation(s)
- H Raza Ali
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Robert B West
- Department of Pathology, Stanford University Medical Center, Stanford, California 94305, USA
| |
Collapse
|
3
|
An M, Mehta A, Min BH, Heo YJ, Wright SJ, Parikh M, Bi L, Lee H, Kim TJ, Lee SY, Moon J, Park RJ, Strickland MR, Park WY, Kang WK, Kim KM, Kim ST, Klempner SJ, Lee J. Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer. Cancer Discov 2024; 14:766-785. [PMID: 38319303 PMCID: PMC11061611 DOI: 10.1158/2159-8290.cd-23-0857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/28/2023] [Accepted: 02/02/2024] [Indexed: 02/07/2024]
Abstract
Adding anti-programmed cell death protein 1 (anti-PD-1) to 5-fluorouracil (5-FU)/platinum improves survival in some advanced gastroesophageal adenocarcinomas (GEA). To understand the effects of chemotherapy and immunotherapy, we conducted a phase II first-line trial (n = 47) sequentially adding pembrolizumab to 5-FU/platinum in advanced GEA. Using serial biopsy of the primary tumor at baseline, after one cycle of 5-FU/platinum, and after the addition of pembrolizumab, we transcriptionally profiled 358,067 single cells to identify evolving multicellular tumor microenvironment (TME) networks. Chemotherapy induced early on-treatment multicellular hubs with tumor-reactive T-cell and M1-like macrophage interactions in slow progressors. Faster progression featured increased MUC5A and MSLN containing treatment resistance programs in tumor cells and M2-like macrophages with immunosuppressive stromal interactions. After pembrolizumab, we observed increased CD8 T-cell infiltration and development of an immunity hub involving tumor-reactive CXCL13 T-cell program and epithelial interferon-stimulated gene programs. Strategies to drive increases in antitumor immune hub formation could expand the portion of patients benefiting from anti-PD-1 approaches. SIGNIFICANCE The benefit of 5-FU/platinum with anti-PD-1 in first-line advanced gastric cancer is limited to patient subgroups. Using a trial with sequential anti-PD-1, we show coordinated induction of multicellular TME hubs informs the ability of anti-PD-1 to potentiate T cell-driven responses. Differential TME hub development highlights features that underlie clinical outcomes. This article is featured in Selected Articles from This Issue, p. 695.
Collapse
Affiliation(s)
- Minae An
- Experimental Therapeutics Development Center, Samsung Medical Center, Seoul, Korea
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Arnav Mehta
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Division of Hematology-Oncology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Byung Hoon Min
- Department of Medicine, Division of Gastroenterology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | | | - Samuel J. Wright
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Milan Parikh
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Division of Hematology-Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Lynn Bi
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Division of Hematology-Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Hyuk Lee
- Department of Medicine, Division of Gastroenterology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Tae Jun Kim
- Department of Medicine, Division of Gastroenterology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Song-Yi Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jeonghyeon Moon
- Departments of Neurology and Immunology, Yale School of Medicine, New Haven, Connecticut
| | - Ryan J. Park
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Division of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Matthew R. Strickland
- Department of Medicine, Division of Hematology-Oncology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | | | - Won Ki Kang
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kyoung-Mee Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seung Tae Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Samuel J. Klempner
- Department of Medicine, Division of Hematology-Oncology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Jeeyun Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| |
Collapse
|
4
|
van Eijck CWF, Real FX, Malats N, Vadgama D, van den Bosch TPP, Doukas M, van Eijck CHJ, Mustafa DAM. GATA6 identifies an immune-enriched phenotype linked to favorable outcomes in patients with pancreatic cancer undergoing upfront surgery. Cell Rep Med 2024:101557. [PMID: 38733987 DOI: 10.1016/j.xcrm.2024.101557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/14/2024] [Accepted: 04/16/2024] [Indexed: 05/13/2024]
Abstract
This study underscores GATA6's role in distinguishing classical and basal-like pancreatic ductal adenocarcinoma (PDAC) phenotypes. Retrospective studies associate GATA6 immunohistochemistry (IHC) expression with survival outcomes, warranting prospective validation. In a prospective treatment-naive cohort of patients with resected PDAC, GATA6 IHC proves a prognostic discriminator, associating high GATA6 expression with extended survival and the classical PDAC phenotype. However, GATA6's prognostic significance is numerically lower after gemcitabine-based neoadjuvant chemoradiotherapy compared to its significance in patients treated with upfront surgery. Furthermore, GATA6 is implicated in immunomodulation, although a comprehensive investigation of its immunological role is lacking. Treatment-naive PDAC tumors with varying GATA6 expression yield distinct immunological landscapes. Tumors highly expressing GATA6 show reduced infiltration of immunosuppressive regulatory T cells and M2 macrophages but increased infiltration of immune-stimulating, antigen-presenting, and activated T cells. Our findings caution against solely relying on GATA6 for molecular subtyping in clinical trials and open avenues for exploring immune-based combination therapies.
Collapse
Affiliation(s)
- Casper W F van Eijck
- Department of Surgery, Erasmus University Medical Centre, Rotterdam, the Netherlands; Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre, Madrid, Spain.
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre, Madrid, Spain; Centro de Investigación Biomédica en Red-Cáncer, Madrid, Spain; Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre, Madrid, Spain; Centro de Investigación Biomédica en Red-Cáncer, Madrid, Spain
| | - Disha Vadgama
- Department of Pathology and Clinical Bioinformatics, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Thierry P P van den Bosch
- Department of Pathology and Clinical Bioinformatics, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Michail Doukas
- Department of Pathology and Clinical Bioinformatics, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Casper H J van Eijck
- Department of Surgery, Erasmus University Medical Centre, Rotterdam, the Netherlands; Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre, Madrid, Spain
| | - Dana A M Mustafa
- Department of Pathology and Clinical Bioinformatics, Erasmus University Medical Centre, Rotterdam, the Netherlands; The Tumor Immuno-Pathology Laboratory, Erasmus University Medical Centre, Rotterdam, the Netherlands.
| |
Collapse
|
5
|
Lupo F, Pezzini F, Pasini D, Fiorini E, Adamo A, Veghini L, Bevere M, Frusteri C, Delfino P, D'agosto S, Andreani S, Piro G, Malinova A, Wang T, De Sanctis F, Lawlor RT, Hwang CI, Carbone C, Amelio I, Bailey P, Bronte V, Tuveson D, Scarpa A, Ugel S, Corbo V. Axon guidance cue SEMA3A promotes the aggressive phenotype of basal-like PDAC. Gut 2024:gutjnl-2023-329807. [PMID: 38670629 DOI: 10.1136/gutjnl-2023-329807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/05/2024] [Indexed: 04/28/2024]
Abstract
OBJECTIVE The dysregulation of the axon guidance pathway is common in pancreatic ductal adenocarcinoma (PDAC), yet our understanding of its biological relevance is limited. Here, we investigated the functional role of the axon guidance cue SEMA3A in supporting PDAC progression. DESIGN We integrated bulk and single-cell transcriptomic datasets of human PDAC with in situ hybridisation analyses of patients' tissues to evaluate SEMA3A expression in molecular subtypes of PDAC. Gain and loss of function experiments in PDAC cell lines and organoids were performed to dissect how SEMA3A contributes to define a biologically aggressive phenotype. RESULTS In PDAC tissues, SEMA3A is expressed by stromal elements and selectively enriched in basal-like/squamous epithelial cells. Accordingly, expression of SEMA3A in PDAC cells is induced by both cell-intrinsic and cell-extrinsic determinants of the basal-like phenotype. In vitro, SEMA3A promotes cell migration as well as anoikis resistance. At the molecular level, these phenotypes are associated with increased focal adhesion kinase signalling through canonical SEMA3A-NRP1 axis. SEMA3A provides mouse PDAC cells with greater metastatic competence and favours intratumoural infiltration of tumour-associated macrophages and reduced density of T cells. Mechanistically, SEMA3A functions as chemoattractant for macrophages and skews their polarisation towards an M2-like phenotype. In SEMA3Ahigh tumours, depletion of macrophages results in greater intratumour infiltration by CD8+T cells and better control of the disease from antitumour treatment. CONCLUSIONS Here, we show that SEMA3A is a stress-sensitive locus that promotes the malignant phenotype of basal-like PDAC through both cell-intrinsic and cell-extrinsic mechanisms.
Collapse
Affiliation(s)
- Francesca Lupo
- Department of Engineering for Innovation Medicine, University of Verona, Verona, Italy
| | - Francesco Pezzini
- Department of Engineering for Innovation Medicine, University of Verona, Verona, Italy
| | - Davide Pasini
- Department of Engineering for Innovation Medicine, University of Verona, Verona, Italy
- Department of Medicine, University of Verona, Verona, Italy
| | - Elena Fiorini
- Department of Engineering for Innovation Medicine, University of Verona, Verona, Italy
| | - Annalisa Adamo
- Department of Medicine, University of Verona, Verona, Italy
| | - Lisa Veghini
- Department of Engineering for Innovation Medicine, University of Verona, Verona, Italy
| | - Michele Bevere
- ARC-Net Research Centre, University of Verona, Verona, Italy
| | | | - Pietro Delfino
- Department of Diagnostic and Public Health, University of Verona, Verona, Italy
- Division of Immunology, Transplantation and Infectious Diseases, IRCSS San Raffaele, Milan, Italy
| | - Sabrina D'agosto
- Department of Diagnostic and Public Health, University of Verona, Verona, Italy
- Human Technopole, Milan, Italy
| | - Silvia Andreani
- ARC-Net Research Centre, University of Verona, Verona, Italy
- Department of Biochemistry and Molecular Biology, University of Würzburg, Wurzburg, Germany
| | - Geny Piro
- Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy
| | - Antonia Malinova
- Department of Engineering for Innovation Medicine, University of Verona, Verona, Italy
| | - Tian Wang
- Department of Medicine, University of Verona, Verona, Italy
| | | | | | - Chang-Il Hwang
- Microbiology and Molecular Genetics, UC Davis Department of Microbiology, Davis, California, USA
| | - Carmine Carbone
- Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy
| | - Ivano Amelio
- Division of Systems Toxicology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Peter Bailey
- Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, UK
| | | | - David Tuveson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Aldo Scarpa
- ARC-Net Research Centre, University of Verona, Verona, Italy
- Department of Diagnostic and Public Health, University of Verona, Verona, Italy
| | - Stefano Ugel
- Department of Medicine, University of Verona, Verona, Italy
| | - Vincenzo Corbo
- Department of Engineering for Innovation Medicine, University of Verona, Verona, Italy
| |
Collapse
|
6
|
Matchett KP, Paris J, Teichmann SA, Henderson NC. Spatial genomics: mapping human steatotic liver disease. Nat Rev Gastroenterol Hepatol 2024:10.1038/s41575-024-00915-2. [PMID: 38654090 DOI: 10.1038/s41575-024-00915-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/28/2024] [Indexed: 04/25/2024]
Abstract
Metabolic dysfunction-associated steatotic liver disease (MASLD, formerly known as non-alcoholic fatty liver disease) is a leading cause of chronic liver disease worldwide. MASLD can progress to metabolic dysfunction-associated steatohepatitis (MASH, formerly known as non-alcoholic steatohepatitis) with subsequent liver cirrhosis and hepatocellular carcinoma formation. The advent of current technologies such as single-cell and single-nuclei RNA sequencing have transformed our understanding of the liver in homeostasis and disease. The next frontier is contextualizing this single-cell information in its native spatial orientation. This understanding will markedly accelerate discovery science in hepatology, resulting in a further step-change in our knowledge of liver biology and pathobiology. In this Review, we discuss up-to-date knowledge of MASLD development and progression and how the burgeoning field of spatial genomics is driving exciting new developments in our understanding of human liver disease pathogenesis and therapeutic target identification.
Collapse
Affiliation(s)
- Kylie P Matchett
- Centre for Inflammation Research, Institute for Regeneration and Repair, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK
| | - Jasmin Paris
- Centre for Inflammation Research, Institute for Regeneration and Repair, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Cambridge, UK
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Neil C Henderson
- Centre for Inflammation Research, Institute for Regeneration and Repair, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
7
|
Salas-Escabillas DJ, Hoffman MT, Moore JS, Brender SM, Wen HJ, Benitz S, Davis ET, Long D, Wombwell AM, Steele NG, Sears RC, Matsumoto I, DelGiorno KE, Crawford HC. Tuft cells transdifferentiate to neural-like progenitor cells in the progression of pancreatic cancer. bioRxiv 2024:2024.02.12.579982. [PMID: 38405804 PMCID: PMC10888969 DOI: 10.1101/2024.02.12.579982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDA) is partly initiated through the transdifferentiation of acinar cells to metaplastic ducts that act as precursors of neoplasia and cancer. Tuft cells are solitary chemosensory cells not found in the normal pancreas but arise in metaplasia and neoplasia, diminishing as neoplastic lesions progress to carcinoma. Metaplastic tuft cells (mTCs) function to suppress tumor progression through communication with the tumor microenvironment, but their fate during progression is unknown. To determine the fate of mTCs during PDA progression, we have created a lineage tracing model that uses a tamoxifen-inducible tuft-cell specific Pou2f3CreERT/+ driver to induce transgene expression, including the lineage tracer tdTomato or the oncogene Myc. mTC lineage trace models of pancreatic neoplasia and carcinoma were used to follow mTC fate. We found that mTCs, in the carcinoma model, transdifferentiate into neural-like progenitor cells (NRPs), a cell type associated with poor survival in PDA patients. Using conditional knock-out and overexpression systems, we found that Myc activity in mTCs is necessary and sufficient to induce this Tuft-to-Neuroendocrine-Transition (TNT).
Collapse
Affiliation(s)
- Daniel J. Salas-Escabillas
- Cancer Biology, University of Michigan, Ann Arbor, MI
- Department of Surgery, Henry Ford Health, Detroit, MI
| | - Megan T. Hoffman
- Department of Immunology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | | | | | - Hui-Ju Wen
- Department of Surgery, Henry Ford Health, Detroit, MI
| | - Simone Benitz
- Department of Surgery, Henry Ford Health, Detroit, MI
| | | | - Dan Long
- Department of Surgery, Henry Ford Health, Detroit, MI
| | | | | | - Rosalie C. Sears
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR
| | | | - Kathleen E. DelGiorno
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN
| | - Howard C. Crawford
- Department of Surgery, Henry Ford Health, Detroit, MI
- Cancer Biology Program, Wayne State University, Detroit, MI
| |
Collapse
|
8
|
Waldron RT, Lugea A, Chang HH, Su HY, Quiros C, Lewis MS, Che M, Ramanujan VK, Rozengurt E, Eibl G, Pandol SJ. Upregulated Matrisomal Proteins and Extracellular Matrix Mechanosignaling Underlie Obesity-Associated Promotion of Pancreatic Ductal Adenocarcinoma. Cancers (Basel) 2024; 16:1593. [PMID: 38672675 PMCID: PMC11048773 DOI: 10.3390/cancers16081593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/05/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Diet-induced obesity (DIO) promotes pancreatic ductal adenocarcinoma (PDAC) in mice expressing KRasG12D in the pancreas (KC mice), but the precise mechanisms remain unclear. Here, we performed multiplex quantitative proteomic and phosphoproteomic analysis by liquid chromatography-tandem mass spectrometry and further bioinformatic and spatial analysis of pancreas tissues from control-fed versus DIO KC mice after 3, 6, and 9 months. Normal pancreatic parenchyma and associated proteins were steadily eliminated and the novel proteins, phosphoproteins, and signaling pathways associated with PDAC tumorigenesis increased until 6 months, when most males exhibited cancer, but females did not. Differentially expressed proteins and phosphoproteins induced by DIO revealed the crucial functional role of matrisomal proteins, which implies the roles of upstream regulation by TGFβ, extracellular matrix-receptor signaling to downstream PI3K-Akt-mTOR-, MAPK-, and Yap/Taz activation, and crucial effects in the tumor microenvironment such as metabolic alterations and signaling crosstalk between immune cells, cancer-associated fibroblasts (CAFs), and tumor cells. Staining tissues from KC mice localized the expression of several prognostic PDAC biomarkers and elucidated tumorigenic features, such as robust macrophage infiltration, acinar-ductal metaplasia, mucinous PanIN, distinct nonmucinous atypical flat lesions (AFLs) surrounded by smooth muscle actin-positive CAFs, invasive tumors with epithelial-mesenchymal transition arising close to AFLs, and expanding deserted areas by 9 months. We next used Nanostring GeoMX to characterize the early spatial distribution of specific immune cell subtypes in distinct normal, stromal, and PanIN areas. Taken together, these data richly contextualize DIO promotion of Kras-driven PDAC tumorigenesis and provide many novel insights into the signaling pathways and processes involved.
Collapse
Affiliation(s)
- Richard T. Waldron
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Aurelia Lugea
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Hui-Hua Chang
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Hsin-Yuan Su
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Crystal Quiros
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Michael S. Lewis
- Department of Medicine and Department of Pathology & Laboratory Medicine, VA Greater Los Angeles Health System, Cedars-Sinai Medical Center, Los Angeles, CA 90073, USA;
| | - Mingtian Che
- Biobank and Research Pathology Resource, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - V. Krishnan Ramanujan
- Biobank and Research Pathology Resource, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Enrique Rozengurt
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Guido Eibl
- Department of Surgery, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Stephen J. Pandol
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| |
Collapse
|
9
|
Guo T, Xu J. Cancer-associated fibroblasts: a versatile mediator in tumor progression, metastasis, and targeted therapy. Cancer Metastasis Rev 2024:10.1007/s10555-024-10186-7. [PMID: 38602594 DOI: 10.1007/s10555-024-10186-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/31/2024] [Indexed: 04/12/2024]
Abstract
Tumor microenvironment (TME) has been demonstrated to play a significant role in tumor initiation, progression, and metastasis. Cancer-associated fibroblasts (CAFs) are the major component of TME and exhibit heterogeneous properties in their communication with tumor cells. This heterogeneity of CAFs can be attributed to various origins, including quiescent fibroblasts, mesenchymal stem cells (MSCs), adipocytes, pericytes, endothelial cells, and mesothelial cells. Moreover, single-cell RNA sequencing has identified diverse phenotypes of CAFs, with myofibroblastic CAFs (myCAFs) and inflammatory CAFs (iCAFs) being the most acknowledged, alongside newly discovered subtypes like antigen-presenting CAFs (apCAFs). Due to these heterogeneities, CAFs exert multiple functions in tumorigenesis, cancer stemness, angiogenesis, immunosuppression, metabolism, and metastasis. As a result, targeted therapies aimed at the TME, particularly focusing on CAFs, are rapidly developing, fueling the promising future of advanced tumor-targeted therapy.
Collapse
Affiliation(s)
- Tianchen Guo
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China
| | - Junfen Xu
- Department of Gynecologic Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China.
| |
Collapse
|
10
|
Di Chiaro P, Nacci L, Arco F, Brandini S, Polletti S, Palamidessi A, Donati B, Soriani C, Gualdrini F, Frigè G, Mazzarella L, Ciarrocchi A, Zerbi A, Spaggiari P, Scita G, Rodighiero S, Barozzi I, Diaferia GR, Natoli G. Mapping functional to morphological variation reveals the basis of regional extracellular matrix subversion and nerve invasion in pancreatic cancer. Cancer Cell 2024; 42:662-681.e10. [PMID: 38518775 DOI: 10.1016/j.ccell.2024.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 12/07/2023] [Accepted: 02/27/2024] [Indexed: 03/24/2024]
Abstract
Intratumor morphological heterogeneity of pancreatic ductal adenocarcinoma (PDAC) predicts clinical outcomes but is only partially understood at the molecular level. To elucidate the gene expression programs underpinning intratumor morphological variation in PDAC, we investigated and deconvoluted at single cell level the molecular profiles of histologically distinct clusters of PDAC cells. We identified three major morphological and functional variants that co-exist in varying proportions in all PDACs, display limited genetic diversity, and are associated with a distinct organization of the extracellular matrix: a glandular variant with classical ductal features; a transitional variant displaying abortive ductal structures and mixed endodermal and myofibroblast-like gene expression; and a poorly differentiated variant lacking ductal features and basement membrane, and showing neuronal lineage priming. Ex vivo and in vitro evidence supports the occurrence of dynamic transitions among these variants in part influenced by extracellular matrix composition and stiffness and associated with local, specifically neural, invasion.
Collapse
Affiliation(s)
- Pierluigi Di Chiaro
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy.
| | - Lucia Nacci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Fabiana Arco
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Stefania Brandini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Sara Polletti
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Andrea Palamidessi
- IFOM, The FIRC Institute for Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Benedetta Donati
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Chiara Soriani
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Francesco Gualdrini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Gianmaria Frigè
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Luca Mazzarella
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy; Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors, IEO, European Institute of Oncology, IRCCS, Milano, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Alessandro Zerbi
- IRCCS Humanitas Research Hospital, Rozzano, Milano, Italy; Humanitas University, Pieve Emanuele - Milano, Italy
| | | | - Giorgio Scita
- IFOM, The FIRC Institute for Molecular Oncology, Via Adamello 16, 20139 Milan, Italy; Department of Oncology and Haemato-Oncology, University of Milan, Milano, Italy
| | - Simona Rodighiero
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Iros Barozzi
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Giuseppe R Diaferia
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy.
| | - Gioacchino Natoli
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy.
| |
Collapse
|
11
|
Zhang Y, Zuo C, Li Y, Liu L, Yang B, Xia J, Cui J, Xu K, Wu X, Gong W, Liu Y. Single-cell characterization of infiltrating T cells identifies novel targets for gallbladder cancer immunotherapy. Cancer Lett 2024; 586:216675. [PMID: 38280478 DOI: 10.1016/j.canlet.2024.216675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 01/29/2024]
Abstract
Gallbladder cancer (GBC) is among the most common malignancies of biliary tract system due to its limited treatments. The immunotherapeutic targets for T cells are appealing, however, heterogeneity of T cells hinds its further development. We systematically construct T cell atlas by single-cell RNA sequencing; and utilized the identified gene signatures of high_CNV_T cells to predict molecular subtyping towards personalized therapeutic treatments for GBC. We identified 12 T cell subtypes, where exhausted CD8+ T cells, activated/exhausted CD8+ T cells, and regulatory T cells were predominant in tumors. There appeared to be an inverse relationship between Th17 and Treg populations with Th17 levels significantly reduced, whereas Tregs were concomitantly increased. Furthermore, we first established subtyping criterion to identify three subtypes of GBC based on their pro-tumorigenic microenvironments, e.g., the type 1 group shows more M2 macrophages infiltration, while the type 2 group is infiltrated by highly exhausted CD8+ T cells, B cells and Tregs with suppressive activities. Our study provides valuable insights into T cell heterogeneity and suggests that molecular subtyping based on T cells might provide a potential immunotherapeutic strategy to improve GBC treatment.
Collapse
Affiliation(s)
- Yijian Zhang
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China; Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, 200092, China; Shanghai Research Center of Biliary Tract Disease, Shanghai, 200092, China
| | - Chunman Zuo
- Institute of Artificial Intelligence, Donghua University, Shanghai, 201620, China; Key Laboratory of Symbolic Computation and knowledge Engineering of Ministry of Education, Jilin University, Changchun, 130022, China.
| | - Yang Li
- Department of Biliary-Pancreatic Surgery, Renji Hospital Affliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China; Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, 200092, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai, 200127, China; Shanghai Research Center of Biliary Tract Disease, Shanghai, 200092, China
| | - Liguo Liu
- Department of Biliary-Pancreatic Surgery, Renji Hospital Affliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China; Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, 200092, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai, 200127, China; Shanghai Research Center of Biliary Tract Disease, Shanghai, 200092, China
| | - Bo Yang
- Department of Biliary-Pancreatic Surgery, Renji Hospital Affliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China; Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, 200092, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai, 200127, China; Shanghai Research Center of Biliary Tract Disease, Shanghai, 200092, China
| | - Junjie Xia
- Institute of Artificial Intelligence, Donghua University, Shanghai, 201620, China
| | - Jiangnan Cui
- Institute of Artificial Intelligence, Donghua University, Shanghai, 201620, China
| | - Keren Xu
- CAS Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xiangsong Wu
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China; Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, 200092, China; Shanghai Research Center of Biliary Tract Disease, Shanghai, 200092, China.
| | - Wei Gong
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China; Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, 200092, China; Shanghai Research Center of Biliary Tract Disease, Shanghai, 200092, China.
| | - Yingbin Liu
- Department of Biliary-Pancreatic Surgery, Renji Hospital Affliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China; Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, 200092, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai, 200127, China; Shanghai Research Center of Biliary Tract Disease, Shanghai, 200092, China.
| |
Collapse
|
12
|
Fu Y, Li J, Cai W, Huang Y, Liu X, Ma Z, Tang Z, Bian X, Zheng J, Jiang J, Li C. The emerging tumor microbe microenvironment: From delineation to multidisciplinary approach-based interventions. Acta Pharm Sin B 2024; 14:1560-1591. [PMID: 38572104 PMCID: PMC10985043 DOI: 10.1016/j.apsb.2023.11.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/20/2023] [Accepted: 11/03/2023] [Indexed: 04/05/2024] Open
Abstract
Intratumoral microbiota has become research hotspots, and emerges as a non-negligent new component of tumor microenvironments (TME), due to its powerful influence on tumor initiation, metastasis, immunosurveillance and prognosis despite in low-biomass. The accumulations of microbes, and their related components and metabolites within tumor tissues, endow TME with additional pluralistic features which are distinct from the conventional one. Therefore, it's definitely necessary to comprehensively delineate the sophisticated landscapes of tumor microbe microenvironment, as well as their functions and related underlying mechanisms. Herein, in this review, we focused on the fields of tumor microbe microenvironment, including the heterogeneity of intratumor microbiota in different types of tumors, the controversial roles of intratumoral microbiota, the basic features of tumor microbe microenvironment (i.e., pathogen-associated molecular patterns (PAMPs), typical microbial metabolites, autophagy, inflammation, multi-faceted immunomodulation and chemoresistance), as well as the multidisciplinary approach-based intervention of tumor microbiome for cancer therapy by applying wild-type or engineered live microbes, microbiota metabolites, antibiotics, synthetic biology and rationally designed biomaterials. We hope our work will provide valuable insight to deeply understand the interplay of cancer-immune-microbial, and facilitate the development of microbes-based tumor-specific treatments.
Collapse
Affiliation(s)
- Yu Fu
- Medical Research Institute, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Jia Li
- Department of Urology, Urologic Surgery Center, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing 400037, China
| | - Wenyun Cai
- Medical Research Institute, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Yulan Huang
- Medical Research Institute, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Xinlong Liu
- Medical Research Institute, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Zhongyi Ma
- Medical Research Institute, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Zhongjie Tang
- Medical Research Institute, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Xufei Bian
- Medical Research Institute, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Ji Zheng
- Department of Urology, Urologic Surgery Center, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing 400037, China
| | - Jiayun Jiang
- Institute of Hepatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Chong Li
- Medical Research Institute, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| |
Collapse
|
13
|
Ahn S, Lee HS. Applicability of Spatial Technology in Cancer Research. Cancer Res Treat 2024; 56:343-356. [PMID: 38291743 PMCID: PMC11016655 DOI: 10.4143/crt.2023.1302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 01/29/2024] [Indexed: 02/01/2024] Open
Abstract
This review explores spatial mapping technologies in cancer research, highlighting their crucial role in understanding the complexities of the tumor microenvironment (TME). The TME, which is an intricate ecosystem of diverse cell types, has a significant impact on tumor dynamics and treatment outcomes. This review closely examines cutting-edge spatial mapping technologies, categorizing them into capture-, imaging-, and antibody-based approaches. Each technology was scrutinized for its advantages and disadvantages, factoring in aspects such as spatial profiling area, multiplexing capabilities, and resolution. Additionally, we draw attention to the nuanced choices researchers face, with capture-based methods lending themselves to hypothesis generation, and imaging/antibody-based methods that fit neatly into hypothesis testing. Looking ahead, we anticipate a scenario in which multi-omics data are seamlessly integrated, artificial intelligence enhances data analysis, and spatiotemporal profiling opens up new dimensions.
Collapse
Affiliation(s)
- Sangjeong Ahn
- Department of Pathology, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea
- Artificial Intelligence Center, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea
- Department of Medical Informatics, Korea University College of Medicine, Seoul, Korea
| | - Hye Seung Lee
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| |
Collapse
|
14
|
Luo Z, Zheng Q, Ye S, Li Y, Chen J, Fan C, Chen J, Lei Y, Liao Q, Xi Y. HMGA2 alleviates ferroptosis by promoting GPX4 expression in pancreatic cancer cells. Cell Death Dis 2024; 15:220. [PMID: 38493165 PMCID: PMC10944463 DOI: 10.1038/s41419-024-06592-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/02/2024] [Accepted: 03/05/2024] [Indexed: 03/18/2024]
Abstract
Pancreatic cancer is one of the most malignant tumor types and is characterized by high metastasis ability and a low survival rate. As a chromatin-binding protein, HMGA2 is widely overexpressed and considered an oncogene with various undefined regulatory mechanisms. Herein, we demonstrated that HMGA2 is highly expressed in pancreatic cancer tissues, mainly distributed in epithelial cells, and represents a subtype of high epithelial-mesenchymal transition. Deletion of HMGA2 inhibits tumor malignancy through cell proliferation, metastasis, and xenograft tumor growth in vivo. Moreover, HMGA2 enhanced the cellular redox status by inhibiting reactive oxygen species and promoting glutathione production. Importantly, ferroptotic cell death was significantly ameliorated in cells overexpressing HMGA2. Conversely, HMGA2 deletion exacerbated ferroptosis. Mechanistically, HMGA2 activated GPX4 expression through transcriptional and translational regulation. HMGA2 binds and promotes cis-element modification in the promoter region of the GPX4 gene by enhancing enhancer activity through increased H3K4 methylation and H3K27 acetylation. Furthermore, HMGA2 stimulated GPX4 protein synthesis via the mTORC1-4EBP1 and -S6K signaling axes. The overexpression of HMGA2 alleviated the decrease in GPX4 protein levels resulting from the pharmacologic inhibition of mTORC1. Conversely, compared with the control, HMGA2 deletion more strongly reduced the phosphorylation of 4EBP1 and S6K. A strong positive correlation between HMGA2 and GPX4 expression was confirmed using immunohistochemical staining. We also demonstrated that HMGA2 mitigated the sensitivity of cancer cells to combination treatment with a ferroptosis inducer and mTORC1 inhibition or gemcitabine. In summary, our results revealed a regulatory mechanism by which HMGA2 coordinates GPX4 expression and underscores the potential value of targeting HMGA2 in cancer treatment.
Collapse
Affiliation(s)
- Ziyang Luo
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Qingfang Zheng
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Shazhou Ye
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Yanguo Li
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, 315211, China
| | - Jiayi Chen
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Chengjiang Fan
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Jianing Chen
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Yuxin Lei
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Qi Liao
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, 315211, China.
| | - Yang Xi
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, 315211, China.
| |
Collapse
|
15
|
Geuenich MJ, Gong DW, Campbell KR. The impacts of active and self-supervised learning on efficient annotation of single-cell expression data. Nat Commun 2024; 15:1014. [PMID: 38307875 PMCID: PMC10837127 DOI: 10.1038/s41467-024-45198-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 01/16/2024] [Indexed: 02/04/2024] Open
Abstract
A crucial step in the analysis of single-cell data is annotating cells to cell types and states. While a myriad of approaches has been proposed, manual labeling of cells to create training datasets remains tedious and time-consuming. In the field of machine learning, active and self-supervised learning methods have been proposed to improve the performance of a classifier while reducing both annotation time and label budget. However, the benefits of such strategies for single-cell annotation have yet to be evaluated in realistic settings. Here, we perform a comprehensive benchmarking of active and self-supervised labeling strategies across a range of single-cell technologies and cell type annotation algorithms. We quantify the benefits of active learning and self-supervised strategies in the presence of cell type imbalance and variable similarity. We introduce adaptive reweighting, a heuristic procedure tailored to single-cell data-including a marker-aware version-that shows competitive performance with existing approaches. In addition, we demonstrate that having prior knowledge of cell type markers improves annotation accuracy. Finally, we summarize our findings into a set of recommendations for those implementing cell type annotation procedures or platforms. An R package implementing the heuristic approaches introduced in this work may be found at https://github.com/camlab-bioml/leader .
Collapse
Affiliation(s)
- Michael J Geuenich
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1×5, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| | - Dae-Won Gong
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1×5, Canada
| | - Kieran R Campbell
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1×5, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Department of Statistical Sciences, University of Toronto, Toronto, ON, M5S 3G3, Canada.
- Department of Computer Science, University of Toronto, Toronto, ON, M5T 3A1, Canada.
- Ontario Institute of Cancer Research, Toronto, ON, M5G 1M1, Canada.
- Vector Institute, Toronto, ON, M5G 1M1, Canada.
| |
Collapse
|
16
|
Hartupee C, Nagalo BM, Chabu CY, Tesfay MZ, Coleman-Barnett J, West JT, Moaven O. Pancreatic cancer tumor microenvironment is a major therapeutic barrier and target. Front Immunol 2024; 15:1287459. [PMID: 38361931 PMCID: PMC10867137 DOI: 10.3389/fimmu.2024.1287459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/04/2024] [Indexed: 02/17/2024] Open
Abstract
Pancreatic Ductal Adenocarcinoma (PDAC) is projected to become the 2nd leading cause of cancer-related deaths in the United States. Limitations in early detection and treatment barriers contribute to the lack of substantial success in the treatment of this challenging-to-treat malignancy. Desmoplasia is the hallmark of PDAC microenvironment that creates a physical and immunologic barrier. Stromal support cells and immunomodulatory cells face aberrant signaling by pancreatic cancer cells that shifts the complex balance of proper repair mechanisms into a state of dysregulation. The product of this dysregulation is the desmoplastic environment that encases the malignant cells leading to a dense, hypoxic environment that promotes further tumorigenesis, provides innate systemic resistance, and suppresses anti-tumor immune invasion. This desmoplastic environment combined with the immunoregulatory events that allow it to persist serve as the primary focus of this review. The physical barrier and immune counterbalance in the tumor microenvironment (TME) make PDAC an immunologically cold tumor. To convert PDAC into an immunologically hot tumor, tumor microenvironment could be considered alongside the tumor cells. We discuss the complex network of microenvironment molecular and cellular composition and explore how they can be targeted to overcome immuno-therapeutic challenges.
Collapse
Affiliation(s)
- Conner Hartupee
- Division of Surgical Oncology, Department of Surgery, Louisiana State University (LSU) Health, New Orleans, LA, United States
| | - Bolni Marius Nagalo
- Department of Pathology, University of Arkansas for Medical Sciences (UAMS), Little Rock, AR, United States
- The Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences (UAMS), Little Rock, AR, United States
| | - Chiswili Y. Chabu
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, United States
- Siteman Cancer Center, Washington University, St. Louis, MO, United States
| | - Mulu Z. Tesfay
- Department of Pathology, University of Arkansas for Medical Sciences (UAMS), Little Rock, AR, United States
| | - Joycelynn Coleman-Barnett
- Division of Surgical Oncology, Department of Surgery, Louisiana State University (LSU) Health, New Orleans, LA, United States
- Department of Interdisciplinary Oncology, Louisiana Cancer Research Center, Louisiana State University (LSU) Health, New Orleans, LA, United States
| | - John T. West
- Department of Interdisciplinary Oncology, Louisiana Cancer Research Center, Louisiana State University (LSU) Health, New Orleans, LA, United States
| | - Omeed Moaven
- Division of Surgical Oncology, Department of Surgery, Louisiana State University (LSU) Health, New Orleans, LA, United States
- Department of Interdisciplinary Oncology, Louisiana Cancer Research Center, Louisiana State University (LSU) Health, New Orleans, LA, United States
- Louisiana State University - Louisiana Children's Medical Center (LSU - LCMC) Cancer Center, New Orleans, LA, United States
| |
Collapse
|
17
|
Xu J, Roe J, Lee E, Tonelli C, Ji KY, Younis OW, Somervile TD, Yao M, Milazzo JP, Tiriac H, Kolarzyk AM, Lee E, Grem JL, Lazenby AJ, Grunkemeyer JA, Hollingsworth MA, Grandgenett PM, Borowsky AD, Park Y, Vakoc CR, Tuveson DA, Hwang C. Engrailed-1 Promotes Pancreatic Cancer Metastasis. Adv Sci (Weinh) 2024; 11:e2308537. [PMID: 38110836 PMCID: PMC10853725 DOI: 10.1002/advs.202308537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Indexed: 12/20/2023]
Abstract
Engrailed-1 (EN1) is a critical homeodomain transcription factor (TF) required for neuronal survival, and EN1 expression has been shown to promote aggressive forms of triple negative breast cancer. Here, it is reported that EN1 is aberrantly expressed in a subset of pancreatic ductal adenocarcinoma (PDA) patients with poor outcomes. EN1 predominantly repressed its target genes through direct binding to gene enhancers and promoters, implicating roles in the activation of MAPK pathways and the acquisition of mesenchymal cell properties. Gain- and loss-of-function experiments demonstrated that EN1 promoted PDA transformation and metastasis in vitro and in vivo. The findings nominate the targeting of EN1 and downstream pathways in aggressive PDA.
Collapse
Affiliation(s)
- Jihao Xu
- Department of Microbiology and Molecular GeneticsUniversity of California DavisDavisCA95616USA
- Comprehensive Cancer CenterUniversity of California DavisSacramentoCA95817USA
| | - Jae‐Seok Roe
- Department of BiochemistryYonsei UniversitySeoul03722South Korea
- Cold Spring Harbor LaboratoryCold Spring HarborNY11724USA
| | - EunJung Lee
- Department of Microbiology and Molecular GeneticsUniversity of California DavisDavisCA95616USA
- Cold Spring Harbor LaboratoryCold Spring HarborNY11724USA
- Lustgarten Foundation Pancreatic Cancer Research LaboratoryCold Spring HarborNY11724USA
| | - Claudia Tonelli
- Cold Spring Harbor LaboratoryCold Spring HarborNY11724USA
- Lustgarten Foundation Pancreatic Cancer Research LaboratoryCold Spring HarborNY11724USA
| | - Keely Y. Ji
- Department of Microbiology and Molecular GeneticsUniversity of California DavisDavisCA95616USA
| | - Omar W. Younis
- Department of Microbiology and Molecular GeneticsUniversity of California DavisDavisCA95616USA
| | | | - Melissa Yao
- Cold Spring Harbor LaboratoryCold Spring HarborNY11724USA
- Lustgarten Foundation Pancreatic Cancer Research LaboratoryCold Spring HarborNY11724USA
| | | | - Herve Tiriac
- Cold Spring Harbor LaboratoryCold Spring HarborNY11724USA
- Lustgarten Foundation Pancreatic Cancer Research LaboratoryCold Spring HarborNY11724USA
| | - Anna M. Kolarzyk
- Nancy E. and Peter C. Meinig School of Biomedical EngineeringCornell UniversityIthacaNY14853USA
| | - Esak Lee
- Nancy E. and Peter C. Meinig School of Biomedical EngineeringCornell UniversityIthacaNY14853USA
| | - Jean L. Grem
- Department of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
| | - Audrey J. Lazenby
- Department of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
| | | | | | | | - Alexander D. Borowsky
- Department of PathologySchool of MedicineUniversity of California DavisSacramentoCA95817USA
| | - Youngkyu Park
- Cold Spring Harbor LaboratoryCold Spring HarborNY11724USA
- Lustgarten Foundation Pancreatic Cancer Research LaboratoryCold Spring HarborNY11724USA
| | | | - David A. Tuveson
- Cold Spring Harbor LaboratoryCold Spring HarborNY11724USA
- Lustgarten Foundation Pancreatic Cancer Research LaboratoryCold Spring HarborNY11724USA
| | - Chang‐Il Hwang
- Department of Microbiology and Molecular GeneticsUniversity of California DavisDavisCA95616USA
- Comprehensive Cancer CenterUniversity of California DavisSacramentoCA95817USA
| |
Collapse
|
18
|
Caputo A, Vipparthi K, Bazeley P, Downs-Kelly E, McIntire P, Duckworth LA, Ni Y, Hu B, Keri RA, Karaayvaz M. Spatial Transcriptomics Suggests That Alterations Occur in the Preneoplastic Breast Microenvironment of BRCA1/2 Mutation Carriers. Mol Cancer Res 2024; 22:169-180. [PMID: 37878345 PMCID: PMC10872731 DOI: 10.1158/1541-7786.mcr-23-0489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/28/2023] [Accepted: 10/23/2023] [Indexed: 10/26/2023]
Abstract
Breast cancer is the most common cancer in females, affecting one in every eight women and accounting for the majority of cancer-related deaths in women worldwide. Germline mutations in the BRCA1 and BRCA2 genes are significant risk factors for specific subtypes of breast cancer. BRCA1 mutations are associated with basal-like breast cancers, whereas BRCA2 mutations are associated with luminal-like disease. Defects in mammary epithelial cell differentiation have been previously recognized in germline BRCA1/2 mutation carriers even before cancer incidence. However, the underlying mechanism is largely unknown. Here, we employ spatial transcriptomics to investigate defects in mammary epithelial cell differentiation accompanied by distinct microenvironmental alterations in preneoplastic breast tissues from BRCA1/2 mutation carriers and normal breast tissues from noncarrier controls. We uncovered spatially defined receptor-ligand interactions in these tissues for the investigation of autocrine and paracrine signaling. We discovered that β1-integrin-mediated autocrine signaling in BRCA2-deficient mammary epithelial cells may differ from BRCA1-deficient mammary epithelial cells. In addition, we found that the epithelial-to-stromal paracrine signaling in the breast tissues of BRCA1/2 mutation carriers is greater than in control tissues. More integrin-ligand pairs were differentially correlated in BRCA1/2-mutant breast tissues than noncarrier breast tissues with more integrin receptor-expressing stromal cells. IMPLICATIONS These results suggest alterations in the communication between mammary epithelial cells and the microenvironment in BRCA1 and BRCA2 mutation carriers, laying the foundation for designing innovative breast cancer chemo-prevention strategies for high-risk patients.
Collapse
Affiliation(s)
- Anthony Caputo
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Kavya Vipparthi
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Peter Bazeley
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Erinn Downs-Kelly
- Department of Pathology, Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Patrick McIntire
- Department of Pathology, Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Lauren A. Duckworth
- Department of Pathology, Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ying Ni
- Center for Immunotherapy & Precision Immuno-Oncology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Bo Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ruth A. Keri
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Mihriban Karaayvaz
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA
| |
Collapse
|
19
|
Tu C, Kulasinghe A, Barbour A, Souza-Fonseca-Guimaraes F. Leveraging spatial omics for the development of precision sarcoma treatments. Trends Pharmacol Sci 2024; 45:134-144. [PMID: 38212196 DOI: 10.1016/j.tips.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/13/2024]
Abstract
Sarcomas are rare and heterogeneous cancers that arise from bone or soft tissue, and are the second most prevalent solid cancer in children and adolescents. Owing to the complex nature of pediatric sarcomas, the development of therapeutics for pediatric sarcoma has seen little progress in the past decades. Existing treatments are largely limited to chemotherapy, radiation, and surgery. Limited knowledge of the sarcoma tumor microenvironment (TME) and of well-defined target antigens in the different subtypes necessitates an alternative investigative approach to improve treatments. Recent advances in spatial omics technologies have enabled a more comprehensive study of the TME in multiple cancers. In this opinion article we discuss advances in our understanding of the TME of some cancers enabled by spatial omics technologies, and we explore how these technologies might advance the development of precision treatments for sarcoma, especially pediatric sarcoma.
Collapse
Affiliation(s)
- Cui Tu
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Arutha Kulasinghe
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Andrew Barbour
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD 4102, Australia; Department of Surgery, Princess Alexandra Hospital, Brisbane, QLD 4102, Australia
| | | |
Collapse
|
20
|
Chen H, Fang X, Shao J, Zhang Q, Xu L, Chen J, Mei Y, Jiang M, Wang Y, Li Z, Chen Z, Chen Y, Yu C, Ma L, Zhang P, Zhang T, Liao Y, Lv Y, Wang X, Yang L, Fu Y, Chen D, Jiang L, Yan F, Lu W, Chen G, Shen H, Wang J, Wang C, Liang T, Han X, Wang Y, Guo G. Pan-Cancer Single-Nucleus Total RNA Sequencing Using snHH-Seq. Adv Sci (Weinh) 2024; 11:e2304755. [PMID: 38010945 PMCID: PMC10837386 DOI: 10.1002/advs.202304755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/11/2023] [Indexed: 11/29/2023]
Abstract
Tumor heterogeneity and its drivers impair tumor progression and cancer therapy. Single-cell RNA sequencing is used to investigate the heterogeneity of tumor ecosystems. However, most methods of scRNA-seq amplify the termini of polyadenylated transcripts, making it challenging to perform total RNA analysis and somatic mutation analysis.Therefore, a high-throughput and high-sensitivity method called snHH-seq is developed, which combines random primers and a preindex strategy in the droplet microfluidic platform. This innovative method allows for the detection of total RNA in single nuclei from clinically frozen samples. A robust pipeline to facilitate the analysis of full-length RNA-seq data is also established. snHH-seq is applied to more than 730 000 single nuclei from 32 patients with various tumor types. The pan-cancer study enables it to comprehensively profile data on the tumor transcriptome, including expression levels, mutations, splicing patterns, clone dynamics, etc. New malignant cell subclusters and exploring their specific function across cancers are identified. Furthermore, the malignant status of epithelial cells is investigated among different cancer types with respect to mutation and splicing patterns. The ability to detect full-length RNA at the single-nucleus level provides a powerful tool for studying complex biological systems and has broad implications for understanding tumor pathology.
Collapse
Affiliation(s)
- Haide Chen
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
- M20 Genomics, Hangzhou, 311121, China
| | - Xiunan Fang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, 999077, China
| | - Jikai Shao
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
| | - Qi Zhang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, 310006, China
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, 310006, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Liwei Xu
- Department of Thoracic Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, China
| | | | - Yuqing Mei
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Mengmeng Jiang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
| | - Yuting Wang
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Zhouyang Li
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Zihang Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, 310009, China
| | - Yang Chen
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology, Hangzhou, 310022, China
- The Second Clinical Medical College of Zhejiang Chinese Medical University Hangzhou, Hangzhou, 310053, China
| | - Chengxuan Yu
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Zhejiang Provincial Clinical Research Center for Cancer, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Lifeng Ma
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Peijing Zhang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, 310058, China
| | | | - Yuan Liao
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- M20 Genomics, Hangzhou, 311121, China
| | | | - Xueyi Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Lei Yang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yuting Fu
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Daobao Chen
- Department of Breast Surgery, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Liming Jiang
- Department of Radiology, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Feng Yan
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, 310009, China
| | - Wei Lu
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Zhejiang Provincial Clinical Research Center for Cancer, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Gao Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, 310009, China
| | - Huahao Shen
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- State Key Laboratory of Respiratory Disease, Guangzhou, 510120, China
| | - Jingjing Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
| | - Changchun Wang
- Department of Thoracic Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, China
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology, Hangzhou, 310022, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, 310006, China
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, 310006, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Xiaoping Han
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yongcheng Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, 310058, China
- Institute of Hematology, Zhejiang University, Hangzhou, 310006, China
| |
Collapse
|
21
|
Yun WG, Han Y, Cho YJ, Jung HS, Lee M, Kwon W, Jang JY. In Neoadjuvant FOLFIRINOX Chemotherapy for Pancreatic Ductal Adenocarcinoma, Which Response is the More Reliable Indicator for Prognosis, Radiologic or Biochemical? Ann Surg Oncol 2024; 31:1336-1346. [PMID: 37991581 DOI: 10.1245/s10434-023-14532-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 10/18/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND In this era of increasing neoadjuvant chemotherapy, methods for evaluating responses to neoadjuvant chemotherapy are still diverse among institutions. Additionally, the efficacy of adjuvant chemotherapy for patients undergoing neoadjuvant chemotherapy remains unclear. Therefore, this retrospective study was performed to evaluate the effectiveness of methods for assessing response to neoadjuvant chemotherapy and the need for adjuvant chemotherapy in treating patients with non-metastatic pancreatic ductal adenocarcinoma. METHODS The study identified 150 patients who underwent neoadjuvant FOLFIRINOX chemotherapy followed by curative-intent pancreatectomy. The patients were stratified by biochemical response based on the normalization of carbohydrate antigen 19-9 and by radiologic response based on size change at imaging. RESULTS The patients were classified into the following three groups based on their response to neoadjuvant chemotherapy and prognosis: biochemical responders (BR+), radiology-only responders (BR-/RR+), and non-responders (BR-/RR-). The 3-year overall survival rate was higher for BR+ (71.0%) than for BR-/RR+ (53.6%) or BR-/RR- (33.1%) (P < 0.001). Response to neoadjuvant chemotherapy also was identified as a significant risk factor for recurrence in a comparison between BR-/RR+ and BR+ (hazard ratio [HR], 2.15; 95% confidence interval [CI] 1.19-3.88; P = 0.011) and BR-/RR- (HR, 3.82; 95% CI 2.41-6.08; P < 0.001). Additionally, regardless of the response to neoadjuvant chemotherapy, patients who completed adjuvant chemotherapy had a significantly higher 3-year overall survival rate than those who did not. CONCLUSIONS This response evaluation criterion for neoadjuvant chemotherapy is feasible and can significantly predict prognosis. Additionally, completion of adjuvant chemotherapy could be helpful to patients who undergo neoadjuvant chemotherapy regardless of their response to neoadjuvant chemotherapy.
Collapse
Affiliation(s)
- Won-Gun Yun
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Youngmin Han
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Young Jae Cho
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hye-Sol Jung
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Mirang Lee
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Wooil Kwon
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jin-Young Jang
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
| |
Collapse
|
22
|
Zhou Z, Lin T, Chen S, Zhang G, Xu Y, Zou H, Zhou A, Zhang Y, Weng S, Han X, Liu Z. Omics-based molecular classifications empowering in precision oncology. Cell Oncol (Dordr) 2024:10.1007/s13402-023-00912-8. [PMID: 38294647 DOI: 10.1007/s13402-023-00912-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2023] [Indexed: 02/01/2024] Open
Abstract
BACKGROUND In the past decades, cancer enigmatical heterogeneity at distinct expression levels could interpret disparities in therapeutic response and prognosis. It built hindrances to precision medicine, a tactic to tailor customized treatment informed by the tumors' molecular profile. Single-omics analysis dissected the biological features associated with carcinogenesis to some extent but still failed to revolutionize cancer treatment as expected. Integrated omics analysis incorporated tumor biological networks from diverse layers and deciphered a holistic overview of cancer behaviors, yielding precise molecular classification to facilitate the evolution and refinement of precision medicine. CONCLUSION This review outlined the biomarkers at multiple expression layers to tutor molecular classification and pinpoint tumor diagnosis, and explored the paradigm shift in precision therapy: from single- to multi-omics-based subtyping to optimize therapeutic regimens. Ultimately, we firmly believe that by parsing molecular characteristics, omics-based typing will be a powerful assistant for precision oncology.
Collapse
Affiliation(s)
- Zhaokai Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Ting Lin
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Shuang Chen
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Ge Zhang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yudi Xu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Haijiao Zou
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Aoyang Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Yuyuan Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Siyuan Weng
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China.
- Interventional Institute of Zhengzhou University, Zhengzhou, Henan, 450052, China.
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan, 450052, China.
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China.
- Interventional Institute of Zhengzhou University, Zhengzhou, Henan, 450052, China.
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan, 450052, China.
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| |
Collapse
|
23
|
Li J, Meng Z, Cao Z, Lu W, Yang Y, Li Z, Lu S. ADGRE5-centered Tsurv model in T cells recognizes responders to neoadjuvant cancer immunotherapy. Front Immunol 2024; 15:1304183. [PMID: 38343549 PMCID: PMC10853338 DOI: 10.3389/fimmu.2024.1304183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/02/2024] [Indexed: 02/15/2024] Open
Abstract
Background Neoadjuvant immunotherapy with anti-programmed death-1 (neo-antiPD1) has revolutionized perioperative methods for improvement of overall survival (OS), while approaches for major pathologic response patients' (MPR) recognition along with methods for overcoming non-MPR resistance are still in urgent need. Methods We utilized and integrated publicly-available immune checkpoint inhibitors regimens (ICIs) single-cell (sc) data as the discovery datasets, and innovatively developed a cell-communication analysis pipeline, along with a VIPER-based-SCENIC process, to thoroughly dissect MPR-responding subsets. Besides, we further employed our own non-small cell lung cancer (NSCLC) ICIs cohort's sc data for validation in-silico. Afterward, we resorted to ICIs-resistant murine models developed by us with multimodal investigation, including bulk-RNA-sequencing, Chip-sequencing and high-dimensional cytometry by time of flight (CYTOF) to consolidate our findings in-vivo. To comprehensively explore mechanisms, we adopted 3D ex-vivo hydrogel models for analysis. Furthermore, we constructed an ADGRE5-centered Tsurv model from our discovery dataset by machine learning (ML) algorithms for a wide range of tumor types (NSCLC, melanoma, urothelial cancer, etc.) and verified it in peripheral blood mononuclear cells (PBMCs) sc datasets. Results Through a meta-analysis of multimodal sequential sc sequencing data from pre-ICIs and post-ICIs, we identified an MPR-expanding T cells meta-cluster (MPR-E) in the tumor microenvironment (TME), characterized by a stem-like CD8+ T cluster (survT) with STAT5-ADGRE5 axis enhancement compared to non-MPR or pre-ICIs TME. Through multi-omics analysis of murine TME, we further confirmed the existence of survT with silenced function and immune checkpoints (ICs) in MPR-E. After verification of the STAT5-ADGRE5 axis of survT in independent ICIs cohorts, an ADGRE5-centered Tsurv model was then developed through ML for identification of MPR patients pre-ICIs and post-ICIs, both in TME and PBMCs, which was further verified in pan-cancer immunotherapy cohorts. Mechanistically, we unveiled ICIs stimulated ADGRE5 upregulation in a STAT5-IL32 dependent manner in a 3D ex-vivo system (3D-HYGTIC) developed by us previously, which marked Tsurv with better survival flexibility, enhanced stemness and potential cytotoxicity within TME. Conclusion Our research provides insights into mechanisms underlying MPR in neo-antiPD1 and a well-performed model for the identification of non-MPR.
Collapse
Affiliation(s)
| | | | | | | | | | - Ziming Li
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Shun Lu
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| |
Collapse
|
24
|
Zhang Y, Petukhov V, Biederstedt E, Que R, Zhang K, Kharchenko PV. Gene panel selection for targeted spatial transcriptomics. Genome Biol 2024; 25:35. [PMID: 38273415 PMCID: PMC10811939 DOI: 10.1186/s13059-024-03174-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
Targeted spatial transcriptomics hold particular promise in analyzing complex tissues. Most such methods, however, measure only a limited panel of transcripts, which need to be selected in advance to inform on the cell types or processes being studied. A limitation of existing gene selection methods is their reliance on scRNA-seq data, ignoring platform effects between technologies. Here we describe gpsFISH, a computational method performing gene selection through optimizing detection of known cell types. By modeling and adjusting for platform effects, gpsFISH outperforms other methods. Furthermore, gpsFISH can incorporate cell type hierarchies and custom gene preferences to accommodate diverse design requirements.
Collapse
Affiliation(s)
- Yida Zhang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Neurobiology, Duke University, Durham, NC, USA
| | - Viktor Petukhov
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Evan Biederstedt
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Richard Que
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Kun Zhang
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA.
| |
Collapse
|
25
|
Wattenberg MM, Colby S, Garrido-Laguna I, Xue Y, Chang R, Delman D, Lee J, Affolter K, Mulvihill SJ, Beg MS, Wang-Gillam A, Wade JL, Guthrie KA, Chiorean EG, Ahmad SA, Lowy AM, Philip PA, Sohal DPS, Beatty GL. Intratumoral Cell Neighborhoods Coordinate Outcomes in Pancreatic Ductal Adenocarcinoma. Gastroenterology 2024:S0016-5085(24)00049-0. [PMID: 38244727 DOI: 10.1053/j.gastro.2024.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 01/22/2024]
Abstract
BACKGROUND & AIMS Pancreatic ductal adenocarcinoma (PDA) is a highly lethal disease characterized by a spatially heterogeneous tumor microenvironment. Within the PDA microenvironment, cells organize into communities where cell fate is influenced by neighboring cells of diverse ontogeny and function. However, it remains unclear how cell neighborhoods in the tumor microenvironment evolve with treatment and impact clinical outcomes. METHODS Here, using automated chromogenic multiplex immunohistochemistry and unsupervised computational image analysis of human PDA tumors, we investigated cell neighborhoods in surgically resected tumors from patients with chemotherapy-naïve PDA (n = 59) and neoadjuvant chemotherapy-treated PDA (n = 57). Single cells were defined by lineage markers (CD3, CD8, Foxp3, CD68, CK19), proliferation (Ki67), and neighboring cells. RESULTS Distinct intratumoral immune and tumor cell subsets were defined by neighboring cells. Higher content of stromal-associated macrophages was seen in chemotherapy-naïve tumors from long-term survivors (overall survival >3 years) compared with short-term survivors (overall survival <1 year), whereas immune-excluded tumor cells were higher in short-term survivors. Chemotherapy-treated vs -naïve tumors showed lower content of tumor-associated T cells and macrophages but similar densities of stromal-associated immune cells. However, proliferating tumor cell subsets with immune-rich neighborhoods were higher in chemotherapy-treated tumors. In a blinded analysis of tumors from patients treated with neoadjuvant chemotherapy, a composite index comprising lower quantities of immune-excluded tumor cells and higher spatially distinct immune cell subsets was associated with prolonged survival. CONCLUSIONS Together, these data provide new insights into discrete cell communities in PDA and show their clinical relevance.
Collapse
Affiliation(s)
- Max M Wattenberg
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sarah Colby
- SWOG Statistics and Data Management Center, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Ignacio Garrido-Laguna
- Division of Oncology, Department of Internal Medicine, University of Utah School of Medicine, University of Utah, Salt Lake City, Utah
| | - Yuqing Xue
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Renee Chang
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Devora Delman
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jesse Lee
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kajsa Affolter
- Department of Pathology, University of Utah School of Medicine, University of Utah, Salt Lake City, Utah
| | - Sean J Mulvihill
- Department of Surgery, University of Utah School of Medicine, University of Utah, Salt Lake City, Utah
| | | | | | | | - Katherine A Guthrie
- SWOG Statistics and Data Management Center, Fred Hutchinson Cancer Center, Seattle, Washington
| | - E Gabriela Chiorean
- University of Washington, Fred Hutchinson Cancer Center, Seattle, Washington
| | | | - Andrew M Lowy
- Division of Surgical Oncology, Department of Surgery, UC San Diego, La Jolla, California
| | - Philip Agop Philip
- Henry Ford Health, Wayne State University, Oncology and Pharmacology, Detroit, Michigan
| | | | - Gregory L Beatty
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| |
Collapse
|
26
|
Benitz S, Steep A, Nasser M, Preall J, Mahajan UM, McQuithey H, Loveless I, Davis ET, Wen HJ, Long DW, Metzler T, Zwernik S, Louw M, Rempinski D, Salas-Escabillas D, Brender S, Song L, Huang L, Zhang Z, Steele NG, Regel I, Bednar F, Crawford HC. ROR2 regulates cellular plasticity in pancreatic neoplasia and adenocarcinoma. bioRxiv 2024:2023.12.13.571566. [PMID: 38168289 PMCID: PMC10760092 DOI: 10.1101/2023.12.13.571566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Cellular plasticity is a hallmark of pancreatic ductal adenocarcinoma (PDAC) starting from the conversion of normal cells into precancerous lesions to the progression of carcinoma subtypes associated with aggressiveness and therapeutic response. We discovered that normal acinar cell differentiation, maintained by the transcription factor Pdx1, suppresses a broad gastric cell identity that is maintained in metaplasia, neoplasia, and the classical subtype of PDAC in mouse and human. We have identified the receptor tyrosine kinase Ror2 as marker of a gastric metaplasia (SPEM)-like identity in the pancreas. Ablation of Ror2 in a mouse model of pancreatic tumorigenesis promoted a switch to a gastric pit cell identity that largely persisted through progression to the classical subtype of PDAC. In both human and mouse pancreatic cancer, ROR2 activity continued to antagonize the gastric pit cell identity, strongly promoting an epithelial to mesenchymal transition, conferring resistance to KRAS inhibition, and vulnerability to AKT inhibition.
Collapse
Affiliation(s)
- Simone Benitz
- Department of Surgery, Henry Ford Health System, Detroit, Michigan, USA
| | - Alec Steep
- Center of Translational Data Science, University of Chicago, Chicago, Illinois, USA
| | - Malak Nasser
- Department of Surgery, Henry Ford Health System, Detroit, Michigan, USA
| | - Jonathan Preall
- Cold Spring Harbor Laboratory Cancer Center, Cold Spring Harbor, New York, USA
| | - Ujjwal M Mahajan
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - Holly McQuithey
- Department of Surgery, Henry Ford Health System, Detroit, Michigan, USA
| | - Ian Loveless
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan, USA
| | - Erick T Davis
- Department of Surgery, Henry Ford Health System, Detroit, Michigan, USA
| | - Hui-Ju Wen
- Department of Surgery, Henry Ford Health System, Detroit, Michigan, USA
| | - Daniel W Long
- Department of Surgery, Henry Ford Health System, Detroit, Michigan, USA
| | - Thomas Metzler
- Comparative Experimental Pathology (CEP), Institute of Pathology, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Samuel Zwernik
- Department of Surgery, Henry Ford Health System, Detroit, Michigan, USA
| | - Michaela Louw
- Department of Surgery, Henry Ford Health System, Detroit, Michigan, USA
| | - Donald Rempinski
- Department of Surgery, Henry Ford Health System, Detroit, Michigan, USA
| | | | - Sydney Brender
- Department of Surgery, Henry Ford Health System, Detroit, Michigan, USA
| | - Linghao Song
- Center of Translational Data Science, University of Chicago, Chicago, Illinois, USA
| | - Ling Huang
- Department of Surgery, Henry Ford Health System, Detroit, Michigan, USA
| | - Zhenyu Zhang
- Center of Translational Data Science, University of Chicago, Chicago, Illinois, USA
| | - Nina G Steele
- Department of Surgery, Henry Ford Health System, Detroit, Michigan, USA
- Department of Pathology, Wayne State University, Detroit, Michigan, USA
- Department of Pharmacology and Toxicology, Michigan State University, Lansing, Michigan, USA
- Department of Oncology, Wayne State University, Detroit, Michigan, USA
| | - Ivonne Regel
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - Filip Bednar
- Department of Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Howard C Crawford
- Department of Surgery, Henry Ford Health System, Detroit, Michigan, USA
- Department of Pharmacology and Toxicology, Michigan State University, Lansing, Michigan, USA
- Department of Oncology, Wayne State University, Detroit, Michigan, USA
| |
Collapse
|
27
|
Patel AG, Ashenberg O, Collins NB, Segerstolpe Å, Jiang S, Slyper M, Huang X, Caraccio C, Jin H, Sheppard H, Xu K, Chang TC, Orr BA, Shirinifard A, Chapple RH, Shen A, Clay MR, Tatevossian RG, Reilly C, Patel J, Lupo M, Cline C, Dionne D, Porter CBM, Waldman J, Bai Y, Zhu B, Barrera I, Murray E, Vigneau S, Napolitano S, Wakiro I, Wu J, Grimaldi G, Dellostritto L, Helvie K, Rotem A, Lako A, Cullen N, Pfaff KL, Karlström Å, Jané-Valbuena J, Todres E, Thorner A, Geeleher P, Rodig SJ, Zhou X, Stewart E, Johnson BE, Wu G, Chen F, Yu J, Goltsev Y, Nolan GP, Rozenblatt-Rosen O, Regev A, Dyer MA. A spatial cell atlas of neuroblastoma reveals developmental, epigenetic and spatial axis of tumor heterogeneity. bioRxiv 2024:2024.01.07.574538. [PMID: 38260392 PMCID: PMC10802404 DOI: 10.1101/2024.01.07.574538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Neuroblastoma is a pediatric cancer arising from the developing sympathoadrenal lineage with complex inter- and intra-tumoral heterogeneity. To chart this complexity, we generated a comprehensive cell atlas of 55 neuroblastoma patient tumors, collected from two pediatric cancer institutions, spanning a range of clinical, genetic, and histologic features. Our atlas combines single-cell/nucleus RNA-seq (sc/scRNA-seq), bulk RNA-seq, whole exome sequencing, DNA methylation profiling, spatial transcriptomics, and two spatial proteomic methods. Sc/snRNA-seq revealed three malignant cell states with features of sympathoadrenal lineage development. All of the neuroblastomas had malignant cells that resembled sympathoblasts and the more differentiated adrenergic cells. A subset of tumors had malignant cells in a mesenchymal cell state with molecular features of Schwann cell precursors. DNA methylation profiles defined four groupings of patients, which differ in the degree of malignant cell heterogeneity and clinical outcomes. Using spatial proteomics, we found that neuroblastomas are spatially compartmentalized, with malignant tumor cells sequestered away from immune cells. Finally, we identify spatially restricted signaling patterns in immune cells from spatial transcriptomics. To facilitate the visualization and analysis of our atlas as a resource for further research in neuroblastoma, single cell, and spatial-omics, all data are shared through the Human Tumor Atlas Network Data Commons at www.humantumoratlas.org.
Collapse
Affiliation(s)
- Anand G Patel
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
- These authors contributed equally
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- These authors contributed equally
| | - Natalie B Collins
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
- These authors contributed equally
| | - Åsa Segerstolpe
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sizun Jiang
- Department of Pathology, Stanford University, Stanford, CA, USA
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xin Huang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Chiara Caraccio
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Heather Sheppard
- Comparative Pathology Core, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ke Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ti-Cheng Chang
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Brent A Orr
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Abbas Shirinifard
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Richard H Chapple
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Amber Shen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael R Clay
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Ruth G Tatevossian
- Cancer Biomarkers Laboratory, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Colleen Reilly
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jaimin Patel
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Marybeth Lupo
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cynthia Cline
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Caroline B M Porter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia Waldman
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yunhao Bai
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Bokai Zhu
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Evan Murray
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sébastien Vigneau
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sara Napolitano
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Isaac Wakiro
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jingyi Wu
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Grace Grimaldi
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Laura Dellostritto
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Karla Helvie
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Asaf Rotem
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ana Lako
- Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicole Cullen
- Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kathleen L Pfaff
- Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Åsa Karlström
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Judit Jané-Valbuena
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ellen Todres
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aaron Thorner
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paul Geeleher
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Elizabeth Stewart
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Bruce E Johnson
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Fei Chen
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yury Goltsev
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Current address: Research and Early Development, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Current address: Research and Early Development, Genentech Inc., South San Francisco, CA, 94080, USA
- Lead contacts
| | - Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Lead contacts
| |
Collapse
|
28
|
Mehta A, Stanger BZ. Lineage Plasticity: The New Cancer Hallmark on the Block. Cancer Res 2024; 84:184-191. [PMID: 37963209 PMCID: PMC10841583 DOI: 10.1158/0008-5472.can-23-1067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/12/2023] [Accepted: 11/07/2023] [Indexed: 11/16/2023]
Abstract
Plasticity refers to the ability of cells to adopt a spectrum of states or phenotypes. In cancer, it is a critical contributor to tumor initiation, progression, invasiveness, and therapy resistance, and it has recently been recognized as an emerging cancer hallmark. Plasticity can occur as a result of cell-intrinsic factors (e.g., genetic, transcriptional, or epigenetic fluctuations), or through cell-extrinsic cues (e.g., signaling from components of the tumor microenvironment or selective pressure from therapy). Over the past decade, technological advances, analysis of patient samples, and studies in mouse model systems have led to a deeper understanding of how such plastic states come about. In this review, we discuss: (i) the definition of plasticity; (ii) methods to measure and quantify plasticity; (iii) the clinical relevance of plasticity; and (iv) therapeutic hypotheses to modulate plasticity in the clinic.
Collapse
Affiliation(s)
- Arnav Mehta
- Department of Medicine, Massachusetts General Hospital, Boston, MA
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA
- Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Ben Z. Stanger
- Abramson Family Cancer Research Institute, Perelman School of Medicine at University of Pennsylvania, Philadelphia, PA
- Department of Medicine, Perelman School of Medicine at University of Pennsylvania, Philadelphia, PA
- Department of Cell and Developmental Biology, Perelman School of Medicine at University of Pennsylvania, Philadelphia, PA
| |
Collapse
|
29
|
Zhou W, Su M, Jiang T, Yang Q, Sun Q, Xu K, Shi J, Yang C, Ding N, Li Y, Xu J. SORC: an integrated spatial omics resource in cancer. Nucleic Acids Res 2024; 52:D1429-D1437. [PMID: 37811897 PMCID: PMC10768140 DOI: 10.1093/nar/gkad820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/31/2023] [Accepted: 09/20/2023] [Indexed: 10/10/2023] Open
Abstract
The interactions between tumor cells and the microenvironment play pivotal roles in the initiation, progression and metastasis of cancer. The advent of spatial transcriptomics data offers an opportunity to unravel the intricate dynamics of cellular states and cell-cell interactions in cancer. Herein, we have developed an integrated spatial omics resource in cancer (SORC, http://bio-bigdata.hrbmu.edu.cn/SORC), which interactively visualizes and analyzes the spatial transcriptomics data in cancer. We manually curated currently available spatial transcriptomics datasets for 17 types of cancer, comprising 722 899 spots across 269 slices. Furthermore, we matched reference single-cell RNA sequencing data in the majority of spatial transcriptomics datasets, involving 334 379 cells and 46 distinct cell types. SORC offers five major analytical modules that address the primary requirements of spatial transcriptomics analysis, including slice annotation, identification of spatially variable genes, co-occurrence of immune cells and tumor cells, functional analysis and cell-cell communications. All these spatial transcriptomics data and in-depth analyses have been integrated into easy-to-browse and explore pages, visualized through intuitive tables and various image formats. In summary, SORC serves as a valuable resource for providing an unprecedented spatially resolved cellular map of cancer and identifying specific genes and functional pathways to enhance our understanding of the tumor microenvironment.
Collapse
Affiliation(s)
- Weiwei Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, Heilongjiang Province, China
| | - Minghai Su
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, Heilongjiang Province, China
| | - Tiantongfei Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, Heilongjiang Province, China
| | - Qingyi Yang
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin 150081, Heilongjiang Province, China
| | - Qisen Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, Heilongjiang Province, China
| | - Kang Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, Heilongjiang Province, China
| | - Jingyi Shi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, Heilongjiang Province, China
| | - Changbo Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, Heilongjiang Province, China
| | - Na Ding
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, Heilongjiang Province, China
| | - Yongsheng Li
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin 150081, Heilongjiang Province, China
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, Heilongjiang Province, China
| |
Collapse
|
30
|
Luo W, Wen T, Qu X. Tumor immune microenvironment-based therapies in pancreatic ductal adenocarcinoma: time to update the concept. J Exp Clin Cancer Res 2024; 43:8. [PMID: 38167055 PMCID: PMC10759657 DOI: 10.1186/s13046-023-02935-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal solid tumors. The tumor immune microenvironment (TIME) formed by interactions among cancer cells, immune cells, cancer-associated fibroblasts (CAF), and extracellular matrix (ECM) components drives PDAC in a more immunosuppressive direction: this is a major cause of therapy resistance and poor prognosis. In recent years, research has advanced our understanding of the signaling mechanism by which TIME components interact with the tumor and the evolution of immunophenotyping. Through revolutionary technologies such as single-cell sequencing, we have gone from simply classifying PDACs as "cold" and "hot" to a more comprehensive approach of immunophenotyping that considers all the cells and matrix components. This is key to improving the clinical efficacy of PDAC treatments. In this review, we elaborate on various TIME components in PDAC, the signaling mechanisms underlying their interactions, and the latest research into PDAC immunophenotyping. A deep understanding of these network interactions will contribute to the effective combination of TIME-based therapeutic approaches, such as immune checkpoint inhibitors (ICI), adoptive cell therapy, therapies targeting myeloid cells, CAF reprogramming, and stromal normalization. By selecting the appropriate integrated therapies based on precise immunophenotyping, significant advances in the future treatment of PDAC are possible.
Collapse
Affiliation(s)
- Wenyu Luo
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, 110001, Liaoning, China
- Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001, Liaoning, China
- Clinical Cancer Research Center of Shenyang, the First Hospital of China Medical University, Shenyang, 110001, China
- Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang, 110001, Liaoning, China
| | - Ti Wen
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, 110001, Liaoning, China.
- Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001, Liaoning, China.
- Clinical Cancer Research Center of Shenyang, the First Hospital of China Medical University, Shenyang, 110001, China.
- Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang, 110001, Liaoning, China.
| | - Xiujuan Qu
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, 110001, Liaoning, China.
- Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001, Liaoning, China.
- Clinical Cancer Research Center of Shenyang, the First Hospital of China Medical University, Shenyang, 110001, China.
- Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang, 110001, Liaoning, China.
| |
Collapse
|
31
|
van Eijck CWF, Strijk G, Vietsch EE, van der Sijde F, Verheij M, Mustafa DAM, Vink M, Aerts JGJV, van Eijck CHJ, Willemsen M. FOLFIRINOX chemotherapy modulates the peripheral immune landscape in pancreatic cancer: Implications for combination therapies and early response prediction. Eur J Cancer 2024; 196:113440. [PMID: 37988843 DOI: 10.1016/j.ejca.2023.113440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/01/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND FOLFIRINOX chemotherapy has improved outcomes for pancreatic cancer patients, but poor long-term survival outcomes and high toxicity remain challenges. This study investigates the impact of FOLFIRINOX on plasma proteins and peripheral immune cells to guide immune-based combination therapies and, ideally, to identify a potential biomarker to predict early disease progression during FOLFIRINOX. METHODS Blood samples were collected from 86 pancreatic cancer patients before and two weeks after the first FOLFIRINOX cycle and subjected to comprehensive immune cell and proteome profiling. Principal Component Analysis and Linear Mixed Effect Regression models were used for data analysis. FOLFIRINOX efficacy was radiologically evaluated after the fourth cycle. RESULTS One cycle of FOLFIRINOX diminished tumour-cell-related pathways and enhanced pathways related to immune activation, illustrated by an increase in pro-inflammatory IL-18, IL-15, and TNFRSF4. Similarly, FOLFIRINOX promoted the activation of CD4 + and CD8 + T cells, the proliferation of NK(T), and the activation of antigen-presenting cells. Furthermore, high pre-treatment levels of VEGFA and PRDX3 and an elevation in FCRL3 levels after one cycle predicted early progression under FOLFIRINOX. Finally, patients with progressive disease exhibited high levels of inhibitory markers on B cells and CD8 + T cells, while responding patients exhibited high levels of activation markers on CD4 + and CD8 + T cell subsets. CONCLUSION FOLFIRINOX has immunomodulatory effects, providing a foundation for clinical trials exploring immune-based combination therapies that harness the immune system to treat pancreatic cancer. In addition, several plasma proteins hold potential as circulating predictive biomarkers for early prediction of FOLFIRINOX response in patients with pancreatic cancer.
Collapse
Affiliation(s)
- Casper W F van Eijck
- Department of Surgery, Erasmus University Medical Centre, Rotterdam, the Netherlands; Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre, Madrid, Spain
| | - Gaby Strijk
- Department of Surgery, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Eveline E Vietsch
- Department of Surgery, Erasmus University Medical Centre, Rotterdam, the Netherlands; Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Fleur van der Sijde
- Department of Surgery, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Maaike Verheij
- Department of Surgery, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Dana A M Mustafa
- Department of Pathology, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Madelief Vink
- Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands; Department of Pulmonary Medicine, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Joachim G J V Aerts
- Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands; Department of Pulmonary Medicine, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Casper H J van Eijck
- Department of Surgery, Erasmus University Medical Centre, Rotterdam, the Netherlands; Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre, Madrid, Spain
| | - Marcella Willemsen
- Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands; Department of Pulmonary Medicine, Erasmus University Medical Centre, Rotterdam, the Netherlands.
| |
Collapse
|
32
|
Michiels E, Madhloum H, Van Lint S, Messaoudi N, Kunda R, Martens S, Giron P, Olsen C, Lefesvre P, Dusetti N, El Mohajer L, Tomasini R, Hawinkels LJ, Ahsayni F, Nicolle R, Arsenijevic T, Bouchart C, Van Laethem JL, Rooman I. High-resolution and quantitative spatial analysis reveal intra-ductal phenotypic and functional diversification in pancreatic cancer. J Pathol 2024; 262:76-89. [PMID: 37842959 DOI: 10.1002/path.6212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 08/23/2023] [Accepted: 09/02/2023] [Indexed: 10/17/2023]
Abstract
A 'classical' and a 'basal-like' subtype of pancreatic cancer have been reported, with differential expression of GATA6 and different dosages of mutant KRAS. We established in situ detection of KRAS point mutations and mRNA panels for the consensus subtypes aiming to project these findings to paraffin-embedded clinical tumour samples for spatial quantitative analysis. We unveiled that, next to inter-patient and intra-patient inter-ductal heterogeneity, intraductal spatial phenotypes exist with anti-correlating expression levels of GATA6 and KRASG12D . The basal-like mRNA panel better captured the basal-like cell states than widely used protein markers. The panels corroborated the co-existence of the classical and basal-like cell states in a single tumour duct with functional diversification, i.e. proliferation and epithelial-to-mesenchymal transition respectively. Mutant KRASG12D detection ascertained an epithelial origin of vimentin-positive cells in the tumour. Uneven spatial distribution of cancer-associated fibroblasts could recreate similar intra-organoid diversification. This extensive heterogeneity with functional cooperation of plastic tumour cells poses extra challenges to therapeutic approaches. © 2023 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)
- Ellis Michiels
- Laboratory of Medical & Molecular Oncology (LMMO), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Hediel Madhloum
- Laboratory of Medical & Molecular Oncology (LMMO), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Silke Van Lint
- Laboratory of Medical & Molecular Oncology (LMMO), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Nouredin Messaoudi
- Department of Surgery, Department of Gastroenterology-Hepatology, Department of Advanced Interventional Endoscopy, Universitair Ziekenhuis Brussel (UZB), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Rastislav Kunda
- Department of Surgery, Department of Gastroenterology-Hepatology, Department of Advanced Interventional Endoscopy, Universitair Ziekenhuis Brussel (UZB), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Sandrina Martens
- Laboratory of Medical & Molecular Oncology (LMMO), Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Department of Cardio and Organ Systems, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Philippe Giron
- Centre for Medical Genetics, Clinical Sciences, Reproduction and Genetics Research Group, Universitair Ziekenhuis Brussel (UZB), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Catharina Olsen
- Centre for Medical Genetics, Clinical Sciences, Reproduction and Genetics Research Group, Universitair Ziekenhuis Brussel (UZB), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Pierre Lefesvre
- Department of Anatomo-Pathology, Universitair Ziekenhuis Brussel (UZB), Brussels, Belgium
| | - Nelson Dusetti
- Cancer Research Center of Marseille (CRCM), INSERM, CNRS, Institut Paoli-Calmettes, Aix-Marseille, Marseille University, Marseille, France
| | - Leila El Mohajer
- Cancer Research Center of Marseille (CRCM), INSERM, CNRS, Institut Paoli-Calmettes, Aix-Marseille, Marseille University, Marseille, France
| | - Richard Tomasini
- Cancer Research Center of Marseille (CRCM), INSERM, CNRS, Institut Paoli-Calmettes, Aix-Marseille, Marseille University, Marseille, France
| | - Lukas Jac Hawinkels
- Department of Gastroenterology and Hepatology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Farah Ahsayni
- Department of Surgery, Department of Gastroenterology-Hepatology, Department of Advanced Interventional Endoscopy, Universitair Ziekenhuis Brussel (UZB), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Rémy Nicolle
- Centre de Recherche sur l'inflammation (CRI), INSERM, Paris, France
| | - Tatjana Arsenijevic
- Laboratory of Experimental Gastroenterology, Faculty of Medicine, Université Libre de Bruxelles (ULB), Bruxelles, Belgium
- Department of Gastroenterology, Hepatology and Digestive Oncology, HUB Bordet Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Christelle Bouchart
- Department of Radiation-Oncology, Université Libre de Bruxelles (ULB), Hospital Universitaire de Bruxelles (HUB) Institut Jules Bordet, Brussels, Belgium
| | - Jean-Luc Van Laethem
- Laboratory of Experimental Gastroenterology, Faculty of Medicine, Université Libre de Bruxelles (ULB), Bruxelles, Belgium
- Department of Gastroenterology, Hepatology and Digestive Oncology, HUB Bordet Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Ilse Rooman
- Laboratory of Medical & Molecular Oncology (LMMO), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| |
Collapse
|
33
|
Dang HX, Saha D, Jayasinghe R, Zhao S, Coonrod E, Mudd J, Goedegebuure S, Fields R, Ding L, Maher C. Single-cell transcriptomics reveals long noncoding RNAs associated with tumor biology and the microenvironment in pancreatic cancer. NAR Cancer 2023; 5:zcad055. [PMID: 38023733 PMCID: PMC10664695 DOI: 10.1093/narcan/zcad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 10/31/2023] [Accepted: 11/09/2023] [Indexed: 12/01/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is highly heterogeneous and lethal. Long noncoding RNAs (lncRNAs) are an important class of genes regulating tumorigenesis and progression. Prior bulk transcriptomic studies in PDAC have revealed the dysregulation of lncRNAs but lack single-cell resolution to distinguish lncRNAs in tumor-intrinsic biology and the tumor microenvironment (TME). We analyzed single-cell transcriptome data from 73 multiregion samples in 21 PDAC patients to evaluate lncRNAs associated with intratumoral heterogeneity and the TME in PDAC. We found 111 cell-specific lncRNAs that reflected tumor, immune and stromal cell contributions, associated with outcomes, and validated across orthogonal datasets. Single-cell analysis of tumor cells revealed lncRNAs associated with TP53 mutations and FOLFIRINOX treatment that were obscured in bulk tumor analysis. Lastly, tumor subcluster analysis revealed widespread intratumor heterogeneity and intratumoral lncRNAs associated with cancer hallmarks and tumor processes such as angiogenesis, epithelial-mesenchymal transition, metabolism and immune signaling. Intratumoral subclusters and lncRNAs were validated across six datasets and showed clinically relevant associations with patient outcomes. Our study provides the first comprehensive assessment of the lncRNA landscape in PDAC using single-cell transcriptomic data and can serve as a resource, PDACLncDB (accessible at https://www.maherlab.com/pdaclncdb-overview), to guide future functional studies.
Collapse
Affiliation(s)
- Ha X Dang
- Department of Internal Medicine, Washington University in St Louis, St Louis, MO 63110, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO 63110, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO 63108, USA
| | - Debanjan Saha
- Department of Internal Medicine, Washington University in St Louis, St Louis, MO 63110, USA
- MD–PhD Program, Washington University in St Louis, St Louis, MO 63110, USA
| | - Reyka Jayasinghe
- Department of Internal Medicine, Washington University in St Louis, St Louis, MO 63110, USA
| | - Sidi Zhao
- Department of Internal Medicine, Washington University in St Louis, St Louis, MO 63110, USA
| | - Emily Coonrod
- Department of Internal Medicine, Washington University in St Louis, St Louis, MO 63110, USA
| | - Jacqueline Mudd
- Department of Surgery, Washington University in St Louis, St Louis, MO 63110, USA
| | - S Peter Goedegebuure
- Department of Surgery, Washington University in St Louis, St Louis, MO 63110, USA
| | - Ryan Fields
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO 63110, USA
- Department of Surgery, Washington University in St Louis, St Louis, MO 63110, USA
| | - Li Ding
- Department of Internal Medicine, Washington University in St Louis, St Louis, MO 63110, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO 63110, USA
| | - Christopher A Maher
- Department of Internal Medicine, Washington University in St Louis, St Louis, MO 63110, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO 63110, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO 63108, USA
- Department of Biomedical Engineering, Washington University in St Louis, St Louis, MO 63130, USA
| |
Collapse
|
34
|
Jiang Z, Zheng X, Li M, Liu M. Improving the prognosis of pancreatic cancer: insights from epidemiology, genomic alterations, and therapeutic challenges. Front Med 2023; 17:1135-1169. [PMID: 38151666 DOI: 10.1007/s11684-023-1050-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/15/2023] [Indexed: 12/29/2023]
Abstract
Pancreatic cancer, notorious for its late diagnosis and aggressive progression, poses a substantial challenge owing to scarce treatment alternatives. This review endeavors to furnish a holistic insight into pancreatic cancer, encompassing its epidemiology, genomic characterization, risk factors, diagnosis, therapeutic strategies, and treatment resistance mechanisms. We delve into identifying risk factors, including genetic predisposition and environmental exposures, and explore recent research advancements in precursor lesions and molecular subtypes of pancreatic cancer. Additionally, we highlight the development and application of multi-omics approaches in pancreatic cancer research and discuss the latest combinations of pancreatic cancer biomarkers and their efficacy. We also dissect the primary mechanisms underlying treatment resistance in this malignancy, illustrating the latest therapeutic options and advancements in the field. Conclusively, we accentuate the urgent demand for more extensive research to enhance the prognosis for pancreatic cancer patients.
Collapse
Affiliation(s)
- Zhichen Jiang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
- Department of General Surgery, Division of Gastroenterology and Pancreas, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310014, China
| | - Xiaohao Zheng
- Department of Pancreatic and Gastric Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Min Li
- Department of Medicine, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.
| | - Mingyang Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| |
Collapse
|
35
|
Ghaddar B, De S. Hierarchical and automated cell-type annotation and inference of cancer cell of origin with Census. Bioinformatics 2023; 39:btad714. [PMID: 38011649 PMCID: PMC10713118 DOI: 10.1093/bioinformatics/btad714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 10/26/2023] [Accepted: 11/25/2023] [Indexed: 11/29/2023] Open
Abstract
MOTIVATION Cell-type annotation is a time-consuming yet critical first step in the analysis of single-cell RNA-seq data, especially when multiple similar cell subtypes with overlapping marker genes are present. Existing automated annotation methods have a number of limitations, including requiring large reference datasets, high computation time, shallow annotation resolution, and difficulty in identifying cancer cells or their most likely cell of origin. RESULTS We developed Census, a biologically intuitive and fully automated cell-type identification method for single-cell RNA-seq data that can deeply annotate normal cells in mammalian tissues and identify malignant cells and their likely cell of origin. Motivated by the inherently stratified developmental programs of cellular differentiation, Census infers hierarchical cell-type relationships and uses gradient-boosted \decision trees that capitalize on nodal cell-type relationships to achieve high prediction speed and accuracy. When benchmarked on 44 atlas-scale normal and cancer, human and mouse tissues, Census significantly outperforms state-of-the-art methods across multiple metrics and naturally predicts the cell-of-origin of different cancers. Census is pretrained on the Tabula Sapiens to classify 175 cell-types from 24 organs; however, users can seamlessly train their own models for customized applications. AVAILABILITY AND IMPLEMENTATION Census is available at Zenodo https://zenodo.org/records/7017103 and on our Github https://github.com/sjdlabgroup/Census.
Collapse
Affiliation(s)
- Bassel Ghaddar
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 08901, United States
| | - Subhajyoti De
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 08901, United States
| |
Collapse
|
36
|
Al-Bzour NN, Al-Bzour AN, Ababneh OE, Al-Jezawi MM, Saeed A, Saeed A. Cancer-Associated Fibroblasts in Gastrointestinal Cancers: Unveiling Their Dynamic Roles in the Tumor Microenvironment. Int J Mol Sci 2023; 24:16505. [PMID: 38003695 PMCID: PMC10671196 DOI: 10.3390/ijms242216505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
Gastrointestinal cancers are highly aggressive malignancies with significant mortality rates. Recent research emphasizes the critical role of the tumor microenvironment (TME) in these cancers, which includes cancer-associated fibroblasts (CAFs), a key component of the TME that have diverse origins, including fibroblasts, mesenchymal stem cells, and endothelial cells. Several markers, such as α-SMA and FAP, have been identified to label CAFs, and some specific markers may serve as potential therapeutic targets. In this review article, we summarize the literature on the multifaceted role of CAFs in tumor progression, including their effects on angiogenesis, immune suppression, invasion, and metastasis. In addition, we highlight the use of single-cell transcriptomics to understand CAF heterogeneity and their interactions within the TME. Moreover, we discuss the dynamic interplay between CAFs and the immune system, which contributes to immunosuppression in the TME, and the potential for CAF-targeted therapies and combination approaches with immunotherapy to improve cancer treatment outcomes.
Collapse
Affiliation(s)
- Noor N. Al-Bzour
- Department of Medicine, Division of Hematology & Oncology, University of Pittsburgh Medical Center (UPMC), Pittsburgh, PA 15232, USA; (N.N.A.-B.); (A.N.A.-B.)
| | - Ayah N. Al-Bzour
- Department of Medicine, Division of Hematology & Oncology, University of Pittsburgh Medical Center (UPMC), Pittsburgh, PA 15232, USA; (N.N.A.-B.); (A.N.A.-B.)
| | - Obada E. Ababneh
- Faculty of Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan; (O.E.A.); (M.M.A.-J.)
| | - Moayad M. Al-Jezawi
- Faculty of Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan; (O.E.A.); (M.M.A.-J.)
| | - Azhar Saeed
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, VT 05401, USA;
| | - Anwaar Saeed
- Department of Medicine, Division of Hematology & Oncology, University of Pittsburgh Medical Center (UPMC), Pittsburgh, PA 15232, USA; (N.N.A.-B.); (A.N.A.-B.)
- UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| |
Collapse
|
37
|
Sun X, Yang D, Chen Y. Single-Cell Analysis Differentiates the Effects of p53 Mutation and p53 Loss on Cell Compositions of Oncogenic Kras-Driven Pancreatic Cancer. Cells 2023; 12:2614. [PMID: 37998349 PMCID: PMC10670612 DOI: 10.3390/cells12222614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/06/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a devastating malignant disease with a dismal prognosis. In the past decades, a plethora of genetically engineered mouse models (GEMMs) with autochthonous pancreatic tumor development have greatly facilitated studies of pancreatic cancer. Commonly used GEMMs of PDAC often harbor the oncogenic KRAS driver mutation (KrasG12D), in combination with either p53 mutation by knock-in strategy (Trp53R172H) or p53 loss by conditional knockout (Trp53cKO) strategy, in pancreatic cell lineages. However, the systematic comparison of the tumor microenvironment between KrasG12D; Trp53R172H (KPmut) mouse models and KrasG12D; Trp53cKO (KPloss) mouse models is still lacking. In this study, we conducted cross-dataset single-cell RNA-sequencing (scRNA-seq) analyses to compare the pancreatic tumor microenvironment from KPmut mouse models and KPloss mouse models, especially focusing on the cell compositions and transcriptomic phenotypes of major cell types including cancer cells, B cells, T cells, granulocytes, myeloid cells, cancer-associated fibroblasts, and endothelial cells. We identified the similarities and differences between KPmut and KPloss mouse models, revealing the effects of p53 mutation and p53 loss on oncogenic KRAS-driven pancreatic tumor progression.
Collapse
Affiliation(s)
- Xinlei Sun
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Daowei Yang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yang Chen
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| |
Collapse
|
38
|
Zhang X, Cao Q, Rajachandran S, Grow EJ, Evans M, Chen H. Dissecting mammalian reproduction with spatial transcriptomics. Hum Reprod Update 2023; 29:794-810. [PMID: 37353907 PMCID: PMC10628492 DOI: 10.1093/humupd/dmad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/15/2023] [Indexed: 06/25/2023] Open
Abstract
BACKGROUND Mammalian reproduction requires the fusion of two specialized cells: an oocyte and a sperm. In addition to producing gametes, the reproductive system also provides the environment for the appropriate development of the embryo. Deciphering the reproductive system requires understanding the functions of each cell type and cell-cell interactions. Recent single-cell omics technologies have provided insights into the gene regulatory network in discrete cellular populations of both the male and female reproductive systems. However, these approaches cannot examine how the cellular states of the gametes or embryos are regulated through their interactions with neighboring somatic cells in the native tissue environment owing to tissue disassociations. Emerging spatial omics technologies address this challenge by preserving the spatial context of the cells to be profiled. These technologies hold the potential to revolutionize our understanding of mammalian reproduction. OBJECTIVE AND RATIONALE We aim to review the state-of-the-art spatial transcriptomics (ST) technologies with a focus on highlighting the novel biological insights that they have helped to reveal about the mammalian reproductive systems in the context of gametogenesis, embryogenesis, and reproductive pathologies. We also aim to discuss the current challenges of applying ST technologies in reproductive research and provide a sneak peek at what the field of spatial omics can offer for the reproduction community in the years to come. SEARCH METHODS The PubMed database was used in the search for peer-reviewed research articles and reviews using combinations of the following terms: 'spatial omics', 'fertility', 'reproduction', 'gametogenesis', 'embryogenesis', 'reproductive cancer', 'spatial transcriptomics', 'spermatogenesis', 'ovary', 'uterus', 'cervix', 'testis', and other keywords related to the subject area. All relevant publications until April 2023 were critically evaluated and discussed. OUTCOMES First, an overview of the ST technologies that have been applied to studying the reproductive systems was provided. The basic design principles and the advantages and limitations of these technologies were discussed and tabulated to serve as a guide for researchers to choose the best-suited technologies for their own research. Second, novel biological insights into mammalian reproduction, especially human reproduction revealed by ST analyses, were comprehensively reviewed. Three major themes were discussed. The first theme focuses on genes with non-random spatial expression patterns with specialized functions in multiple reproductive systems; The second theme centers around functionally interacting cell types which are often found to be spatially clustered in the reproductive tissues; and the thrid theme discusses pathological states in reproductive systems which are often associated with unique cellular microenvironments. Finally, current experimental and computational challenges of applying ST technologies to studying mammalian reproduction were highlighted, and potential solutions to tackle these challenges were provided. Future directions in the development of spatial omics technologies and how they will benefit the field of human reproduction were discussed, including the capture of cellular and tissue dynamics, multi-modal molecular profiling, and spatial characterization of gene perturbations. WIDER IMPLICATIONS Like single-cell technologies, spatial omics technologies hold tremendous potential for providing significant and novel insights into mammalian reproduction. Our review summarizes these novel biological insights that ST technologies have provided while shedding light on what is yet to come. Our review provides reproductive biologists and clinicians with a much-needed update on the state of art of ST technologies. It may also facilitate the adoption of cutting-edge spatial technologies in both basic and clinical reproductive research.
Collapse
Affiliation(s)
- Xin Zhang
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Qiqi Cao
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Shreya Rajachandran
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Edward J Grow
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Melanie Evans
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Haiqi Chen
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| |
Collapse
|
39
|
Zwart ES, van Ee T, Doppenberg D, Farina A, Wilmink JW, Versteijne E, Busch OR, Besselink MG, Meijer LL, van Kooyk Y, Mebius RE, Kazemier G. The immune microenvironment after neoadjuvant therapy compared to upfront surgery in patients with pancreatic cancer. J Cancer Res Clin Oncol 2023; 149:14731-14743. [PMID: 37587309 PMCID: PMC10603010 DOI: 10.1007/s00432-023-05219-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/27/2023] [Indexed: 08/18/2023]
Abstract
BACKGROUND Patients with resectable and borderline resectable pancreatic ductal adenocarcinoma increasingly receive neoadjuvant therapy prior to surgery. However, the effect of neoadjuvant therapy on the immune microenvironment remains largely unknown. We analyzed the immune microenvironment in pancreatic cancer tumor tissue samples from patients treated with neoadjuvant therapy compared to patients after upfront surgery to gain knowledge about the immunological environment after therapy. METHODS Multispectral imaging was performed on tissue from resected specimens from patients with PDAC who underwent upfront surgery (n = 10), neoadjuvant FOLFIRINOX (n = 10) or gemcitabine + radiotherapy (gem-RT) (n = 9) followed by surgery. The samples were selected by a dedicated pancreas pathologist from both the central part and the invasive front of the tumor (by the resected vein or venous surface) and subsequently analyzed using the Vectra Polaris. RESULTS Patients receiving neoadjuvant FOLFIRINOX display a more pro-inflammatory immune profile, with less regulatory T cells and more CD8 T cells in the tumor tissue compared to patients receiving neoadjuvant gem-RTgem-RT or undergoing upfront surgery. Furthermore, CD163+ macrophages were decreased, and a higher CD163- macrophages versus CD163+ macrophages ratio was found in patients with neoadjuvant FOLFIRINOX. In all treatment groups, percentage of FoxP3+ B cells was significantly higher in tumor tissue compared to adjacent tissue. Furthermore, an increase in regulatory T cells in the tumor tissue was found in patients undergoing upfront surgery or receiving neoadjuvant gem-RT. In the gem-RT group, less CD8 T cells and a higher CD163+ macrophages to CD8 ratio were noted in the tumor tissue, suggesting a more immune suppressive profile in the tumor tissue. CONCLUSION Patients receiving neoadjuvant FOLFIRINOX display a more pro-inflammatory immune profile compared to patients receiving neoadjuvant gem-RT or undergoing upfront surgery. Furthermore, in all treatment groups, a more immune suppressive microenvironment was found in the tumor tissue compared to the adjacent non-tumorous tissue.
Collapse
Affiliation(s)
- Eline S Zwart
- Department of Surgery, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Department of Molecular Biology and Immunology, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Thomas van Ee
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Department of Molecular Biology and Immunology, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Oncology Graduate School, Amsterdam, The Netherlands
| | - Deesje Doppenberg
- Department of Surgery, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Surgery, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Arantza Farina
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Department of Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Johanna W Wilmink
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Department of Oncology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Eva Versteijne
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Department of Radiation Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Olivier R Busch
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Department of Surgery, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Marc G Besselink
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Department of Surgery, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Laura L Meijer
- Department of Surgery, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Yvette van Kooyk
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Department of Molecular Biology and Immunology, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Reina E Mebius
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Department of Molecular Biology and Immunology, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Geert Kazemier
- Department of Surgery, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
- Cancer Center Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
40
|
Karamitopoulou E. Emerging Prognostic and Predictive Factors in Pancreatic Cancer. Mod Pathol 2023; 36:100328. [PMID: 37714333 DOI: 10.1016/j.modpat.2023.100328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/23/2023] [Accepted: 08/29/2023] [Indexed: 09/17/2023]
Abstract
Pancreatic cancer is a lethal disease with increasing incidence and high recurrence rates and is currently resistant to conventional therapies. Moreover, it displays extensive morphologic and molecular intratumoral and intertumoral heterogeneity and a mostly low mutational burden, failing to induce significant antitumor immunity. Thus, immunotherapy has shown limited effect in pancreatic cancer, except in rare tumors with microsatellite instability, constituting <1% of the cases. Currently, new methods, including single-cell and single-nucleus RNA sequencing, have refined and expanded the 2-group molecular classification based on bulk RNA sequencing (classical and basal-like subtypes), identifying hybrid forms and providing us with a comprehensive map of the tumor cell subsets that drive gene expression during tumor evolution, simultaneously giving us insight into therapy resistance and metastasis. Additionally, deeper profiling of the tumor microenvironment of pancreatic cancer by using spatial analyses and multiplex imaging techniques has improved our understanding of the heterogeneous distribution of both adaptive and innate immune components with their protumor and antitumor properties. By integrating host immune response patterns, as defined by spatial transcriptomic and proteomic analysis and multiplex immunofluorescence, with molecular and morphologic features of the tumors, we can increasingly understand the genetic, immunologic, and morphologic background of pancreatic cancer and recognize the potential predictors for different treatment modalities.
Collapse
Affiliation(s)
- Eva Karamitopoulou
- Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland; Pathology Institute Enge, Zurich, Switzerland.
| |
Collapse
|
41
|
Mu K, Fu J, Gai J, Ravichandran H, Zheng L, Sun WC. Genetic alterations in the neuronal development genes are associated with changes of the tumor immune microenvironment in pancreatic cancer. Ann Pancreat Cancer 2023; 6:10.21037/apc-23-13. [PMID: 38495381 PMCID: PMC10942730 DOI: 10.21037/apc-23-13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Background Pancreatic ductal adenocarcinoma (PDAC) has a poor prognosis and is highly metastatic. Our prior studies have demonstrated the critical role of axon guidance pathway genes in PDAC and the connection between neuronal development and the tumor microenvironment. A recent study newly identified 20 neuronal development genes [disks large homolog 2 (DLG2), neuron-glial-related cell adhesion molecule (NRCAM), neurexin3 (NRXN3), mitogen-activated protein kinase 10 (MAPK10), platelet-derived growth factor D (PDGFD), protein kinase C epsilon (PRKCE), potassium calcium-activated channel subfamily M alpha 1 (KCNMA1), polycystic kidney and hepatic disease 1 (PKHD1), neural cell adhesion molecule 1 (NCAM1), neuregulin-1 (NRG1), zinc finger protein 667 (ZNF667), cystic fibrosis transmembrane conductance regulator (CFTR), acyl-CoA medium-chain synthetase-3 (ACSM3), complement 6 (C6), protein tyrosine phosphatase receptor type M (PTPRM), hypoxia-inducible factor 1 alpha (HIF1A), adenylyl cyclase 5 (ADCY5), adherens junctions-associated protein 1 (AJAP1), neurobeachin (NBEA), sodium voltage-gated channel alpha subunit 9 (SCN9A)] that are associated with perineural invasion and poor prognosis of PDAC. The relationship between genetic alterations in these 20 genes and tumor immune microenvironment (TME) has not previously been investigated. Methods We hence applied the sequential multiplex immunohistochemistry results of biopsy specimens from 63 PDAC patients to investigate this relationship. Results We found that, except for PTPRM and NBEA, genetic alterations involving these 20 genes are associated with significant changes in the densities of major immune cell subtypes. Except for AJAP1, the copy number loss involving this panel of neuronal development genes is significantly associated with changes in immune cell infiltrates. In contrast, the copy number gain in fewer genes, including NRXN3, ZNF667, ACSM3, C6, ADCY5, SCN9A, and PRKCE, is significantly associated with changes in immune cell infiltrates. Conclusions Our study suggested that neuronal development genes play a role in modulating TME in a pancreatic cancer setting.
Collapse
Affiliation(s)
- Kaiyi Mu
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Juan Fu
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jessica Gai
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Harshitha Ravichandran
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lei Zheng
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Wei-Chih Sun
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| |
Collapse
|
42
|
Thielman NRJ, Funes V, Davuluri S, Ibanez HE, Sun WC, Fu J, Li K, Muth S, Pan X, Fujiwara K, Thomas D, Henderson M, Teh SS, Zhu Q, Thompson E, Jaffee EM, Kolodkin A, Meng F, Zheng L. Tumor- and Nerve-Derived Axon Guidance Molecule Promotes Pancreatic Ductal Adenocarcinoma Progression and Metastasis through Macrophage Reprogramming. bioRxiv 2023:2023.10.24.563862. [PMID: 37961340 PMCID: PMC10634802 DOI: 10.1101/2023.10.24.563862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Axon guidance molecules were found to be the gene family most frequently altered in pancreatic ductal adenocarcinoma (PDA) through mutations and copy number changes. However, the exact molecular mechanism regarding PDA development remained unclear. Using genetically engineered mouse models to examine one of the axon guidance molecules, semaphorin 3D (SEMA3D), we found a dual role for tumor-derived SEMA3D in malignant transformation of pancreatic epithelial cells and a role for nerve-derived SEMA3D in PDA development. This was demonstrated by the pancreatic-specific knockout of the SEMA3D gene from the KRAS G12D and TP53 R 172 H mutation knock-in, PDX1-Cre (KPC) mouse model which demonstrated a delayed tumor initiation and growth comparing to the original KPC mouse model. Our results showed that SEMA3D knockout skews the macrophages in the pancreas away from M2 polarization, providing a potential mechanistic role of tumor-derived SEMA3D in PDA development. The KPC mice with the SEMA3D knockout remained metastasis-free, however, died from primary tumor growth. We then tested the hypothesis that a potential compensation mechanism could result from SEMA3D which is naturally expressed by the intratumoral nerves. Our study further revealed that nerve-derived SEMA3D does not reprogram macrophages directly, but reprograms macrophages indirectly through ARF6 signaling and lactate production in PDA tumor cells. SEMA3D increases tumor-secreted lactate which is sensed by GPCR132 on macrophages and subsequently stimulates pro-tumorigenic M2 polarization in vivo. Tumor intrinsic- and extrinsic-SEMA3D induced ARF6 signaling through its receptor Plexin D1 in a mutant KRAS-dependent manner. Consistently, RNA sequencing database analysis revealed an association of higher KRAS MUT expression with an increase in SEMA3D and ARF6 expression in human PDAs. Moreover, multiplex immunohistochemistry analysis showed an increased number of M2-polarized macrophages proximal to nerves in human PDA tissue expressing SEMA3D. Thus, this study suggests altered expression of SEMA3D in tumor cells lead to acquisition of cancer-promoting functions and the axon guidance signaling originating from nerves is "hijacked" by tumor cells to support their growth. Other axon guidance and neuronal development molecules may play a similar dual role which is worth further investigation. One sentence summary Tumor- and nerve-derived SEMA3D promotes tumor progression and metastasis through macrophage reprogramming in the tumor microenvironment. STATEMENT OF SIGNIFICANCE This study established the dual role of axon guidance molecule, SEMA3D, in the malignant transformation of pancreatic epithelial cells and of nerve-derived SEMA3D in PDA progression and metastasis. It revealed macrophage reprogramming as the mechanism underlying bothroles. Together, this research elucidated how inflammatory responses promote invasive PDA progression and metastasis through an oncogenic process.
Collapse
|
43
|
Zhao S, Chen DP, Fu T, Yang JC, Ma D, Zhu XZ, Wang XX, Jiao YP, Jin X, Xiao Y, Xiao WX, Zhang HY, Lv H, Madabhushi A, Yang WT, Jiang YZ, Xu J, Shao ZM. Single-cell morphological and topological atlas reveals the ecosystem diversity of human breast cancer. Nat Commun 2023; 14:6796. [PMID: 37880211 PMCID: PMC10600153 DOI: 10.1038/s41467-023-42504-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 10/12/2023] [Indexed: 10/27/2023] Open
Abstract
Digital pathology allows computerized analysis of tumor ecosystem using whole slide images (WSIs). Here, we present single-cell morphological and topological profiling (sc-MTOP) to characterize tumor ecosystem by extracting the features of nuclear morphology and intercellular spatial relationship for individual cells. We construct a single-cell atlas comprising 410 million cells from 637 breast cancer WSIs and dissect the phenotypic diversity within tumor, inflammatory and stroma cells respectively. Spatially-resolved analysis identifies recurrent micro-ecological modules representing locoregional multicellular structures and reveals four breast cancer ecotypes correlating with distinct molecular features and patient prognosis. Further analysis with multiomics data uncovers clinically relevant ecosystem features. High abundance of locally-aggregated inflammatory cells indicates immune-activated tumor microenvironment and favorable immunotherapy response in triple-negative breast cancers. Morphological intratumor heterogeneity of tumor nuclei correlates with cell cycle pathway activation and CDK inhibitors responsiveness in hormone receptor-positive cases. sc-MTOP enables using WSIs to characterize tumor ecosystems at the single-cell level.
Collapse
Affiliation(s)
- Shen Zhao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - De-Pin Chen
- Institute for Artificial Intelligence in Medicine, School of Artificial Intelligence, Nanjing University of Information Science and Technology, Nanjing, China
| | - Tong Fu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Jing-Cheng Yang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Greater Bay Area Institute of Precision Medicine, Guangzhou, China
| | - Ding Ma
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiu-Zhi Zhu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiang-Xue Wang
- Institute for Artificial Intelligence in Medicine, School of Artificial Intelligence, Nanjing University of Information Science and Technology, Nanjing, China
| | - Yi-Ping Jiao
- Institute for Artificial Intelligence in Medicine, School of Artificial Intelligence, Nanjing University of Information Science and Technology, Nanjing, China
| | - Xi Jin
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yi Xiao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Wen-Xuan Xiao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Hu-Yunlong Zhang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Hong Lv
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Anant Madabhushi
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Atlanta Veterans Affairs Medical Center, Atlanta, GA, USA
| | - Wen-Tao Yang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China.
| | - Yi-Zhou Jiang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
| | - Jun Xu
- Institute for Artificial Intelligence in Medicine, School of Artificial Intelligence, Nanjing University of Information Science and Technology, Nanjing, China.
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
| |
Collapse
|
44
|
Cohn DE, Forder A, Marshall EA, Vucic EA, Stewart GL, Noureddine K, Lockwood WW, MacAulay CE, Guillaud M, Lam WL. Delineating spatial cell-cell interactions in the solid tumour microenvironment through the lens of highly multiplexed imaging. Front Immunol 2023; 14:1275890. [PMID: 37936700 PMCID: PMC10627006 DOI: 10.3389/fimmu.2023.1275890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/11/2023] [Indexed: 11/09/2023] Open
Abstract
The growth and metastasis of solid tumours is known to be facilitated by the tumour microenvironment (TME), which is composed of a highly diverse collection of cell types that interact and communicate with one another extensively. Many of these interactions involve the immune cell population within the TME, referred to as the tumour immune microenvironment (TIME). These non-cell autonomous interactions exert substantial influence over cell behaviour and contribute to the reprogramming of immune and stromal cells into numerous pro-tumourigenic phenotypes. The study of some of these interactions, such as the PD-1/PD-L1 axis that induces CD8+ T cell exhaustion, has led to the development of breakthrough therapeutic advances. Yet many common analyses of the TME either do not retain the spatial data necessary to assess cell-cell interactions, or interrogate few (<10) markers, limiting the capacity for cell phenotyping. Recently developed digital pathology technologies, together with sophisticated bioimage analysis programs, now enable the high-resolution, highly-multiplexed analysis of diverse immune and stromal cell markers within the TME of clinical specimens. In this article, we review the tumour-promoting non-cell autonomous interactions in the TME and their impact on tumour behaviour. We additionally survey commonly used image analysis programs and highly-multiplexed spatial imaging technologies, and we discuss their relative advantages and limitations. The spatial organization of the TME varies enormously between patients, and so leveraging these technologies in future studies to further characterize how non-cell autonomous interactions impact tumour behaviour may inform the personalization of cancer treatment..
Collapse
Affiliation(s)
- David E. Cohn
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Aisling Forder
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Erin A. Marshall
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Emily A. Vucic
- Department of Biochemistry and Molecular Pharmacology, New York University (NYU) Langone Medical Center, New York, NY, United States
| | - Greg L. Stewart
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Kouther Noureddine
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - William W. Lockwood
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Calum E. MacAulay
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Martial Guillaud
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Wan L. Lam
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| |
Collapse
|
45
|
Tang R, Xu J, Wang W, Meng Q, Shao C, Zhang Y, Lei Y, Zhang Z, Liu Y, Du Q, Sun X, Wu D, Liang C, Hua J, Zhang B, Yu X, Shi S. Targeting neoadjuvant chemotherapy-induced metabolic reprogramming in pancreatic cancer promotes anti-tumor immunity and chemo-response. Cell Rep Med 2023; 4:101234. [PMID: 37852179 PMCID: PMC10591062 DOI: 10.1016/j.xcrm.2023.101234] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 09/06/2023] [Accepted: 09/19/2023] [Indexed: 10/20/2023]
Abstract
The molecular dynamics of pancreatic ductal adenocarcinoma (PDAC) under chemotherapy remain incompletely understood. The widespread use of neoadjuvant chemotherapy (NAC) provides a unique opportunity to investigate PDAC samples post-chemotherapy. Leveraging a cohort from Fudan University Shanghai Cancer Center, encompassing PDAC samples with and without exposure to neoadjuvant albumin-bound paclitaxel and gemcitabine (AG), we have compiled data from single-cell and spatial transcriptomes, proteomes, bulk transcriptomes, and metabolomes, deepening our comprehension of the molecular changes in PDACs in response to chemotherapy. Metabolic flux analysis reveals that NAC induces a reprogramming of PDAC metabolic patterns and enhances immunogenicity. Notably, NAC leads to the downregulation of glycolysis and the upregulation of CD36. Tissue microarray analysis demonstrates that high CD36 expression is linked to poorer survival in patients receiving postoperative AG. Targeting CD36 synergistically improves the PDAC response to AG both in vitro and in vivo, including patient-derived preclinical models.
Collapse
Affiliation(s)
- Rong Tang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jin Xu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wei Wang
- Shanghai Pancreatic Cancer Institute, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Qingcai Meng
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chenghao Shao
- Department of Pancreatic-Biliary Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Yiyin Zhang
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Yubin Lei
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
| | - Zifeng Zhang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuan Liu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Department of Endoscopy, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Qiong Du
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Department of Pharmacy, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiangjie Sun
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Di Wu
- Shanghai Pancreatic Cancer Institute, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Chen Liang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jie Hua
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Bo Zhang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xianjun Yu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Si Shi
- Shanghai Pancreatic Cancer Institute, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China.
| |
Collapse
|
46
|
Digomann D, Heiduk M, Reiche C, Glück J, Kahlert C, Mirtschink P, Klimova A, Bösch F, Tonn T, Gaedcke J, Ghadimi M, Weitz J, Seifert L, Seifert AM. Serum immune checkpoint profiling identifies soluble CD40 as a biomarker for pancreatic cancer. NPJ Precis Oncol 2023; 7:104. [PMID: 37838778 PMCID: PMC10576756 DOI: 10.1038/s41698-023-00459-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 09/26/2023] [Indexed: 10/16/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) responds poorly to systemic treatment, including new immunotherapeutic approaches. Biomarkers are urgently needed for early disease detection, patient stratification for treatment, and response prediction. The role of soluble CD40 (sCD40) is unknown in PDAC. In this study, we performed a quantitative multiplex analysis of 17 immune checkpoint proteins in serum samples from patients with various stages of PDAC in a discovery study (n = 107) and analyzed sCD40 by ELISA in a validation study (n = 317). Youden's J statistic was used for diagnostic cut-off optimization. A Cox proportional hazards regression model was applied in an empiric approach for prognostic threshold optimization. Kaplan-Meier estimator and multivariable Cox regression analyses were used for survival analysis. sCD40 was significantly increased in the serum of patients with PDAC compared to healthy cohorts and patients with IPMN. In the validation cohort, the area under the receiver operating characteristic (ROC) c-statistic was 0.8, and combining sCD40 with CA19-9 yielded a c-statistic of 0.95. sCD40 levels were independent of the tumor stage. However, patients who received neoadjuvant chemotherapy had significantly lower sCD40 levels than those who underwent upfront surgery. Patients with a sCD40 level above the empirical threshold of 0.83 ng/ml had a significantly reduced overall survival with a hazard ratio of 1.4. This observation was pronounced in patients after neoadjuvant chemotherapy. Collectively, soluble CD40 may be considered as both a diagnostic and prognostic non-invasive biomarker in PDAC.
Collapse
Affiliation(s)
- David Digomann
- Department of Visceral, Thoracic and Vascular Surgery, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Max Heiduk
- Department of Visceral, Thoracic and Vascular Surgery, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Charlotte Reiche
- Department of Visceral, Thoracic and Vascular Surgery, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Jessica Glück
- Department of Visceral, Thoracic and Vascular Surgery, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Christoph Kahlert
- Department of Visceral, Thoracic and Vascular Surgery, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter Mirtschink
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Anna Klimova
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Core Unit for Data Management and Analytics (CDMA), National Center for Tumor Diseases (NCT), Dresden, Germany
| | - Florian Bösch
- Department of Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Torsten Tonn
- German Cancer Consortium (DKTK), Partner Site Dresden, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute for Transfusion Medicine, German Red Cross Blood Donation Service North-East, Dresden, Germany
- Experimental Transfusion Medicine, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Jochen Gaedcke
- Department of Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Michael Ghadimi
- Department of Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Jürgen Weitz
- Department of Visceral, Thoracic and Vascular Surgery, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lena Seifert
- Department of Visceral, Thoracic and Vascular Surgery, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Else Kröner Clinician Scientist Professor for Translational Tumor Immunological Research, 01307, Dresden, Germany
| | - Adrian M Seifert
- Department of Visceral, Thoracic and Vascular Surgery, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
- National Center for Tumor Diseases (NCT), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany.
- German Cancer Consortium (DKTK), Partner Site Dresden, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| |
Collapse
|
47
|
Pedrazzoli S. Currently Debated Topics on Surgical Treatment of Pancreatic Ductal Adenocarcinoma: A Narrative Review on Surgical Treatment of Borderline Resectable, Locally Advanced, and Synchronous or Metachronous Oligometastatic Tumor. J Clin Med 2023; 12:6461. [PMID: 37892599 PMCID: PMC10607532 DOI: 10.3390/jcm12206461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Previously considered inoperable patients (borderline resectable, locally advanced, synchronous oligometastatic or metachronous pancreatic adenocarcinoma (PDAC)) are starting to become resectable thanks to advances in chemo/radiotherapy and the reduction in operative mortality. METHODS This narrative review presents a chosen literature selection, giving a picture of the current state of treatment of these patients. RESULTS Neoadjuvant therapy (NAT) is generally recognized as the treatment of choice before surgery. However, despite the increased efficacy, the best pathological response is still limited to 10.9-27.9% of patients. There are still limited data on the selection of possible NAT responders and how to diagnose non-responders early. Multidetector computed tomography has high sensitivity and low specificity in evaluating resectability after NAT, limiting the resection rate of resectable patients. Ca 19-9 and Positron emission tomography are giving promising results. The prediction of early recurrence after a radical resection of synchronous or metachronous metastatic PDAC, thus identifying patients with poor prognosis and saving them from a resection of little benefit, is still ongoing, although some promising data are available. CONCLUSION In conclusion, high-level evidence demonstrating the benefit of the surgical treatment of such patients is still lacking and should not be performed outside of high-volume centers with interdisciplinary teams of surgeons and oncologists.
Collapse
|
48
|
Li J, D’Amico S, Kirillov V, Petrenko O, Reich NC. Oncogenic dependency plays a dominant role in the immune response to cancer. Proc Natl Acad Sci U S A 2023; 120:e2308635120. [PMID: 37782788 PMCID: PMC10576078 DOI: 10.1073/pnas.2308635120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/01/2023] [Indexed: 10/04/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest human malignancies. Advanced PDAC is considered incurable. Nearly 90% of pancreatic cancers are caused by oncogenic KRAS mutations. The mechanisms of primary or acquired resistance to KRAS inhibition are currently unknown. Here, we propose that oncogenic dependency, rather than KRAS mutation per se, plays a dominant role in the immune response to cancer, including late-stage PDAC. Classifying tumor samples according to KRAS activity scores allows accurate prediction of tumor immune composition and therapy response. Dual RAS/MAPK pathway blockade combining KRAS and MEK inhibitors is more effective than the selective KRAS inhibitor alone in attenuating MAPK activation and unblocking the influx of T cells into the tumor. Lowering KRAS activity in established tumors promotes immune infiltration, but with a limited antitumor effect, whereas combining KRAS/MEK inhibition with immune checkpoint blockade achieves durable regression in preclinical models. The results are directly applicable to stratifying human PDAC based on KRAS dependency values and immune cell composition to improve therapeutic design.
Collapse
Affiliation(s)
- Jinyu Li
- Department of Pathology, Stony Brook University, Stony Brook, NY11794
| | - Stephen D’Amico
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY11794
| | - Varvara Kirillov
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY11794
| | - Oleksi Petrenko
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY11794
| | - Nancy C. Reich
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY11794
| |
Collapse
|
49
|
Yousuf S, Qiu M, Voith von Voithenberg L, Hulkkonen J, Macinkovic I, Schulz AR, Hartmann D, Mueller F, Mijatovic M, Ibberson D, AlHalabi KT, Hetzer J, Anders S, Brüne B, Mei HE, Imbusch CD, Brors B, Heikenwälder M, Gaida MM, Büchler MW, Weigert A, Hackert T, Roth S. Spatially Resolved Multi-Omics Single-Cell Analyses Inform Mechanisms of Immune Dysfunction in Pancreatic Cancer. Gastroenterology 2023; 165:891-908.e14. [PMID: 37263303 DOI: 10.1053/j.gastro.2023.05.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND & AIMS As pancreatic ductal adenocarcinoma (PDAC) continues to be recalcitrant to therapeutic interventions, including poor response to immunotherapy, albeit effective in other solid malignancies, a more nuanced understanding of the immune microenvironment in PDAC is urgently needed. We aimed to unveil a detailed view of the immune micromilieu in PDAC using a spatially resolved multimodal single-cell approach. METHODS We applied single-cell RNA sequencing, spatial transcriptomics, multiplex immunohistochemistry, and mass cytometry to profile the immune compartment in treatment-naïve PDAC tumors and matched adjacent normal pancreatic tissue, as well as in the systemic circulation. We determined prognostic associations of immune signatures and performed a meta-analysis of the immune microenvironment in PDAC and lung adenocarcinoma on single-cell level. RESULTS We provided a spatially resolved fine map of the immune landscape in PDAC. We substantiated the exhausted phenotype of CD8 T cells and immunosuppressive features of myeloid cells, and highlighted immune subsets with potentially underappreciated roles in PDAC that diverged from immune populations within adjacent normal areas, particularly CD4 T cell subsets and natural killer T cells that are terminally exhausted and acquire a regulatory phenotype. Differential analysis of immune phenotypes in PDAC and lung adenocarcinoma revealed the presence of extraordinarily immunosuppressive subtypes in PDAC, along with a distinctive immune checkpoint composition. CONCLUSIONS Our study sheds light on the multilayered immune dysfunction in PDAC and presents a holistic view of the immune landscape in PDAC and lung adenocarcinoma, providing a comprehensive resource for functional studies and the exploration of therapeutically actionable targets in PDAC.
Collapse
Affiliation(s)
- Suhail Yousuf
- Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Mengjie Qiu
- Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Johannes Hulkkonen
- Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Igor Macinkovic
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, Frankfurt, Germany
| | | | - Domenic Hartmann
- Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Florian Mueller
- Division of Chronic Inflammation and Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Margarete Mijatovic
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, Frankfurt, Germany
| | - David Ibberson
- Deep Sequencing Core Facility, BioQuant, Heidelberg University, Heidelberg, Germany
| | - Karam T AlHalabi
- Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Jenny Hetzer
- Division of Chronic Inflammation and Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Simon Anders
- BioQuant Center, Heidelberg University, Heidelberg, Germany
| | - Bernhard Brüne
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, Frankfurt, Germany; Frankfurt Cancer Institute, Goethe-University Frankfurt, Frankfurt, Germany; German Cancer Consortium, Partner Site Frankfurt, Germany
| | - Henrik E Mei
- German Rheumatism Research Center, Berlin, Germany
| | - Charles D Imbusch
- Division of Applied Bioinformatics, German Cancer Research Center, Heidelberg, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center, Heidelberg, Germany
| | - Mathias Heikenwälder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Matthias M Gaida
- Institute of Pathology, University Medical Center Mainz, Johannes Gutenberg University, Mainz, Germany; Research Center for Immunotherapy, University Medical Center Mainz, Johannes Gutenberg University, Mainz, Germany; Joint Unit Immunopathology, Institute of Pathology, University Medical Center, Johannes Gutenberg University and Translational Oncology, University Medical Center Mainz, Mainz, Germany
| | - Markus W Büchler
- Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas Weigert
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, Frankfurt, Germany; Frankfurt Cancer Institute, Goethe-University Frankfurt, Frankfurt, Germany; German Cancer Consortium, Partner Site Frankfurt, Germany
| | - Thilo Hackert
- Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Susanne Roth
- Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany.
| |
Collapse
|
50
|
Wang Q, Zhi Y, Zi M, Mo Y, Wang Y, Liao Q, Zhang S, Gong Z, Wang F, Zeng Z, Guo C, Xiong W. Spatially Resolved Transcriptomics Technology Facilitates Cancer Research. Adv Sci (Weinh) 2023; 10:e2302558. [PMID: 37632718 PMCID: PMC10602551 DOI: 10.1002/advs.202302558] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/16/2023] [Indexed: 08/28/2023]
Abstract
Single cell RNA sequencing (scRNA-seq) provides a great convenience for studying tumor occurrence and development for its ability to study gene expression at the individual cell level. However, patient-derived tumor tissues are composed of multiple types of cells including tumor cells and adjacent non-malignant cells such as stromal cells and immune cells. The spatial locations of various cells in situ tissues plays a pivotal role in the occurrence and development of tumors, which cannot be elucidated by scRNA-seq alone. Spatially resolved transcriptomics (SRT) technology emerges timely to explore the unrecognized relationship between the spatial background of a particular cell and its functions, and is increasingly used in cancer research. This review provides a systematic overview of the SRT technologies that are developed, in particular the more widely used cutting-edge SRT technologies based on next-generation sequencing (NGS). In addition, the main achievements by SRT technologies in precisely unveiling the underappreciated spatial locations on gene expression and cell function with unprecedented high-resolution in cancer research are emphasized, with the aim of developing more effective clinical therapeutics oriented to a deeper understanding of the interaction between tumor cells and surrounding non-malignant cells.
Collapse
Affiliation(s)
- Qian Wang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer MetabolismHunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaHunan410008P. R. China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCancer Research InstituteCentral South UniversityChangshaHunan410008P. R. China
| | - Yuan Zhi
- Department of Oral and Maxillofacial SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaHunan410012P. R. China
| | - Moxin Zi
- Department of Oral and Maxillofacial SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaHunan410012P. R. China
| | - Yongzhen Mo
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCancer Research InstituteCentral South UniversityChangshaHunan410008P. R. China
- Department of Otolaryngology Head and Neck SurgeryXiangya HospitalCentral South UniversityChangshaHunan410008P. R. China
| | - Yumin Wang
- Department of Otolaryngology Head and Neck SurgeryXiangya HospitalCentral South UniversityChangshaHunan410008P. R. China
| | - Qianjin Liao
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer MetabolismHunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaHunan410008P. R. China
| | - Shanshan Zhang
- Department of Otolaryngology Head and Neck SurgeryXiangya HospitalCentral South UniversityChangshaHunan410008P. R. China
| | - Zhaojian Gong
- Department of Oral and Maxillofacial SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaHunan410012P. R. China
| | - Fuyan Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCancer Research InstituteCentral South UniversityChangshaHunan410008P. R. China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer MetabolismHunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaHunan410008P. R. China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCancer Research InstituteCentral South UniversityChangshaHunan410008P. R. China
| | - Can Guo
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer MetabolismHunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaHunan410008P. R. China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCancer Research InstituteCentral South UniversityChangshaHunan410008P. R. China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer MetabolismHunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaHunan410008P. R. China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCancer Research InstituteCentral South UniversityChangshaHunan410008P. R. China
| |
Collapse
|