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Kirthiga Devi SS, Singh S, Joga R, Patil SY, Meghana Devi V, Chetan Dushantrao S, Dwivedi F, Kumar G, Kumar Jindal D, Singh C, Dhamija I, Kumar S. Enhancing cancer immunotherapy: Exploring strategies to target the PD-1/PD-L1 axis and analyzing the associated patent, regulatory, and clinical trial landscape. Eur J Pharm Biopharm 2024:114323. [PMID: 38754524 DOI: 10.1016/j.ejpb.2024.114323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/10/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
Cancer treatment modalities and their progression is guided by the specifics of cancer, including its type and site of localization. Surgery, radiation, and chemotherapy are the most often used conventional treatments. Conversely, emerging treatment techniques include immunotherapy, hormone therapy, anti-angiogenic therapy, dendritic cell-based immunotherapy, and stem cell therapy. Immune checkpoint inhibitors' anticancer properties have drawn considerable attention in recent studies in the cancer research domain. Programmed Cell Death Protein-1 (PD-1) and its ligand (PD-L1) checkpoint pathway are key regulators of the interactions between activated T-cells and cancer cells, protecting the latter from immune destruction. When the ligand PD-L1 attaches to the receptor PD-1, T-cells are prevented from destroying cells that contain PD-L1, including cancer cells. The PD-1/PD-L1 checkpoint inhibitors block them, boosting the immune response and strengthening the body's defenses against tumors. Recent years have seen incredible progress and tremendous advancement in developing anticancer therapies using PD-1/PD-L1 targeting antibodies. While immune-related adverse effects and low response rates significantly limit these therapies, there is a need for research on methods that raise their efficacy and lower their toxicity. This review discusses various recent innovative nanomedicine strategies such as PLGA nanoparticles, carbon nanotubes and drug loaded liposomes to treat cancer targeting PD-1/PD-L1 axis. The biological implications of PD-1/PD-L1 in cancer treatment and the fundamentals of nanotechnology, focusing on the novel strategies used in nanomedicine, are widely discussed along with the corresponding guidelines, clinical trial status, and the patent landscape of such formulations.
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Affiliation(s)
- S S Kirthiga Devi
- Department of Regulatory Affairs, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana 500037, India
| | - Sidhartha Singh
- School of Bioscience and Bioengineering, D Y Patil International University, Akurdi, Pune 411044, India
| | - Ramesh Joga
- Department of Regulatory Affairs, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana 500037, India
| | - Sharvari Y Patil
- Department of Regulatory Affairs, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana 500037, India
| | - Vakalapudi Meghana Devi
- Department of Regulatory Affairs, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana 500037, India
| | - Sabnis Chetan Dushantrao
- Department of Regulatory Affairs, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana 500037, India
| | - Falguni Dwivedi
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana 500037, India
| | - Gautam Kumar
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana 500037, India
| | - Deepak Kumar Jindal
- Department of Pharmaceutical Sciences, Guru Jambheshwar University of Science & Technology, Hisar 125001, India
| | - Charan Singh
- Department of Pharmaceutical Sciences, School of Sciences, Hemvati Nandan Bahuguna Garhwal University (A Central University), Srinagar, Garhwal, Uttarakhand 246174, India
| | - Isha Dhamija
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana 500037, India
| | - Sandeep Kumar
- Department of Regulatory Affairs, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana 500037, India; Department of Pharmaceutics, NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan 303121, India.
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2
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Kuwata T. Molecular classification and intratumoral heterogeneity of gastric adenocarcinoma. Pathol Int 2024. [PMID: 38651937 DOI: 10.1111/pin.13427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 03/25/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024]
Abstract
Gastric cancers frequently harbor striking histological complexity and diversity between lesions as well as within single lesions, known as inter- and intratumoral heterogeneity, respectively. The latest World Health Organization Classification of Tumors designated more than 30 histological subtypes for gastric epithelial tumors, assigning 12 subtypes for gastric adenocarcinoma (GAD). Meanwhile, recent advances in genome-wide analyses have provided molecular aspects to the histological classification of GAD, and consequently revealed different molecular traits underlying these histological subtypes. Moreover, accumulating knowledge of comprehensive molecular profiles has led to establishing molecular classifications of GAD, which are often associated with clinical biomarkers for therapeutics and prognosis. However, most of our knowledge of GAD molecular profiles is based on inter-tumoral heterogeneity, and the molecular profiles underlying intratumoral heterogeneity are yet to be determined. In this review, recently established molecular classifications of GAD are introduced in the aspect of pathological diagnosis and are discussed in the context of intratumoral heterogeneity.
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Affiliation(s)
- Takeshi Kuwata
- Department of Genetic Medicine and Services, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
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3
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Challoner BR, Woolston A, Lau D, Buzzetti M, Fong C, Barber LJ, Anandappa G, Crux R, Assiotis I, Fenwick K, Begum R, Begum D, Lund T, Sivamanoharan N, Sansano HB, Domingo-Arada M, Tran A, Pandha H, Church D, Eccles B, Ellis R, Falk S, Hill M, Krell D, Murugaesu N, Nolan L, Potter V, Saunders M, Shiu KK, Guettler S, Alexander JL, Lázare-Iglesias H, Kinross J, Murphy J, von Loga K, Cunningham D, Chau I, Starling N, Ruiz-Bañobre J, Dhillon T, Gerlinger M. Genetic and immune landscape evolution in MMR-deficient colorectal cancer. J Pathol 2024; 262:226-239. [PMID: 37964706 DOI: 10.1002/path.6228] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/17/2023] [Accepted: 10/10/2023] [Indexed: 11/16/2023]
Abstract
Mismatch repair-deficient (MMRd) colorectal cancers (CRCs) have high mutation burdens, which make these tumours immunogenic and many respond to immune checkpoint inhibitors. The MMRd hypermutator phenotype may also promote intratumour heterogeneity (ITH) and cancer evolution. We applied multiregion sequencing and CD8 and programmed death ligand 1 (PD-L1) immunostaining to systematically investigate ITH and how genetic and immune landscapes coevolve. All cases had high truncal mutation burdens. Despite pervasive ITH, driver aberrations showed a clear hierarchy. Those in WNT/β-catenin, mitogen-activated protein kinase, and TGF-β receptor family genes were almost always truncal. Immune evasion (IE) drivers, such as inactivation of genes involved in antigen presentation or IFN-γ signalling, were predominantly subclonal and showed parallel evolution. These IE drivers have been implicated in immune checkpoint inhibitor resistance or sensitivity. Clonality assessments are therefore important for the development of predictive immunotherapy biomarkers in MMRd CRCs. Phylogenetic analysis identified three distinct patterns of IE driver evolution: pan-tumour evolution, subclonal evolution, and evolutionary stasis. These, but neither mutation burdens nor heterogeneity metrics, significantly correlated with T-cell densities, which were used as a surrogate marker of tumour immunogenicity. Furthermore, this revealed that genetic and T-cell infiltrates coevolve in MMRd CRCs. Low T-cell densities in the subgroup without any known IE drivers may indicate an, as yet unknown, IE mechanism. PD-L1 was expressed in the tumour microenvironment in most samples and correlated with T-cell densities. However, PD-L1 expression in cancer cells was independent of T-cell densities but strongly associated with loss of the intestinal homeobox transcription factor CDX2. This explains infrequent PD-L1 expression by cancer cells and may contribute to a higher recurrence risk of MMRd CRCs with impaired CDX2 expression. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
| | - Andrew Woolston
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - David Lau
- The Royal Marsden NHS Foundation Trust, London, UK
| | - Marta Buzzetti
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | - Louise J Barber
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | - Richard Crux
- The Royal Marsden NHS Foundation Trust, London, UK
| | | | | | | | - Dipa Begum
- The Institute of Cancer Research, London, UK
- The Royal Marsden NHS Foundation Trust, London, UK
| | - Tom Lund
- The Institute of Cancer Research, London, UK
- The Royal Marsden NHS Foundation Trust, London, UK
| | - Nanna Sivamanoharan
- The Institute of Cancer Research, London, UK
- The Royal Marsden NHS Foundation Trust, London, UK
| | | | | | - Amina Tran
- The Royal Marsden NHS Foundation Trust, London, UK
| | | | - David Church
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Bryony Eccles
- University Hospitals Dorset NHS Foundation Trust, Bournemouth, UK
| | | | - Stephen Falk
- University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Mark Hill
- Maidstone and Tunbridge Wells NHS Trust, Maidstone, UK
| | - Daniel Krell
- Royal Free London NHS Foundation Trust, London, UK
| | - Nirupa Murugaesu
- St George's University Hospitals NHS Foundation Trust, London, UK
- Genomics England, London, UK
| | - Luke Nolan
- Hampshire Hospitals NHS Foundation Trust, Winchester, UK
| | - Vanessa Potter
- University Hospitals Coventry and Warwickshire NHS Trust, Coventry, UK
| | | | - Kai-Keen Shiu
- University College London Hospitals NHS Foundation Trust, London, UK
| | | | | | | | | | - Jamie Murphy
- Imperial College Healthcare NHS Trust, London, UK
| | - Katharina von Loga
- The Institute of Cancer Research, London, UK
- The Royal Marsden NHS Foundation Trust, London, UK
| | | | - Ian Chau
- The Royal Marsden NHS Foundation Trust, London, UK
| | | | - Juan Ruiz-Bañobre
- University Clinical Hospital of Santiago de Compostela, Santiago de Compostela, Spain
- University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Tony Dhillon
- Royal Surrey Hospital NHS Foundation Trust, Guildford, UK
| | - Marco Gerlinger
- Barts Cancer Institute, Queen Mary University of London, London, UK
- St Bartholomew's Hospital Cancer Centre, London, UK
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Kobayashi G, Imai T, Sentani K. Distribution and Clinicopathological Features of Mott Cells (Plasma Cells Containing Russell Bodies) in Gastric Cancer: Presence of Mott Cells Is Associated with Favorable Prognosis. J Clin Med 2024; 13:658. [PMID: 38337351 PMCID: PMC10856670 DOI: 10.3390/jcm13030658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
Gastric cancer (GC) is still one of the leading causes of cancer-related mortality. We previously reported the relationship between histological heterogeneity of tumor cells and molecular features in GC. The tumor microenvironment also has a crucial role in GC progression and therapeutic resistance. In this study, we focused on the tumor microenvironment, especially inflammatory cells in GC. Using GC tissue slides, we investigated the distribution and clinicopathological significance of inflammatory cell counts including eosinophils, neutrophils, lymphocytes, and plasma cells. Additionally, we investigated the relationship between Mott cells (plasma cells containing Russell bodies) and clinicopathological features. In neoplastic gastric mucosa, a high number of plasma cells was associated with low T-grade, early stage, and good prognosis. We then focused on Mott cells and found that their presence in neoplastic gastric mucosa was associated with lower T and N grades, early stage, and Helicobacter pylori infection and was inversely associated with CD44 and EGFR expression. Additionally, the presence of Mott cells was associated with good prognosis in advanced GC and was an independent favorable prognostic predictor. The presence of Mott cells in GC might be one useful prognostic predictor, and Mott cells might have an important role in the carcinogenesis of H. pylori infection.
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Affiliation(s)
- Go Kobayashi
- Laboratory of Molecular Pathology, Department of Molecular Biosciences, Radiation Effects Research Foundation, Hiroshima 732-0815, Japan;
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Takeharu Imai
- Department of Surgical Oncology, Graduate School of Medicine Gifu University, Gifu 501-1194, Japan;
| | - Kazuhiro Sentani
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
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Fornaro L, Lonardi S, Catanese S, Nappo F, Pietrantonio F, Pellino A, Angerilli V, Signorini F, Salani F, Murgioni S, Neculaescu IA, Bruno R, Vivaldi C, Ricagno G, Masi G, Bergamo F, Ugolini C, Fassan M. Concordance of microsatellite instability and mismatch repair status in paired biopsies and surgical specimens of resectable gastroesophageal adenocarcinoma: time for a call to action. Gastric Cancer 2023; 26:958-968. [PMID: 37382783 DOI: 10.1007/s10120-023-01411-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/12/2023] [Indexed: 06/30/2023]
Abstract
BACKGROUND Reliability of mismatch repair proteins and microsatellite instability assessment is essential in order to define treatment strategy and identify candidates to immune checkpoint inhibitors in locally advanced gastroesophageal carcinoma. We evaluated the concordance of deficient mismatch repair (dMMR) and microsatellite instability-high (MSI-H) status between endoscopic biopsies and surgical specimens. METHODS Consecutive patients with resectable gastric or gastroesophageal junction adenocarcinoma classified as MSI-H/dMMR by polymerase chain reaction (PCR) or immunohistochemistry (IHC) and operated at three referral Institutions were included. The primary endpoint was the rate of concordance between biopsy and surgical samples. If needed, central revision by IHC/PCR was performed by specialized pathologists from coordinating Institutions. RESULTS Thirteen (19.7%) out of 66 patients showed discordant MSI-H/dMMR results in the original pathology reports. In most cases (11, 16.7%) this was due to the diagnosis of proficient mismatch repair status on biopsies. Among the ten cases available for central review, four were due to sample issues, four were reclassified as dMMR, one case showed dMMR status but was classified as microsatellite stable by PCR, one was linked to misdiagnosis of endoscopic biopsy by the local pathologist. Heterogeneity of mismatch repair proteins staining was observed in two cases. CONCLUSIONS Available methods can lead to conflicting results in MSI-H/dMMR evaluation between endoscopic biopsies and surgical samples of gastroesophageal adenocarcinoma. Strategies aiming to improve the reliability of assessment should be primarily focused on the optimization of tissue collection and management during endoscopy and adequate training of dedicated gastrointestinal pathologists within the multidisciplinary team.
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Affiliation(s)
- Lorenzo Fornaro
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy.
| | - Sara Lonardi
- Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy
| | - Silvia Catanese
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
- Unit of Medical Oncology, Ospedale Misericordia, Azienda Toscana Sud-Est, Grosseto, Italy
| | - Floriana Nappo
- Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy
| | - Filippo Pietrantonio
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Antonio Pellino
- Department of Oncology, Division of Medical Oncology, Azienda Toscana Nord Ovest, Livorno, Italy
| | - Valentina Angerilli
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, Padua, Italy
| | - Francesca Signorini
- Department of Surgical, Medical and Molecular Pathology and Critical Care Medicine, University of Pisa, Pisa, Italy
| | - Francesca Salani
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
- Institute of Interdisciplinary Research "Health Science", Scuola Superiore Sant'Anna, Pisa, Italy
| | - Sabina Murgioni
- Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy
| | | | - Rossella Bruno
- Unit of Pathology 3, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Caterina Vivaldi
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Gianmarco Ricagno
- Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy
| | - Gianluca Masi
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Francesca Bergamo
- Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy
| | - Clara Ugolini
- Department of Surgical, Medical and Molecular Pathology and Critical Care Medicine, University of Pisa, Pisa, Italy
| | - Matteo Fassan
- Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, Padua, Italy
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6
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Chen S, Zhou Z, Li Y, Du Y, Chen G. Application of single-cell sequencing to the research of tumor microenvironment. Front Immunol 2023; 14:1285540. [PMID: 37965341 PMCID: PMC10641410 DOI: 10.3389/fimmu.2023.1285540] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023] Open
Abstract
Single-cell sequencing is a technique for detecting and analyzing genomes, transcriptomes, and epigenomes at the single-cell level, which can detect cellular heterogeneity lost in conventional sequencing hybrid samples, and it has revolutionized our understanding of the genetic heterogeneity and complexity of tumor progression. Moreover, the tumor microenvironment (TME) plays a crucial role in the formation, development and response to treatment of tumors. The application of single-cell sequencing has ushered in a new age for the TME analysis, revealing not only the blueprint of the pan-cancer immune microenvironment, but also the heterogeneity and differentiation routes of immune cells, as well as predicting tumor prognosis. Thus, the combination of single-cell sequencing and the TME analysis provides a unique opportunity to unravel the molecular mechanisms underlying tumor development and progression. In this review, we summarize the recent advances in single-cell sequencing and the TME analysis, highlighting their potential applications in cancer research and clinical translation.
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Affiliation(s)
| | | | | | | | - Guoan Chen
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, China
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7
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Kobayashi Y, Niida A, Nagayama S, Saeki K, Haeno H, Takahashi KK, Hayashi S, Ozato Y, Saito H, Hasegawa T, Nakamura H, Tobo T, Kitagawa A, Sato K, Shimizu D, Hirata H, Hisamatsu Y, Toshima T, Yonemura Y, Masuda T, Mizuno S, Kawazu M, Kohsaka S, Ueno T, Mano H, Ishihara S, Uemura M, Mori M, Doki Y, Eguchi H, Oshima M, Suzuki Y, Shibata T, Mimori K. Subclonal accumulation of immune escape mechanisms in microsatellite instability-high colorectal cancers. Br J Cancer 2023; 129:1105-1118. [PMID: 37596408 PMCID: PMC10539316 DOI: 10.1038/s41416-023-02395-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 08/20/2023] Open
Abstract
BACKGROUND Intratumor heterogeneity (ITH) in microsatellite instability-high (MSI-H) colorectal cancer (CRC) has been poorly studied. We aimed to clarify how the ITH of MSI-H CRCs is generated in cancer evolution and how immune selective pressure affects ITH. METHODS We reanalyzed public whole-exome sequencing data on 246 MSI-H CRCs. In addition, we performed a multi-region analysis from 6 MSI-H CRCs. To verify the process of subclonal immune escape accumulation, a novel computational model of cancer evolution under immune pressure was developed. RESULTS Our analysis presented the enrichment of functional genomic alterations in antigen-presentation machinery (APM). Associative analysis of neoantigens indicated the generation of immune escape mechanisms via HLA alterations. Multiregion analysis revealed the clonal acquisition of driver mutations and subclonal accumulation of APM defects in MSI-H CRCs. Examination of variant allele frequencies demonstrated that subclonal mutations tend to be subjected to selective sweep. Computational simulations of tumour progression with the interaction of immune cells successfully verified the subclonal accumulation of immune escape mutations and suggested the efficacy of early initiation of an immune checkpoint inhibitor (ICI) -based treatment. CONCLUSIONS Our results demonstrate the heterogeneous acquisition of immune escape mechanisms in MSI-H CRCs by Darwinian selection, providing novel insights into ICI-based treatment strategies.
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Affiliation(s)
- Yuta Kobayashi
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka, 565-0871, Japan
| | - Atsushi Niida
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1, Sirokane-dai, Minato-Ku, Tokyo, 108-8639, Japan
| | - Satoshi Nagayama
- Gastroenterological Center, Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-Ku, Tokyo, 135-8550, Japan
- Department of Surgery, Uji-Tokushukai Medical Center, Kyoto, 611-0041, Japan
| | - Koichi Saeki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, 227-8561, Japan
| | - Hiroshi Haeno
- Division of Integrated Research, Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda City, Chiba, 278-0022, Japan
| | - Kazuki K Takahashi
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1, Sirokane-dai, Minato-Ku, Tokyo, 108-8639, Japan
| | - Shuto Hayashi
- Division of Systems Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yuki Ozato
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka, 565-0871, Japan
| | - Hideyuki Saito
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Takanori Hasegawa
- Division of Health Medical Data Science, Health Intelligence Center, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Hiromi Nakamura
- Division of Cancer Genomics, National Cancer Center Japan, Research Institute 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Taro Tobo
- Department of Pathology, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Akihiro Kitagawa
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka, 565-0871, Japan
| | - Kuniaki Sato
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
- Department of Head and Neck Surgery, National Hospital Organization Kyushu Cancer Center, Fukuoka, 811-1395, Japan
| | - Dai Shimizu
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Hidenari Hirata
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
- Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Yuichi Hisamatsu
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Takeo Toshima
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Yusuke Yonemura
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Takaaki Masuda
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Shinichi Mizuno
- Division of Cancer Research, Center for Advanced Medical Innovation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Masahito Kawazu
- Division of Cellular Signaling, National Cancer Center Japan, Research Institute 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Shinji Kohsaka
- Division of Cellular Signaling, National Cancer Center Japan, Research Institute 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Toshihide Ueno
- Division of Cellular Signaling, National Cancer Center Japan, Research Institute 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Japan, Research Institute 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Soichiro Ishihara
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Mamoru Uemura
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka, 565-0871, Japan
| | - Masaki Mori
- Faculty of Medicine, Tokai University, Isegahara, 259-1193, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka, 565-0871, Japan
| | - Hidetoshi Eguchi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka, 565-0871, Japan
| | - Masanobu Oshima
- Division of Genetics, Cancer Research Institute, Kanazawa University, Kadoma-Cho, Kanazawa, 920-1164, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Tatsuhiro Shibata
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1, Sirokane-dai, Minato-Ku, Tokyo, 108-8639, Japan
- Division of Cancer Genomics, National Cancer Center Japan, Research Institute 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan.
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Huang J, Zhao G, Peng Q, Yi X, Ji L, Li J, Li P, Guan Y, Ge J, Chen L, Chen R, Hu X, Lee W, Reuben A, Futreal PA, Xia X, Ma J, Zhang J, Chen Z. Analysis of genomic and immune intratumor heterogeneity in linitis plastica via multiregional exome and T-cell receptor sequencing. Mol Oncol 2023; 17:1531-1544. [PMID: 36703611 PMCID: PMC10399711 DOI: 10.1002/1878-0261.13381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 11/25/2022] [Accepted: 01/20/2023] [Indexed: 01/28/2023] Open
Abstract
The molecular landscape and the intratumor heterogeneity (ITH) architecture of gastric linitis plastica (LP) are poorly understood. We performed whole-exome sequencing (WES) and T-cell receptor (TCR) sequencing on 40 tumor regions from four LP patients. The landscape and ITH at the genomic and immunological levels in LP tumors were compared with multiple cancers that have previously been reported. The lymphocyte infiltration was further assessed by immunohistochemistry (IHC) in LP tumors. In total, we identified 6339 non-silent mutations from multi-samples, with a median tumor mutation burden (TMB) of 3.30 mutations per Mb, comparable to gastric adenocarcinoma from the Cancer Genome Atlas (TCGA) cohort (P = 0.53). An extremely high level of genomic ITH was observed, with only 12.42%, 5.37%, 5.35%, and 30.67% of mutations detectable across 10 regions within the same tumors of each patient, respectively. TCR sequencing revealed that TCR clonality was substantially lower in LP than in multi-cancers. IHC using antibodies against CD4, CD8, and PD-L1 demonstrated scant T-cell infiltration in the four LP tumors. Furthermore, profound TCR ITH was observed in all LP tumors, with no T-cell clones shared across tumor regions in any of the patients, while over 94% of T-cell clones were restricted to individual tumor regions. The Morisita overlap index (MOI) ranged from 0.21 to 0.66 among multi-regions within the same tumors, significantly lower than that of lung cancer (P = 0.002). Our results show that LP harbored extremely high genomic and TCR ITH and suppressed T-cell infiltration, suggesting a potential contribution to the frequent recurrence and poor therapeutic response of this adenocarcinoma.
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Affiliation(s)
- Jin Huang
- The Hunan Provincial Key Lab of Precision Diagnosis and Treatment for Gastrointestinal TumorXiangya Hospital, Central South UniversityChangshaHunanChina
- Department of Oncology, Xiangya HospitalXiangya HospitalCentral South UniversityChangshaChina
- Department of General Surgery, Xiangya HospitalCentral South UniversityChangshaChina
- International Joint Research Center of Minimally Invasive Endoscopic Technology Equipment & StandardizationChangshaChina
- National Clinical Research Center for Geriatric DisordersXiangya HospitalChangshaChina
| | - Guofeng Zhao
- Geneplus‐Beijing InstituteBeijingChina
- Geneplus‐BeijingBeijingChina
| | - Qiu Peng
- Cancer Research Institute, School of Basic Medical ScienceCentral South UniversityChangshaChina
| | - Xin Yi
- Geneplus‐Beijing InstituteBeijingChina
- Geneplus‐BeijingBeijingChina
| | - Liyan Ji
- Geneplus‐Beijing InstituteBeijingChina
- Geneplus‐BeijingBeijingChina
| | - Jing Li
- Geneplus‐Beijing InstituteBeijingChina
- Geneplus‐BeijingBeijingChina
| | - Pansong Li
- Geneplus‐Beijing InstituteBeijingChina
- Geneplus‐BeijingBeijingChina
| | - Yanfang Guan
- Geneplus‐Beijing InstituteBeijingChina
- Geneplus‐BeijingBeijingChina
| | - Jie Ge
- Department of General Surgery, Xiangya HospitalCentral South UniversityChangshaChina
| | - Ling Chen
- Department of General Surgery, Xiangya HospitalCentral South UniversityChangshaChina
| | - Runzhe Chen
- Department of Thoracic and Head and Neck Medical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
- Department of Genomic MedicineThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
| | - Xin Hu
- Department of Thoracic and Head and Neck Medical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
- Department of Genomic MedicineThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
| | - Won‐Chul Lee
- Department of Thoracic and Head and Neck Medical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
| | - Alexandre Reuben
- Department of Thoracic and Head and Neck Medical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
| | - P. Andrew Futreal
- Department of Genomic MedicineThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
| | | | - Jian Ma
- The Hunan Provincial Key Lab of Precision Diagnosis and Treatment for Gastrointestinal TumorXiangya Hospital, Central South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric DisordersXiangya HospitalChangshaChina
- Cancer Research Institute, School of Basic Medical ScienceCentral South UniversityChangshaChina
| | - Jianjun Zhang
- Department of Thoracic and Head and Neck Medical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
- Department of Genomic MedicineThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
| | - Zihua Chen
- The Hunan Provincial Key Lab of Precision Diagnosis and Treatment for Gastrointestinal TumorXiangya Hospital, Central South UniversityChangshaHunanChina
- Department of General Surgery, Xiangya HospitalCentral South UniversityChangshaChina
- International Joint Research Center of Minimally Invasive Endoscopic Technology Equipment & StandardizationChangshaChina
- National Clinical Research Center for Geriatric DisordersXiangya HospitalChangshaChina
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9
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Monahan KJ, Swinyard O, Latchford A. Biology of Precancers and Opportunities for Cancer Interception: Lesson from Colorectal Cancer Susceptibility Syndromes. Cancer Prev Res (Phila) 2023; 16:421-427. [PMID: 37001883 DOI: 10.1158/1940-6207.capr-22-0500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/28/2023] [Accepted: 03/28/2023] [Indexed: 04/04/2023]
Abstract
Hereditary gastrointestinal cancer is associated with molecular and neoplastic precursors which have revealed much about sporadic carcinogenesis. Therefore, an appreciation of constitutional and somatic events linked to these syndromes have provided a useful model for the development of risk models and preventative strategies. In this review, we focus of two of the best characterized syndromes, Lynch syndrome (LS) and familial adenomatous polyposis (FAP). Our understanding of the neoplasia-immune interaction in LS has contributed to the development of immune mediated therapies including cancer preventing vaccines and immunotherapy for cancer precursors. Chemoprevention in LS with aspirin and nonsteroidal anti-inflammatory drugs has also translated into clinical cancer, however the efficacy of such agents in FAP remains elusive when cancer is applied as an endpoint in trials rather than the use of 'indirect' endpoints such as polyp burden, and requires further elucidation of biological mechanisms in FAP. Finally, we review controversies in gastrointestinal surveillance for LS and FAP, including limitations and opportunities of upper and lower gastrointestinal endoscopy in the prevention and early detection of cancer.
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Affiliation(s)
- Kevin J Monahan
- Centre for Familial Intestinal Cancer, St. Marks Hospital & Imperial College, London, United Kingdom
| | - Ottilie Swinyard
- Evolution and Cancer Lab, Centre of Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
- Genomics and Evolutionary Dynamics Lab, Division of Molecular Pathology, Institute of Cancer Research, Sutton, London, United Kingdom
| | - Andrew Latchford
- Centre for Familial Intestinal Cancer, St. Marks Hospital & Imperial College, London, United Kingdom
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10
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Hui P, Ni F, Zheng L, Jia L, Wang Z. Identification of immunotherapy-related lncRNA signature for predicting prognosis, immunotherapy responses and drug candidates in bladder cancer. BMC Cancer 2023; 23:355. [PMID: 37072750 PMCID: PMC10111848 DOI: 10.1186/s12885-023-10828-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 04/08/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND Bladder cancer (BC) is one of the most common malignant diseases and the most common causes of cancer death worldwide. Immunotherapy has opened new avenues for precision treatment of bladder tumours, and immune checkpoint inhibitors (ICIs) have revolutionized the clinical treatment strategy of bladder tumours. In addition, long non-coding RNA (lncRNA) plays an important role in regulating tumour development and immunotherapy efficacy. METHODS We obtained genes with significant differences between anti-PD-L1 response and non-response from the Imvogor210 data set and combined with the bladder cancer expression data in the TCGA cohort to obtain immunotherapy-related lncRNA. Based on these lncRNAs, the prognostic risk model of bladder cancer was constructed and verified by GEO external data set. The characterization of immune cell infiltration and immunotherapy effects between high-risk and low-risk groups were then analysed. We predicted the ceRNA network and performed molecular docking of key target proteins. The functional experiments verified the function of SBF2-AS1. RESULTS Three immunotherapy-related lncRNAs were identified as independent prognostic biomarkers for bladder cancer and a prognostic model of immunotherapy-related prognosis was constructed. Prognosis, immune cell infiltration, and immunotherapy efficacy were significantly different between high- and low-risk groups based on risk scores. Additionally, we established a ceRNA network of lncRNA(SBF2-AS1)-miRNA(has-miR-582-5p)-mRNA (HNRNPA2B1). Targeting the protein HNRNPA2B1 identified the top eight small molecule drugs with the highest affinity. CONCLUSION We developed a prognostic risk score model based on immune-therapy-related lncRNA, which was subsequently determined to be significantly associated with immune cell infiltration and immunotherapy response. This study not only helps to promote our understanding of immunotherapy-related lncRNA in the prognosis of BC, but also provides new ideas for clinical immunotherapy and the development of novel therapeutic drugs for patients.
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Affiliation(s)
- Pengyu Hui
- Department of Urology, The Second Affiliated Hospital of Xi'an Medical University, No.167 Fangzhicheng East Road, Baqiao District, Xi'an, Shaanxi, 710038, China
| | - Feng Ni
- Department of Urology, The Second Affiliated Hospital of Xi'an Medical University, No.167 Fangzhicheng East Road, Baqiao District, Xi'an, Shaanxi, 710038, China
| | - Liang Zheng
- Department of Urology, The Second Affiliated Hospital of Xi'an Medical University, No.167 Fangzhicheng East Road, Baqiao District, Xi'an, Shaanxi, 710038, China
| | - Lei Jia
- Department of Urology, The Second Affiliated Hospital of Xi'an Medical University, No.167 Fangzhicheng East Road, Baqiao District, Xi'an, Shaanxi, 710038, China
| | - Zhe Wang
- Department of Urology, Cancer Hospital of China Medical University, No.44 Xiaoheyan Road, Dadong District, Shenyang, 110042, Liaoning, China.
- Department of Urology, Liaoning Cancer Hospital & Institute, No.44 Xiaoheyan Road, Dadong District, Shenyang, 110042, Liaoning, China.
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11
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Tang Z, Gu Y, Shi Z, Min L, Zhang Z, Zhou P, Luo R, Wang Y, Cui Y, Sun Y, Wang X. Multiplex immune profiling reveals the role of serum immune proteomics in predicting response to preoperative chemotherapy of gastric cancer. Cell Rep Med 2023; 4:100931. [PMID: 36724786 PMCID: PMC9975277 DOI: 10.1016/j.xcrm.2023.100931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/23/2022] [Accepted: 01/11/2023] [Indexed: 02/03/2023]
Abstract
Responses toward preoperative chemotherapy are heterogeneous in patients with gastric adenocarcinoma. Existing studies in the field focus heavily on the tumor microenvironment (TME), whereas little is known about the relationship between systemic immunity and chemotherapy response. In this study, we collect serum samples from patients with gastric adenocarcinoma before, on, and after preoperative chemotherapy and study their immune proteomics using an antibody-based proteomics panel. We also collect surgically resected tumor samples and incorporate multiple methods to assess their TME. We find that both local and systemic immune features are associated with treatment response. Preoperative chemotherapy induces a sophisticated systemic immune response indicated by dynamic serum immune proteomics. A pretreatment serum protein scoring system is established for response prediction. Together, these findings highlight the fundamental but largely underestimated role of systemic immunity in the treatment of gastric cancer, suggesting a patient stratification strategy based on pretreatment serum immune proteomics.
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Affiliation(s)
- Zhaoqing Tang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Gastric Cancer Center, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Department of General Surgery, Zhongshan Hospital (Xiamen), Fudan University, Shanghai 200032, China
| | - Yuan Gu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Zhongyi Shi
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Lingqiang Min
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Ziwei Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Peng Zhou
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Rongkui Luo
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yan Wang
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yuehong Cui
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai 200032, China.
| | - Yihong Sun
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Gastric Cancer Center, Zhongshan Hospital, Fudan University, Shanghai 200032, China.
| | - Xuefei Wang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Gastric Cancer Center, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Department of General Surgery, Zhongshan Hospital (Xiamen), Fudan University, Shanghai 200032, China.
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12
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Boutin M, Gill S. Controversies and management of deficient mismatch repair gastrointestinal cancers in the neoadjuvant setting. Ther Adv Med Oncol 2023; 15:17588359231162577. [PMID: 37007634 PMCID: PMC10064478 DOI: 10.1177/17588359231162577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 02/17/2023] [Indexed: 03/31/2023] Open
Abstract
High microsatellite instability (MSI-H)/deficient mismatch repair (dMMR) phenotype is a distinct molecular signature across gastrointestinal cancers characterized by high tumor mutational burden and high neoantigen load. Tumors harboring dMMR are highly immunogenic and heavily infiltrated by immune cells; consequently, they are uniquely vulnerable to therapeutic strategies enhancing immune antitumor response such as checkpoint inhibitors. The MSI-H/dMMR phenotype arose as a powerful predictor of response to immune checkpoint inhibitors with evidence supporting significantly improved outcomes in the metastatic setting. On the other hand, the genomic instability characteristic of MSI-H/dMMR tumors appears to be associated with decreased sensitivity to chemotherapy, and the benefits of standard adjuvant or neoadjuvant chemotherapy approaches in this subtype are being increasingly questioned. Here, we review the prognostic and predictive impact of MMR status in localized gastric and colorectal cancers, and highlight the emerging clinical data incorporating checkpoint inhibitors in the neoadjuvant setting.
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Affiliation(s)
- Mélina Boutin
- BC Cancer, University of British Columbia, Vancouver, BC, Canada
- Centre Intégré de Cancérologie de la Montérégie-Centre, Université de Sherbrooke, Greenfield Park, QC, Canada
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13
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Relationships of tumor differentiation and immune infiltration in gastric cancers revealed by single-cell RNA-seq analyses. Cell Mol Life Sci 2023; 80:57. [PMID: 36729271 PMCID: PMC9894979 DOI: 10.1007/s00018-023-04702-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/08/2023] [Accepted: 01/17/2023] [Indexed: 02/03/2023]
Abstract
Gastric cancers are highly heterogeneous malignant tumors. To reveal the relationship between differentiation status of cancer cells and tumor immune microenvironments in gastric cancer, single-cell RNA-sequencing was performed on normal mucosa tissue, differentiated gastric cancer (DGC) tissue, poorly differentiated gastric cancer (PDGC) tissue and neuroendocrine carcinoma (NEC) tissue sampled from surgically resected gastric cancer specimens. We identified the signature genes for both DGC and PDGC, and found that signature genes of PDGC strongly enriched in the epithelial-mesenchymal transition (EMT) program. Furthermore, we found that DGC tends to be immune-rich type whereas PDGC tends to be immune-poor type defined according to the density of tumor-infiltrating CD8+ T cells. Additionally, interferon alpha and gamma responding genes were specifically expressed in the immune-rich malignant cells compared with immune-poor malignant cells. Through analyzing the mixed adenoneuroendocrine carcinoma, we identified intermediate state malignant cells during the trans-differentiation process from DGC to NEC, which showed double-negative expressions of both DGC marker genes and NEC marker genes. Interferon-related pathways were gradually downregulated along the DGC to NEC trans-differentiation path, which was accompanied by reduced CD8+ cytotoxic T-cell infiltration. In summary, molecular features of both malignant cells and immune microenvironment cells of DGC, PDGC and NEC were systematically revealed, which may partially explain the strong tumor heterogeneities of gastric cancer. Especially along the DGC to NEC trans-differentiation path, immune-evasion was gradually enhanced with the decreasing activities of interferon pathway responses in malignant cells.
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14
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Chen B, Xi Y, Zhao J, Hong Y, Tian S, Zhai X, Chen Q, Ren X, Fan L, Xie X, Jiang C. m5C regulator-mediated modification patterns and tumor microenvironment infiltration characterization in colorectal cancer: One step closer to precision medicine. Front Immunol 2022; 13:1049435. [PMID: 36532062 PMCID: PMC9751490 DOI: 10.3389/fimmu.2022.1049435] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/09/2022] [Indexed: 12/04/2022] Open
Abstract
Background The RNA modification 5-methylcytosine (m5C) is one of the most prevalent post-transcriptional modifications, with increasing evidence demonstrating its extensive involvement in the tumorigenesis and progression of various cancers. Colorectal cancer (CRC) is the third most common cancer and second leading cause of cancer-related deaths worldwide. However, the role of m5C modulators in shaping tumor microenvironment (TME) heterogeneity and regulating immune cell infiltration in CRC requires further clarification. Results The transcriptomic sequencing data of 18 m5C regulators and clinical data of patients with CRC were obtained from The Cancer Genome Atlas (TCGA) and systematically evaluated. We found that 16 m5C regulators were differentially expressed between CRC and normal tissues. Unsupervised cluster analysis was then performed and revealed two distinct m5C modification patterns that yielded different clinical prognoses and biological functions in CRC. We demonstrated that the m5C score constructed from eight m5C-related genes showed excellent prognostic performance, with a subsequent independent analysis confirming its predictive ability in the CRC cohort. Then we developed a nomogram containing five clinical risk factors and the m5C risk score and found that the m5C score exhibited high prognostic prediction accuracy and favorable clinical applicability. Moreover, the CRC patients with low m5C score were characterized by "hot" TME exhibiting increased immune cell infiltration and higher immune checkpoint expression. These characteristics were highlighted as potential identifiers of suitable candidates for anticancer immunotherapy. Although the high m5C score represented the non-inflammatory phenotype, the CRC patients in this group exhibited high level of sensitivity to molecular-targeted therapy. Conclusion Our comprehensive analysis indicated that the novel m5C clusters and scoring system accurately reflected the distinct prognostic signature, clinicopathological characteristics, immunological phenotypes, and stratifying therapeutic opportunities of CRC. Our findings, therefore, offer valuable insights into factors that may be targeted in the development of precision medicine-based therapeutic strategies for CRC.
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Affiliation(s)
- Baoxiang Chen
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China,Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University), Wuhan, China,Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University), Wuhan, China
| | - Yiqing Xi
- Department of Breast and Thyroid Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jianhong Zhao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China,Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, China
| | - Yuntian Hong
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China,Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University), Wuhan, China,Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University), Wuhan, China
| | - Shunhua Tian
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China,Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University), Wuhan, China,Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University), Wuhan, China
| | - Xiang Zhai
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China,Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University), Wuhan, China,Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University), Wuhan, China
| | - Quanjiao Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, CAS Center for Influenza Research and Early Warning, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Xianghai Ren
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China,Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University), Wuhan, China,Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University), Wuhan, China,*Correspondence: Congqing Jiang, ; Xiaoyu Xie, ; Lifang Fan, ; Xianghai Ren,
| | - Lifang Fan
- Department of Pathology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,*Correspondence: Congqing Jiang, ; Xiaoyu Xie, ; Lifang Fan, ; Xianghai Ren,
| | - Xiaoyu Xie
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China,Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University), Wuhan, China,Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University), Wuhan, China,*Correspondence: Congqing Jiang, ; Xiaoyu Xie, ; Lifang Fan, ; Xianghai Ren,
| | - Congqing Jiang
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China,Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University), Wuhan, China,Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University), Wuhan, China,*Correspondence: Congqing Jiang, ; Xiaoyu Xie, ; Lifang Fan, ; Xianghai Ren,
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15
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Zhou X, Ni Y, Liang X, Lin Y, An B, He X, Zhao X. Mechanisms of tumor resistance to immune checkpoint blockade and combination strategies to overcome resistance. Front Immunol 2022; 13:915094. [PMID: 36189283 PMCID: PMC9520263 DOI: 10.3389/fimmu.2022.915094] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 08/19/2022] [Indexed: 11/24/2022] Open
Abstract
Immune checkpoint blockade (ICB) has rapidly transformed the treatment paradigm for various cancer types. Multiple single or combinations of ICB treatments have been approved by the US Food and Drug Administration, providing more options for patients with advanced cancer. However, most patients could not benefit from these immunotherapies due to primary and acquired drug resistance. Thus, a better understanding of the mechanisms of ICB resistance is urgently needed to improve clinical outcomes. Here, we focused on the changes in the biological functions of CD8+ T cells to elucidate the underlying resistance mechanisms of ICB therapies and summarized the advanced coping strategies to increase ICB efficacy. Combinational ICB approaches and individualized immunotherapies require further in-depth investigation to facilitate longer-lasting efficacy and a more excellent safety of ICB in a broader range of patients.
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16
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Zhao H, Xie R, Zhang C, Lu G, Kong H. Pan-cancer analysis of prognostic and immunological role of DTYMK in human tumors. Front Genet 2022; 13:989460. [PMID: 36159971 PMCID: PMC9493117 DOI: 10.3389/fgene.2022.989460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/22/2022] [Indexed: 12/03/2022] Open
Abstract
Background: Deoxythymidylate kinase (DTYMK) has been reported to correlate with the progression of hepatocellular carcinoma. However, the role of DTYMK in human cancers is not studied. In this study, we studied the prognostic value, functional states, and correlations with immune infiltration of DTYMK in human cancers. Methods: The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), UALCAN, Clinical Proteomic Tumor Analysis Consortium (CPTAC), the search tool for the retrieval of interacting genes (STRING), GeneMANIA, cBioPortal, Cancer Single-cell State Atlas (CancerSEA), and Tumor IMmune Estimation Resource (TIMER) databases were utilized to analyze DTYMK in cancers. Results: In general, DTYMK is abnormally expressed between most human cancer and normal tissues from a pan-cancer perspective. DTYMK can be used as a diagnostic biomarker to differentiate tumor tissues from normal tissues in most tumors. Upregulation of DTYMK predicted poor survival status in most cancer types in TCGA. Moreover, DTYMK expression was correlated with the T stage in ACC, BRCA, KIRC, LIHC, and LUAD, with the N stage in BLCA, HNSC, KICH, KIRC, LUAD, LUSC, and THCA, with the M stage in ACC, KIRC, KIRP, and LUAD, with TNM stage in ACC, KIRC, LIHC, LUAD, and LUSC. In addition, based on single-cell sequencing data, we concluded that the expression of DTYMK was correlated with the functional status of the cell cycle, DNA damage, DNA repair, invasion, EMT, and proliferation. Finally, DTYMK expression was correlated with six infiltrating immune cells, including B cells, CD4+ T cells, CD8+ T cells, neutrophils, macrophages, and dendritic cells by investigating TIMER. Conclusion: Our findings suggested that abnormally expressed DTYMK was correlated with poor survival, malignant functional status, and immune infiltrates. DTYMK might be served as a potential biomarker for diagnosis and poor prognosis in various cancer types. DTYMK might act as a potential target for immune therapy.
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Affiliation(s)
- Huihui Zhao
- Department of Oncology, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Rongrong Xie
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chenxi Zhang
- Central Laboratory, Nanjing Chest Hospital, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, China
| | - Guojun Lu
- Department of Respiratory Medicine, Nanjing Chest Hospital, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, China
- *Correspondence: Guojun Lu, ; Hui Kong,
| | - Hui Kong
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Guojun Lu, ; Hui Kong,
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17
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Khatib SA, Ma L, Dang H, Forgues M, Chung JY, Ylaya K, Hewitt SM, Chaisaingmongkol J, Rucchirawat M, Wang XW. Single-cell biology uncovers apoptotic cell death and its spatial organization as a potential modifier of tumor diversity in HCC. Hepatology 2022; 76:599-611. [PMID: 35034369 DOI: 10.1002/hep.32345] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND AIMS HCC is a highly aggressive and heterogeneous cancer type with limited treatment options. Identifying drivers of tumor heterogeneity may lead to better therapeutic options and favorable patient outcomes. We investigated whether apoptotic cell death and its spatial architecture is linked to tumor molecular heterogeneity using single-cell in situ hybridization analysis. APPROACH AND RESULTS We analyzed 254 tumor samples from two HCC cohorts using tissue microarrays. We developed a mathematical model to quantify cellular diversity among HCC samples using two tumor markers, cyclin-dependent kinase inhibitor 3 and protein regulator of cytokinesis 1 as surrogates for heterogeneity and caspase 3 (CASP3) as an apoptotic cell death marker. We further explored the impact of potential dying-cell hubs on tumor cell diversity and patient outcome by density contour mapping and spatial proximity analysis. We also developed a selectively controlled in vitro model of cell death using CRISPR/CRISPR-associated 9 to determine therapy response and growth under hypoxic conditions. We found that increasing levels of CASP3+ tumor cells are associated with higher tumor diversity. Interestingly, we discovered regions of densely populated CASP3+ , which we refer to as CASP3+ cell islands, in which the nearby cellular heterogeneity was found to be the greatest compared to cells farther away from these islands and that this phenomenon was associated with survival. Additionally, cell culture experiments revealed that higher levels of cell death, accompanied by increased CASP3 expression, led to greater therapy resistance and growth under hypoxia. CONCLUSIONS These results are consistent with the hypothesis that increased apoptotic cell death may lead to greater tumor heterogeneity and thus worse patient outcomes.
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Affiliation(s)
- Subreen A Khatib
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA.,Department of Tumor Biology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Lichun Ma
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Hien Dang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA.,Division of Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Marshonna Forgues
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Joon-Yong Chung
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Kris Ylaya
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Stephen M Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Jittporn Chaisaingmongkol
- Laboratory of Chemical Carcinogenesis, Chulabhorn Research Institute, Bangkok, Thailand.,Center of Excellence on Environmental Health and Toxicology, Office of the Higher Education Commission, Ministry of Education, Bangkok, Thailand
| | - Mathuros Rucchirawat
- Laboratory of Chemical Carcinogenesis, Chulabhorn Research Institute, Bangkok, Thailand.,Center of Excellence on Environmental Health and Toxicology, Office of the Higher Education Commission, Ministry of Education, Bangkok, Thailand
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA.,Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
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18
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van den Bosch T, Vermeulen L, Miedema DM. Quantitative models for the inference of intratumor heterogeneity. COMPUTATIONAL AND SYSTEMS ONCOLOGY 2022. [DOI: 10.1002/cso2.1034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Tom van den Bosch
- Laboratory for Experimental Oncology and Radiobiology Center for Experimental and Molecular Medicine Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism Amsterdam University Medical Centers Amsterdam The Netherlands
- Oncode Institute Amsterdam The Netherlands
| | - Louis Vermeulen
- Laboratory for Experimental Oncology and Radiobiology Center for Experimental and Molecular Medicine Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism Amsterdam University Medical Centers Amsterdam The Netherlands
- Oncode Institute Amsterdam The Netherlands
| | - Daniël M. Miedema
- Laboratory for Experimental Oncology and Radiobiology Center for Experimental and Molecular Medicine Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism Amsterdam University Medical Centers Amsterdam The Netherlands
- Oncode Institute Amsterdam The Netherlands
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19
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Jia Q, Wang A, Yuan Y, Zhu B, Long H. Heterogeneity of the tumor immune microenvironment and its clinical relevance. Exp Hematol Oncol 2022; 11:24. [PMID: 35461288 PMCID: PMC9034473 DOI: 10.1186/s40164-022-00277-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/10/2022] [Indexed: 02/08/2023] Open
Abstract
During the course of tumorigenesis and subsequent metastasis, malignant cells gradually diversify and become more heterogeneous. Consequently, the tumor mass might be infiltrated by diverse immune-related components, including the cytokine/chemokine environment, cytotoxic activity, or immunosuppressive elements. This immunological heterogeneity is universally presented spatially or varies temporally along with tumor evolution or therapeutic intervention across almost all solid tumors. The heterogeneity of anti-tumor immunity shows a profound association with the progression of disease and responsiveness to treatment, particularly in the realm of immunotherapy. Therefore, an accurate understanding of tumor immunological heterogeneity is essential for the development of effective therapies. Facilitated by multi-regional and -omics sequencing, single cell sequencing, and longitudinal liquid biopsy approaches, recent studies have demonstrated the potential to investigate the complexity of immunological heterogeneity of the tumors and its clinical relevance in immunotherapy. Here, we aimed to review the mechanism underlying the heterogeneity of the immune microenvironment. We also explored how clinical assessments of tumor heterogeneity might facilitate the development of more effective personalized therapies.
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Affiliation(s)
- Qingzhu Jia
- Institute of Cancer, Xinqiao Hospital, Army Military Medical University, Xinqiao Main Street, Chongqing, 400037, China.,Chongqing Key Laboratory of Immunotherapy, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Aoyun Wang
- Institute of Cancer, Xinqiao Hospital, Army Military Medical University, Xinqiao Main Street, Chongqing, 400037, China.,Chongqing Key Laboratory of Immunotherapy, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Yixiao Yuan
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, 650118, China
| | - Bo Zhu
- Institute of Cancer, Xinqiao Hospital, Army Military Medical University, Xinqiao Main Street, Chongqing, 400037, China. .,Chongqing Key Laboratory of Immunotherapy, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China.
| | - Haixia Long
- Institute of Cancer, Xinqiao Hospital, Army Military Medical University, Xinqiao Main Street, Chongqing, 400037, China. .,Chongqing Key Laboratory of Immunotherapy, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China.
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20
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Ouellette TW, Awadalla P. Inferring ongoing cancer evolution from single tumour biopsies using synthetic supervised learning. PLoS Comput Biol 2022; 18:e1010007. [PMID: 35482653 PMCID: PMC9049314 DOI: 10.1371/journal.pcbi.1010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/09/2022] [Indexed: 11/18/2022] Open
Abstract
Variant allele frequencies (VAF) encode ongoing evolution and subclonal selection in growing tumours. However, existing methods that utilize VAF information for cancer evolutionary inference are compressive, slow, or incorrectly specify the underlying cancer evolutionary dynamics. Here, we provide a proof-of-principle synthetic supervised learning method, TumE, that integrates simulated models of cancer evolution with Bayesian neural networks, to infer ongoing selection in bulk-sequenced single tumour biopsies. Analyses in synthetic and patient tumours show that TumE significantly improves both accuracy and inference time per sample when detecting positive selection, deconvoluting selected subclonal populations, and estimating subclone frequency. Importantly, we show how transfer learning can leverage stored knowledge within TumE models for related evolutionary inference tasks-substantially reducing data and computational time for further model development and providing a library of recyclable deep learning models for the cancer evolution community. This extensible framework provides a foundation and future directions for harnessing progressive computational methods for the benefit of cancer genomics and, in turn, the cancer patient.
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Affiliation(s)
- Tom W. Ouellette
- Ontario Institute for Cancer Research, Department of Computational Biology, Toronto, Ontario, Canada
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Philip Awadalla
- Ontario Institute for Cancer Research, Department of Computational Biology, Toronto, Ontario, Canada
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
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21
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Noble R, Burri D, Le Sueur C, Lemant J, Viossat Y, Kather JN, Beerenwinkel N. Spatial structure governs the mode of tumour evolution. Nat Ecol Evol 2022; 6:207-217. [PMID: 34949822 PMCID: PMC8825284 DOI: 10.1038/s41559-021-01615-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/10/2021] [Indexed: 12/12/2022]
Abstract
Characterizing the mode-the way, manner or pattern-of evolution in tumours is important for clinical forecasting and optimizing cancer treatment. Sequencing studies have inferred various modes, including branching, punctuated and neutral evolution, but it is unclear why a particular pattern predominates in any given tumour. Here we propose that tumour architecture is key to explaining the variety of observed genetic patterns. We examine this hypothesis using spatially explicit population genetics models and demonstrate that, within biologically relevant parameter ranges, different spatial structures can generate four tumour evolutionary modes: rapid clonal expansion, progressive diversification, branching evolution and effectively almost neutral evolution. Quantitative indices for describing and classifying these evolutionary modes are presented. Using these indices, we show that our model predictions are consistent with empirical observations for cancer types with corresponding spatial structures. The manner of cell dispersal and the range of cell-cell interactions are found to be essential factors in accurately characterizing, forecasting and controlling tumour evolution.
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Affiliation(s)
- Robert Noble
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland. .,SIB Swiss Institute of Bioinformatics, Basel, Switzerland. .,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland. .,Department of Mathematics, City, University of London, London, UK.
| | - Dominik Burri
- grid.5801.c0000 0001 2156 2780Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland ,grid.6612.30000 0004 1937 0642Biozentrum, University of Basel, Basel, Switzerland
| | - Cécile Le Sueur
- grid.5801.c0000 0001 2156 2780Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Jeanne Lemant
- grid.5801.c0000 0001 2156 2780Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Yannick Viossat
- grid.11024.360000000120977052Ceremade, Université Paris Dauphine-PSL, Paris, France
| | - Jakob Nikolas Kather
- grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Applied Tumor Immunity, German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.412301.50000 0000 8653 1507Internal Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland. .,SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
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22
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Röcken C, Amallraja A, Halske C, Opasic L, Traulsen A, Behrens HM, Krüger S, Liu A, Haag J, Egberts JH, Rosenstiel P, Meißner T. Multiscale heterogeneity in gastric adenocarcinoma evolution is an obstacle to precision medicine. Genome Med 2021; 13:177. [PMID: 34749812 PMCID: PMC8576943 DOI: 10.1186/s13073-021-00975-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 09/22/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Cancer is a somatic evolutionary disease and adenocarcinomas of the stomach and gastroesophageal junction (GC) may serve as a two-dimensional model of cancer expansion, in which tumor subclones are not evenly mixed during tumor progression but rather spatially separated and diversified. We hypothesize that precision medicine efforts are compromised when clinical decisions are based on a single-sample analysis, which ignores the mechanisms of cancer evolution and resulting intratumoral heterogeneity. Using multiregional whole-exome sequencing, we investigated the effect of somatic evolution on intratumoral heterogeneity aiming to shed light on the evolutionary biology of GC. METHODS The study comprised a prospective discovery cohort of 9 and a validation cohort of 463 GCs. Multiregional whole-exome sequencing was performed using samples form 45 primary tumors and 3 lymph node metastases (range 3-10 tumor samples/patient) of the discovery cohort. RESULTS In total, the discovery cohort harbored 16,537 non-synonymous mutations. Intratumoral heterogeneity of somatic mutations and copy number variants were present in all tumors of the discovery cohort. Of the non-synonymous mutations, 53-91% were not present in each patient's sample; 399 genes harbored 2-4 different non-synonymous mutations in the same patient; 175 genes showed copy number variations, the majority being heterogeneous, including CD274 (PD-L1). Multi-sample tree-based analyses provided evidence for branched evolution being most complex in a microsatellite instable GC. The analysis of the mode of evolution showed a high degree of heterogeneity in deviation from neutrality within each tumor. We found evidence of parallel evolution and evolutionary trajectories: different mutations of SMAD4 aligned with different subclones and were found only in TP53 mutant GCs. CONCLUSIONS Neutral and non-neutral somatic evolution shape the mutational landscape in GC along its lateral expansions. It leads to complex spatial intratumoral heterogeneity, where lymph node metastases may stem from different areas of the primary tumor, synchronously. Our findings may have profound effects on future patient management. They illustrate the risk of mis-interpreting tumor genetics based on single-sample analysis and open new avenues for an evolutionary classification of GC, i.e., the discovery of distinct evolutionary trajectories which can be utilized for precision medicine.
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Affiliation(s)
- Christoph Röcken
- Department of Pathology, Christian-Albrechts-University, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Arnold-Heller-Str. 3, Haus U33, D-24105, Kiel, Germany.
- Institute for Clinical Molecular Biology, Christian-Albrechts-University, 24105, Kiel, Germany.
| | - Anu Amallraja
- Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, USA
| | - Christine Halske
- Department of Pathology, Christian-Albrechts-University, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Arnold-Heller-Str. 3, Haus U33, D-24105, Kiel, Germany
| | - Luka Opasic
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Arne Traulsen
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Hans-Michael Behrens
- Department of Pathology, Christian-Albrechts-University, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Arnold-Heller-Str. 3, Haus U33, D-24105, Kiel, Germany
| | - Sandra Krüger
- Department of Pathology, Christian-Albrechts-University, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Arnold-Heller-Str. 3, Haus U33, D-24105, Kiel, Germany
| | - Anne Liu
- Department of Pathology, Christian-Albrechts-University, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Arnold-Heller-Str. 3, Haus U33, D-24105, Kiel, Germany
| | - Jochen Haag
- Department of Pathology, Christian-Albrechts-University, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Arnold-Heller-Str. 3, Haus U33, D-24105, Kiel, Germany
| | - Jan-Hendrik Egberts
- Department of General Surgery, Visceral, Thoracic, Transplantation and Pediatric Surgery, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Kiel, Germany
| | - Philip Rosenstiel
- Department of General Surgery, Visceral, Thoracic, Transplantation and Pediatric Surgery, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Kiel, Germany
| | - Tobias Meißner
- Institute for Clinical Molecular Biology, Christian-Albrechts-University, 24105, Kiel, Germany
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23
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Sundar R, Liu DHW, Hutchins GGA, Slaney HL, Silva ANS, Oosting J, Hayden JD, Hewitt LC, Ng CCY, Mangalvedhekar A, Ng SB, Tan IBH, Tan P, Grabsch HI. Spatial profiling of gastric cancer patient-matched primary and locoregional metastases reveals principles of tumour dissemination. Gut 2021; 70:1823-1832. [PMID: 33229445 PMCID: PMC8458060 DOI: 10.1136/gutjnl-2020-320805] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Endoscopic mucosal biopsies of primary gastric cancers (GCs) are used to guide diagnosis, biomarker testing and treatment. Spatial intratumoural heterogeneity (ITH) may influence biopsy-derived information. We aimed to study ITH of primary GCs and matched lymph node metastasis (LNmet). DESIGN GC resection samples were annotated to identify primary tumour superficial (PTsup), primary tumour deep (PTdeep) and LNmet subregions. For each subregion, we determined (1) transcriptomic profiles (NanoString 'PanCancer Progression Panel', 770 genes); (2) next-generation sequencing (NGS, 225 gastrointestinal cancer-related genes); (3) DNA copy number profiles by multiplex ligation-dependent probe amplification (MLPA, 16 genes); and (4) histomorphological phenotypes. RESULTS NanoString profiling of 64 GCs revealed no differences between PTsup1 and PTsup2, while 43% of genes were differentially expressed between PTsup versus PTdeep and 38% in PTsup versus LNmet. Only 16% of genes were differently expressed between PTdeep and LNmet. Several genes with therapeutic potential (eg IGF1, PIK3CD and TGFB1) were overexpressed in LNmet and PTdeep compared with PTsup. NGS data revealed orthogonal support of NanoString results with 40% mutations present in PTdeep and/or LNmet, but not in PTsup. Conversely, only 6% of mutations were present in PTsup and were absent in PTdeep and LNmet. MLPA demonstrated significant ITH between subregions and progressive genomic changes from PTsup to PTdeep/LNmet. CONCLUSION In GC, regional lymph node metastases are likely to originate from deeper subregions of the primary tumour. Future clinical trials of novel targeted therapies must consider assessment of deeper subregions of the primary tumour and/or metastases as several therapeutically relevant genes are only mutated, overexpressed or amplified in these regions.
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Affiliation(s)
- Raghav Sundar
- Department of Haematology-Oncology, National University Cancer Institute Singapore, National University Health System, Singapore,Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore,Yong Loo Lin School of Medicine, National University of Singapore, Singapore,The N.1 Institute for Health, National University of Singapore, Singapore
| | - Drolaiz HW Liu
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Gordon GA Hutchins
- Division of Pathology and Data Analytics, Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, West Yorkshire, UK
| | - Hayley L Slaney
- Division of Pathology and Data Analytics, Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, West Yorkshire, UK
| | - Arnaldo NS Silva
- Division of Pathology and Data Analytics, Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, West Yorkshire, UK,Department of Surgery, University of Cambridge, Cambridge University Hospitals, Addenbrookes, Cambridge, UK
| | - Jan Oosting
- Department of Pathology, Leiden University Medical Center, Leiden, Zuid-Holland, The Netherlands
| | - Jeremy D Hayden
- Department of Upper Gastrointestinal Surgery, Institute of Oncology, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Lindsay C Hewitt
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Cedric CY Ng
- Laboratory of Cancer Epigenome, Department of Medical Sciences, National Cancer Centre Singapore, Singapore
| | | | - Sarah B Ng
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Iain BH Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore,Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Patrick Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore .,Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Heike I Grabsch
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht, The Netherlands .,Division of Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, West Yorkshire, UK
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24
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Hoppe S, Jonas C, Wenzel MC, Velazquez Camacho O, Arolt C, Zhao Y, Büttner R, Quaas A, Plum PS, Hillmer AM. Genomic and Transcriptomic Characteristics of Esophageal Adenocarcinoma. Cancers (Basel) 2021; 13:cancers13174300. [PMID: 34503107 PMCID: PMC8428370 DOI: 10.3390/cancers13174300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/20/2021] [Accepted: 08/22/2021] [Indexed: 12/28/2022] Open
Abstract
Simple Summary Cancer of the esophagus is a deadly disease. There are two main subtypes, adenocarcinoma and squamous cell carcinoma, with adenocarcinoma of the esophagus (EAC) being more common in Western countries. Barrett’s esophagus (BE) describes a change in the esophageal surface near the stomach in response to reflux of gastric acid into the esophagus. BE increases the risk of developing EAC, and the incidence of EAC has risen dramatically over recent decades. One likely reason for the poor prognosis of EAC is based on the fact that each tumor has many genes affected by mutations, and most of these genes differ across patients, hampering the efficacy of therapies that target specific cancer driver proteins. In this review, we provide an overview of the gene mutations and gene activity changes in EAC and how these features can be used to divide patients into groups that might have different clinical characteristics. Abstract Esophageal adenocarcinoma (EAC) is a deadly disease with limited options for targeted therapy. With the help of next-generation sequencing studies over the last decade, we gained an understanding of the genomic architecture of EAC. The tumor suppressor gene TP53 is mutated in 70 to 80% of tumors followed by genomic alterations in CDKN2A, KRAS, ERBB2, ARID1A, SMAD4 and a long tail of less frequently mutated genes. EAC is characterized by a high burden of point mutations and genomic rearrangements, resulting in amplifications and deletions of genomic regions. The genomic complexity is likely hampering the efficacy of targeted therapies. Barrett’s esophagus (BE), a metaplastic response of the esophagus to gastro-esophageal reflux disease, is the main risk factor for the development of EAC. Almost all EACs are derived from BE. The sequence from BE to EAC provides an opportunity to study the genomic evolution towards EAC. While the overlap of point mutations between BE and EAC within the same patient is, at times, surprisingly low, there is a correlation between the complexity of the genomic copy number profile and the development of EAC. Transcriptomic analyses separated EAC into a basal and a classical subtype, with the basal subtype showing a higher level of resistance to chemotherapy. In this review, we provide an overview of the current knowledge of the genomic and transcriptomic characteristics of EAC and their relevance for the development of the disease and patient care.
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Affiliation(s)
- Sascha Hoppe
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (S.H.); (C.J.); (M.C.W.); (O.V.C.); (C.A.); (R.B.); (A.Q.); (P.S.P.)
| | - Christoph Jonas
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (S.H.); (C.J.); (M.C.W.); (O.V.C.); (C.A.); (R.B.); (A.Q.); (P.S.P.)
| | - Marten Christian Wenzel
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (S.H.); (C.J.); (M.C.W.); (O.V.C.); (C.A.); (R.B.); (A.Q.); (P.S.P.)
| | - Oscar Velazquez Camacho
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (S.H.); (C.J.); (M.C.W.); (O.V.C.); (C.A.); (R.B.); (A.Q.); (P.S.P.)
| | - Christoph Arolt
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (S.H.); (C.J.); (M.C.W.); (O.V.C.); (C.A.); (R.B.); (A.Q.); (P.S.P.)
| | - Yue Zhao
- Department of General, Visceral, Cancer and Transplantation Surgery, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany;
| | - Reinhard Büttner
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (S.H.); (C.J.); (M.C.W.); (O.V.C.); (C.A.); (R.B.); (A.Q.); (P.S.P.)
| | - Alexander Quaas
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (S.H.); (C.J.); (M.C.W.); (O.V.C.); (C.A.); (R.B.); (A.Q.); (P.S.P.)
| | - Patrick Sven Plum
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (S.H.); (C.J.); (M.C.W.); (O.V.C.); (C.A.); (R.B.); (A.Q.); (P.S.P.)
- Department of General, Visceral, Cancer and Transplantation Surgery, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany;
| | - Axel Maximilian Hillmer
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (S.H.); (C.J.); (M.C.W.); (O.V.C.); (C.A.); (R.B.); (A.Q.); (P.S.P.)
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
- Correspondence:
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25
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[Influence of molecular pathology on oncological surgery of tumors of the upper gastrointestinal tract]. Chirurg 2021; 92:981-985. [PMID: 34287671 DOI: 10.1007/s00104-021-01466-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND In the recent past tumors of the upper gastrointestinal (GI) tract, e.g. esophageal squamous cell carcinoma (ESCC), esophageal adenocarcinoma (EAC) and gastric adenocarcinoma, have been increasingly characterized by molecular genetics. The resulting subtypes provide potential targets for novel targeted treatment based on the biological characteristics. OBJECTIVE This article summarizes the current state of molecular subtyping in all three tumor entities and the individualized treatment strategies derived from these categories are discussed. MATERIAL AND METHODS A selective literature search was performed focusing on molecular subtyping, current targeted treatment and the impact on the oncological treatment concepts. Databases such as PubMed were used. RESULTS Based on molecular characteristics ESCC is nowadays categorized into three subtypes. Genetically, at least one subgroup resembles oropharyngeal carcinomas rather than those of the upper GI tract. In contrast, EAC is characterized by its high tumor burden and large chromosomal instability. In gastric carcinoma 4 subtypes are distinguished: 1) Epstein-Barr virus (EBV) positive, 2) microsatellite instability (MSI), 3) genomically stable (GS) and 4) chromosomally unstable (CIN) tumors. CONCLUSION To date, only a few targeted therapeutic options have been successfully transferred into daily routine derived from the genetic characterization of the three tumor entities. These include selective ERBB2 inhibition, immunotherapy using PD-L1 inhibition or combined blockade of ERBB2/VEGF.
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Deregulation of Transcriptional Enhancers in Cancer. Cancers (Basel) 2021; 13:cancers13143532. [PMID: 34298745 PMCID: PMC8303223 DOI: 10.3390/cancers13143532] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/29/2021] [Accepted: 07/08/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary One of the major challenges in cancer treatments is the dynamic adaptation of tumor cells to cancer therapies. In this regard, tumor cells can modify their response to environmental cues without altering their DNA sequence. This cell plasticity enables cells to undergo morphological and functional changes, for example, during the process of tumour metastasis or when acquiring resistance to cancer therapies. Central to cell plasticity, are the dynamic changes in gene expression that are controlled by a set of molecular switches called enhancers. Enhancers are DNA elements that determine when, where and to what extent genes should be switched on and off. Thus, defects in enhancer function can disrupt the gene expression program and can lead to tumour formation. Here, we review how enhancers control the activity of cancer-associated genes and how defects in these regulatory elements contribute to cell plasticity in cancer. Understanding enhancer (de)regulation can provide new strategies for modulating cell plasticity in tumour cells and can open new research avenues for cancer therapy. Abstract Epigenetic regulations can shape a cell’s identity by reversible modifications of the chromatin that ultimately control gene expression in response to internal and external cues. In this review, we first discuss the concept of cell plasticity in cancer, a process that is directly controlled by epigenetic mechanisms, with a particular focus on transcriptional enhancers as the cornerstone of epigenetic regulation. In the second part, we discuss mechanisms of enhancer deregulation in adult stem cells and epithelial-to-mesenchymal transition (EMT), as two paradigms of cell plasticity that are dependent on epigenetic regulation and serve as major sources of tumour heterogeneity. Finally, we review how genetic variations at enhancers and their epigenetic modifiers contribute to tumourigenesis, and we highlight examples of cancer drugs that target epigenetic modifications at enhancers.
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Cancer: a mirrored room between tumor bulk and tumor microenvironment. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:217. [PMID: 34183054 PMCID: PMC8240272 DOI: 10.1186/s13046-021-02022-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/18/2021] [Indexed: 12/11/2022]
Abstract
It has been well documented that the tumor microenvironment (TME) plays a key role in the promotion of drug resistance, the support of tumor progression, invasiveness, metastasis, and even the maintenance of a cancer stem-like phenotype. Here, we reviewed TME formation presenting it as a reflection of a tumor’s own organization during the different stages of tumor development. Interestingly, functionally different groups of stromal cells seem to have specific spatial distributions within the TME that change as the tumor evolves into advanced stage progression which correlates with the fact that cancer stem-like cells (CSCs) are located in the edges of solid tumor masses in advanced tumors. We also focus on the continuos feedback that is established between a tumor and its surroundings. The “talk” between tumor mass cells and TME stromal cells, marks the evolution of both interlocuting cell types. For instance, the metabolic and functional transformations that stromal cells undergo due to tumor corrupting activity. Moreover, the molecular basis of metastatic spread is also approached, making special emphasis on the site-specific pre-metastatic niche formation as another reflection of the primary tumor molecular signature. Finally, several therapeutic approaches targeting primary TME and pre-metastatic niche are suggested. For instance, a systematic analysis of the TME just adjacent to the tumor mass to establish the proportion of myofibroblasts-like cancer-associated fibroblasts (CAFs) which may in turn correspond to stemness and metastases-promotion. Or the implementation of “re-education” therapies consisting of switching tumor-supportive stromal cells into tumor-suppressive ones. In summary, to improve our clinical management of cancer, it is crucial to understand and learn how to manage the close interaction between TME and metastasis.
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Challoner BR, von Loga K, Woolston A, Griffiths B, Sivamanoharan N, Semiannikova M, Newey A, Barber LJ, Mansfield D, Hewitt LC, Saito Y, Davarzani N, Starling N, Melcher A, Grabsch HI, Gerlinger M. Computational Image Analysis of T-Cell Infiltrates in Resectable Gastric Cancer: Association with Survival and Molecular Subtypes. J Natl Cancer Inst 2021; 113:88-98. [PMID: 32324860 PMCID: PMC7781469 DOI: 10.1093/jnci/djaa051] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/05/2020] [Accepted: 04/02/2020] [Indexed: 01/08/2023] Open
Abstract
Background Gastric and gastro-esophageal junction cancers (GCs) frequently recur after resection, but markers to predict recurrence risk are missing. T-cell infiltrates have been validated as prognostic markers in other cancer types, but not in GC because of methodological limitations of past studies. We aimed to define and validate the prognostic role of major T-cell subtypes in GC by objective computational quantification. Methods Surgically resected chemotherapy-naïve GCs were split into discovery (n = 327) and validation (n = 147) cohorts. CD8 (cytotoxic), CD45RO (memory), and FOXP3 (regulatory) T-cell densities were measured through multicolor immunofluorescence and computational image analysis. Cancer-specific survival (CSS) was assessed. All statistical tests were two-sided. Results CD45RO-cell and FOXP3-cell densities statistically significantly predicted CSS in both cohorts. Stage, CD45RO-cell, and FOXP3-cell densities were independent predictors of CSS in multivariable analysis; mismatch repair (MMR) and Epstein–Barr virus (EBV) status were not statistically significant. Combining CD45RO-cell and FOXP3-cell densities into the Stomach Cancer Immune Score showed highly statistically significant (all P ≤ .002) CSS differences (0.9 years median CSS to not reached). T-cell infiltrates were highest in EBV-positive GCs and similar in MMR-deficient and MMR-proficient GCs. Conclusion The validation of CD45RO-cell and FOXP3-cell densities as prognostic markers in GC may guide personalized follow-up or (neo)adjuvant treatment strategies. Only those 20% of GCs with the highest T-cell infiltrates showed particularly good CSS, suggesting that a small subgroup of GCs is highly immunogenic. The potential for T-cell densities to predict immunotherapy responses should be assessed. The association of high FOXP3-cell densities with longer CSS warrants studies into the biology of regulatory T cells in GC.
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Affiliation(s)
- Benjamin R Challoner
- Translational Oncogenomics Laboratory, Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Katharina von Loga
- Translational Oncogenomics Laboratory, Division of Molecular Pathology, The Institute of Cancer Research, London, UK.,Translational Immuno-Oncology Team, Centre for Molecular Pathology, The Royal Marsden Hospital NHS Foundation Trust and The Institute of Cancer Research, Sutton, UK
| | - Andrew Woolston
- Translational Oncogenomics Laboratory, Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Beatrice Griffiths
- Translational Oncogenomics Laboratory, Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Nanna Sivamanoharan
- Translational Oncogenomics Laboratory, Division of Molecular Pathology, The Institute of Cancer Research, London, UK.,Translational Immuno-Oncology Team, Centre for Molecular Pathology, The Royal Marsden Hospital NHS Foundation Trust and The Institute of Cancer Research, Sutton, UK
| | - Maria Semiannikova
- Translational Oncogenomics Laboratory, Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Alice Newey
- Translational Oncogenomics Laboratory, Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Louise J Barber
- Translational Oncogenomics Laboratory, Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - David Mansfield
- Targeted Therapy Team, Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
| | - Lindsay C Hewitt
- Department of Pathology, Maastricht University Medical Center, Limburg, The Netherlands
| | - Yuichi Saito
- Department of Surgery, Teikyo University School of Medicine, Tokyo, Japan
| | - Naser Davarzani
- Department of Pathology, Maastricht University Medical Center, Limburg, The Netherlands.,Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Naureen Starling
- Gastrointestinal Cancer Unit, The Royal Marsden Hospital NHS Foundation Trust, London, UK
| | - Alan Melcher
- Translational Immunotherapy Team, Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
| | - Heike I Grabsch
- Department of Pathology, Maastricht University Medical Center, Limburg, The Netherlands.,Pathology & Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, St James's University Hospital, Leeds, UK
| | - Marco Gerlinger
- Translational Oncogenomics Laboratory, Division of Molecular Pathology, The Institute of Cancer Research, London, UK.,Gastrointestinal Cancer Unit, The Royal Marsden Hospital NHS Foundation Trust, London, UK
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Dujon AM, Aktipis A, Alix‐Panabières C, Amend SR, Boddy AM, Brown JS, Capp J, DeGregori J, Ewald P, Gatenby R, Gerlinger M, Giraudeau M, Hamede RK, Hansen E, Kareva I, Maley CC, Marusyk A, McGranahan N, Metzger MJ, Nedelcu AM, Noble R, Nunney L, Pienta KJ, Polyak K, Pujol P, Read AF, Roche B, Sebens S, Solary E, Staňková K, Swain Ewald H, Thomas F, Ujvari B. Identifying key questions in the ecology and evolution of cancer. Evol Appl 2021; 14:877-892. [PMID: 33897809 PMCID: PMC8061275 DOI: 10.1111/eva.13190] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/24/2020] [Accepted: 12/26/2020] [Indexed: 12/17/2022] Open
Abstract
The application of evolutionary and ecological principles to cancer prevention and treatment, as well as recognizing cancer as a selection force in nature, has gained impetus over the last 50 years. Following the initial theoretical approaches that combined knowledge from interdisciplinary fields, it became clear that using the eco-evolutionary framework is of key importance to understand cancer. We are now at a pivotal point where accumulating evidence starts to steer the future directions of the discipline and allows us to underpin the key challenges that remain to be addressed. Here, we aim to assess current advancements in the field and to suggest future directions for research. First, we summarize cancer research areas that, so far, have assimilated ecological and evolutionary principles into their approaches and illustrate their key importance. Then, we assembled 33 experts and identified 84 key questions, organized around nine major themes, to pave the foundations for research to come. We highlight the urgent need for broadening the portfolio of research directions to stimulate novel approaches at the interface of oncology and ecological and evolutionary sciences. We conclude that progressive and efficient cross-disciplinary collaborations that draw on the expertise of the fields of ecology, evolution and cancer are essential in order to efficiently address current and future questions about cancer.
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Affiliation(s)
- Antoine M. Dujon
- School of Life and Environmental SciencesCentre for Integrative EcologyDeakin UniversityWaurn PondsVic.Australia
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRDMontpellierFrance
| | - Athena Aktipis
- Biodesign InstituteDepartment of PsychologyArizona State UniversityTempeAZUSA
| | - Catherine Alix‐Panabières
- Laboratory of Rare Human Circulating Cells (LCCRH)University Medical Center of MontpellierMontpellierFrance
| | - Sarah R. Amend
- Brady Urological InstituteThe Johns Hopkins School of MedicineBaltimoreMDUSA
| | - Amy M. Boddy
- Department of AnthropologyUniversity of California Santa BarbaraSanta BarbaraCAUSA
| | - Joel S. Brown
- Department of Integrated MathematicsMoffitt Cancer CenterTampaFLUSA
| | - Jean‐Pascal Capp
- Toulouse Biotechnology InstituteINSA/University of ToulouseCNRSINRAEToulouseFrance
| | - James DeGregori
- Department of Biochemistry and Molecular GeneticsIntegrated Department of ImmunologyDepartment of PaediatricsDepartment of Medicine (Section of Hematology)University of Colorado School of MedicineAuroraCOUSA
| | - Paul Ewald
- Department of BiologyUniversity of LouisvilleLouisvilleKYUSA
| | - Robert Gatenby
- Department of RadiologyH. Lee Moffitt Cancer Center & Research InstituteTampaFLUSA
| | - Marco Gerlinger
- Translational Oncogenomics LabThe Institute of Cancer ResearchLondonUK
| | - Mathieu Giraudeau
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRDMontpellierFrance
- Littoral Environnement et Sociétés (LIENSs)UMR 7266CNRS‐Université de La RochelleLa RochelleFrance
| | | | - Elsa Hansen
- Center for Infectious Disease Dynamics, Biology DepartmentPennsylvania State UniversityUniversity ParkPAUSA
| | - Irina Kareva
- Mathematical and Computational Sciences CenterSchool of Human Evolution and Social ChangeArizona State UniversityTempeAZUSA
| | - Carlo C. Maley
- Arizona Cancer Evolution CenterBiodesign Institute and School of Life SciencesArizona State UniversityTempeAZUSA
| | - Andriy Marusyk
- Department of Cancer PhysiologyH Lee Moffitt Cancer Centre and Research InstituteTampaFLUSA
| | - Nicholas McGranahan
- Translational Cancer Therapeutics LaboratoryThe Francis Crick InstituteLondonUK
- Cancer Research UK Lung Cancer Centre of ExcellenceUniversity College London Cancer InstituteLondonUK
| | | | | | - Robert Noble
- Department of Biosystems Science and EngineeringETH ZurichBaselSwitzerland
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Leonard Nunney
- Department of Evolution, Ecology, and Organismal BiologyUniversity of California RiversideRiversideCAUSA
| | - Kenneth J. Pienta
- Brady Urological InstituteThe Johns Hopkins School of MedicineBaltimoreMDUSA
| | - Kornelia Polyak
- Department of Medical OncologyDana‐Farber Cancer InstituteBostonMAUSA
- Department of MedicineHarvard Medical SchoolBostonMAUSA
| | - Pascal Pujol
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRDMontpellierFrance
- Centre Hospitalier Universitaire Arnaud de VilleneuveMontpellierFrance
| | - Andrew F. Read
- Center for Infectious Disease DynamicsHuck Institutes of the Life SciencesDepartments of Biology and EntomologyPennsylvania State UniversityUniversity ParkPAUSA
| | - Benjamin Roche
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRDMontpellierFrance
- Unité Mixte Internationale de Modélisation Mathématique et Informatique des Systèmes ComplexesUMI IRD/Sorbonne UniversitéUMMISCOBondyFrance
| | - Susanne Sebens
- Institute for Experimental Cancer Research Kiel University and University Hospital Schleswig‐HolsteinKielGermany
| | - Eric Solary
- INSERM U1287Gustave RoussyVillejuifFrance
- Faculté de MédecineUniversité Paris‐SaclayLe Kremlin‐BicêtreFrance
| | - Kateřina Staňková
- Department of Data Science and Knowledge EngineeringMaastricht UniversityMaastrichtThe Netherlands
- Delft Institute of Applied MathematicsDelft University of TechnologyDelftThe Netherlands
| | | | - Frédéric Thomas
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRDMontpellierFrance
| | - Beata Ujvari
- School of Life and Environmental SciencesCentre for Integrative EcologyDeakin UniversityWaurn PondsVic.Australia
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Takano S, Fukasawa M, Shindo H, Takahashi E, Fukasawa Y, Kawakami S, Hayakawa H, Kuratomi N, Kadokura M, Maekawa S, Enomoto N. Digital next-generation sequencing of cell-free DNA for pancreatic cancer. JGH OPEN 2021; 5:508-516. [PMID: 33860102 PMCID: PMC8035455 DOI: 10.1002/jgh3.12530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/28/2021] [Accepted: 03/08/2021] [Indexed: 12/26/2022]
Abstract
Background and Aim The clinical applicability of digital next‐generation sequencing (dNGS), which eliminates polymerase chain reaction (PCR) and sequencing error‐derived noise by using molecular barcodes (MBs), has not been fully evaluated. We evaluated the utility of dNGS of cell‐free DNA (cfDNA) in liquid biopsies obtained from patients with pancreatic cancer. Methods Fifty‐eight patients with pancreatic cancer undergoing endoscopic ultrasound‐guided fine‐needle aspiration (EUS‐FNA) were included. Samples were subjected to sequencing of 50 cancer‐related genes using next‐generation sequencing (NGS). The results were used as reference gene alterations. NGS of cfDNA from plasma was performed for patients with a mutant allele frequency (MAF) >1% and an absolute mutant number > 10 copies/plasma mL in KRAS or GNAS by digital PCR. Sequence readings with and without MBs were compared with reference to EUS‐FNA‐derived gene alterations. Results The concordance rate between dNGS of cfDNA and EUS‐FNA‐derived gene alterations was higher with than without MBs (p = 0.039), and MAF cut‐off values in dNGS could be decreased to 0.2%. dNGS using MBs eliminated PCR and sequencing error by 74% and 68% for TP53 and all genes, respectively. Overall, dNGS detected mutations in KRAS (45%) and TP53 (26%) and copy number alterations in CCND2, CCND3, CDK4, FGFR1, and MYC, which are targets of molecular‐targeted drugs. Conclusions dNGS of cfDNA using MBs is useful for accurate detection of gene alterations even with low levels of MAFs. These results may be used to inform the development of diagnostics and therapeutics that can improve the prognosis of pancreatic cancer.
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Affiliation(s)
- Shinichi Takano
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Chuo Japan
| | - Mitsuharu Fukasawa
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Chuo Japan
| | - Hiroko Shindo
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Chuo Japan
| | - Ei Takahashi
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Chuo Japan
| | - Yoshimitsu Fukasawa
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Chuo Japan
| | - Satoshi Kawakami
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Chuo Japan
| | - Hiroshi Hayakawa
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Chuo Japan
| | - Natsuhiko Kuratomi
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Chuo Japan
| | - Makoto Kadokura
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Chuo Japan
| | - Shinya Maekawa
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Chuo Japan
| | - Nobuyuki Enomoto
- First Department of Internal Medicine, Faculty of Medicine University of Yamanashi Chuo Japan
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31
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Puliga E, Corso S, Pietrantonio F, Giordano S. Microsatellite instability in Gastric Cancer: Between lights and shadows. Cancer Treat Rev 2021; 95:102175. [PMID: 33721595 DOI: 10.1016/j.ctrv.2021.102175] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 12/11/2022]
Abstract
Gastric cancer (GC) represents an important contributor to the global burden of cancer, being one of the most common and deadly malignancies worldwide. According to TCGA and ACRG classifications, the microsatellite instable (MSI) group represents a significant subset of GCs and is currently in the limelight of many researches due to its favorable survival outcome in resectable stages compared to microsatellite stable tumors. MSI GCs hypermutated phenotype triggers immunosurveillance, making this molecular subgroup a promising candidate for immune checkpoint inhibitors treatment. Conversely, conflicting outcomes have been reported in chemotherapy settings. Due to the clinical relevance of these observations, in this review we report and discuss the molecular, pathological, prognostic, and predictive features of MSI gastric tumors.
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Affiliation(s)
- Elisabetta Puliga
- Department of Oncology, University of Torino, Candiolo, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.
| | - Simona Corso
- Department of Oncology, University of Torino, Candiolo, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Filippo Pietrantonio
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Silvia Giordano
- Department of Oncology, University of Torino, Candiolo, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.
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32
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Guan J, Lu C, Jin Q, Lu H, Chen X, Tian L, Zhang Y, Ortega J, Zhang J, Siteni S, Chen M, Gu L, Shay JW, Davis AJ, Chen ZJ, Fu YX, Li GM. MLH1 Deficiency-Triggered DNA Hyperexcision by Exonuclease 1 Activates the cGAS-STING Pathway. Cancer Cell 2021; 39:109-121.e5. [PMID: 33338427 PMCID: PMC8666006 DOI: 10.1016/j.ccell.2020.11.004] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/22/2020] [Accepted: 11/13/2020] [Indexed: 12/15/2022]
Abstract
Tumors with defective mismatch repair (dMMR) are responsive to immunotherapy because of dMMR-induced neoantigens and activation of the cGAS-STING pathway. While neoantigens result from the hypermutable nature of dMMR, it is unknown how dMMR activates the cGAS-STING pathway. We show here that loss of the MutLα subunit MLH1, whose defect is responsible for ~50% of dMMR cancers, results in loss of MutLα-specific regulation of exonuclease 1 (Exo1) during DNA repair. This leads to unrestrained DNA excision by Exo1, which causes increased single-strand DNA formation, RPA exhaustion, DNA breaks, and aberrant DNA repair intermediates. Ultimately, this generates chromosomal abnormalities and the release of nuclear DNA into the cytoplasm, activating the cGAS-STING pathway. In this study, we discovered a hitherto unknown MMR mechanism that modulates genome stability and has implications for cancer therapy.
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Affiliation(s)
- Junhong Guan
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Changzheng Lu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Qihuang Jin
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Huiming Lu
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiang Chen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lei Tian
- Department of Cancer Biology, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yanbin Zhang
- Department of Biochemistry & Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Janice Ortega
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Junqiu Zhang
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Silvia Siteni
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mingyi Chen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Liya Gu
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jerry W Shay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Anthony J Davis
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Zhijian J Chen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yang-Xin Fu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Guo-Min Li
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Lu C, Guan J, Lu S, Jin Q, Rousseau B, Lu T, Stephens D, Zhang H, Zhu J, Yang M, Ren Z, Liang Y, Liu Z, Han C, Liu L, Cao X, Zhang A, Qiao J, Batten K, Chen M, Castrillon DH, Wang T, Li B, Diaz LA, Li GM, Fu YX. DNA Sensing in Mismatch Repair-Deficient Tumor Cells Is Essential for Anti-tumor Immunity. Cancer Cell 2021; 39:96-108.e6. [PMID: 33338425 PMCID: PMC9477183 DOI: 10.1016/j.ccell.2020.11.006] [Citation(s) in RCA: 148] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/23/2020] [Accepted: 11/13/2020] [Indexed: 12/21/2022]
Abstract
Increased neoantigens in hypermutated cancers with DNA mismatch repair deficiency (dMMR) are proposed as the major contributor to the high objective response rate in anti-PD-1 therapy. However, the mechanism of drug resistance is not fully understood. Using tumor models defective in the MMR gene Mlh1 (dMLH1), we show that dMLH1 tumor cells accumulate cytosolic DNA and produce IFN-β in a cGAS-STING-dependent manner, which renders dMLH1 tumors slowly progressive and highly sensitive to checkpoint blockade. In neoantigen-fixed models, dMLH1 tumors potently induce T cell priming and lose resistance to checkpoint therapy independent of tumor mutational burden. Accordingly, loss of STING or cGAS in tumor cells decreases tumor infiltration of T cells and endows resistance to checkpoint blockade. Clinically, downregulation of cGAS/STING in human dMMR cancers correlates with poor prognosis. We conclude that DNA sensing within tumor cells is essential for dMMR-triggered anti-tumor immunity. This study provides new mechanisms and biomarkers for anti-dMMR-cancer immunotherapy.
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Affiliation(s)
- Changzheng Lu
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Junhong Guan
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Steve Lu
- Ludwig Center and Howard Hughes Medical Institute at Johns Hopkins, Baltimore, MD 21287, USA
| | - Qihuang Jin
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Benoit Rousseau
- Department of Medicine, Division of Solid Tumors, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Tianshi Lu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Dennis Stephens
- Department of Medicine, Division of Solid Tumors, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hongyi Zhang
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiankun Zhu
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mingming Yang
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhenhua Ren
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yong Liang
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhida Liu
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chuanhui Han
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Longchao Liu
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xuezhi Cao
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Anli Zhang
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jian Qiao
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kimberly Batten
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mingyi Chen
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Diego H Castrillon
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Obstetrics and Gynecology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tao Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bo Li
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Luis A Diaz
- Department of Medicine, Division of Solid Tumors, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Guo-Min Li
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Yang-Xin Fu
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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Abstract
Abundant neoantigens are considered responsible for the immunotherapy sensitivity of mismatch repair-deficient (MMRd) cancers. In this issue of Cancer Cell, two papers show that MLH1 mismatch repair gene loss promotes cGAS-STING activation, interferon secretion, and T cell priming. This may be essential for the high immunotherapy sensitivity in MMRd cancer.
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Affiliation(s)
- Marco Gerlinger
- The Institute of Cancer Research, London, UK; The Royal Marsden Hospital, GI Cancer Unit, London, UK.
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35
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Jeevanandam J, Sabbih G, Tan KX, Danquah MK. Oncological Ligand-Target Binding Systems and Developmental Approaches for Cancer Theranostics. Mol Biotechnol 2021; 63:167-183. [PMID: 33423212 DOI: 10.1007/s12033-020-00296-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2020] [Indexed: 02/07/2023]
Abstract
Targeted treatment of cancer hinges on the identification of specific intracellular molecular receptors on cancer cells to stimulate apoptosis for eventually inhibiting growth; the development of novel ligands to target biomarkers expressed by the cancer cells; and the creation of novel multifunctional carrier systems for targeted delivery of anticancer drugs to specific malignant sites. There are numerous receptors, antigens, and biomarkers that have been discovered as oncological targets (oncotargets) for cancer diagnosis and treatment applications. Oncotargets are critically important to navigate active anticancer drug ingredients to specific disease sites with no/minimal effect on surrounding normal cells. In silico techniques relating to genomics, proteomics, and bioinformatics have catalyzed the discovery of oncotargets for various cancer types. Effective oncotargeting requires high-affinity probes engineered for specific binding of receptors associated with the malignancy. Computational methods such as structural modeling and molecular dynamic (MD) simulations offer opportunities to structurally design novel ligands and optimize binding affinity for specific oncotargets. This article proposes a streamlined approach for the development of ligand-oncotarget bioaffinity systems via integrated structural modeling and MD simulations, making use of proteomics, genomic, and X-ray crystallographic resources, to support targeted diagnosis and treatment of cancers and tumors.
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Affiliation(s)
- Jaison Jeevanandam
- CQM-Centro de Química da Madeira, MMRG, Universidade da Madeira, Campus da Penteada, 9020-105, Funchal, Portugal
| | - Godfred Sabbih
- Chemical Engineering Department, University of Tennessee, Chattanooga, TN, 37403, USA
| | - Kei X Tan
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Michael K Danquah
- Chemical Engineering Department, University of Tennessee, Chattanooga, TN, 37403, USA.
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Chung J, Maruvka YE, Sudhaman S, Kelly J, Haradhvala NJ, Bianchi V, Edwards M, Forster VJ, Nunes NM, Galati MA, Komosa M, Deshmukh S, Cabric V, Davidson S, Zatzman M, Light N, Hayes R, Brunga L, Anderson ND, Ho B, Hodel KP, Siddaway R, Morrissy AS, Bowers DC, Larouche V, Bronsema A, Osborn M, Cole KA, Opocher E, Mason G, Thomas GA, George B, Ziegler DS, Lindhorst S, Vanan M, Yalon-Oren M, Reddy AT, Massimino M, Tomboc P, Van Damme A, Lossos A, Durno C, Aronson M, Morgenstern DA, Bouffet E, Huang A, Taylor MD, Villani A, Malkin D, Hawkins CE, Pursell ZF, Shlien A, Kunkel TA, Getz G, Tabori U. DNA Polymerase and Mismatch Repair Exert Distinct Microsatellite Instability Signatures in Normal and Malignant Human Cells. Cancer Discov 2020; 11:1176-1191. [PMID: 33355208 DOI: 10.1158/2159-8290.cd-20-0790] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 09/23/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022]
Abstract
Although replication repair deficiency, either by mismatch repair deficiency (MMRD) and/or loss of DNA polymerase proofreading, can cause hypermutation in cancer, microsatellite instability (MSI) is considered a hallmark of MMRD alone. By genome-wide analysis of tumors with germline and somatic deficiencies in replication repair, we reveal a novel association between loss of polymerase proofreading and MSI, especially when both components are lost. Analysis of indels in microsatellites (MS-indels) identified five distinct signatures (MS-sigs). MMRD MS-sigs are dominated by multibase losses, whereas mutant-polymerase MS-sigs contain primarily single-base gains. MS deletions in MMRD tumors depend on the original size of the MS and converge to a preferred length, providing mechanistic insight. Finally, we demonstrate that MS-sigs can be a powerful clinical tool for managing individuals with germline MMRD and replication repair-deficient cancers, as they can detect the replication repair deficiency in normal cells and predict their response to immunotherapy. SIGNIFICANCE: Exome- and genome-wide MSI analysis reveals novel signatures that are uniquely attributed to mismatch repair and DNA polymerase. This provides new mechanistic insight into MS maintenance and can be applied clinically for diagnosis of replication repair deficiency and immunotherapy response prediction.This article is highlighted in the In This Issue feature, p. 995.
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Affiliation(s)
- Jiil Chung
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Yosef E Maruvka
- Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Sumedha Sudhaman
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jacalyn Kelly
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nicholas J Haradhvala
- Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Harvard Graduate Program in Biophysics, Harvard University, Cambridge, Massachusetts
| | - Vanessa Bianchi
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Melissa Edwards
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Victoria J Forster
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nuno M Nunes
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Melissa A Galati
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Martin Komosa
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Shriya Deshmukh
- Department of Experimental Medicine, McGill University, Montreal, Quebec, Canada.,The Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - Vanja Cabric
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Scott Davidson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Matthew Zatzman
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Nicholas Light
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Reid Hayes
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ledia Brunga
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nathaniel D Anderson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ben Ho
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Karl P Hodel
- Department of Biochemistry and Molecular Biology, Tulane Cancer Center, Tulane University of Medicine, New Orleans, Louisiana
| | - Robert Siddaway
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - A Sorana Morrissy
- Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Charbonneau Cancer Institute and Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada
| | - Daniel C Bowers
- Department of Pediatrics and Harold C. Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, Texas.,Pauline Allen Gill Center for Cancer and Blood Disorders, Children's Health, Dallas, Texas
| | - Valérie Larouche
- Department of Pediatrics, Centre Mere-enfant Soleil du CHU de Quebec, CRCHU de Quebec, Universite Laval, Quebec City, Quebec, Canada
| | - Annika Bronsema
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Osborn
- Department of Haematology and Oncology, Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - Kristina A Cole
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Enrico Opocher
- Pediatric Oncology and Hematology, Azienda Ospedaliera-Universita' degli Studi di Padova, Padova, Italy
| | - Gary Mason
- Department of Pediatric Hematology-Oncology, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania
| | - Gregory A Thomas
- Division of Pediatric Hematology-Oncology, Oregon Health and Science University, Portland, Oregon
| | - Ben George
- Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - David S Ziegler
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, New South Wales, Australia.,Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales, Australia
| | - Scott Lindhorst
- Neuro-Oncology, Department of Neurosurgery, and Department of Medicine, Division of Hematology/Medical Oncology, Medical University of South Carolina Charleston, South Carolina
| | - Magimairajan Vanan
- Department of Pediatric Hematology-Oncology, Cancer Care Manitoba; Research Institute in Oncology and Hematology (RIOH), University of Manitoba, Winnipeg, Manitoba, Canada
| | - Michal Yalon-Oren
- Pediatric Hemato-Oncology, Edmond and Lilly Safra Children's Hospital and Cancer Research Center, Sheba Medical Center, Tel Hashomer Affiliated to the Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Alyssa T Reddy
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Maura Massimino
- Pediatric Unit, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milano, Italy
| | - Patrick Tomboc
- Department of Pediatrics Section of Hematology-Oncology, WVU Medicine Children's, Morgantown, West Virginia
| | - An Van Damme
- Division of Hematology and Oncology, Department of Pediatrics, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Alexander Lossos
- Department of Neurology, Agnes Ginges Center for Human Neurogenetics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Carol Durno
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada.,Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Melyssa Aronson
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Daniel A Morgenstern
- Department of Paediatrics, Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
| | - Eric Bouffet
- Department of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Annie Huang
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.,Department of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Neurosurgery, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Anita Villani
- Department of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - David Malkin
- Department of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Cynthia E Hawkins
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.,Program in Cell Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology, Tulane Cancer Center, Tulane University of Medicine, New Orleans, Louisiana
| | - Adam Shlien
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Thomas A Kunkel
- Genome Integrity Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Durham, North Carolina
| | - Gad Getz
- Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts. .,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Uri Tabori
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada. .,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
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Plum PS, Löser H, Zander T, Essakly A, Bruns CJ, Hillmer AM, Alakus H, Schröder W, Büttner R, Gebauer F, Quaas A. GATA binding protein 6 (GATA6) is co-amplified with PIK3CA in patients with esophageal adenocarcinoma and is linked to neoadjuvant therapy. J Cancer Res Clin Oncol 2020; 147:1031-1040. [PMID: 33300112 PMCID: PMC7954758 DOI: 10.1007/s00432-020-03486-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 11/27/2020] [Indexed: 12/20/2022]
Abstract
Purpose Driver mutations are typically absent in esophageal adenocarcinoma (EAC). Mostly, oncogenes are amplified as driving molecular events (including GATA6-amplification in 14% of cases). However, only little is known about its biological function and clinical relevance. Methods We examined a large number of EAC (n = 496) for their GATA6 amplification by fluorescence in situ hybridization (FISH) analyzing both primary resected (n = 219) and neoadjuvant treated EAC (n = 277). Results were correlated to clinicopathological data and known mutations/amplifications in our EAC-cohort. Results GATA6 amplification was detectable in 49 (9.9%) EACs of our cohort. We observed an enrichment of GATA6-positive tumors among patients after neoadjuvant treatment (12,3% amplified tumors versus 6,8% in the primary resected group; p = 0.044). Additionally, there was a simultaneous amplification of PIK3CA and GATA6 (p < 0.001) not detectable when analyzing other genes such as EGFR, ERBB2, KRAS or MDM2. Although we did not identify a survival difference depending on GATA6 in the entire cohort (p = 0.212), GATA6 amplification was associated with prolonged overall survival among patients with primary surgery (median overall-survival 121.1 vs. 41.4 months, p = 0.032). Multivariate cox-regression analysis did not confirm GATA6 as an independent prognostic marker, neither in the entire cohort (p = 0.210), nor in the subgroup with (p = 0.655) or without pretreatment (p = 0.961). Conclusions Our study investigates the relevance of GATA6 amplification on a large tumor collective, which includes primary resected tumors and the clinically relevant group of neoadjuvant treated EACs. Especially in the pretreated group, we found an accumulation of GATA6-amplified tumors (12.3%) and a frequent co-amplification of PIK3CA. Our data suggest an increased resistance to radio-chemotherapy in GATA6-amplified tumors.
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Affiliation(s)
- Patrick Sven Plum
- Department of General, Visceral, Cancer, and Transplantation Surgery, University of Cologne, Faculty of Medicine, and University Hospital Cologne, Kerpener Straße 62, 50937, Cologne, Germany.
- Gastrointestinal Cancer Group Cologne (GCGC), Cologne, Germany.
- Else Kröner Forschungskolleg Cologne "Clonal Evolution in Cancer", Cologne, Germany.
- Centre for Integrated Oncology (CIO), Cologne Bonn, Cologne, Germany.
| | - Heike Löser
- Gastrointestinal Cancer Group Cologne (GCGC), Cologne, Germany
- Institute of Pathology, University of Cologne, Faculty of Medicine, and University Hospital Cologne, Kerpener Straße 62, 50937, Cologne, Germany
| | - Thomas Zander
- Centre for Integrated Oncology (CIO), Cologne Bonn, Cologne, Germany
- Department of Internal Medicine I, University of Cologne, Faculty of Medicine, and University Hospital Cologne, Kerpener Straße 62, 50937, Cologne, Germany
| | - Ahlem Essakly
- Institute of Pathology, University of Cologne, Faculty of Medicine, and University Hospital Cologne, Kerpener Straße 62, 50937, Cologne, Germany
| | - Christiane J Bruns
- Department of General, Visceral, Cancer, and Transplantation Surgery, University of Cologne, Faculty of Medicine, and University Hospital Cologne, Kerpener Straße 62, 50937, Cologne, Germany
- Centre for Integrated Oncology (CIO), Cologne Bonn, Cologne, Germany
| | - Axel M Hillmer
- Institute of Pathology, University of Cologne, Faculty of Medicine, and University Hospital Cologne, Kerpener Straße 62, 50937, Cologne, Germany
| | - Hakan Alakus
- Department of General, Visceral, Cancer, and Transplantation Surgery, University of Cologne, Faculty of Medicine, and University Hospital Cologne, Kerpener Straße 62, 50937, Cologne, Germany
- Centre for Integrated Oncology (CIO), Cologne Bonn, Cologne, Germany
| | - Wolfgang Schröder
- Department of General, Visceral, Cancer, and Transplantation Surgery, University of Cologne, Faculty of Medicine, and University Hospital Cologne, Kerpener Straße 62, 50937, Cologne, Germany
- Centre for Integrated Oncology (CIO), Cologne Bonn, Cologne, Germany
| | - Reinhard Büttner
- Institute of Pathology, University of Cologne, Faculty of Medicine, and University Hospital Cologne, Kerpener Straße 62, 50937, Cologne, Germany
| | - Florian Gebauer
- Department of General, Visceral, Cancer, and Transplantation Surgery, University of Cologne, Faculty of Medicine, and University Hospital Cologne, Kerpener Straße 62, 50937, Cologne, Germany
- Centre for Integrated Oncology (CIO), Cologne Bonn, Cologne, Germany
| | - Alexander Quaas
- Gastrointestinal Cancer Group Cologne (GCGC), Cologne, Germany
- Centre for Integrated Oncology (CIO), Cologne Bonn, Cologne, Germany
- Institute of Pathology, University of Cologne, Faculty of Medicine, and University Hospital Cologne, Kerpener Straße 62, 50937, Cologne, Germany
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38
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Nowak KM, Chetty R. SWI/SNF-deficient cancers of the Gastroenteropancreatic tract: an in-depth review of the literature and pathology. Semin Diagn Pathol 2020; 38:195-198. [PMID: 33288347 DOI: 10.1053/j.semdp.2020.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/16/2020] [Accepted: 11/25/2020] [Indexed: 12/13/2022]
Abstract
The SWItch Sucrose non-fermentable (SWI/SNF) complex is a large, multi-subunit ATP-dependent nucleosome remodeling complex that acts as a tumor suppressor by modulating transcription. Mutations of SWI/SNF subunits have been described in relation to developmental disorders, hereditary SWI/SNF deficiency syndromes, as well as malignancies. In this review we summarize the current literature in regards to SWI/SNF-deficient tumors of the luminal gastrointestinal tract (GIT) and pancreas. As a group they range from moderately to undifferentiated tumors composed of monotonous anaplastic cells, prominent macronucleoli and a variable rhabdoid cell component. Deficiency of a SWI/SNF subunit is typified by complete loss of nuclear staining by immunohistochemistry for respective subunit.
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Affiliation(s)
- Klaudia M Nowak
- Division of Anatomical Pathology, Laboratory Medicine Programme, University Health Network, Toronto, Canada
| | - Runjan Chetty
- Department of Histopathology, Brighton and Sussex University Hospitals, Brighton; United Kingdom and Deciphex Ltd, Ireland.
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39
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Mismatch Repair System Genomic Scars in Gastroesophageal Cancers: Biology and Clinical Testing. GASTROINTESTINAL DISORDERS 2020. [DOI: 10.3390/gidisord2040031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Alterations in the mismatch repair (MMR) system result in genomic instability, neoantigen production, and immune response in cancer. There is evidence that gastroesophageal tumors with MMR deficiency may be susceptible to immune-checkpoint inhibitors treatment, especially in those presenting at advanced-stage disease. Although a number of biomarkers have been developed in histology-agnostic settings to assess MMR status, there is evidence that a tumor-specific testing approach would improve the selection of patients for immunotherapy. However, no testing methods have been developed specifically for gastroesophageal cancers so far. Here, we discuss the state of the art, current advances, and future perspectives of MMR-related biomarkers’ biologic and clinical role in gastroesophageal cancers.
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40
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Affiliation(s)
- Steven Maron
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Adam Bass
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge
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