1
|
Jost TA, Gardner AL, Morgan D, Brock A. Deep learning identifies heterogeneous subpopulations in breast cancer cell lines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.02.601576. [PMID: 39005432 PMCID: PMC11245002 DOI: 10.1101/2024.07.02.601576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Motivation Cells exhibit a wide array of morphological features, enabling computer vision methods to identify and track relevant parameters. Morphological analysis has long been implemented to identify specific cell types and cell responses. Here we asked whether morphological features might also be used to classify transcriptomic subpopulations within in vitro cancer cell lines. Identifying cell subpopulations furthers our understanding of morphology as a reflection of underlying cell phenotype and could enable a better understanding of how subsets of cells compete and cooperate in disease progression and treatment. Results We demonstrate that cell morphology can reflect underlying transcriptomic differences in vitro using convolutional neural networks. First, we find that changes induced by chemotherapy treatment are highly identifiable in a breast cancer cell line. We then show that the intra cell line subpopulations that comprise breast cancer cell lines under standard growth conditions are also identifiable using cell morphology. We find that cell morphology is influenced by neighborhood effects beyond the cell boundary, and that including image information surrounding the cell can improve model discrimination ability.
Collapse
|
2
|
Lai J, Yang Y, Liu Y, Scharpf RB, Karchin R. Assessing the merits: an opinion on the effectiveness of simulation techniques in tumor subclonal reconstruction. BIOINFORMATICS ADVANCES 2024; 4:vbae094. [PMID: 38948008 PMCID: PMC11213631 DOI: 10.1093/bioadv/vbae094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/28/2024] [Accepted: 06/15/2024] [Indexed: 07/02/2024]
Abstract
Summary Neoplastic tumors originate from a single cell, and their evolution can be traced through lineages characterized by mutations, copy number alterations, and structural variants. These lineages are reconstructed and mapped onto evolutionary trees with algorithmic approaches. However, without ground truth benchmark sets, the validity of an algorithm remains uncertain, limiting potential clinical applicability. With a growing number of algorithms available, there is urgent need for standardized benchmark sets to evaluate their merits. Benchmark sets rely on in silico simulations of tumor sequence, but there are no accepted standards for simulation tools, presenting a major obstacle to progress in this field. Availability and implementation All analysis done in the paper was based on publicly available data from the publication of each accessed tool.
Collapse
Affiliation(s)
- Jiaying Lai
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Yi Yang
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Yunzhou Liu
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Robert B Scharpf
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, United States
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21231, United States
| | - Rachel Karchin
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, United States
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, United States
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21231, United States
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, United States
| |
Collapse
|
3
|
El-Sayed MM, Bianco JR, Li Y, Fabian Z. Tumor-Agnostic Therapy-The Final Step Forward in the Cure for Human Neoplasms? Cells 2024; 13:1071. [PMID: 38920700 PMCID: PMC11201516 DOI: 10.3390/cells13121071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 06/27/2024] Open
Abstract
Cancer accounted for 10 million deaths in 2020, nearly one in every six deaths annually. Despite advancements, the contemporary clinical management of human neoplasms faces a number of challenges. Surgical removal of tumor tissues is often not possible technically, while radiation and chemotherapy pose the risk of damaging healthy cells, tissues, and organs, presenting complex clinical challenges. These require a paradigm shift in developing new therapeutic modalities moving towards a more personalized and targeted approach. The tumor-agnostic philosophy, one of these new modalities, focuses on characteristic molecular signatures of transformed cells independently of their traditional histopathological classification. These include commonly occurring DNA aberrations in cancer cells, shared metabolic features of their homeostasis or immune evasion measures of the tumor tissues. The first dedicated, FDA-approved tumor-agnostic agent's profound progression-free survival of 78% in mismatch repair-deficient colorectal cancer paved the way for the accelerated FDA approvals of novel tumor-agnostic therapeutic compounds. Here, we review the historical background, current status, and future perspectives of this new era of clinical oncology.
Collapse
Affiliation(s)
| | | | | | - Zsolt Fabian
- School of Medicine and Dentistry, Faculty of Clinical and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, UK; (M.M.E.-S.); (J.R.B.); (Y.L.)
| |
Collapse
|
4
|
Strobl MAR, Martin AL, West J, Gallaher J, Robertson-Tessi M, Gatenby R, Wenham R, Maini PK, Damaghi M, Anderson ARA. To modulate or to skip: De-escalating PARP inhibitor maintenance therapy in ovarian cancer using adaptive therapy. Cell Syst 2024; 15:510-525.e6. [PMID: 38772367 PMCID: PMC11190943 DOI: 10.1016/j.cels.2024.04.003] [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: 05/19/2023] [Revised: 02/27/2024] [Accepted: 04/17/2024] [Indexed: 05/23/2024]
Abstract
Toxicity and emerging drug resistance pose important challenges in poly-adenosine ribose polymerase inhibitor (PARPi) maintenance therapy of ovarian cancer. We propose that adaptive therapy, which dynamically reduces treatment based on the tumor dynamics, might alleviate both issues. Utilizing in vitro time-lapse microscopy and stepwise model selection, we calibrate and validate a differential equation mathematical model, which we leverage to test different plausible adaptive treatment schedules. Our model indicates that adjusting the dosage, rather than skipping treatments, is more effective at reducing drug use while maintaining efficacy due to a delay in cell kill and a diminishing dose-response relationship. In vivo pilot experiments confirm this conclusion. Although our focus is toxicity mitigation, reducing drug use may also delay resistance. This study enhances our understanding of PARPi treatment scheduling and illustrates the first steps in developing adaptive therapies for new treatment settings. A record of this paper's transparent peer review process is included in the supplemental information.
Collapse
Affiliation(s)
- Maximilian A R Strobl
- Department of Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, FL, USA; Department of Translational Hematology & Oncology Research, Cleveland Clinic, Cleveland, OH, USA.
| | - Alexandra L Martin
- Department of Obstetrics and Gynecology, University of Tennessee Health Science Center, Memphis, TN, USA; Division of Gynecologic Oncology, West Cancer Center and Research Institute, Memphis, TN, USA
| | - Jeffrey West
- Department of Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Jill Gallaher
- Department of Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Mark Robertson-Tessi
- Department of Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Robert Gatenby
- Department of Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, FL, USA; Cancer Biology and Evolution Program, Moffitt Cancer Center, Tampa, FL, USA
| | - Robert Wenham
- Gynecologic Oncology Program, Moffitt Cancer Center, Tampa, FL, USA
| | - Philip K Maini
- Wolfson Centre for Mathematical Biology, University of Oxford, Oxford, UK.
| | - Mehdi Damaghi
- Department of Pathology, Stony Brook Medicine, SUNY, Brookhaven, NY, USA; Stony Brook Cancer Center, Stony Brook Medicine, SUNY, Brookhaven, NY, USA.
| | | |
Collapse
|
5
|
Gorlov IP, Gorlova OY, Tsavachidis S, Amos CI. Strength of selection in lung tumors correlates with clinical features better than tumor mutation burden. Sci Rep 2024; 14:12732. [PMID: 38831004 PMCID: PMC11148192 DOI: 10.1038/s41598-024-63468-z] [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: 12/08/2023] [Accepted: 05/29/2024] [Indexed: 06/05/2024] Open
Abstract
Single nucleotide substitutions are the most common type of somatic mutations in cancer genome. The goal of this study was to use publicly available somatic mutation data to quantify negative and positive selection in individual lung tumors and test how strength of directional and absolute selection is associated with clinical features. The analysis found a significant variation in strength of selection (both negative and positive) among tumors, with median selection tending to be negative even though tumors with strong positive selection also exist. Strength of selection estimated as the density of missense mutations relative to the density of silent mutations showed only a weak correlation with tumor mutation burden. In the "all histology together" analysis we found that absolute strength of selection was strongly correlated with all clinically relevant features analyzed. In histology-stratified analysis selection was strongest in small cell lung cancer. Selection in adenocarcinoma was somewhat higher compared to squamous cell carcinoma. The study suggests that somatic mutation- based quantifying of directional and absolute selection in individual tumors can be a useful biomarker of tumor aggressiveness.
Collapse
Affiliation(s)
- Ivan P Gorlov
- Institute for Clinical and Translational Research, Baylor College of Medicine, One Baylor Plaza, Mailstop: BCM451, Houston, TX, 77030, USA.
| | - Olga Y Gorlova
- Institute for Clinical and Translational Research, Baylor College of Medicine, One Baylor Plaza, Mailstop: BCM451, Houston, TX, 77030, USA
| | - Spyridon Tsavachidis
- Institute for Clinical and Translational Research, Baylor College of Medicine, One Baylor Plaza, Mailstop: BCM451, Houston, TX, 77030, USA
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, One Baylor Plaza, Mailstop: BCM451, Houston, TX, 77030, USA
| |
Collapse
|
6
|
Pei F, He W, Duan Y, Yao Q, Zhao Y, Fan X, Liu S, Chen H, He F, Liu T, Chen J, Zheng Y, Li H, Guo X, Shi L, Ling L, Chen Y, He J, Liu M, Huang M, Bai Y, Wang J, Huang M, Huang J. PD-1 blockade enhances the effect of targeted chemotherapy on locally advanced pMMR/MSS colorectal cancer. Cancer Med 2024; 13:e7224. [PMID: 38888366 PMCID: PMC11184646 DOI: 10.1002/cam4.7224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 04/06/2024] [Accepted: 04/14/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Patients with DNA mismatch repair-proficient/microsatellite stable (pMMR/MSS) colorectal cancer (CRC), which accounts for 85% of all CRC cases, display a poor respond to immune checkpoint inhibitors (i.e., anti-PD-1 antibodies). pMMR/MSS CRC patients with locally advanced cancers need effective combined therapies. METHODS In this pilot study, we administered six preoperative doses of each 2-week cycle of the anti-PD-1 antibody sintilimab (at a fixed dose of 200 mg), oxaliplatin, and 5-FU/CF (mFOLFOX6) combined with five doses of bevacizumab (the number of doses was reduced to prevent surgical delays) to patients with cT4NxM0 colon or upper rectal cancers. And radical surgery was performed approximately 2 weeks after the last dose of neoadjuvant therapy. The primary endpoint was a pathologic complete response (pCR). We also evaluated major pathologic response (MPR, ≤10% residual viable tumor), radiological and pathological regression, safety, and tumor mutation burden (TMB), and tumor microenvironment (TME) characteristics. RESULTS By the cutoff date (September 2023), 22 patients with cT4NxM0 pMMR/MSS colon or upper rectal cancers were enrolled and the median follow-up was 24.7 months (IQR: 21.1-26.1). All patients underwent R0 surgical resection without treatment-related surgical delays. pCR occurred in 12 of 22 resected tumors (54.5%) and MPR occurred in 18 of 22 (81.8%) patients. At the cutoff date, all patients were alive, and 21/22 were recurrence-free. Treatment-related adverse events of grade 3 or higher occurred in of 2/22 (9.1%) patients. Among the pCR tumors, two were found to harbor POLE mutations. The degree of pathological regression was significantly greater than that of radiological regression (p = 1.35 × 10-8). The number of CD3+/CD4+ cells in the tumor and stroma in pretreated biopsied tissues was markedly lower in pCR tumors than in non-pCR tumors (p = 0.038 and p = 0.015, respectively). CONCLUSIONS Neoadjuvant sintilimab combined with bevacizumab and mFOLFOX6 was associated with few side effects, did not delay surgery, and led to pCR and non-pCR in 54.5% and 81.8% of the cases, respectively. Downregulation of CD3/CD4 expression in the tumor and stroma is related to pCR. However, the molecular mechanisms underlying PD-1 blockade-enhanced targeted chemotherapy require further investigation.
Collapse
Affiliation(s)
- Fengyun Pei
- Department of Colorectal Surgery, The Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
- Department of General Surgery, The Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Wan He
- Department of OncologyShenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology)ShenzhenChina
| | - Yinghua Duan
- Department of Traditional Chinese Medicine, The First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Qijun Yao
- Department of Colorectal Surgery, The Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
- Department of General Surgery, The Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Yandong Zhao
- Department of Pathology, The Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Xinjuan Fan
- Department of Pathology, The Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Shuai Liu
- Department of Radiation Oncology, The Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Haiyang Chen
- Department of Radiation Oncology, The Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Fang He
- Department of Radiation Oncology, The Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Tingzhi Liu
- Department of Hematology, The Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Jiaoting Chen
- Department of Hematology, The Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Yijia Zheng
- Department of Hematology, The Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Heping Li
- Department of Medical Oncology of the Eastern Hospital, The First Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Xiaofang Guo
- Department of Medical Oncology of the Eastern Hospital, The First Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Lishuo Shi
- Clinical Research Center, The Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Li Ling
- Faculty of Medical Statistics, School of Public HealthSun Yat‐sen UniversityGuangzhouChina
| | - Yaoxu Chen
- Medical Affairs3D Medicines, Inc.ShanghaiChina
| | - Jiapeng He
- Medical Affairs3D Medicines, Inc.ShanghaiChina
| | - Miao Liu
- Medical Affairs3D Medicines, Inc.ShanghaiChina
| | | | - Yuezong Bai
- Medical Affairs3D Medicines, Inc.ShanghaiChina
| | - Jianping Wang
- Department of Colorectal Surgery, The Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
- Department of General Surgery, The Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
- Guangdong Institute of GastroenterologyGuangzhouChina
| | - Meijin Huang
- Department of Colorectal Surgery, The Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
- Department of General Surgery, The Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
- Guangdong Institute of GastroenterologyGuangzhouChina
| | - Jun Huang
- Department of Colorectal Surgery, The Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
- Department of General Surgery, The Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
- Guangdong Institute of GastroenterologyGuangzhouChina
| |
Collapse
|
7
|
De Meester L, Vázquez-Domínguez E, Kassen R, Forest F, Bellon MR, Koskella B, Scherson RA, Colli L, Hendry AP, Crandall KA, Faith DP, Starger CJ, Geeta R, Araki H, Dulloo EM, Souffreau C, Schroer S, Johnson MTJ. A link between evolution and society fostering the UN sustainable development goals. Evol Appl 2024; 17:e13728. [PMID: 38884021 PMCID: PMC11178947 DOI: 10.1111/eva.13728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 06/18/2024] Open
Abstract
Given the multitude of challenges Earth is facing, sustainability science is of key importance to our continued existence. Evolution is the fundamental biological process underlying the origin of all biodiversity. This phylogenetic diversity fosters the resilience of ecosystems to environmental change, and provides numerous resources to society, and options for the future. Genetic diversity within species is also key to the ability of populations to evolve and adapt to environmental change. Yet, the value of evolutionary processes and the consequences of their impairment have not generally been considered in sustainability research. We argue that biological evolution is important for sustainability and that the concepts, theory, data, and methodological approaches used in evolutionary biology can, in crucial ways, contribute to achieving the UN Sustainable Development Goals (SDGs). We discuss how evolutionary principles are relevant to understanding, maintaining, and improving Nature Contributions to People (NCP) and how they contribute to the SDGs. We highlight specific applications of evolution, evolutionary theory, and evolutionary biology's diverse toolbox, grouped into four major routes through which evolution and evolutionary insights can impact sustainability. We argue that information on both within-species evolutionary potential and among-species phylogenetic diversity is necessary to predict population, community, and ecosystem responses to global change and to make informed decisions on sustainable production, health, and well-being. We provide examples of how evolutionary insights and the tools developed by evolutionary biology can not only inspire and enhance progress on the trajectory to sustainability, but also highlight some obstacles that hitherto seem to have impeded an efficient uptake of evolutionary insights in sustainability research and actions to sustain SDGs. We call for enhanced collaboration between sustainability science and evolutionary biology to understand how integrating these disciplines can help achieve the sustainable future envisioned by the UN SDGs.
Collapse
Affiliation(s)
- Luc De Meester
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Laboratory of Aquatic Ecology, Evolution and Conservation KU Leuven Leuven Belgium
- Institute of Biology Freie University Berlin Berlin Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - Ella Vázquez-Domínguez
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México Ciudad Universitaria Ciudad de México Mexico
- Conservation and Evolutionary Genetics Group Estación Biológica de Doñana (EBD-CSIC) Sevilla Spain
| | - Rees Kassen
- Department of Biology McGill University Montreal Quebec Canada
| | | | - Mauricio R Bellon
- Comisión Nacional Para el Conocimiento y Uso de la Biodiversidad (CONABIO) México City Mexico
- Swette Center for Sustainable Food Systems Arizona State University Tempe Arizona USA
| | - Britt Koskella
- Department of Integrative Biology University of California Berkeley California USA
| | - Rosa A Scherson
- Laboratorio Evolución y Sistemática, Departamento de Silvicultura y Conservación de la Naturaleza Universidad de Chile Santiago Chile
| | - Licia Colli
- Dipartimento di Scienze Animali, Della Nutrizione e Degli Alimenti, BioDNA Centro di Ricerca Sulla Biodiversità e Sul DNA Antico, Facoltà di Scienze Agrarie, Alimentari e Ambientali Università Cattolica del Sacro Cuore Piacenza Italy
| | - Andrew P Hendry
- Redpath Museum & Department of Biology McGill University Montreal Quebec Canada
| | - Keith A Crandall
- Department of Biostatistics and Bioinformatics George Washington University Washington DC USA
- Department of Invertebrate Zoology, US National Museum of Natural History Smithsonian Institution Washington DC USA
| | | | - Craig J Starger
- School of Global Environmental Sustainability Colorado State University Fort Collins Colorado USA
| | - R Geeta
- Department of Botany University of Delhi New Delhi India
| | - Hitoshi Araki
- Research Faculty of Agriculture Hokkaido University Sapporo Japan
| | - Ehsan M Dulloo
- Effective Genetic Resources Conservation and Use Alliance of Bioversity International and CIAT Rome Italy
| | - Caroline Souffreau
- Laboratory of Aquatic Ecology, Evolution and Conservation KU Leuven Leuven Belgium
| | - Sibylle Schroer
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
| | - Marc T J Johnson
- Department of Biology & Centre for Urban Environments University of Toronto Mississauga Mississauga Ontario Canada
| |
Collapse
|
8
|
Chen K, Shuen TWH, Chow PKH. The association between tumour heterogeneity and immune evasion mechanisms in hepatocellular carcinoma and its clinical implications. Br J Cancer 2024:10.1038/s41416-024-02684-w. [PMID: 38760445 DOI: 10.1038/s41416-024-02684-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 05/19/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related mortality worldwide. The emergence of combination therapy, atezolizumab (anti-PDL1, immune checkpoint inhibitor) and bevacizumab (anti-VEGF) has revolutionised the management of HCC. Despite this breakthrough, the best overall response rate with first-line systemic therapy is only about 30%, owing to intra-tumoural heterogeneity, complex tumour microenvironment and the lack of predictive biomarkers. Many groups have attempted to classify HCC based on the immune microenvironment and have consistently observed better outcomes in immunologically "hot" HCC. We summarised possible mechanisms of tumour immune evasion based on the latest literature and the rationale for combination/sequential therapy to improve treatment response. Lastly, we proposed future strategies and therapies to overcome HCC immune evasion to further improve treatment outcomes of HCC.
Collapse
Affiliation(s)
- Kaina Chen
- Department of Gastroenterology & Hepatology, Singapore General Hospital, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Timothy W H Shuen
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Pierce K H Chow
- Duke-NUS Medical School, Singapore, Singapore.
- Department of Hepato-pancreato-biliary and Transplant Surgery, National Cancer Centre Singapore and Singapore General Hospital, Singapore, Singapore.
- Program in Translational and Clinical Liver Cancer Research, National Cancer Centre Singapore, Singapore, Singapore.
| |
Collapse
|
9
|
Gourmet L, Walker-Samuel S, Mallick P. Examination of the role of mutualism in immune evasion. Front Oncol 2024; 14:1406744. [PMID: 38779085 PMCID: PMC11109368 DOI: 10.3389/fonc.2024.1406744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024] Open
Abstract
Though the earliest stages of oncogenesis, post initiation, are not well understood, it is generally appreciated that a successful transition from a collection of dysregulated cells to an aggressive tumour requires complex ecological interactions between cancer cells and their environment. One key component of tumorigenesis is immune evasion. To investigate the interplay amongst the ecological behaviour of mutualism and immune evasion, we used a computational simulation framework. Sensitivity analyses of the growth of a virtual tumour implemented as a 2D-hexagonal lattice model suggests tumour survival depends on the interplay between growth rates, mutualism and immune evasion. In 60% of simulations, cancer clones with low growth rates, but exhibiting mutualism were able to evade the immune system and continue progressing suggesting that tumours with equivalent growth rates and no mutualism are more likely to be eliminated than tumours with mutualism. Tumours with faster growth rates showed a lower dependence upon mutualism for progression. Geostatistical analysis showed decreased spatial heterogeneity over time for polyclonal tumours with a high division rate. Overall, these results suggest that in slow growing tumours, mutualism is critical for early tumorigenesis.
Collapse
Affiliation(s)
- Lucie Gourmet
- Centre for Computational Medicine, Division of Medicine, University College London, London, United Kingdom
| | - Simon Walker-Samuel
- Centre for Computational Medicine, Division of Medicine, University College London, London, United Kingdom
| | - Parag Mallick
- Canary Center for Cancer Early Detection, Stanford University, Palo Alto, CA, United States
| |
Collapse
|
10
|
Zhang P, Chen T, Yang M. Comparative analysis of prognosis and gene expression in prostate cancer patients with site-specific visceral metastases. Urol Oncol 2024; 42:160.e1-160.e10. [PMID: 38433022 DOI: 10.1016/j.urolonc.2024.01.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 03/05/2024]
Abstract
INTRODUCTION Prostate cancer patients with visceral metastases often exhibited poor prognoses. Few researches had compared the prognostic impact and gene expression profiles among distinct visceral metastatic sites. Therefore, we conducted a comprehensive study utilizing data from the Surveillance, Epidemiology, and End Results (SEER) database and the Gene Expression Omnibus database. PATIENTS AND METHODS We analyzed the prostate cancer-specific mortality (PCSM) risk for 8,170 patients diagnosed with metastatic prostate cancer (mPCa) between 2000 and 2019, utilizing data from the SEER 17 registry database. Patients with metastatic disease in nonregional lymph nodes, bones, brains, livers, and lungs were identified. Competing risks regression was employed to evaluate the effect of visceral metastatic disease sites on PCSM. Differentially expressed genes (DEGs) between visceral metastases were assessed using data from the GSE6752 dataset. A relative protein-protein interaction (PPI) network was constructed based on STRING analysis. Furthermore, we explored the distribution of DEGs in various normal tissues and tumor tissues using the Human Protein Atlas and GEPIA. RESULTS Competing risks regression analysis revealed that liver and lung metastases had a substantial impact on PCSM (hazard ratio 2.24, 95% confidence interval 1.70-2.95, P < 0.001; hazard ratio 1.30, 95% confidence interval 1.06-1.59, P = 0.012, respectively). Seven significant DEGs were identified from samples of liver and lung metastases (HERV-FRD, NUDT12, FAM63A, SCGB3A1, CEACAM6, LOC440416, SFTPB) and were associated with respiratory gaseous exchange, pulmonary surfactant metabolism, and fibronectin matrix formation in PPI network analysis. Notably, the expression levels of the three DEGs significantly upregulated in lung metastases were also found to be higher in normal lung tissues compared to normal liver tissues. CONCLUSION Patients diagnosed with mPCa and presenting with liver and/or lung metastases exhibit poorer prognoses. SCGB3A1, identified as a tumor suppressor gene, may contribute to the better survival prognosis observed in patients with prostate cancer lung metastases compared to those with liver metastases. The gene expression profiles in these two specific metastatic sites reveal a combination of both heterogeneity and homogeneity.
Collapse
Affiliation(s)
- Peng Zhang
- Department of Urology, Ningbo Medical Center Lihuili Hospital, Ningbo, Zhejiang, China.
| | - Tieding Chen
- Department of Urology, Ningbo Medical Center Lihuili Hospital, Ningbo, Zhejiang, China
| | - Ming Yang
- Department of Urology, Ningbo Medical Center Lihuili Hospital, Ningbo, Zhejiang, China
| |
Collapse
|
11
|
Colyer B, Bak M, Basanta D, Noble R. A seven-step guide to spatial, agent-based modelling of tumour evolution. Evol Appl 2024; 17:e13687. [PMID: 38707992 PMCID: PMC11064804 DOI: 10.1111/eva.13687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 05/07/2024] Open
Abstract
Spatial agent-based models are frequently used to investigate the evolution of solid tumours subject to localized cell-cell interactions and microenvironmental heterogeneity. As spatial genomic, transcriptomic and proteomic technologies gain traction, spatial computational models are predicted to become ever more necessary for making sense of complex clinical and experimental data sets, for predicting clinical outcomes, and for optimizing treatment strategies. Here we present a non-technical step by step guide to developing such a model from first principles. Stressing the importance of tailoring the model structure to that of the biological system, we describe methods of increasing complexity, from the basic Eden growth model up to off-lattice simulations with diffusible factors. We examine choices that unavoidably arise in model design, such as implementation, parameterization, visualization and reproducibility. Each topic is illustrated with examples drawn from recent research studies and state of the art modelling platforms. We emphasize the benefits of simpler models that aim to match the complexity of the phenomena of interest, rather than that of the entire biological system. Our guide is aimed at both aspiring modellers and other biologists and oncologists who wish to understand the assumptions and limitations of the models on which major cancer studies now so often depend.
Collapse
Affiliation(s)
- Blair Colyer
- Department of MathematicsCity, University of LondonLondonUK
| | - Maciej Bak
- Department of MathematicsCity, University of LondonLondonUK
| | - David Basanta
- Department of Integrated Mathematical OncologyH. Lee Moffitt Cancer Center and Research InstituteTampaFloridaUSA
| | - Robert Noble
- Department of MathematicsCity, University of LondonLondonUK
| |
Collapse
|
12
|
Aguadé-Gorgorió G, Anderson AR, Solé R. Modeling tumors as species-rich ecological communities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590504. [PMID: 38712062 PMCID: PMC11071393 DOI: 10.1101/2024.04.22.590504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Many advanced cancers resist therapeutic intervention. This process is fundamentally related to intra-tumor heterogeneity: multiple cell populations, each with different mutational and phenotypic signatures, coexist within a tumor and its metastatic nodes. Like species in an ecosystem, many cancer cell populations are intertwined in a complex network of ecological interactions. Most mathematical models of tumor ecology, however, cannot account for such phenotypic diversity nor are able to predict its consequences. Here we propose that the Generalized Lotka-Volterra model (GLV), a standard tool to describe complex, species-rich ecological communities, provides a suitable framework to describe the ecology of heterogeneous tumors. We develop a GLV model of tumor growth and discuss how its emerging properties, such as outgrowth and multistability, provide a new understanding of the disease. Additionally, we discuss potential extensions of the model and their application to three active areas of cancer research, namely phenotypic plasticity, the cancer-immune interplay and the resistance of metastatic tumors to treatment. Our work outlines a set of questions and a tentative road map for further research in cancer ecology.
Collapse
Affiliation(s)
| | - Alexander R.A. Anderson
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa, USA
| | - Ricard Solé
- ICREA-Complex Systems Lab, UPF-PRBB, Dr. Aiguader 80, 08003 Barcelona, Spain
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| |
Collapse
|
13
|
Ten A, Kumeiko V, Farniev V, Gao H, Shevtsov M. Tumor Microenvironment Modulation by Cancer-Derived Extracellular Vesicles. Cells 2024; 13:682. [PMID: 38667297 PMCID: PMC11049026 DOI: 10.3390/cells13080682] [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: 02/11/2024] [Revised: 04/06/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
The tumor microenvironment (TME) plays an important role in the process of tumorigenesis, regulating the growth, metabolism, proliferation, and invasion of cancer cells, as well as contributing to tumor resistance to the conventional chemoradiotherapies. Several types of cells with relatively stable phenotypes have been identified within the TME, including cancer-associated fibroblasts (CAFs), tumor-associated macrophages (TAMs), neutrophils, and natural killer (NK) cells, which have been shown to modulate cancer cell proliferation, metastasis, and interaction with the immune system, thus promoting tumor heterogeneity. Growing evidence suggests that tumor-cell-derived extracellular vesicles (EVs), via the transfer of various molecules (e.g., RNA, proteins, peptides, and lipids), play a pivotal role in the transformation of normal cells in the TME into their tumor-associated protumorigenic counterparts. This review article focuses on the functions of EVs in the modulation of the TME with a view to how exosomes contribute to the transformation of normal cells, as well as their importance for cancer diagnosis and therapy.
Collapse
Affiliation(s)
- Artem Ten
- School of Medicine and Life Sciences, Far Eastern Federal University, 690922 Vladivostok, Russia; (A.T.); (V.K.); (V.F.)
| | - Vadim Kumeiko
- School of Medicine and Life Sciences, Far Eastern Federal University, 690922 Vladivostok, Russia; (A.T.); (V.K.); (V.F.)
| | - Vladislav Farniev
- School of Medicine and Life Sciences, Far Eastern Federal University, 690922 Vladivostok, Russia; (A.T.); (V.K.); (V.F.)
| | - Huile Gao
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610064, China;
| | - Maxim Shevtsov
- School of Medicine and Life Sciences, Far Eastern Federal University, 690922 Vladivostok, Russia; (A.T.); (V.K.); (V.F.)
- Laboratory of Biomedical Nanotechnologies, Institute of Cytology of the Russian Academy of Sciences, Tikhoretsky Ave., 4, 194064 St. Petersburg, Russia
- Personalized Medicine Centre, Almazov National Medical Research Centre, Akkuratova Str., 2, 197341 St. Petersburg, Russia
- Department of Radiation Oncology, Technishe Universität München (TUM), Klinikum Rechts der Isar, Ismaninger Str., 22, 81675 Munich, Germany
| |
Collapse
|
14
|
Marrone L, Romano S, Malasomma C, Di Giacomo V, Cerullo A, Abate R, Vecchione MA, Fratantonio D, Romano MF. Metabolic vulnerability of cancer stem cells and their niche. Front Pharmacol 2024; 15:1375993. [PMID: 38659591 PMCID: PMC11039812 DOI: 10.3389/fphar.2024.1375993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Abstract
Cancer stem cells (CSC) are the leading cause of the failure of anti-tumor treatments. These aggressive cancer cells are preserved and sustained by adjacent cells forming a specialized microenvironment, termed niche, among which tumor-associated macrophages (TAMs) are critical players. The cycle of tricarboxylic acids, fatty acid oxidation path, and electron transport chain have been proven to play central roles in the development and maintenance of CSCs and TAMs. By improving their oxidative metabolism, cancer cells are able to extract more energy from nutrients, which allows them to survive in nutritionally defective environments. Because mitochondria are crucial bioenergetic hubs and sites of these metabolic pathways, major hopes are posed for drugs targeting mitochondria. A wide range of medications targeting mitochondria, electron transport chain complexes, or oxidative enzymes are currently investigated in phase 1 and phase 2 clinical trials against hard-to-treat tumors. This review article aims to highlight recent literature on the metabolic adaptations of CSCs and their supporting macrophages. A focus is provided on the resistance and dormancy behaviors that give CSCs a selection advantage and quiescence capacity in particularly hostile microenvironments and the role of TAMs in supporting these attitudes. The article also describes medicaments that have demonstrated a robust ability to disrupt core oxidative metabolism in preclinical cancer studies and are currently being tested in clinical trials.
Collapse
Affiliation(s)
- Laura Marrone
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Simona Romano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Chiara Malasomma
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Valeria Di Giacomo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Andrea Cerullo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Rosetta Abate
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | | | - Deborah Fratantonio
- Department of Medicine and Surgery, LUM University Giuseppe Degennaro, Bari, Italy
| | - Maria Fiammetta Romano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| |
Collapse
|
15
|
Lu Q, Kou D, Lou S, Ashrafizadeh M, Aref AR, Canadas I, Tian Y, Niu X, Wang Y, Torabian P, Wang L, Sethi G, Tergaonkar V, Tay F, Yuan Z, Han P. Nanoparticles in tumor microenvironment remodeling and cancer immunotherapy. J Hematol Oncol 2024; 17:16. [PMID: 38566199 PMCID: PMC10986145 DOI: 10.1186/s13045-024-01535-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
Cancer immunotherapy and vaccine development have significantly improved the fight against cancers. Despite these advancements, challenges remain, particularly in the clinical delivery of immunomodulatory compounds. The tumor microenvironment (TME), comprising macrophages, fibroblasts, and immune cells, plays a crucial role in immune response modulation. Nanoparticles, engineered to reshape the TME, have shown promising results in enhancing immunotherapy by facilitating targeted delivery and immune modulation. These nanoparticles can suppress fibroblast activation, promote M1 macrophage polarization, aid dendritic cell maturation, and encourage T cell infiltration. Biomimetic nanoparticles further enhance immunotherapy by increasing the internalization of immunomodulatory agents in immune cells such as dendritic cells. Moreover, exosomes, whether naturally secreted by cells in the body or bioengineered, have been explored to regulate the TME and immune-related cells to affect cancer immunotherapy. Stimuli-responsive nanocarriers, activated by pH, redox, and light conditions, exhibit the potential to accelerate immunotherapy. The co-application of nanoparticles with immune checkpoint inhibitors is an emerging strategy to boost anti-tumor immunity. With their ability to induce long-term immunity, nanoarchitectures are promising structures in vaccine development. This review underscores the critical role of nanoparticles in overcoming current challenges and driving the advancement of cancer immunotherapy and TME modification.
Collapse
Affiliation(s)
- Qiang Lu
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Medical University, 569 Xinsi Road, Xi'an, 710038, China
| | - Dongquan Kou
- Department of Rehabilitation Medicine, Chongqing Public Health Medical Center, Chongqing, China
| | - Shenghan Lou
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Milad Ashrafizadeh
- Department of General Surgery, Institute of Precision Diagnosis and Treatment of Digestive System Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, 518055, Guangdong, China
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, 250000, Shandong, China
| | - Amir Reza Aref
- Xsphera Biosciences, Translational Medicine Group, 6 Tide Street, Boston, MA, 02210, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Israel Canadas
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Yu Tian
- School of Public Health, Benedictine University, Lisle, USA
| | - Xiaojia Niu
- Department of Urologic Sciences and Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, V6H3Z6, Canada
| | - Yuzhuo Wang
- Department of Urologic Sciences and Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, V6H3Z6, Canada
| | - Pedram Torabian
- Cumming School of Medicine, Arnie Charbonneau Cancer Research Institute, University of Calgary, Calgary, AB, T2N 4Z6, Canada
- Department of Medical Sciences, University of Calgary, Calgary, AB, T2N 4Z6, Canada
| | - Lingzhi Wang
- NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 16 Medical Drive, Singapore, 117600, Singapore
| | - Gautam Sethi
- NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 16 Medical Drive, Singapore, 117600, Singapore.
| | - Vinay Tergaonkar
- Laboratory of NF-κB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, 138673, Singapore, Republic of Singapore
| | - Franklin Tay
- The Graduate School, Augusta University, 30912, Augusta, GA, USA
| | - Zhennan Yuan
- Department of Oncology Surgery, Harbin Medical University Cancer Hospital, Harbin, China.
| | - Peng Han
- Department of Oncology Surgery, Harbin Medical University Cancer Hospital, Harbin, China.
- Key Laboratory of Tumor Immunology in Heilongjiang, Harbin, China.
| |
Collapse
|
16
|
Alejandre C, Calle-Espinosa J, Iranzo J. Synergistic epistasis among cancer drivers can rescue early tumors from the accumulation of deleterious passengers. PLoS Comput Biol 2024; 20:e1012081. [PMID: 38687804 PMCID: PMC11087069 DOI: 10.1371/journal.pcbi.1012081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 05/10/2024] [Accepted: 04/16/2024] [Indexed: 05/02/2024] Open
Abstract
Epistasis among driver mutations is pervasive and explains relevant features of cancer, such as differential therapy response and convergence towards well-characterized molecular subtypes. Furthermore, a growing body of evidence suggests that tumor development could be hampered by the accumulation of slightly deleterious passenger mutations. In this work, we combined empirical epistasis networks, computer simulations, and mathematical models to explore how synergistic interactions among driver mutations affect cancer progression under the burden of slightly deleterious passengers. We found that epistasis plays a crucial role in tumor development by promoting the transformation of precancerous clones into rapidly growing tumors through a process that is analogous to evolutionary rescue. The triggering of epistasis-driven rescue is strongly dependent on the intensity of epistasis and could be a key rate-limiting step in many tumors, contributing to their unpredictability. As a result, central genes in cancer epistasis networks appear as key intervention targets for cancer therapy.
Collapse
Affiliation(s)
- Carla Alejandre
- Centro de Astrobiología (CAB) CSIC-INTA, Torrejón de Ardoz, Madrid, Spain
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Jorge Calle-Espinosa
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Jaime Iranzo
- Centro de Astrobiología (CAB) CSIC-INTA, Torrejón de Ardoz, Madrid, Spain
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain
| |
Collapse
|
17
|
Guo J, Ma RY, Qian BZ. Macrophage heterogeneity in bone metastasis. J Bone Oncol 2024; 45:100598. [PMID: 38585688 PMCID: PMC10997910 DOI: 10.1016/j.jbo.2024.100598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/16/2024] [Accepted: 03/20/2024] [Indexed: 04/09/2024] Open
Abstract
Previous studies illustrated that macrophage, a type of innate immune cell, plays critical roles in tumour progression and metastasis. Bone is the most frequent site of metastasis for several cancer types including breast, prostate, and lung. In bone metastasis, osteoclast, a macrophage subset specialized in bone resorption, was heavily investigated in the past. Recent studies illustrated that other macrophage subsets, e.g. monocyte-derived macrophages, and bone resident macrophages, promoted bone metastasis independent of osteoclast function. These novel mechanisms further improved our understanding of macrophage heterogeneity in the context of bone metastasis and illustrated new opportunities for future studies.
Collapse
Affiliation(s)
| | | | - Bin-Zhi Qian
- Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, The Human Phenome Institute, Zhangjiang-Fudan International Innovation Center, Fudan University, Shanghai 200438, China
| |
Collapse
|
18
|
Bao K, Liang G, Tian T, Zhang X. Mathematical modeling of combined therapies for treating tumor drug resistance. Math Biosci 2024; 371:109170. [PMID: 38467302 DOI: 10.1016/j.mbs.2024.109170] [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: 06/25/2023] [Revised: 02/27/2024] [Accepted: 03/03/2024] [Indexed: 03/13/2024]
Abstract
Drug resistance is one of the most intractable issues to the targeted therapy for cancer diseases. To explore effective combination therapy schemes, we propose a mathematical model to study the effects of different treatment schemes on the dynamics of cancer cells. Then we characterize the dynamical behavior of the model by finding the equilibrium points and exploring their local stability. Lyapunov functions are constructed to investigate the global asymptotic stability of the model equilibria. Numerical simulations are carried out to verify the stability of equilibria and treatment outcomes using a set of collected model parameters and experimental data on murine colon carcinoma. Simulation results suggest that immunotherapy combined with chemotherapy contributes significantly to the control of tumor growth compared to monotherapy. Sensitivity analysis is performed to identify the importance of model parameters on the variations of model outcomes.
Collapse
Affiliation(s)
- Kangbo Bao
- School of Mathematics and Statistics, Central China Normal University, Wuhan, 430079, PR China.
| | - Guizhen Liang
- School of Mathematics and Information Science, Xinxiang University, Xinxiang, 453003, PR China.
| | - Tianhai Tian
- School of Mathematics, Monash University, Melbourne, VIC 3800, Australia.
| | - Xinan Zhang
- School of Mathematics and Statistics, Central China Normal University, Wuhan, 430079, PR China.
| |
Collapse
|
19
|
Katsikis PD, Ishii KJ, Schliehe C. Challenges in developing personalized neoantigen cancer vaccines. Nat Rev Immunol 2024; 24:213-227. [PMID: 37783860 DOI: 10.1038/s41577-023-00937-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2023] [Indexed: 10/04/2023]
Abstract
The recent success of cancer immunotherapies has highlighted the benefit of harnessing the immune system for cancer treatment. Vaccines have a long history of promoting immunity to pathogens and, consequently, vaccines targeting cancer neoantigens have been championed as a tool to direct and amplify immune responses against tumours while sparing healthy tissue. In recent years, extensive preclinical research and more than one hundred clinical trials have tested different strategies of neoantigen discovery and vaccine formulations. However, despite the enthusiasm for neoantigen vaccines, proof of unequivocal efficacy has remained beyond reach for the majority of clinical trials. In this Review, we focus on the key obstacles pertaining to vaccine design and tumour environment that remain to be overcome in order to unleash the true potential of neoantigen vaccines in cancer therapy.
Collapse
Affiliation(s)
- Peter D Katsikis
- Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands.
| | - Ken J Ishii
- Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo (IMSUT), Tokyo, Japan
- International Vaccine Design Center (vDesC), The Institute of Medical Science, The University of Tokyo (IMSUT), Tokyo, Japan
| | - Christopher Schliehe
- Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
| |
Collapse
|
20
|
Valcz G, Buzás EI, Gatenby RA, Újvári B, Molnár B. Small extracellular vesicles from surviving cancer cells as multiparametric monitoring tools of measurable residual disease and therapeutic efficiency. Biochim Biophys Acta Rev Cancer 2024; 1879:189088. [PMID: 38387823 DOI: 10.1016/j.bbcan.2024.189088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/13/2023] [Accepted: 02/18/2024] [Indexed: 02/24/2024]
Abstract
Although conventional anti-cancer therapies remove most cells of the tumor mass, small surviving populations may evolve adaptive resistance strategies, which lead to treatment failure. The size of the resistant population initially may not reach the threshold of clinical detection (designated as measurable residual disease/MRD) thus, its investigation requires highly sensitive and specific methods. Here, we discuss that the specific molecular fingerprint of tumor-derived small extracellular vesicles (sEVs) is suitable for longitudinal monitoring of MRD. Furthermore, we present a concept that exploiting the multiparametric nature of sEVs may help early detection of recurrence and the design of dynamic, evolution-adjusted treatments.
Collapse
Affiliation(s)
- Gábor Valcz
- HUN-REN-SU Translational Extracellular Vesicle Research Group, Budapest, Hungary; Department of Image Analysis, 3DHISTECH Ltd, Budapest, Hungary.
| | - Edit I Buzás
- HUN-REN-SU Translational Extracellular Vesicle Research Group, Budapest, Hungary; Institute of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary; HCEMM-SU Extracellular Vesicles Research Group, Budapest, Hungary
| | - Robert A Gatenby
- Cancer Biology and Evolution Program, Moffitt Cancer Center, Tampa, FL, USA
| | - Beáta Újvári
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, Australia
| | - Béla Molnár
- Department of Image Analysis, 3DHISTECH Ltd, Budapest, Hungary; Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| |
Collapse
|
21
|
Revsine M, Wang L, Forgues M, Behrens S, Craig AJ, Liu M, Tran B, Kelly M, Budhu A, Monge C, Xie C, Hernandez JM, Greten TF, Wang XW, Ma L. Lineage and ecology define liver tumor evolution in response to treatment. Cell Rep Med 2024; 5:101394. [PMID: 38280378 PMCID: PMC10897542 DOI: 10.1016/j.xcrm.2024.101394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/09/2023] [Accepted: 01/03/2024] [Indexed: 01/29/2024]
Abstract
A tumor ecosystem constantly evolves over time in the face of immune predation or therapeutic intervention, resulting in treatment failure and tumor progression. Here, we present a single-cell transcriptome-based strategy to determine the evolution of longitudinal tumor biopsies from liver cancer patients by measuring cellular lineage and ecology. We construct a lineage and ecological score as joint dynamics of tumor cells and their microenvironments. Tumors may be classified into four main states in the lineage-ecological space, which are associated with clinical outcomes. Analysis of longitudinal samples reveals the evolutionary trajectory of tumors in response to treatment. We validate the lineage-ecology-based scoring system in predicting clinical outcomes using bulk transcriptomic data of additional cohorts of 716 liver cancer patients. Our study provides a framework for monitoring tumor evolution in response to therapeutic intervention.
Collapse
Affiliation(s)
- Mahler Revsine
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Limin Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Marshonna Forgues
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Shay Behrens
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Amanda J Craig
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Meng Liu
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Bao Tran
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 20701, USA
| | - Michael Kelly
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 20701, USA
| | - Anuradha Budhu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Cecilia Monge
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Changqing Xie
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Jonathan M Hernandez
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Tim F Greten
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
| | - Lichun Ma
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
| |
Collapse
|
22
|
Neagu AN, Whitham D, Bruno P, Arshad A, Seymour L, Morrissiey H, Hukovic AI, Darie CC. Onco-Breastomics: An Eco-Evo-Devo Holistic Approach. Int J Mol Sci 2024; 25:1628. [PMID: 38338903 PMCID: PMC10855488 DOI: 10.3390/ijms25031628] [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: 12/20/2023] [Revised: 01/21/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Known as a diverse collection of neoplastic diseases, breast cancer (BC) can be hyperbolically characterized as a dynamic pseudo-organ, a living organism able to build a complex, open, hierarchically organized, self-sustainable, and self-renewable tumor system, a population, a species, a local community, a biocenosis, or an evolving dynamical ecosystem (i.e., immune or metabolic ecosystem) that emphasizes both developmental continuity and spatio-temporal change. Moreover, a cancer cell community, also known as an oncobiota, has been described as non-sexually reproducing species, as well as a migratory or invasive species that expresses intelligent behavior, or an endangered or parasite species that fights to survive, to optimize its features inside the host's ecosystem, or that is able to exploit or to disrupt its host circadian cycle for improving the own proliferation and spreading. BC tumorigenesis has also been compared with the early embryo and placenta development that may suggest new strategies for research and therapy. Furthermore, BC has also been characterized as an environmental disease or as an ecological disorder. Many mechanisms of cancer progression have been explained by principles of ecology, developmental biology, and evolutionary paradigms. Many authors have discussed ecological, developmental, and evolutionary strategies for more successful anti-cancer therapies, or for understanding the ecological, developmental, and evolutionary bases of BC exploitable vulnerabilities. Herein, we used the integrated framework of three well known ecological theories: the Bronfenbrenner's theory of human development, the Vannote's River Continuum Concept (RCC), and the Ecological Evolutionary Developmental Biology (Eco-Evo-Devo) theory, to explain and understand several eco-evo-devo-based principles that govern BC progression. Multi-omics fields, taken together as onco-breastomics, offer better opportunities to integrate, analyze, and interpret large amounts of complex heterogeneous data, such as various and big-omics data obtained by multiple investigative modalities, for understanding the eco-evo-devo-based principles that drive BC progression and treatment. These integrative eco-evo-devo theories can help clinicians better diagnose and treat BC, for example, by using non-invasive biomarkers in liquid-biopsies that have emerged from integrated omics-based data that accurately reflect the biomolecular landscape of the primary tumor in order to avoid mutilating preventive surgery, like bilateral mastectomy. From the perspective of preventive, personalized, and participatory medicine, these hypotheses may help patients to think about this disease as a process governed by natural rules, to understand the possible causes of the disease, and to gain control on their own health.
Collapse
Affiliation(s)
- Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, “Alexandru Ioan Cuza” University of Iași, Carol I bvd. 20A, 700505 Iasi, Romania
| | - Danielle Whitham
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA; (D.W.); (P.B.); (A.A.); (L.S.); (H.M.); (A.I.H.)
| | - Pathea Bruno
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA; (D.W.); (P.B.); (A.A.); (L.S.); (H.M.); (A.I.H.)
| | - Aneeta Arshad
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA; (D.W.); (P.B.); (A.A.); (L.S.); (H.M.); (A.I.H.)
| | - Logan Seymour
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA; (D.W.); (P.B.); (A.A.); (L.S.); (H.M.); (A.I.H.)
| | - Hailey Morrissiey
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA; (D.W.); (P.B.); (A.A.); (L.S.); (H.M.); (A.I.H.)
| | - Angiolina I. Hukovic
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA; (D.W.); (P.B.); (A.A.); (L.S.); (H.M.); (A.I.H.)
| | - Costel C. Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA; (D.W.); (P.B.); (A.A.); (L.S.); (H.M.); (A.I.H.)
| |
Collapse
|
23
|
Valdivia A, Cowan M, Cardenas H, Isac AM, Zhao G, Huang H, Matei D. E2F1 mediates competition, proliferation and response to cisplatin in cohabitating resistant and sensitive ovarian cancer cells. Front Oncol 2024; 14:1304691. [PMID: 38344207 PMCID: PMC10853425 DOI: 10.3389/fonc.2024.1304691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/09/2024] [Indexed: 02/28/2024] Open
Abstract
Background Tumor heterogeneity is one of the key factors leading to chemo-resistance relapse. It remains unknown how resistant cancer cells influence sensitive cells during cohabitation and growth within a heterogenous tumors. The goal of our study was to identify driving factors that mediate the interactions between resistant and sensitive cancer cells and to determine the effects of cohabitation on both phenotypes. Methods We used isogenic ovarian cancer (OC) cell lines pairs, sensitive and resistant to platinum: OVCAR5 vs. OVCAR5 CisR and PE01 vs. PE04, respectively, to perform long term direct culture and to study the phenotypical changes of the interaction of these cells. Results Long term direct co-culture of sensitive and resistant OC cells promoted proliferation (p < 0.001) of sensitive cells and increased the proportion of cells in the G1 and S cell cycle phase in both PE01 and OVCAR5 cells. Direct co-culture led to a decrease in the IC50 to platinum in the cisplatin-sensitive cells (5.92 µM to 2.79 µM for PE01, and from 2.05 µM to 1.51 µM for OVCAR5). RNAseq analysis of co-cultured cells showed enrichment of Cell Cycle Control, Cyclins and Cell Cycle Regulation pathways. The transcription factor E2F1 was predicted as the main effector responsible for the transcriptomic changes in sensitive cells. Western blot and qRT-PCR confirmed upregulation of E2F1 in co-cultured vs monoculture. Furthermore, an E2F1 inhibitor reverted the increase in proliferation rate induced by co-culture to baseline levels. Conclusion Our data suggest that long term cohabitation of chemo-sensitive and -resistant cancer cells drive sensitive cells to a higher proliferative state, more responsive to platinum. Our results reveal an unexpected effect caused by direct interactions between cancer cells with different proliferative rates and levels of platinum resistance, modelling competition between cells in heterogeneous tumors.
Collapse
Affiliation(s)
- Andres Valdivia
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Matthew Cowan
- Department of Obstetrics & Gynecology and Women’s Health, Montefiore Medical Center, Bronx, NY, United States
| | - Horacio Cardenas
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Ana Maria Isac
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Guangyuan Zhao
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Hao Huang
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Daniela Matei
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Department of Medicine, Jesse Brown Veterans Affairs Medical Center, Chicago, IL, United States
| |
Collapse
|
24
|
Zhang J, Duan Y, Wu P, Chang Y, Wang Y, Hu T, Liu C, Chen X, Zong S, Chen X, Wu Y, Jin L, Lan Y, Liu X, Cheng X, Ding F, Li T, Chen X, Guo Y, Chen Y, Yang W, Zhang L, Zou Y, Cheng T, Zhu X, Zhang Y. Clonal evolution dissection reveals that a high MSI2 level promotes chemoresistance in T-cell acute lymphoblastic leukemia. Blood 2024; 143:320-335. [PMID: 37801708 DOI: 10.1182/blood.2023020490] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 10/08/2023] Open
Abstract
ABSTRACT T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive cancer with resistant clonal propagation in recurrence. We performed high-throughput droplet-based 5' single-cell RNA with paired T-cell receptor (TCR) sequencing of paired diagnosis-relapse (Dx_Rel) T-ALL samples to dissect the clonal diversities. Two leukemic evolutionary patterns, "clonal shift" and "clonal drift" were unveiled. Targeted single-cell DNA sequencing of paired Dx_Rel T-ALL samples further corroborated the existence of the 2 contrasting clonal evolution patterns, revealing that dynamic transcriptional variation might cause the mutationally static clones to evolve chemotherapy resistance. Analysis of commonly enriched drifted gene signatures showed expression of the RNA-binding protein MSI2 was significantly upregulated in the persistent TCR clonotypes at relapse. Integrated in vitro and in vivo functional studies suggested that MSI2 contributed to the proliferation of T-ALL and promoted chemotherapy resistance through the posttranscriptional regulation of MYC, pinpointing MSI2 as an informative biomarker and novel therapeutic target in T-ALL.
Collapse
Affiliation(s)
- Jingliao Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Yongjuan Duan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Peng Wu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | | | - Yue Wang
- Novogene Co, Ltd, Beijing, China
| | - Tianyuan Hu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Chao Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Xiaoyan Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Suyu Zong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Xiaoli Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Yangping Wu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Linlin Jin
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Yang Lan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Xiaoming Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Xuelian Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | | | - Tianyu Li
- Wuxi Children's Hospital, Jiangsu, China
| | - Xiaojuan Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Ye Guo
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Yumei Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Wenyu Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Li Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Yao Zou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Xiaofan Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Yingchi Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| |
Collapse
|
25
|
Feng P, Xue X, Bukhari I, Qiu C, Li Y, Zheng P, Mi Y. Gut microbiota and its therapeutic implications in tumor microenvironment interactions. Front Microbiol 2024; 15:1287077. [PMID: 38322318 PMCID: PMC10844568 DOI: 10.3389/fmicb.2024.1287077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/08/2024] [Indexed: 02/08/2024] Open
Abstract
The development of cancer is not just the growth and proliferation of a single transformed cell, but its tumor microenvironment (TME) also coevolves with it, which is primarily involved in tumor initiation, development, metastasis, and therapeutic responses. Recent years, TME has been emerged as a potential target for cancer diagnosis and treatment. However, the clinical efficacy of treatments targeting the TME, especially its specific components, remains insufficient. In parallel, the gut microbiome is an essential TME component that is crucial in cancer immunotherapy. Thus, assessing and constructing frameworks between the gut microbiota and the TME can significantly enhance the exploration of effective treatment strategies for various tumors. In this review the role of the gut microbiota in human cancers, including its function and relationship with various tumors was summarized. In addition, the interaction between the gut microbiota and the TME as well as its potential applications in cancer therapeutics was described. Furthermore, it was summarized that fecal microbiota transplantation, dietary adjustments, and synthetic biology to introduce gut microbiota-based medical technologies for cancer treatment. This review provides a comprehensive summary for uncovering the mechanism underlying the effects of the gut microbiota on the TME and lays a foundation for the development of personalized medicine in further studies.
Collapse
Affiliation(s)
- Pengya Feng
- Key Laboratory of Helicobacter Pylori, Microbiota and Gastrointestinal Cancer of Henan Province, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Children Rehabilitation Medicine, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Gastroenterology, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xia Xue
- Key Laboratory of Helicobacter Pylori, Microbiota and Gastrointestinal Cancer of Henan Province, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Gastroenterology, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ihtisham Bukhari
- Key Laboratory of Helicobacter Pylori, Microbiota and Gastrointestinal Cancer of Henan Province, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Gastroenterology, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chunjing Qiu
- Key Laboratory of Helicobacter Pylori, Microbiota and Gastrointestinal Cancer of Henan Province, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Gastroenterology, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yingying Li
- Key Laboratory of Helicobacter Pylori, Microbiota and Gastrointestinal Cancer of Henan Province, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Gastroenterology, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Pengyuan Zheng
- Key Laboratory of Helicobacter Pylori, Microbiota and Gastrointestinal Cancer of Henan Province, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Gastroenterology, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yang Mi
- Key Laboratory of Helicobacter Pylori, Microbiota and Gastrointestinal Cancer of Henan Province, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Gastroenterology, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| |
Collapse
|
26
|
Tian J, Fu W, Xie Z, Zhao Y, Yang H, Zhao J. Methionine enkephalin (MENK) protected macrophages from ferroptosis by downregulating HMOX1 and ferritin. Proteome Sci 2024; 22:2. [PMID: 38245706 PMCID: PMC10799539 DOI: 10.1186/s12953-024-00228-x] [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: 05/02/2023] [Accepted: 01/06/2024] [Indexed: 01/22/2024] Open
Abstract
OBJECTIVE The aim of this work was to investigate the immunological effect of MENK by analyzing the protein spectrum and bioinformatics of macrophage RAW264.7, and to explore the relationship between macrophage and ferroptosis. RESULT We employed proteomic analysis to identify differentially expressed proteins (DEPs) between macrophages and macrophages intervened by MENK. A total of 208 DEPs were identified. Among these, 96 proteins had upregulated expression and 112 proteins had downregulated expression. Proteomic analysis revealed a significant enrichment of DEPs associated with iron metabolism. The identification of hub genes was conducted using KEGG pathway diagrams and protein-protein interaction (PPI) analysis. The hub genes identified in this study include HMOX1 and Ferritin (FTH and FTL). A correlation was established between HMOX1, FTH, and FTL in the GO and KEGG databases. The results of PCR, WB and immunofluorescence showed that MENK downregulated the level of HMOX1 and FTH. CONCLUSION MENK had the potential to become an adjuvant chemotherapy drug by regulating iron metabolism in macrophages, reducing levels of HMOX1 and ferritin. We proposed an innovative research direction on the therapeutic potential of MENK, focusing on the relationship between ferroptosis and macrophage activity.
Collapse
Affiliation(s)
- Jing Tian
- Department of Immunology, School of Basic Medical Science, Jinzhou Medical University, Jinzhou, Liaoning, 121000, China.
| | - Wenrui Fu
- Graduate College, Jinzhou Medical University, Jinzhou, Liaoning, 121000, China
| | - Zifeng Xie
- First Clinical Medical College, Jinzhou Medical University, Jinzhou, Liaoning, 121000, China
| | - Yuanlong Zhao
- First Clinical Medical College, Jinzhou Medical University, Jinzhou, Liaoning, 121000, China
| | - Haochen Yang
- First Clinical Medical College, Jinzhou Medical University, Jinzhou, Liaoning, 121000, China
| | - Jiafan Zhao
- First Clinical Medical College, Jinzhou Medical University, Jinzhou, Liaoning, 121000, China
| |
Collapse
|
27
|
Baygin RC, Yilmaz KC, Acar A. Characterization of dabrafenib-induced drug insensitivity via cellular barcoding and collateral sensitivity to second-line therapeutics. Sci Rep 2024; 14:286. [PMID: 38167959 PMCID: PMC10762103 DOI: 10.1038/s41598-023-50443-3] [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: 05/14/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024] Open
Abstract
Drug insensitivity is arguably one of the biggest challenges in cancer therapeutics. Although effective therapeutic solutions in cancer are limited due to the emergence of drug insensitivity, exploiting evolutionary understanding in this context can provide potential second-line therapeutics sensitizing the drug insensitive populations. Targeted therapeutic agent dabrafenib is used to treat CRC patients with BRAF V600E genotype and insensitivity to dabrafenib is often observed. Understanding underlying clonal architecture of dabrafenib-induced drug insensitivity and identification of potential second-line therapeutics that could sensitize dabrafenib insensitive populations remain to be elucidated. For this purpose, we utilized cellular barcoding technology to decipher dabrafenib-induced clonal evolution in BRAF V600E mutant HT-29 cells. This approach revealed the detection of both pre-existing and de novo barcodes with increased frequencies as a result of dabrafenib insensitivity. Furthermore, our longitudinal monitoring of drug insensitivity based on barcode detection from floating DNA within used medium enabled to identify temporal dynamics of pre-existing and de novo barcodes in relation to dabrafenib insensitivity in HT-29 cells. Moreover, whole-exome sequencing analysis exhibited possible somatic CNVs and SNVs contributing to dabrafenib insensitivity in HT-29 cells. Last, collateral drug sensitivity testing demonstrated oxaliplatin and capecitabine, alone or in combination, as successful second-like therapeutics in inducing collateral sensitivity in dabrafenib-insensitive HT-29 cells. Overall, our findings demonstrate clonal dynamics of dabrafenib-insensitivity in HT-29 cells. In addition, oxaliplatin and capecitabine, alone or in combination, were successful second-line therapeutics in inducing collateral sensitivity in dabrafenib-insensitive HT-29 cells.
Collapse
Affiliation(s)
- Rana Can Baygin
- Department of Biological Sciences, Middle East Technical University, Universiteler Mah. Dumlupınar Bulvarı 1, Çankaya, 06800, Ankara, Turkey
| | - Kubra Celikbas Yilmaz
- Department of Biological Sciences, Middle East Technical University, Universiteler Mah. Dumlupınar Bulvarı 1, Çankaya, 06800, Ankara, Turkey
| | - Ahmet Acar
- Department of Biological Sciences, Middle East Technical University, Universiteler Mah. Dumlupınar Bulvarı 1, Çankaya, 06800, Ankara, Turkey.
| |
Collapse
|
28
|
Derbal Y. Adaptive Cancer Therapy in the Age of Generative Artificial Intelligence. Cancer Control 2024; 31:10732748241264704. [PMID: 38897721 PMCID: PMC11189021 DOI: 10.1177/10732748241264704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/17/2024] [Accepted: 06/06/2024] [Indexed: 06/21/2024] Open
Abstract
Therapeutic resistance is a major challenge facing the design of effective cancer treatments. Adaptive cancer therapy is in principle the most viable approach to manage cancer's adaptive dynamics through drug combinations with dose timing and modulation. However, there are numerous open issues facing the clinical success of adaptive therapy. Chief among these issues is the feasibility of real-time predictions of treatment response which represent a bedrock requirement of adaptive therapy. Generative artificial intelligence has the potential to learn prediction models of treatment response from clinical, molecular, and radiomics data about patients and their treatments. The article explores this potential through a proposed integration model of Generative Pre-Trained Transformers (GPTs) in a closed loop with adaptive treatments to predict the trajectories of disease progression. The conceptual model and the challenges facing its realization are discussed in the broader context of artificial intelligence integration in oncology.
Collapse
Affiliation(s)
- Youcef Derbal
- Ted Rogers School of Information Technology Management, Toronto Metropolitan University, Toronto, ON, Canada
| |
Collapse
|
29
|
Di Ieva A. Fractal Analysis in Clinical Neurosciences: An Overview. ADVANCES IN NEUROBIOLOGY 2024; 36:261-271. [PMID: 38468037 DOI: 10.1007/978-3-031-47606-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Over the last years, fractals have entered into the realms of clinical neurosciences. The whole brain and its components (i.e., neurons and astrocytes) have been studied as fractal objects, and even more relevant, the fractal-based quantification of the geometrical complexity of histopathological and neuroradiological images as well as neurophysiopathological time series has suggested the existence of a gradient in the pattern representation of neurological diseases. Computational fractal-based parameters have been suggested as potential diagnostic and prognostic biomarkers in different brain diseases, including brain tumors, neurodegeneration, epilepsy, demyelinating diseases, cerebrovascular malformations, and psychiatric disorders as well. This chapter and the entire third section of this book are focused on practical applications of computational fractal-based analysis into the clinical neurosciences, namely, neurology and neuropsychiatry, neuroradiology and neurosurgery, neuropathology, neuro-oncology and neurorehabilitation, neuro-ophthalmology, and cognitive neurosciences, with special emphasis on the translation of the fractal dimension and other fractal parameters as clinical biomarkers useful from bench to bedside.
Collapse
Affiliation(s)
- Antonio Di Ieva
- Computational NeuroSurgery (CNS) Lab & Macquarie Neurosurgery, Macquarie Medical School, Faculty of Medicine, Human and Health Sciences, Macquarie University, Sydney, NSW, Australia.
| |
Collapse
|
30
|
Wan Y, Mu Q, Krzysztoń R, Cohen J, Coraci D, Helenek C, Tompkins C, Lin A, Farquhar K, Cross E, Wang J, Balázsi G. Adaptive DNA amplification of synthetic gene circuit opens a way to overcome cancer chemoresistance. Proc Natl Acad Sci U S A 2023; 120:e2303114120. [PMID: 38019857 DOI: 10.1073/pnas.2303114120] [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: 02/22/2023] [Accepted: 09/27/2023] [Indexed: 12/01/2023] Open
Abstract
Drug resistance continues to impede the success of cancer treatments, creating a need for experimental model systems that are broad, yet simple, to allow the identification of mechanisms and novel countermeasures applicable to many cancer types. To address these needs, we investigated a set of engineered mammalian cell lines with synthetic gene circuits integrated into their genome that evolved resistance to Puromycin. We identified DNA amplification as the mechanism underlying drug resistance in 4 out of 6 replicate populations. Triplex-forming oligonucleotide (TFO) treatment combined with Puromycin could efficiently suppress the growth of cell populations with DNA amplification. Similar observations in human cancer cell lines suggest that TFOs could be broadly applicable to mitigate drug resistance, one of the major difficulties in treating cancer.
Collapse
Affiliation(s)
- Yiming Wan
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
| | - Quanhua Mu
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong Special Administrative Region 999077, China
| | - Rafał Krzysztoń
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
| | - Joseph Cohen
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
| | - Damiano Coraci
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
| | - Christopher Helenek
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
| | | | - Annie Lin
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
| | - Kevin Farquhar
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
| | | | - Jiguang Wang
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong Special Administrative Region 999077, China
| | - Gábor Balázsi
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11794
| |
Collapse
|
31
|
Liu Z, Zhang Y, Wu C. Single-cell sequencing in pancreatic cancer research: A deeper understanding of heterogeneity and therapy. Biomed Pharmacother 2023; 168:115664. [PMID: 37837881 DOI: 10.1016/j.biopha.2023.115664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/28/2023] [Accepted: 10/06/2023] [Indexed: 10/16/2023] Open
Abstract
Pancreatic cancer, including pancreatic ductal adenocarcinomas (PDACs), is a malignant tumor with characteristics of tumor-stroma interactions. Patients often have a poor prognosis and a poor long-term survival rate. In recent years, rapidly-developing single-cell sequencing techniques have been used to analyze cell populations at a single-cell resolution, so that it is now possible to have a more in-depth and clearer understanding of the genetic composition of pancreatic cancer. In this review, we provide an overview of the current single-cell sequencing techniques and their applications in the exploration of intratumoral heterogeneity, the tumor microenvironment, therapy resistance, and novel treatments. Our hope is to provide new insight into the potential of precision therapy, which will perhaps one day lead to significant advances in PDAC treatment.
Collapse
Affiliation(s)
- Zhuomiao Liu
- Department of Radiation Oncology, the Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Yalin Zhang
- Department of Radiation Oncology, the Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Chunli Wu
- Department of Radiation Oncology, the Fourth Affiliated Hospital of China Medical University, Shenyang, China.
| |
Collapse
|
32
|
Ivanov RA, Lashin SA. Intratumor heterogeneity: models of malignancy emergence and evolution. Vavilovskii Zhurnal Genet Selektsii 2023; 27:815-819. [PMID: 38213707 PMCID: PMC10777286 DOI: 10.18699/vjgb-23-94] [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: 07/13/2023] [Revised: 08/07/2023] [Accepted: 08/17/2023] [Indexed: 01/13/2024] Open
Abstract
Cancer is a complex and heterogeneous disease characterized by the accumulation of genetic alterations that drive uncontrolled cell growth and proliferation. Evolutionary dynamics plays a crucial role in the emergence and development of tumors, shaping the heterogeneity and adaptability of cancer cells. From the perspective of evolutionary theory, tumors are complex ecosystems that evolve through a process of microevolution influenced by genetic mutations, epigenetic changes, tumor microenvironment factors, and therapy-induced changes. This dynamic nature of tumors poses significant challenges for effective cancer treatment, and understanding it is essential for developing effective and personalized therapies. By uncovering the mechanisms that determine tumor heterogeneity, researchers can identify key genetic and epigenetic changes that contribute to tumor progression and resistance to treatment. This knowledge enables the development of innovative strategies for targeting specific tumor clones, minimizing the risk of recurrence and improving patient outcomes. To investigate the evolutionary dynamics of cancer, researchers employ a wide range of experimental and computational approaches. Traditional experimental methods involve genomic profiling techniques such as next-generation sequencing and fluorescence in situ hybridization. These techniques enable the identification of somatic mutations, copy number alterations, and structural rearrangements within cancer genomes. Furthermore, single-cell sequencing methods have emerged as powerful tools for dissecting intratumoral heterogeneity and tracing clonal evolution. In parallel, computational models and algorithms have been developed to simulate and analyze cancer evolution. These models integrate data from multiple sources to predict tumor growth patterns, identify driver mutations, and infer evolutionary trajectories. In this paper, we set out to describe the current approaches to address this evolutionary complexity and theories of its occurrence.
Collapse
Affiliation(s)
- R A Ivanov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - S A Lashin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| |
Collapse
|
33
|
Baglamis S, Sheraton VM, Meijer D, Qian H, Hoebe RA, Lenos KJ, Betjes MA, Betjes MA, Tans S, van Zon J, Vermeulen L, Krawczyk PM. Using picoliter droplet deposition to track clonal competition in adherent and organoid cancer cell cultures. Sci Rep 2023; 13:18832. [PMID: 37914743 PMCID: PMC10620187 DOI: 10.1038/s41598-023-42849-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 09/15/2023] [Indexed: 11/03/2023] Open
Abstract
Clonal growth and competition underlie processes of key relevance in etiology, progression and therapy response across all cancers. Here, we demonstrate a novel experimental approach, based on multi-color, fluorescent tagging of cell nuclei, in combination with picoliter droplet deposition, to study the clonal dynamics in two- and three-dimensional cell cultures. The method allows for the simultaneous visualization and analysis of multiple clones in individual multi-clonal colonies, providing a powerful tool for studying clonal dynamics and identifying clonal populations with distinct characteristics. Results of our experiments validate the utility of the method in studying clonal dynamics in vitro, and reveal differences in key aspects of clonal behavior of different cancer cell lines in monoculture conditions, as well as in co-cultures with stromal fibroblasts.
Collapse
Affiliation(s)
- Selami Baglamis
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Cancer Center Amsterdam, 1081 HV, Amsterdam, The Netherlands
- Oncode Institute, 3521 AL, Utrecht, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ, Amsterdam, The Netherlands
| | - Vivek M Sheraton
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Cancer Center Amsterdam, 1081 HV, Amsterdam, The Netherlands
- Oncode Institute, 3521 AL, Utrecht, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ, Amsterdam, The Netherlands
- Institute for Advanced Study, University of Amsterdam, 1012 WX, Amsterdam, The Netherlands
| | - Debora Meijer
- Cancer Center Amsterdam, 1081 HV, Amsterdam, The Netherlands
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Haibin Qian
- Cancer Center Amsterdam, 1081 HV, Amsterdam, The Netherlands
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Ron A Hoebe
- Cancer Center Amsterdam, 1081 HV, Amsterdam, The Netherlands
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Kristiaan J Lenos
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Cancer Center Amsterdam, 1081 HV, Amsterdam, The Netherlands
- Oncode Institute, 3521 AL, Utrecht, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ, Amsterdam, The Netherlands
| | - Max A Betjes
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Cancer Center Amsterdam, 1081 HV, Amsterdam, The Netherlands
- Oncode Institute, 3521 AL, Utrecht, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ, Amsterdam, The Netherlands
| | | | | | | | - Louis Vermeulen
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
- Cancer Center Amsterdam, 1081 HV, Amsterdam, The Netherlands.
- Oncode Institute, 3521 AL, Utrecht, The Netherlands.
- Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ, Amsterdam, The Netherlands.
| | - Przemek M Krawczyk
- Cancer Center Amsterdam, 1081 HV, Amsterdam, The Netherlands.
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
| |
Collapse
|
34
|
Snell-Rood EC, Ehlman SM. Developing the genotype-to-phenotype relationship in evolutionary theory: A primer of developmental features. Evol Dev 2023; 25:393-409. [PMID: 37026670 DOI: 10.1111/ede.12434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 02/09/2023] [Accepted: 03/16/2023] [Indexed: 04/08/2023]
Abstract
For decades, there have been repeated calls for more integration across evolutionary and developmental biology. However, critiques in the literature and recent funding initiatives suggest this integration remains incomplete. We suggest one way forward is to consider how we elaborate the most basic concept of development, the relationship between genotype and phenotype, in traditional models of evolutionary processes. For some questions, when more complex features of development are accounted for, predictions of evolutionary processes shift. We present a primer on concepts of development to clarify confusion in the literature and fuel new questions and approaches. The basic features of development involve expanding a base model of genotype-to-phenotype to include the genome, space, and time. A layer of complexity is added by incorporating developmental systems, including signal-response systems and networks of interactions. The developmental emergence of function, which captures developmental feedbacks and phenotypic performance, offers further model elaborations that explicitly link fitness with developmental systems. Finally, developmental features such as plasticity and developmental niche construction conceptualize the link between a developing phenotype and the external environment, allowing for a fuller inclusion of ecology in evolutionary models. Incorporating aspects of developmental complexity into evolutionary models also accommodates a more pluralistic focus on the causal importance of developmental systems, individual organisms, or agents in generating evolutionary patterns. Thus, by laying out existing concepts of development, and considering how they are used across different fields, we can gain clarity in existing debates around the extended evolutionary synthesis and pursue new directions in evolutionary developmental biology. Finally, we consider how nesting developmental features in traditional models of evolution can highlight areas of evolutionary biology that need more theoretical attention.
Collapse
Affiliation(s)
- Emilie C Snell-Rood
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, Minnesota, USA
| | - Sean M Ehlman
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, Minnesota, USA
- SCIoI Excellence Cluster, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Humboldt University, Berlin, Germany
| |
Collapse
|
35
|
Savy N, Moodie EE, Drouet I, Chambaz A, Falissard B, Kosorok MR, Krakow EF, Mayo DG, Senn S, Van der Laan M. Statistics, philosophy, and health: the SMAC 2021 webconference. Int J Biostat 2023; 19:261-270. [PMID: 36476947 DOI: 10.1515/ijb-2022-0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 11/08/2022] [Indexed: 11/15/2023]
Abstract
SMAC 2021 was a webconference organized in June 2021. The aim of this conference was to bring together data scientists, (bio)statisticians, philosophers, and any person interested in the questions of causality and Bayesian statistics, ranging from technical to philosophical aspects. This webconference consisted of keynote speakers and contributed speakers, and closed with a round-table organized in an unusual fashion. Indeed, organisers asked world renowned scientists to prepare two videos: a short video presenting a question of interest to them and a longer one presenting their point of view on the question. The first video served as a "teaser" for the conference and the second were presented during the conference as an introduction to the round-table. These videos and this round-table generated original scientific insights and discussion worthy of being shared with the community which we do by means of this paper.
Collapse
Affiliation(s)
- Nicolas Savy
- Toulouse Institute of Mathematics, University of Toulouse III and IFERISS FED 4142, University of Toulouse, Toulouse, France
| | - Erica Em Moodie
- Department of Epidemiology & Biostatistics, McGill University, Montréal, Québec, Canada
| | | | | | - Bruno Falissard
- CESP, INSERM U1018, Université Paris-Saclay, Villejuif, France
| | - Michael R Kosorok
- Department of Biostatistics and Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Elizabeth F Krakow
- Fred Hutchinson Cancer Research Center and University of Washington, Seattle, WA, USA
| | - Deborah G Mayo
- Department of Philosophy, Virginia Tech, Blacksburg, VA, USA
| | | | - Mark Van der Laan
- Division of Biostatistics, School of Public Health, University of California, Berkeley, USA
| |
Collapse
|
36
|
Zhao S, Chen DP, Fu T, Yang JC, Ma D, Zhu XZ, Wang XX, Jiao YP, Jin X, Xiao Y, Xiao WX, Zhang HY, Lv H, Madabhushi A, Yang WT, Jiang YZ, Xu J, Shao ZM. Single-cell morphological and topological atlas reveals the ecosystem diversity of human breast cancer. Nat Commun 2023; 14:6796. [PMID: 37880211 PMCID: PMC10600153 DOI: 10.1038/s41467-023-42504-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 10/12/2023] [Indexed: 10/27/2023] Open
Abstract
Digital pathology allows computerized analysis of tumor ecosystem using whole slide images (WSIs). Here, we present single-cell morphological and topological profiling (sc-MTOP) to characterize tumor ecosystem by extracting the features of nuclear morphology and intercellular spatial relationship for individual cells. We construct a single-cell atlas comprising 410 million cells from 637 breast cancer WSIs and dissect the phenotypic diversity within tumor, inflammatory and stroma cells respectively. Spatially-resolved analysis identifies recurrent micro-ecological modules representing locoregional multicellular structures and reveals four breast cancer ecotypes correlating with distinct molecular features and patient prognosis. Further analysis with multiomics data uncovers clinically relevant ecosystem features. High abundance of locally-aggregated inflammatory cells indicates immune-activated tumor microenvironment and favorable immunotherapy response in triple-negative breast cancers. Morphological intratumor heterogeneity of tumor nuclei correlates with cell cycle pathway activation and CDK inhibitors responsiveness in hormone receptor-positive cases. sc-MTOP enables using WSIs to characterize tumor ecosystems at the single-cell level.
Collapse
Affiliation(s)
- Shen Zhao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - De-Pin Chen
- Institute for Artificial Intelligence in Medicine, School of Artificial Intelligence, Nanjing University of Information Science and Technology, Nanjing, China
| | - Tong Fu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Jing-Cheng Yang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Greater Bay Area Institute of Precision Medicine, Guangzhou, China
| | - Ding Ma
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiu-Zhi Zhu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiang-Xue Wang
- Institute for Artificial Intelligence in Medicine, School of Artificial Intelligence, Nanjing University of Information Science and Technology, Nanjing, China
| | - Yi-Ping Jiao
- Institute for Artificial Intelligence in Medicine, School of Artificial Intelligence, Nanjing University of Information Science and Technology, Nanjing, China
| | - Xi Jin
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yi Xiao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Wen-Xuan Xiao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Hu-Yunlong Zhang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Hong Lv
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Anant Madabhushi
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Atlanta Veterans Affairs Medical Center, Atlanta, GA, USA
| | - Wen-Tao Yang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China.
| | - Yi-Zhou Jiang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
| | - Jun Xu
- Institute for Artificial Intelligence in Medicine, School of Artificial Intelligence, Nanjing University of Information Science and Technology, Nanjing, China.
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
| |
Collapse
|
37
|
Piekuś-Słomka N, Mocan LP, Shkreli R, Grapă C, Denkiewicz K, Wesolowska O, Kornek M, Spârchez Z, Słomka A, Crăciun R, Mocan T. Don't Judge a Book by Its Cover: The Role of Statins in Liver Cancer. Cancers (Basel) 2023; 15:5100. [PMID: 37894467 PMCID: PMC10605163 DOI: 10.3390/cancers15205100] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/16/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
Statins, which are inhibitors of 3-hydroxy-3-methyl-glutaryl-coenzyme A (HMG-CoA) reductase, are an effective pharmacological tool for lowering blood cholesterol levels. This property makes statins one of the most popular drugs used primarily to prevent cardiovascular diseases, where hyperlipidemia is a significant risk factor that increases mortality. Nevertheless, studies conducted mainly in the last decade have shown that statins might prevent and treat liver cancer, one of the leading causes of cancer-related mortality worldwide. This narrative review summarizes the scientific achievements to date regarding the role of statins in liver tumors. Molecular biology tools have revealed that cell growth and proliferation can be inhibited by statins, which further inhibit angiogenesis. Clinical studies, supported by meta-analysis, confirm that statins are highly effective in preventing and treating hepatocellular carcinoma and cholangiocarcinoma. However, this effect may depend on the statin's type and dose, and more clinical trials are required to evaluate clinical effects. Moreover, their potential hepatotoxicity is a significant caveat for using statins in clinical practice. Nevertheless, this group of drugs, initially developed to prevent cardiovascular diseases, is now a key candidate in hepato-oncology patient management. The description of new drug-statin-like structures, e.g., with low toxicity to liver cells, may bring another clinically significant improvement to current cancer therapies.
Collapse
Affiliation(s)
- Natalia Piekuś-Słomka
- Department of Inorganic and Analytical Chemistry, Nicolaus Copernicus University in Toruń, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Jurasza 2, 85-089 Bydgoszcz, Poland;
| | - Lavinia Patricia Mocan
- Department of Histology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania;
| | - Rezarta Shkreli
- Department of Pharmacy, Faculty of Medical Sciences, Aldent University, 1001-1028 Tirana, Albania;
| | - Cristiana Grapă
- Department of Physiology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania;
| | - Kinga Denkiewicz
- Department of Pathophysiology, Nicolaus Copernicus University in Toruń, Ludwik Rydygier Collegium Medicum in Bydgoszcz, 85-094 Bydgoszcz, Poland; (K.D.); (O.W.); (A.S.)
| | - Oliwia Wesolowska
- Department of Pathophysiology, Nicolaus Copernicus University in Toruń, Ludwik Rydygier Collegium Medicum in Bydgoszcz, 85-094 Bydgoszcz, Poland; (K.D.); (O.W.); (A.S.)
| | - Miroslaw Kornek
- Department of Internal Medicine I, University Hospital Bonn of the Rheinische Friedrich-Wilhelms-University, 53127 Bonn, Germany;
| | - Zeno Spârchez
- 3rd Medical Department, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400162 Cluj-Napoca, Romania;
| | - Artur Słomka
- Department of Pathophysiology, Nicolaus Copernicus University in Toruń, Ludwik Rydygier Collegium Medicum in Bydgoszcz, 85-094 Bydgoszcz, Poland; (K.D.); (O.W.); (A.S.)
| | - Rareș Crăciun
- 3rd Medical Department, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400162 Cluj-Napoca, Romania;
- Department of Gastroenterology, “Octavian Fodor” Institute for Gastroenterology and Hepatology, 400162 Cluj-Napoca, Romania
| | - Tudor Mocan
- Department of Gastroenterology, “Octavian Fodor” Institute for Gastroenterology and Hepatology, 400162 Cluj-Napoca, Romania
- UBBMed Department, Babeș-Bolyai University, 400349 Cluj-Napoca, Romania
| |
Collapse
|
38
|
Dwivedi S, Glock C, Germerodt S, Stark H, Schuster S. Game-theoretical description of the go-or-grow dichotomy in tumor development for various settings and parameter constellations. Sci Rep 2023; 13:16758. [PMID: 37798314 PMCID: PMC10555990 DOI: 10.1038/s41598-023-43199-3] [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: 05/19/2023] [Accepted: 09/21/2023] [Indexed: 10/07/2023] Open
Abstract
A medically important feature of several types of tumors is their ability to "decide" between staying at a primary site in the body or leaving it and forming metastases. The present theoretical study aims to provide a better understanding of the ultimate reasons for this so-called "go-or-grow" dichotomy. To that end, we use game theory, which has proven to be useful in analyzing the competition between tumors and healthy tissues or among different tumor cells. We begin by determining the game types in the Basanta-Hatzikirou-Deutsch model, depending on the parameter values. Thereafter, we suggest and analyze five modified variants of the model. For example, in the basic model, the deadlock game, Prisoner's Dilemma, and hawk-dove game can occur. The modified versions lead to several additional game types, such as battle of the sexes, route-choice, and stag-hunt games. For some game types, all cells are predicted to stay on their original site ("grow phenotype"), while for other types, only a certain fraction stay and the other cells migrate away ("go phenotype"). If the nutrient supply at a distant site is high, all the cells are predicted to go. We discuss our predictions in terms of the pros and cons of caloric restriction and limitations of the supply of vitamins or methionine. Our results may help devise treatments to prevent metastasis.
Collapse
Affiliation(s)
- Shalu Dwivedi
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University, Ernst-Abbe-Platz 2, 07743, Jena, Germany
| | - Christina Glock
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University, Ernst-Abbe-Platz 2, 07743, Jena, Germany
| | - Sebastian Germerodt
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University, Ernst-Abbe-Platz 2, 07743, Jena, Germany
| | - Heiko Stark
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University, Ernst-Abbe-Platz 2, 07743, Jena, Germany
- Institute of Zoology and Evolutionary Research, University of Jena, Erbertstr. 1, 07743, Jena, Germany
| | - Stefan Schuster
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University, Ernst-Abbe-Platz 2, 07743, Jena, Germany.
| |
Collapse
|
39
|
Strobl MAR, Gallaher J, Robertson-Tessi M, West J, Anderson ARA. Treatment of evolving cancers will require dynamic decision support. Ann Oncol 2023; 34:867-884. [PMID: 37777307 PMCID: PMC10688269 DOI: 10.1016/j.annonc.2023.08.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 08/01/2023] [Accepted: 08/21/2023] [Indexed: 10/02/2023] Open
Abstract
Cancer research has traditionally focused on developing new agents, but an underexplored question is that of the dose and frequency of existing drugs. Based on the modus operandi established in the early days of chemotherapies, most drugs are administered according to predetermined schedules that seek to deliver the maximum tolerated dose and are only adjusted for toxicity. However, we believe that the complex, evolving nature of cancer requires a more dynamic and personalized approach. Chronicling the milestones of the field, we show that the impact of schedule choice crucially depends on processes driving treatment response and failure. As such, cancer heterogeneity and evolution dictate that a one-size-fits-all solution is unlikely-instead, each patient should be mapped to the strategy that best matches their current disease characteristics and treatment objectives (i.e. their 'tumorscape'). To achieve this level of personalization, we need mathematical modeling. In this perspective, we propose a five-step 'Adaptive Dosing Adjusted for Personalized Tumorscapes (ADAPT)' paradigm to integrate data and understanding across scales and derive dynamic and personalized schedules. We conclude with promising examples of model-guided schedule personalization and a call to action to address key outstanding challenges surrounding data collection, model development, and integration.
Collapse
Affiliation(s)
- M A R Strobl
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa; Translational Hematology and Oncology Research, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, USA
| | - J Gallaher
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa
| | - M Robertson-Tessi
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa
| | - J West
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa
| | - A R A Anderson
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa.
| |
Collapse
|
40
|
Zheng Y, Wang X, Yang X, Xing N. Single-cell RNA sequencing reveals the cellular and molecular characteristics of high-grade and metastatic bladder cancer. Cell Oncol (Dordr) 2023; 46:1415-1427. [PMID: 37170046 DOI: 10.1007/s13402-023-00820-x] [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] [Accepted: 04/21/2023] [Indexed: 05/13/2023] Open
Abstract
PURPOSE Metastatic bladder cancer (BC) has the highest somatic mutation frequency and recurrence rate of all tumors. However, the cellular and molecular characteristics of BC remain unclear. METHODS We performed single-cell RNA sequencing (scRNA-seq) on the samples of paracancerous normal tissue (PNT), primary tumor (PT) and lymph node metastasis (LNM). The proportions and gene expression profiles of different cell types in the tumor microenvironment (TME) were investigated. RESULTS In total, 50,158 cells were classified into six populations. Malignant cells of PT and LNM exhibited large mutant DNA fragments, while the cell phenotypes and gene expression profiles differed during differentiation. Metastasis was associated with a poorer prognosis than PT. Tumor-associated stromal cells and inhibitory immune cells were the main cell populations in PT and LNM. Cell-cell communication analysis revealed the roles of signaling pathways of inflammatory cancer-associated fibroblast (iCAF) and tumor-associated macrophage (TAM) in exhaustion of T cells. In addition, iCAF may recruit TAM to promote formation of the TME earlier than the differentiation of tumor cells. CONCLUSION This study through scRNA-seq enhanced our understanding of new features about the cellular and molecular similarities and differences of high-grade and metastatic bladder cancer, which might provide potential therapeutic targets in future treatment.
Collapse
Affiliation(s)
- Yue Zheng
- Department of Biochemistry and Molecular Biology, Basic Medical College, Shanxi Medical University, No. 56, Xinjiang South Road, Yingze street, Yingze District, Taiyuan City, 030000, Shanxi Province, China
| | - Xin Wang
- Department of Urology, First Hospital of Shanxi Medical University, No. 85, Jiefang South Road, Yingze street, Yingze District, Taiyuan City, 030000, Shanxi Province, China
| | - Xiaofeng Yang
- Department of Urology, First Hospital of Shanxi Medical University, No. 85, Jiefang South Road, Yingze street, Yingze District, Taiyuan City, 030000, Shanxi Province, China.
| | - Nianzeng Xing
- Department of Urology and State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing City, 100021, China
- Department of Urology, Shanxi Hospital Affiliated to Cancer Hospital, Cancer Hospital, Shanxi Province Cancer Hospital, Chinese Academy of Medical Sciences, Shanxi Medical University, Taiyuan, 030013, Shanxi Province, China
| |
Collapse
|
41
|
Zaky MY, Fan C, Zhang H, Sun XF. Unraveling the Anticancer Potential of Statins: Mechanisms and Clinical Significance. Cancers (Basel) 2023; 15:4787. [PMID: 37835481 PMCID: PMC10572000 DOI: 10.3390/cancers15194787] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Statins are an essential medication class in the treatment of lipid diseases because they inhibit 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase. They reduce cholesterol levels and reduce the risk of cardiovascular disease in both primary and secondary prevention. In addition to their powerful pharmacologic suppression of cholesterol production, statins appear to have pleitropic effects in a wide variety of other diseases by modulating signaling pathways. In recent years, statins have seen a large increase in interest due to their putative anticancer effects. Statins appear to cause upregulation or inhibition in key pathways involved in cancer such as inhibition of proliferation, angiogenesis, and metastasis as well as reducing cancer stemness. Further, statins have been found to induce oxidative stress, cell cycle arrest, autophagy, and apoptosis of cancer cells. Interestingly, clinical studies have shown that statin use is associated with a decreased risk of cancer formation, lower cancer grade at diagnosis, reduction in the risk of local reoccurrence, and increasing survival in patients. Therefore, our objective in the present review is to summarize the findings of the publications on the underlying mechanisms of statins' anticancer effects and their clinical implications.
Collapse
Affiliation(s)
- Mohamed Y. Zaky
- Department of Oncology, Linköping University, 581 83 Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
- Molecular Physiology Division, Zoology Department, Faculty of Science, Beni-Suef University, Beni-Suef 62521, Egypt
| | - Chuanwen Fan
- Department of Oncology, Linköping University, 581 83 Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
| | - Huan Zhang
- Department of Oncology, Linköping University, 581 83 Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
| | - Xiao-Feng Sun
- Department of Oncology, Linköping University, 581 83 Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
| |
Collapse
|
42
|
Chang CY, Armstrong D, Corry DB, Kheradmand F. Alveolar macrophages in lung cancer: opportunities challenges. Front Immunol 2023; 14:1268939. [PMID: 37822933 PMCID: PMC10562548 DOI: 10.3389/fimmu.2023.1268939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/12/2023] [Indexed: 10/13/2023] Open
Abstract
Alveolar macrophages (AMs) are critical components of the innate defense mechanism in the lung. Nestled tightly within the alveoli, AMs, derived from the yolk-sac or bone marrow, can phagocytose foreign particles, defend the host against pathogens, recycle surfactant, and promptly respond to inhaled noxious stimuli. The behavior of AMs is tightly dependent on the environmental cues whereby infection, chronic inflammation, and associated metabolic changes can repolarize their effector functions in the lungs. Several factors within the tumor microenvironment can re-educate AMs, resulting in tumor growth, and reducing immune checkpoint inhibitors (ICIs) efficacy in patients treated for non-small cell lung cancer (NSCLC). The plasticity of AMs and their critical function in altering tumor responses to ICIs make them a desirable target in lung cancer treatment. New strategies have been developed to target AMs in solid tumors reprograming their suppressive function and boosting the efficacy of ICIs. Here, we review the phenotypic and functional changes in AMs in response to sterile inflammation and in NSCLC that could be critical in tumor growth and metastasis. Opportunities in altering AMs' function include harnessing their potential function in trained immunity, a concept borrowed from memory response to infections, which could be explored therapeutically in managing lung cancer treatment.
Collapse
Affiliation(s)
- Cheng-Yen Chang
- Department of Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Dominique Armstrong
- Department of Medicine, Baylor College of Medicine, Houston, TX, United States
| | - David B. Corry
- Department of Medicine, Baylor College of Medicine, Houston, TX, United States
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
- Biology of Inflammation Center, Baylor College of Medicine, Houston, TX, United States
- Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey Department of Veterans Affairs Medical Center, Houston, TX, United States
| | - Farrah Kheradmand
- Department of Medicine, Baylor College of Medicine, Houston, TX, United States
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
- Biology of Inflammation Center, Baylor College of Medicine, Houston, TX, United States
- Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey Department of Veterans Affairs Medical Center, Houston, TX, United States
| |
Collapse
|
43
|
Fontana D, Crespiatico I, Crippa V, Malighetti F, Villa M, Angaroni F, De Sano L, Aroldi A, Antoniotti M, Caravagna G, Piazza R, Graudenzi A, Mologni L, Ramazzotti D. Evolutionary signatures of human cancers revealed via genomic analysis of over 35,000 patients. Nat Commun 2023; 14:5982. [PMID: 37749078 PMCID: PMC10519956 DOI: 10.1038/s41467-023-41670-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 09/13/2023] [Indexed: 09/27/2023] Open
Abstract
Recurring sequences of genomic alterations occurring across patients can highlight repeated evolutionary processes with significant implications for predicting cancer progression. Leveraging the ever-increasing availability of cancer omics data, here we unveil cancer's evolutionary signatures tied to distinct disease outcomes, representing "favored trajectories" of acquisition of driver mutations detected in patients with similar prognosis. We present a framework named ASCETIC (Agony-baSed Cancer EvoluTion InferenCe) to extract such signatures from sequencing experiments generated by different technologies such as bulk and single-cell sequencing data. We apply ASCETIC to (i) single-cell data from 146 myeloid malignancy patients and bulk sequencing from 366 acute myeloid leukemia patients, (ii) multi-region sequencing from 100 early-stage lung cancer patients, (iii) exome/genome data from 10,000+ Pan-Cancer Atlas samples, and (iv) targeted sequencing from 25,000+ MSK-MET metastatic patients, revealing subtype-specific single-nucleotide variant signatures associated with distinct prognostic clusters. Validations on several datasets underscore the robustness and generalizability of the extracted signatures.
Collapse
Affiliation(s)
- Diletta Fontana
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Ilaria Crespiatico
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Valentina Crippa
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Federica Malighetti
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Matteo Villa
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Fabrizio Angaroni
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy
- Center of Computational Biology, Human Technopole, Milano, Italy
| | - Luca De Sano
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy
| | - Andrea Aroldi
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- Hematology and Clinical Research Unit, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Marco Antoniotti
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy
- Bicocca Bioinformatics, Biostatistics and Bioimaging Centre-B4, Milan, Italy
| | - Giulio Caravagna
- Department of Mathematics and Geosciences, University of Trieste, Trieste, Italy
| | - Rocco Piazza
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Alex Graudenzi
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy.
- Bicocca Bioinformatics, Biostatistics and Bioimaging Centre-B4, Milan, Italy.
- Institute of Molecular Bioimaging and Physiology, Consiglio Nazionale delle Ricerche (IBFM-CNR), Segrate, Milan, Italy.
| | - Luca Mologni
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Daniele Ramazzotti
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy.
| |
Collapse
|
44
|
Panzeri I, Fagnocchi L, Apostle S, Tompkins M, Wolfrum E, Madaj Z, Hostetter G, Liu Y, Schaefer K, Chih-Hsiang Y, Bergsma A, Drougard A, Dror E, Chandler D, Schramek D, Triche TJ, Pospisilik JA. Developmental priming of cancer susceptibility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557446. [PMID: 37745326 PMCID: PMC10515831 DOI: 10.1101/2023.09.12.557446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
DNA mutations are necessary drivers of cancer, yet only a small subset of mutated cells go on to cause the disease. To date, the mechanisms that determine which rare subset of cells transform and initiate tumorigenesis remain unclear. Here, we take advantage of a unique model of intrinsic developmental heterogeneity (Trim28+/D9) and demonstrate that stochastic early life epigenetic variation can trigger distinct cancer-susceptibility 'states' in adulthood. We show that these developmentally primed states are characterized by differential methylation patterns at typically silenced heterochromatin, and that these epigenetic signatures are detectable as early as 10 days of age. The differentially methylated loci are enriched for genes with known oncogenic potential. These same genes are frequently mutated in human cancers, and their dysregulation correlates with poor prognosis. These results provide proof-of-concept that intrinsic developmental heterogeneity can prime individual, life-long cancer risk.
Collapse
Affiliation(s)
- Ilaria Panzeri
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Luca Fagnocchi
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Stefanos Apostle
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Megan Tompkins
- Vivarium and Transgenics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Emily Wolfrum
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Zachary Madaj
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Galen Hostetter
- Pathology and Biorepository Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Yanqing Liu
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Kristen Schaefer
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Department of Genetics and Genome Science, Case Western Reserve University, Cleveland, Ohio, USA
| | - Yang Chih-Hsiang
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Alexis Bergsma
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Parkinson’s Disease Center, Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Anne Drougard
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Erez Dror
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Darrell Chandler
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Daniel Schramek
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Timothy J. Triche
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - J. Andrew Pospisilik
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| |
Collapse
|
45
|
Borgsmüller N, Valecha M, Kuipers J, Beerenwinkel N, Posada D. Single-cell phylogenies reveal changes in the evolutionary rate within cancer and healthy tissues. CELL GENOMICS 2023; 3:100380. [PMID: 37719146 PMCID: PMC10504633 DOI: 10.1016/j.xgen.2023.100380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 05/03/2023] [Accepted: 07/18/2023] [Indexed: 09/19/2023]
Abstract
Cell lineages accumulate somatic mutations during organismal development, potentially leading to pathological states. The rate of somatic evolution within a cell population can vary due to multiple factors, including selection, a change in the mutation rate, or differences in the microenvironment. Here, we developed a statistical test called the Poisson Tree (PT) test to detect varying evolutionary rates among cell lineages, leveraging the phylogenetic signal of single-cell DNA sequencing (scDNA-seq) data. We applied the PT test to 24 healthy and cancer samples, rejecting a constant evolutionary rate in 11 out of 15 cancer and five out of nine healthy scDNA-seq datasets. In six cancer datasets, we identified subclonal mutations in known driver genes that could explain the rate accelerations of particular cancer lineages. Our findings demonstrate the efficacy of scDNA-seq for studying somatic evolution and suggest that cell lineages often evolve at different rates within cancer and healthy tissues.
Collapse
Affiliation(s)
- Nico Borgsmüller
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Monica Valecha
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Jack Kuipers
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - David Posada
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310 Vigo, Spain
| |
Collapse
|
46
|
Cs AS, Joseph TI, Girish KL, T P, Binu A, Mary J. Comparative Analysis of Cluster of Differentiation 57 and Proliferating Cell Nuclear Antigen Expression in Different Grades of Oral Squamous Cell Carcinoma: An Immunohistochemical Study. Cureus 2023; 15:e44779. [PMID: 37809121 PMCID: PMC10558034 DOI: 10.7759/cureus.44779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023] Open
Abstract
BACKGROUND The immune defense against tumor cells is mainly mediated by the natural killer (NK) cells. Cluster of differentiation 57 (CD57) is a 110-kd glycoprotein, typically expressed by the NK cells, attacks the cancer cells and inhibits tumor development. Proliferating cell nuclear antigen (PCNA) is a 36-kd auxiliary protein for DNA polymerase delta that correlates with cell proliferation and DNA synthesis. It is an essential component of DNA replication, DNA recombination, and DNA repair. The uncoordinated proliferation of PCNA protein characterizes the biological behavior of malignant lesions. AIM The aim of the present study is to compare and correlate the expression of CD57 and PCNA in different grades of oral squamous cell carcinoma (OSCC) by immunohistochemistry. MATERIALS AND METHODS This retrospective analysis comprises 30 samples of various grades of OSCCs and 10 samples of healthy mucosa. Sections of 4-5 µm thickness were done and stained with monoclonal anti-PCNA and anti-CD57 antibodies. The statistical package for social science (SPSS) version 16.0 software (IBM Corp., Armonk, NY) was used to analyze the data in this study. The expression of CD57 and PCNA was compared and correlated between the groups using analysis of variance (ANOVA) post hoc, Dunnet t-test, and Pearson's correlation coefficient test. For statistical significance, a p-value of 0.05 or less was used. RESULTS A significant decrease in CD57 labeling index was seen from well-differentiated squamous cell carcinoma (16.63 ± 2.33) to poorly differentiated squamous cell carcinoma (5.53 ± 1.20) whereas the significant increase in PCNA labeling index was noted from well-differentiated squamous cell carcinoma (45.88 ± 2.20), followed by moderately differentiated and poorly differentiated squamous cell carcinoma (72.77 ± 4.35). CONCLUSION The combination of CD57 and PCNA biomarkers appears to be good indicators of the immune status of the patient and the aggressiveness of the lesion.
Collapse
Affiliation(s)
- Ani Simila Cs
- Oral and Maxillofacial Pathology, Rajas Dental College and Hospital, Kavalkinaru, IND
| | - T Isaac Joseph
- Oral and Maxillofacial Pathology, Sree Mookambika Institute of Dental Sciences, Kulasekaram, IND
| | - K L Girish
- Oral and Maxillofacial Pathology, Sree Mookambika Institute of Dental Sciences, Kulasekaram, IND
| | - Prasanth T
- Oral and Maxillofacial Pathology, Sree Mookambika Institute of Dental Sciences, Kulasekaram, IND
| | - Angelin Binu
- Oral and Maxillofacial Pathology, Sree Mookambika Institute of Dental Sciences, Kulasekaram, IND
| | - Jeslin Mary
- Oral and Maxillofacial Pathology, Sree Mookambika Institute of Dental Sciences, Kulasekaram, IND
| |
Collapse
|
47
|
Park J, Newton PK. Stochastic competitive release and adaptive chemotherapy. Phys Rev E 2023; 108:034407. [PMID: 37849192 DOI: 10.1103/physreve.108.034407] [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: 07/15/2022] [Accepted: 07/10/2023] [Indexed: 10/19/2023]
Abstract
We develop a finite-cell model of tumor natural selection dynamics to investigate the stochastic fluctuations associated with multiple rounds of adaptive chemotherapy. The adaptive cycles are designed to avoid chemoresistance in the tumor by managing the ecological mechanism of competitive release of a resistant subpopulation. Our model is based on a three-component evolutionary game played among healthy (H), sensitive (S), and resistant (R) populations of N cells, with a chemotherapy control parameter, C(t), which we use to dynamically impose selection pressure on the sensitive subpopulation to slow tumor growth and manage competitive release of the resistant population. The adaptive chemoschedule is designed based on the deterministic (N→∞) adjusted replicator dynamical system, then implemented using the finite-cell stochastic frequency dependent Moran process model (N=10K-50K) to ascertain the cumulative effect of the stochastic fluctuations on the efficacy of the adaptive schedules over multiple rounds. We quantify the stochastic fixation probability regions of the R and S populations in the HSR trilinear phase plane as a function of the control parameter C∈[0,1], showing that the size of the R region increases with increasing C. We then implement an adaptive time-dependent schedule C(t) for the stochastic model and quantify the variances (using principal component coordinates) associated with the evolutionary cycles over multiple rounds of adaptive therapy. The variances increase subquadratically through several rounds before the evolutionary cycle begins to break down. Despite this, we show the stochastic adaptive schedules are more effective at delaying resistance than standard maximum tolerated dose and low-dose metronomic schedules. The simplified low-dimensional model provides some insights on how well multiple rounds of adaptive therapies are likely to perform over a range of tumor sizes (i.e., different values of N) if the goal is to maintain a sustained balance among competing subpopulations of cells to avoid chemoresistance via competitive release in a stochastic environment.
Collapse
Affiliation(s)
- J Park
- Department of Mathematics, University of Southern California, Los Angeles, California 90089-1191, USA
| | - P K Newton
- Department of Aerospace & Mechanical Engineering, Department of Mathematics, and Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California 90089-1191, USA
| |
Collapse
|
48
|
Ravikumar V, Xu T, Al-Holou WN, Fattahi S, Rao A. Efficient Inference of Spatially-Varying Gaussian Markov Random Fields With Applications in Gene Regulatory Networks. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:2920-2932. [PMID: 37276119 PMCID: PMC10623339 DOI: 10.1109/tcbb.2023.3282028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this paper, we study the problem of inferring spatially-varying Gaussian Markov random fields (SV-GMRF) where the goal is to learn a network of sparse, context-specific GMRFs representing network relationships between genes. An important application of SV-GMRFs is in inference of gene regulatory networks from spatially-resolved transcriptomics datasets. The current work on inference of SV-GMRFs are based on the regularized maximum likelihood estimation (MLE) and suffer from overwhelmingly high computational cost due to their highly nonlinear nature. To alleviate this challenge, we propose a simple and efficient optimization problem in lieu of MLE that comes equipped with strong statistical and computational guarantees. Our proposed optimization problem is extremely efficient in practice: we can solve instances of SV-GMRFs with more than 2 million variables in less than 2 minutes. We apply the developed framework to study how gene regulatory networks in Glioblastoma are spatially rewired within tissue, and identify prominent activity of the transcription factor HES4 and ribosomal proteins as characterizing the gene expression network in the tumor peri-vascular niche that is known to harbor treatment resistant stem cells.
Collapse
|
49
|
Guidolin D, Tamma R, Annese T, Tortorella C, Ingravallo G, Gaudio F, Musto P, Specchia G, Ribatti D. Different patterns of mast cell distribution in B-cell non-Hodgkin lymphomas. Pathol Res Pract 2023; 248:154661. [PMID: 37406375 DOI: 10.1016/j.prp.2023.154661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 07/07/2023]
Abstract
Tumor growth, progression, and metastatic capability in non-Hodgkin lymphomas (NHLs) are influenced by different component of tumor microenvironment, including inflammatory cells. Among these latter, mast cells play a crucial role. The spatial distribution of mast cells inside the tumor stroma of different types of B-cell NHLs has not yet been investigated. The aim of this study is to analyze the pattern of distribution of mast cells in biopsy samples obtained from three different types of B-cell NHLs by utilizing an image analysis system and a mathematical model to allow a quantitative estimation to characterize their spatial distribution. As concerns the spatial distributions exhibited by mast cells in diffuse large B cell lymphoma (DLBCL), some clustering was detected in both activated B-like (ABC) and germinal center B-like (GBC) groups. In follicular lymphoma (FL), mast cell spatial distribution tends to uniformly fill the tissue space as far as the grade of the pathology increases. Finally, in marginal lymphoma tissue (MALT) lymphoma, mast cells maintain a significantly clustered spatial distribution, suggesting a lower tendency of the cells to fill the tissue space in this pathological condition. Overall, the data of this study confirm that the analysis of the spatial distribution of the tumor cells is of particular significance for the knowledge of the biological processes occurring in tumor stroma and for the development of parameters to characterize the morphologic organization of the cellular patterns in different types of tumors.
Collapse
Affiliation(s)
- Diego Guidolin
- Department of Neuroscience, Section of Anatomy, University of Padova, Padova, Italy
| | - Roberto Tamma
- Department of Translational Biomedicine and Neuroscience, University of Bari Medical School, Bari, Italy
| | - Tiziana Annese
- Department of Medicine and Surgery, University LUM "G. Degennaro", Casamassima, Ba, Italy
| | - Cinzia Tortorella
- Department of Neuroscience, Section of Anatomy, University of Padova, Padova, Italy
| | - Giuseppe Ingravallo
- Section of Pathology, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari Medical School, Bari, Italy
| | - Francesco Gaudio
- Section of Hematology, Department of Precision and Regenerative Medicine and Ionian Area, "Aldo Moro" University of Bari Medical School, Bari, Italy
| | - Pellegrino Musto
- Section of Hematology, Department of Precision and Regenerative Medicine and Ionian Area, "Aldo Moro" University of Bari Medical School, Bari, Italy
| | - Giorgina Specchia
- Section of Hematology, Department of Precision and Regenerative Medicine and Ionian Area, "Aldo Moro" University of Bari Medical School, Bari, Italy
| | - Domenico Ribatti
- Department of Translational Biomedicine and Neuroscience, University of Bari Medical School, Bari, Italy.
| |
Collapse
|
50
|
Chen Z, Lau KS. Advances in Mapping Tumor Progression from Precancer Atlases. Cancer Prev Res (Phila) 2023; 16:439-447. [PMID: 37167978 PMCID: PMC10523872 DOI: 10.1158/1940-6207.capr-22-0473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/22/2023] [Accepted: 04/11/2023] [Indexed: 05/13/2023]
Abstract
Tissue profiling technologies present opportunities for understanding transition from precancerous lesions to malignancy, which may impact risk stratification, prevention, and even cancer treatment. A human precancer atlas building effort is ongoing to tackle the significant challenge of decoding the heterogeneity among cells, specimens, and patients. Here, we discuss the findings resulting from atlases built across precancer types, including those found in colon, breast, lung, stomach, cervix, and skin, using bulk, single-cell, and spatial profiling strategies. We highlight two main themes that emerge across precancer types: the ordering of molecular events that occur during tumor progression and the fluctuation of microenvironmental response during precancer progression. We further highlight the key challenges of data integration across large cohorts of patients, and the need for computational tools to reliably annotate and quality control high-volume, high-dimensional data.
Collapse
Affiliation(s)
- Zhengyi Chen
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ken S. Lau
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| |
Collapse
|