1
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Wang P, Leong QY, Lau NY, Ng WY, Kwek SP, Tan L, Song SW, You K, Chong LM, Zhuang I, Ong YH, Foo N, Tadeo X, Kumar KS, Vijayakumar S, Sapanel Y, Raczkowska MN, Remus A, Blasiak A, Ho D. N-of-1 medicine. Singapore Med J 2024; 65:167-175. [PMID: 38527301 PMCID: PMC11060644 DOI: 10.4103/singaporemedj.smj-2023-243] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/19/2024] [Indexed: 03/27/2024]
Abstract
ABSTRACT The fields of precision and personalised medicine have led to promising advances in tailoring treatment to individual patients. Examples include genome/molecular alteration-guided drug selection, single-patient gene therapy design and synergy-based drug combination development, and these approaches can yield substantially diverse recommendations. Therefore, it is important to define each domain and delineate their commonalities and differences in an effort to develop novel clinical trial designs, streamline workflow development, rethink regulatory considerations, create value in healthcare and economics assessments, and other factors. These and other segments are essential to recognise the diversity within these domains to accelerate their respective workflows towards practice-changing healthcare. To emphasise these points, this article elaborates on the concept of digital health and digital medicine-enabled N-of-1 medicine, which individualises combination regimen and dosing using a patient's own data. We will conclude with recommendations for consideration when developing novel workflows based on emerging digital-based platforms.
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Affiliation(s)
- Peter Wang
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore
| | - Qiao Ying Leong
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
| | - Ni Yin Lau
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
| | - Wei Ying Ng
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
| | - Siong Peng Kwek
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
| | - Lester Tan
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore
| | - Shang-Wei Song
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore
| | - Kui You
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore
| | - Li Ming Chong
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore
| | - Isaiah Zhuang
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
| | - Yoong Hun Ong
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
| | - Nigel Foo
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore
| | - Xavier Tadeo
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
| | - Kirthika Senthil Kumar
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
| | - Smrithi Vijayakumar
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
| | - Yoann Sapanel
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
- Singapore’s Health District @ Queenstown, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Marlena Natalia Raczkowska
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
| | - Alexandria Remus
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore
- Heat Resilience Performance Centre (HRPC), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Agata Blasiak
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Dean Ho
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore
- Singapore’s Health District @ Queenstown, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The Bia-Echo Asia Centre for Reproductive Longevity and Equality, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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2
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Thng DKH, Hooi L, Siew BE, Lee KY, Tan IJW, Lieske B, Lin NS, Kow AWC, Wang S, Rashid MBMA, Ang C, Koh JJM, Toh TB, Tan KK, Chow EKH. A functional personalised oncology approach against metastatic colorectal cancer in matched patient derived organoids. NPJ Precis Oncol 2024; 8:52. [PMID: 38413740 PMCID: PMC10899621 DOI: 10.1038/s41698-024-00543-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/08/2024] [Indexed: 02/29/2024] Open
Abstract
Globally, colorectal cancer (CRC) is the third most frequently occurring cancer. Progression on to an advanced metastatic malignancy (metCRC) is often indicative of poor prognosis, as the 5-year survival rates of patients decline rapidly. Despite the availability of many systemic therapies for the management of metCRC, the long-term efficacies of these regimens are often hindered by the emergence of treatment resistance due to intratumoral and intertumoral heterogeneity. Furthermore, not all systemic therapies have associated biomarkers that can accurately predict patient responses. Hence, a functional personalised oncology (FPO) approach can enable the identification of patient-specific combinatorial vulnerabilities and synergistic combinations as effective treatment strategies. To this end, we established a panel of CRC patient-derived organoids (PDOs) as clinically relevant biological systems, of which three pairs of matched metCRC PDOs were derived from the primary sites (ptCRC) and metastatic lesions (mCRC). Histological and genomic characterisation of these PDOs demonstrated the preservation of histopathological and genetic features found in the parental tumours. Subsequent application of the phenotypic-analytical drug combination interrogation platform, Quadratic Phenotypic Optimisation Platform, in these pairs of PDOs identified patient-specific drug sensitivity profiles to epigenetic-based combination therapies. Most notably, matched PDOs from one patient exhibited differential sensitivity patterns to the rationally designed drug combinations despite being genetically similar. These findings collectively highlight the limitations of current genomic-driven precision medicine in guiding treatment strategies for metCRC patients. Instead, it suggests that epigenomic profiling and application of FPO could complement the identification of novel combinatorial vulnerabilities to target synchronous ptCRC and mCRC.
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Affiliation(s)
- Dexter Kai Hao Thng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Lissa Hooi
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Bei En Siew
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Kai-Yin Lee
- Division of Colorectal Surgery, Department of Surgery, National University Hospital, National University Health System, Singapore, Singapore
| | - Ian Jse-Wei Tan
- Division of Colorectal Surgery, Department of Surgery, National University Hospital, National University Health System, Singapore, Singapore
| | - Bettina Lieske
- Division of Colorectal Surgery, Department of Surgery, National University Hospital, National University Health System, Singapore, Singapore
| | - Norman Sihan Lin
- Division of Colorectal Surgery, Department of Surgery, National University Hospital, National University Health System, Singapore, Singapore
| | - Alfred Wei Chieh Kow
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, National University Hospital, National University Health System, Singapore, Singapore
| | - Shi Wang
- Department of Pathology, National University Hospital, National University Health System, Singapore, Singapore
| | | | - Chermaine Ang
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jasmin Jia Min Koh
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tan Boon Toh
- The N.1 Institute for Health, National University of Singapore, Singapore, Singapore
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ker-Kan Tan
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Division of Colorectal Surgery, Department of Surgery, National University Hospital, National University Health System, Singapore, Singapore.
| | - Edward Kai-Hua Chow
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
- NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- The N.1 Institute for Health, National University of Singapore, Singapore, Singapore.
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore.
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3
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De Mel S, Lee AR, Tan JHI, Tan RZY, Poon LM, Chan E, Lee J, Chee YL, Lakshminarasappa SR, Jaynes PW, Jeyasekharan AD. Targeting the DNA damage response in hematological malignancies. Front Oncol 2024; 14:1307839. [PMID: 38347838 PMCID: PMC10859481 DOI: 10.3389/fonc.2024.1307839] [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: 10/05/2023] [Accepted: 01/03/2024] [Indexed: 02/15/2024] Open
Abstract
Deregulation of the DNA damage response (DDR) plays a critical role in the pathogenesis and progression of many cancers. The dependency of certain cancers on DDR pathways has enabled exploitation of such through synthetically lethal relationships e.g., Poly ADP-Ribose Polymerase (PARP) inhibitors for BRCA deficient ovarian cancers. Though lagging behind that of solid cancers, DDR inhibitors (DDRi) are being clinically developed for haematological cancers. Furthermore, a high proliferative index characterize many such cancers, suggesting a rationale for combinatorial strategies targeting DDR and replicative stress. In this review, we summarize pre-clinical and clinical data on DDR inhibition in haematological malignancies and highlight distinct haematological cancer subtypes with activity of DDR agents as single agents or in combination with chemotherapeutics and targeted agents. We aim to provide a framework to guide the design of future clinical trials involving haematological cancers for this important class of drugs.
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Affiliation(s)
- Sanjay De Mel
- Department of Haematology-Oncology, National University Cancer Institute, Singapore, National University Health System, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University Singapore, Singapore, Singapore
| | - Ainsley Ryan Lee
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Joelle Hwee Inn Tan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Rachel Zi Yi Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Li Mei Poon
- Department of Haematology-Oncology, National University Cancer Institute, Singapore, National University Health System, Singapore, Singapore
- NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University Singapore, Singapore, Singapore
| | - Esther Chan
- Department of Haematology-Oncology, National University Cancer Institute, Singapore, National University Health System, Singapore, Singapore
- NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University Singapore, Singapore, Singapore
| | - Joanne Lee
- Department of Haematology-Oncology, National University Cancer Institute, Singapore, National University Health System, Singapore, Singapore
- NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University Singapore, Singapore, Singapore
| | - Yen Lin Chee
- Department of Haematology-Oncology, National University Cancer Institute, Singapore, National University Health System, Singapore, Singapore
- NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University Singapore, Singapore, Singapore
| | - Satish R. Lakshminarasappa
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Patrick William Jaynes
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Anand D. Jeyasekharan
- Department of Haematology-Oncology, National University Cancer Institute, Singapore, National University Health System, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
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4
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Chen Y, He L, Ianevski A, Ayuda-Durán P, Potdar S, Saarela J, Miettinen JJ, Kytölä S, Miettinen S, Manninen M, Heckman CA, Enserink JM, Wennerberg K, Aittokallio T. Robust scoring of selective drug responses for patient-tailored therapy selection. Nat Protoc 2024; 19:60-82. [PMID: 37996540 DOI: 10.1038/s41596-023-00903-x] [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: 03/24/2023] [Accepted: 08/10/2023] [Indexed: 11/25/2023]
Abstract
Most patients with advanced malignancies are treated with severely toxic, first-line chemotherapies. Personalized treatment strategies have led to improved patient outcomes and could replace one-size-fits-all therapies, yet they need to be tailored by testing of a range of targeted drugs in primary patient cells. Most functional precision medicine studies use simple drug-response metrics, which cannot quantify the selective effects of drugs (i.e., the differential responses of cancer cells and normal cells). We developed a computational method for selective drug-sensitivity scoring (DSS), which enables normalization of the individual patient's responses against normal cell responses. The selective response scoring uses the inhibition of noncancerous cells as a proxy for potential drug toxicity, which can in turn be used to identify effective and safer treatment options. Here, we explain how to apply the selective DSS calculation for guiding precision medicine in patients with leukemia treated across three cancer centers in Europe and the USA; the generic methods are also widely applicable to other malignancies that are amenable to drug testing. The open-source and extendable R-codes provide a robust means to tailor personalized treatment strategies on the basis of increasingly available ex vivo drug-testing data from patients in real-world and clinical trial settings. We also make available drug-response profiles to 527 anticancer compounds tested in 10 healthy bone marrow samples as reference data for selective scoring and de-prioritization of drugs that show broadly toxic effects. The procedure takes <60 min and requires basic skills in R.
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Affiliation(s)
- Yingjia Chen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Liye He
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Aleksandr Ianevski
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Pilar Ayuda-Durán
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Swapnil Potdar
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Jani Saarela
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Juho J Miettinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Sari Kytölä
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Susanna Miettinen
- Adult Stem Cell Group, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Research, Development and Innovation Centre, Tampere University Hospital, Tampere, Finland
| | | | - Caroline A Heckman
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jorrit M Enserink
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Section for Biochemistry and Molecular Biology, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Krister Wennerberg
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
- Centre for Biostatistics and Epidemiology (OCBE), Faculty of Medicine, University of Oslo, Oslo, Norway.
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5
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Åkerlund E, Gudoityte G, Moussaud-Lamodière E, Lind O, Bwanika HC, Lehti K, Salehi S, Carlson J, Wallin E, Fernebro J, Östling P, Kallioniemi O, Joneborg U, Seashore-Ludlow B. The drug efficacy testing in 3D cultures platform identifies effective drugs for ovarian cancer patients. NPJ Precis Oncol 2023; 7:111. [PMID: 37907613 PMCID: PMC10618545 DOI: 10.1038/s41698-023-00463-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 10/06/2023] [Indexed: 11/02/2023] Open
Abstract
Most patients with advanced ovarian cancer (OC) relapse and progress despite systemic therapy, pointing to the need for improved and tailored therapy options. Functional precision medicine can help to identify effective therapies for individual patients in a clinically relevant timeframe. Here, we present a scalable functional precision medicine platform: DET3Ct (Drug Efficacy Testing in 3D Cultures), where the response of patient cells to drugs and drug combinations are quantified with live-cell imaging. We demonstrate the delivery of individual drug sensitivity profiles in 20 samples from 16 patients with ovarian cancer in both 2D and 3D culture formats, achieving over 90% success rate in providing results six days after operation. In this cohort all patients received carboplatin. The carboplatin sensitivity scores were significantly different for patients with a progression free interval (PFI) less than or equal to 12 months and those with more than 12 months (p < 0.05). We find that the 3D culture format better retains proliferation and characteristics of the in vivo setting. Using the DET3Ct platform we evaluate 27 tailored combinations with results available 10 days after operation. Notably, carboplatin and A-1331852 (Bcl-xL inhibitor) showed an additive effect in four of eight OC samples tested, while afatinib and A-1331852 led to synergy in five of seven OC models. In conclusion, our 3D DET3Ct platform can rapidly define potential, clinically relevant data on efficacy of existing drugs in OC for precision medicine purposes, as well as provide insights on emerging drugs and drug combinations that warrant testing in clinical trials.
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Affiliation(s)
- Emma Åkerlund
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Greta Gudoityte
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | | | - Olina Lind
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | | | - Kaisa Lehti
- Department of Biomedical Laboratory Science, Norwegian University of Science and Technology NTNU, Trondheim, Norway
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sahar Salehi
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Pelvic Cancer, Theme Cancer, Karolinska University Hospital, Stockholm, Sweden
- Department of Women's and Children's Health, Division of Obstetrics and Gynecology, Karolinska Institutet, Stockholm, Sweden
| | - Joseph Carlson
- Department of Pathology and Laboratory Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Emelie Wallin
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
- Department of Pelvic Cancer, Theme Cancer, Karolinska University Hospital, Stockholm, Sweden
| | - Josefin Fernebro
- Department of Women's and Children's Health, Division of Obstetrics and Gynecology, Karolinska Institutet, Stockholm, Sweden
- Department of Pelvic Cancer, Theme Cancer, Karolinska University Hospital, Stockholm, Sweden
| | - Päivi Östling
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Olli Kallioniemi
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Ulrika Joneborg
- Department of Pelvic Cancer, Theme Cancer, Karolinska University Hospital, Stockholm, Sweden
- Department of Women's and Children's Health, Division of Obstetrics and Gynecology, Karolinska Institutet, Stockholm, Sweden
| | - Brinton Seashore-Ludlow
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden.
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6
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Wang P, Ho D. Deep Learning and Drug Discovery for Healthy Aging. ACS CENTRAL SCIENCE 2023; 9:1860-1863. [PMID: 37901176 PMCID: PMC10604011 DOI: 10.1021/acscentsci.3c01212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Affiliation(s)
- Peter Wang
- Institute for Digital
Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077
- The N.1 Institute for Health (N.1), National
University of Singapore, Singapore 119077
- Department of Biomedical Engineering, College
of Design and Engineering, National University
of Singapore, Singapore 119077
| | - Dean Ho
- Institute for Digital
Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077
- The N.1 Institute for Health (N.1), National
University of Singapore, Singapore 119077
- Department of Biomedical Engineering, College
of Design and Engineering, National University
of Singapore, Singapore 119077
- Department of Pharmacology, Yong Loo Lin
School of Medicine, National University
of Singapore, Singapore 119077
- Singapore’s Health District @ Queenstown,
Yong Loo Lin School of Medicine, National
University of Singapore, Singapore 119077
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7
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Hahn CK, Palmer AC, Weinstock DM. Genetically informed therapy for lymphoma: the discomfiting benefit of lumping splits. Cancer Cell 2023; 41:1696-1698. [PMID: 37774696 DOI: 10.1016/j.ccell.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 10/01/2023]
Abstract
Zhang et al. report a randomized phase 2 trial for diffuse large B cell lymphoma (DLBCL) that compared standard of care (R-CHOP) to R-CHOP combined with one of 5 agents matched to an individual lymphoma's genetics. Overall, the matching strategy significantly outperformed R-CHOP, laying the foundation for a paradigm-shifting phase 3 trial.
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Affiliation(s)
- Cynthia K Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Adam C Palmer
- Department of Pharmacology, Computational Medicine Program, UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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8
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Rovsing AB, Thomsen EA, Nielsen I, Skov TW, Luo Y, Dybkaer K, Mikkelsen JG. Resistance to vincristine in DLBCL by disruption of p53-induced cell cycle arrest and apoptosis mediated by KIF18B and USP28. Br J Haematol 2023; 202:825-839. [PMID: 37190875 DOI: 10.1111/bjh.18872] [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: 02/14/2023] [Revised: 04/21/2023] [Accepted: 05/04/2023] [Indexed: 05/17/2023]
Abstract
The frontline therapy R-CHOP for patients with diffuse large B-cell lymphoma (DLBCL) has remained unchanged for two decades despite numerous Phase III clinical trials investigating new alternatives. Multiple large studies have uncovered genetic subtypes of DLBCL enabling a targeted approach. To further pave the way for precision oncology, we perform genome-wide CRISPR screening to uncover the cellular response to one of the components of R-CHOP, vincristine, in the DLBCL cell line SU-DHL-5. We discover important pathways and subnetworks using gene-set enrichment analysis and protein-protein interaction networks and identify genes related to mitotic spindle organization that are essential during vincristine treatment. The inhibition of KIF18A, a mediator of chromosome alignment, using the small molecule inhibitor BTB-1 causes complete cell death in a synergistic manner when administered together with vincristine. We also identify the genes KIF18B and USP28 of which CRISPR/Cas9-directed knockout induces vincristine resistance across two DLBCL cell lines. Mechanistic studies show that lack of KIF18B or USP28 counteracts a vincristine-induced p53 response suggesting that resistance to vincristine has origin in the mitotic surveillance pathway (USP28-53BP1-p53). Collectively, our CRISPR screening data uncover potential drug targets and mechanisms behind vincristine resistance, which may support the development of future drug regimens.
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Affiliation(s)
| | | | - Ian Nielsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | | | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Shenzhen, China
| | - Karen Dybkaer
- Department of Hematology, Aalborg University Hospital, Aalborg, Denmark
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9
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Senthil Kumar K, Miskovic V, Blasiak A, Sundar R, Pedrocchi ALG, Pearson AT, Prelaj A, Ho D. Artificial Intelligence in Clinical Oncology: From Data to Digital Pathology and Treatment. Am Soc Clin Oncol Educ Book 2023; 43:e390084. [PMID: 37235822 DOI: 10.1200/edbk_390084] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Recently, a wide spectrum of artificial intelligence (AI)-based applications in the broader categories of digital pathology, biomarker development, and treatment have been explored. In the domain of digital pathology, these have included novel analytical strategies for realizing new information derived from standard histology to guide treatment selection and biomarker development to predict treatment selection and response. In therapeutics, these have included AI-driven drug target discovery, drug design and repurposing, combination regimen optimization, modulated dosing, and beyond. Given the continued advances that are emerging, it is important to develop workflows that seamlessly combine the various segments of AI innovation to comprehensively augment the diagnostic and interventional arsenal of the clinical oncology community. To overcome challenges that remain with regard to the ideation, validation, and deployment of AI in clinical oncology, recommendations toward bringing this workflow to fruition are also provided from clinical, engineering, implementation, and health care economics considerations. Ultimately, this work proposes frameworks that can potentially integrate these domains toward the sustainable adoption of practice-changing AI by the clinical oncology community to drive improved patient outcomes.
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Affiliation(s)
- Kirthika Senthil Kumar
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore
| | - Vanja Miskovic
- Department of Electronics, Informatics, and Bioengineering, Politecnico di Milano, Milan, Italy
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Agata Blasiak
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Raghav Sundar
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
- Department of Haematology-Oncology, National University Cancer Institute, National University Hospital
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Singapore Gastric Cancer Consortium, Singapore
- NUS Centre for Cancer Research (N2CR), National University of Singapore, Singapore
| | | | - Alexander T Pearson
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL
- University of Chicago Comprehensive Cancer Center, Chicago, IL
| | - Arsela Prelaj
- Department of Electronics, Informatics, and Bioengineering, Politecnico di Milano, Milan, Italy
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Dean Ho
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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Wang SSY, Chng WJ, Liu H, de Mel S. Tumor-Associated Macrophages and Related Myelomonocytic Cells in the Tumor Microenvironment of Multiple Myeloma. Cancers (Basel) 2022; 14:5654. [PMID: 36428745 PMCID: PMC9688291 DOI: 10.3390/cancers14225654] [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: 10/08/2022] [Revised: 11/05/2022] [Accepted: 11/11/2022] [Indexed: 11/19/2022] Open
Abstract
Multiple myeloma (MM) is the second-most common hematologic malignancy and remains incurable despite potent plasma cell directed therapeutics. The tumor microenvironment (TME) is a key player in the pathogenesis and progression of MM and is an active focus of research with a view to targeting immune dysregulation. Tumor-associated macrophages (TAM), myeloid derived suppressor cells (MDSC), and dendritic cells (DC) are known to drive progression and treatment resistance in many cancers. They have also been shown to promote MM progression and immune suppression in vitro, and there is growing evidence of their impact on clinical outcomes. The heterogeneity and functional characteristics of myelomonocytic cells in MM are being unraveled through high-dimensional immune profiling techniques. We are also beginning to understand how they may affect and be modulated by current and future MM therapeutics. In this review, we provide an overview of the biology and clinical relevance of TAMs, MDSCs, and DCs in the MM TME. We also highlight key areas to be addressed in future research as well as our perspectives on how the myelomonocytic compartment of the TME may influence therapeutic strategies of the future.
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Affiliation(s)
- Samuel S. Y. Wang
- Department of Rheumatology, Allergy and Immunology, Tan Tock Seng Hospital, Singapore 308433, Singapore
| | - Wee Joo Chng
- Department of Haematology-Oncology, National University Cancer Institute Singapore, National University Health System, Singapore 119228, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Dr, Singapore 117597, Singapore
- Cancer Science Institute, National University of Singapore, 14 Medical Dr, #12-01 Centre for Translational Medicine, Singapore 117599, Singapore
| | - Haiyan Liu
- Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
- Immunology Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
| | - Sanjay de Mel
- Department of Haematology-Oncology, National University Cancer Institute Singapore, National University Health System, Singapore 119228, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Dr, Singapore 117597, Singapore
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