1
|
Nafie MS, Kahwash SH, Youssef MM, Dawood KM. Recent advances on quinoxalines as target-oriented chemotherapeutic anticancer agents through apoptosis. Arch Pharm (Weinheim) 2024:e2400225. [PMID: 38822393 DOI: 10.1002/ardp.202400225] [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: 03/27/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 06/03/2024]
Abstract
The current review outlines all possible recent synthetic platforms to quinoxaline derivatives and the potent stimulated apoptosis mechanisms targeted by anticancer therapies. The currently reported results disclosed that quinoxaline derivatives had promising anticancer potencies against a wide array of cancer cell lines, better than the reference drugs, through target inhibition. This review summarizes some potent quinoxaline derivatives with their synthesis strategies and their potential activities against various molecular targets. Quinoxalines can be considered an important scaffold for apoptosis inducers in cancer cells through inhibiting some molecular targets, so they can be further developed as target-oriented chemotherapeutics.
Collapse
Affiliation(s)
- Mohamed S Nafie
- Department of Chemistry, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Chemistry Department, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Shaima H Kahwash
- Chemistry Department, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Magdy M Youssef
- Chemistry Department, Biochemistry Division, Faculty of Science, Mansoura University, Mansoura, Egypt
| | - Kamal M Dawood
- Chemistry Department, Faculty of Science, Cairo University, Giza, Egypt
| |
Collapse
|
2
|
Mirbahari SN, Da Silva M, Zúñiga AIM, Kooshki Zamani N, St-Laurent G, Totonchi M, Azad T. Recent progress in combination therapy of oncolytic vaccinia virus. Front Immunol 2024; 15:1272351. [PMID: 38558795 PMCID: PMC10979700 DOI: 10.3389/fimmu.2024.1272351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
In recent years, oncolytic viruses have emerged as promising agents for treating various cancers. An oncolytic virus is a non-pathogenic virus that, due to genetic manipulation, tends to replicate in and cause lysis of cancerous cells while leaving healthy cells unaffected. Among these viruses, vaccinia virus is an attractive platform for use as an oncolytic platform due to its 190 Kb genome with a high capacity for encoding therapeutic payloads. Combining oncolytic VV therapy with other conventional cancer treatments has been shown to be synergistic and more effective than monotherapies. Additionally, OVV can be used as a vector to deliver therapeutic payloads, alone or in combination with other treatments, to increase overall efficacy. Here, we present a comprehensive analysis of preclinical and clinical studies that have evaluated the efficacy of oncolytic vaccinia viruses in cancer immunotherapy. We discuss the outcomes of these studies, including tumor regression rates, overall survival benefits, and long-term responses. Moreover, we provide insights into the challenges and limitations associated with oncolytic vaccinia virus- based therapies, including immune evasion mechanisms, potential toxicities, and the development of resistance.
Collapse
Affiliation(s)
- Seyedeh Nasim Mirbahari
- Faculty of Sciences and Advanced Technologies in Biology, University of Science and Culture, Academic Center for Education, Culture and Research (ACECR), Tehran, Iran
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, Academic Center for Education, Culture and Research (ACECR), Tehran, Iran
| | - Miles Da Silva
- Department of Microbiology and Immunology, University of British Colombia, Vancouver, BC, Canada
- Ottawa Hospital Research Institute, The Ottawa Hospital, Ottawa, ON, Canada
| | - Abril Ixchel Muñoz Zúñiga
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC, Canada
- Centre de Recherche du CHUS, Sherbrooke, QC, Canada
| | - Nika Kooshki Zamani
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC, Canada
- Centre de Recherche du CHUS, Sherbrooke, QC, Canada
| | - Gabriel St-Laurent
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC, Canada
- Centre de Recherche du CHUS, Sherbrooke, QC, Canada
| | - Mehdi Totonchi
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, Academic Center for Education, Culture and Research (ACECR), Tehran, Iran
| | - Taha Azad
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC, Canada
- Centre de Recherche du CHUS, Sherbrooke, QC, Canada
| |
Collapse
|
3
|
Gram SB, Alosi D, Bagger FO, Østrup O, von Buchwald C, Friborg J, Wessel I, Vogelius IR, Rohrberg K, Rasmussen JH. Clinical implication of genetic intratumor heterogeneity for targeted therapy in head and neck cancer. Acta Oncol 2023; 62:1831-1839. [PMID: 37902999 DOI: 10.1080/0284186x.2023.2272293] [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: 07/24/2023] [Accepted: 10/15/2023] [Indexed: 11/01/2023]
Abstract
BACKGROUND Genomic profiling is increasingly used both in therapeutic decision-making and as inclusion criteria for trials testing targeted therapies. However, the mutational landscape may vary across different areas of a tumor and intratumor heterogeneity will challenge treatments or clinical decisions based on single tumor biopsies. The purpose of this study was to assess the clinical relevance of genetic intratumor heterogeneity in head and neck squamous cell carcinomas (HNSCC) using the ESMO Scale for Clinical Actionability of Molecular Targets (ESCAT). MATERIALS AND METHODS This prospective study included 33 whole tumor specimens from 28 patients with primary or recurrent HNSCC referred for surgery. Three tumor blocks were selected from central, semi-peripheral, and peripheral positions, mimicking biopsies in three different locations. Genetic analysis of somatic copy number alterations (SCNAs) was performed on the three biopsies using Oncoscan, focusing on 45 preselected HNSCC genes of interest. Clinical relevance was assessed using the ESCAT score to investigate whether and how treatment decisions would change based on the three biopsies from the same tumor. RESULTS The SCNAs identified among 45 preselected genes within the three tumor biopsies derived from the same tumor revealed distinct variations. The detected discrepancies could potentially influence treatment approaches or clinical decisions in 36% of the patients if only one tumor biopsy was used. Recurrent tumors exhibited significantly higher variation in SCNAs than primary tumors (p = .024). No significant correlation between tumor size and heterogeneity (p = .7) was observed. CONCLUSION In 36% of patients diagnosed with HNSCC, clinically significant intratumor heterogeneity was observed which may have implications for patient management. This finding substantiates the need for future studies that specifically investigate the clinical implications associated with intratumor heterogeneity.
Collapse
Affiliation(s)
- Signe Buhl Gram
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Daniela Alosi
- Center for Genomic Medicine, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Frederik Otzen Bagger
- Center for Genomic Medicine, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Olga Østrup
- Center for Genomic Medicine, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Christian von Buchwald
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Jeppe Friborg
- Department of Oncology, Section of Radiotherapy, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Irene Wessel
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Ivan Richter Vogelius
- Department of Oncology, Section of Radiotherapy, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Kristoffer Rohrberg
- Department of Oncology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Jacob Høygaard Rasmussen
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| |
Collapse
|
4
|
Boeschen M, Kuhn CK, Wirtz H, Seyfarth HJ, Frille A, Lordick F, Hacker UT, Obeck U, Stiller M, Bläker H, von Laffert M. Comparative bioinformatic analysis of KRAS, STK11 and KEAP1 (co-)mutations in non-small cell lung cancer with a special focus on KRAS G12C. Lung Cancer 2023; 184:107361. [PMID: 37699269 DOI: 10.1016/j.lungcan.2023.107361] [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: 07/25/2023] [Accepted: 09/04/2023] [Indexed: 09/14/2023]
Abstract
OBJECTIVES Mutations in STK11 (STK11MUT) and KEAP1 (KEAP1MUT) occur frequently in non-small cell lung cancer (NSCLC) and are often co-mutated with KRAS. Several studies linked the co-occurrence of KRASMUT + STK11MUT, as well as KRASMUT + KEAP1MUT to reduced response to immune checkpoint inhibitors (ICI) and even a negative impact on survival. Data focusing STK11 + KEAP1 co-mutations or the triple mutation (KRAS + STK11 + KEAP1) are scarce. The recent availability of KRAS-G12C inhibitors increases the clinical relevance of those co-mutations in KRAS-mutated NSCLC. MATERIALS AND METHODS We present a comprehensive bioinformatic analysis encompassing six datasets retrieved from cBioPortal. RESULTS Independent of the treatment, triple mutations and STK11MUT + KEAP1MUT were significantly associated with a reduced overall survival (OS). Across treatments, OS of patients with a KRAS G12C triple mutation was significantly reduced compared to patients with KRAS G12C-only. Under ICI-therapy, there was no significant difference in OS between patients harboring the KRAS G12C-only and patients with the KRAS G12C triple mutation, but a significant difference between patients harboring KRAS non-G12C and KRAS non-G12C triple mutations. Triple mutated primary tumors showed a significantly increased frequency of distant metastases to bone and adrenal glands compared to KRAS-only mutated tumors. Additionally, our drug response analysis in cancer cell lines harboring the triple mutations revealed the WNT pathway inhibitor XAV-939 as a potential future drug candidate for this mutational situation. CONCLUSION The triple mutation status may serve as a negative prognostic and predictive factor across treatments compared to KRASMUT-only. KRAS G12C generally seems to be a negative predictive marker for ICI-therapy.
Collapse
Affiliation(s)
- Myriam Boeschen
- Institute of Pathology, Leipzig University Medical Center, Liebigstraße 26, 04103 Leipzig, Germany.
| | - Christina Katharina Kuhn
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, Johannisallee 30, 04103 Leipzig, Germany
| | - Hubert Wirtz
- Department of Respiratory Medicine, Leipzig University Medical Center, Liebigstrasse 20, 04103 Leipzig
| | - Hans-Jürgen Seyfarth
- Department of Respiratory Medicine, Leipzig University Medical Center, Liebigstrasse 20, 04103 Leipzig
| | - Armin Frille
- Department of Respiratory Medicine, Leipzig University Medical Center, Liebigstrasse 20, 04103 Leipzig
| | - Florian Lordick
- Department of Medicine II, University Cancer Center Leipzig (UCCL), Leipzig University Medical Center, Leipzig, Germany
| | - Ulrich T Hacker
- Department of Medicine II, University Cancer Center Leipzig (UCCL), Leipzig University Medical Center, Leipzig, Germany
| | - Ulrike Obeck
- Institute of Pathology, Leipzig University Medical Center, Liebigstraße 26, 04103 Leipzig, Germany
| | - Mathias Stiller
- Institute of Pathology, Leipzig University Medical Center, Liebigstraße 26, 04103 Leipzig, Germany
| | - Hendrik Bläker
- Institute of Pathology, Leipzig University Medical Center, Liebigstraße 26, 04103 Leipzig, Germany
| | - Maximilian von Laffert
- Institute of Pathology, Leipzig University Medical Center, Liebigstraße 26, 04103 Leipzig, Germany.
| |
Collapse
|
5
|
Tarazi D, Maynes JT. Impact of Opioids on Cellular Metabolism: Implications for Metabolic Pathways Involved in Cancer. Pharmaceutics 2023; 15:2225. [PMID: 37765194 PMCID: PMC10534826 DOI: 10.3390/pharmaceutics15092225] [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: 08/01/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Opioid utilization for pain management is prevalent among cancer patients. There is significant evidence describing the many effects of opioids on cancer development. Despite the pivotal role of metabolic reprogramming in facilitating cancer growth and metastasis, the specific impact of opioids on crucial oncogenic metabolic pathways remains inadequately investigated. This review provides an understanding of the current research on opioid-mediated changes to cellular metabolic pathways crucial for oncogenesis, including glycolysis, the tricarboxylic acid cycle, glutaminolysis, and oxidative phosphorylation (OXPHOS). The existing literature suggests that opioids affect energy production pathways via increasing intracellular glucose levels, increasing the production of lactic acid, and reducing ATP levels through impediment of OXPHOS. Opioids modulate pathways involved in redox balance which may allow cancer cells to overcome ROS-mediated apoptotic signaling. The majority of studies have been conducted in healthy tissue with a predominant focus on neuronal cells. To comprehensively understand the impact of opioids on metabolic pathways critical to cancer progression, research must extend beyond healthy tissue and encompass patient-derived cancer tissue, allowing for a better understanding in the context of the metabolic reprogramming already undergone by cancer cells. The current literature is limited by a lack of direct experimentation exploring opioid-induced changes to cancer metabolism as they relate to tumor growth and patient outcome.
Collapse
Affiliation(s)
- Doorsa Tarazi
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1A8, Canada;
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Jason T. Maynes
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1A8, Canada;
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Anesthesia and Pain Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Anesthesiology and Pain Medicine, University of Toronto, Toronto, ON M5G 1E2, Canada
| |
Collapse
|
6
|
Anand U, Dey A, Chandel AKS, Sanyal R, Mishra A, Pandey DK, De Falco V, Upadhyay A, Kandimalla R, Chaudhary A, Dhanjal JK, Dewanjee S, Vallamkondu J, Pérez de la Lastra JM. Cancer chemotherapy and beyond: Current status, drug candidates, associated risks and progress in targeted therapeutics. Genes Dis 2023; 10:1367-1401. [PMID: 37397557 PMCID: PMC10310991 DOI: 10.1016/j.gendis.2022.02.007] [Citation(s) in RCA: 146] [Impact Index Per Article: 146.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 02/15/2022] [Accepted: 02/21/2022] [Indexed: 11/28/2022] Open
Abstract
Cancer is an abnormal state of cells where they undergo uncontrolled proliferation and produce aggressive malignancies that causes millions of deaths every year. With the new understanding of the molecular mechanism(s) of disease progression, our knowledge about the disease is snowballing, leading to the evolution of many new therapeutic regimes and their successive trials. In the past few decades, various combinations of therapies have been proposed and are presently employed in the treatment of diverse cancers. Targeted drug therapy, immunotherapy, and personalized medicines are now largely being employed, which were not common a few years back. The field of cancer discoveries and therapeutics are evolving fast as cancer type-specific biomarkers are progressively being identified and several types of cancers are nowadays undergoing systematic therapies, extending patients' disease-free survival thereafter. Although growing evidence shows that a systematic and targeted approach could be the future of cancer medicine, chemotherapy remains a largely opted therapeutic option despite its known side effects on the patient's physical and psychological health. Chemotherapeutic agents/pharmaceuticals served a great purpose over the past few decades and have remained the frontline choice for advanced-stage malignancies where surgery and/or radiation therapy cannot be prescribed due to specific reasons. The present report succinctly reviews the existing and contemporary advancements in chemotherapy and assesses the status of the enrolled drugs/pharmaceuticals; it also comprehensively discusses the emerging role of specific/targeted therapeutic strategies that are presently being employed to achieve better clinical success/survival rate in cancer patients.
Collapse
Affiliation(s)
- Uttpal Anand
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, West Bengal 700073, India
| | - Arvind K. Singh Chandel
- Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Rupa Sanyal
- Department of Botany, Bhairab Ganguly College (affiliated to West Bengal State University), Kolkata, West Bengal 700056, India
| | - Amarnath Mishra
- Faculty of Science and Technology, Amity Institute of Forensic Sciences, Amity University Uttar Pradesh, Noida 201313, India
| | - Devendra Kumar Pandey
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab 144411, India
| | - Valentina De Falco
- Institute of Endocrinology and Experimental Oncology (IEOS), National Research Council (CNR), Department of Molecular Medicine and Medical Biotechnology (DMMBM), University of Naples Federico II, Naples 80131, Italy
| | - Arun Upadhyay
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandar Sindari, Kishangarh Ajmer, Rajasthan 305817, India
| | - Ramesh Kandimalla
- CSIR-Indian Institute of Chemical Technology, Hyderabad, Telangana 500007, India
- Department of Biochemistry, Kakatiya Medical College, Warangal, Telangana 506007, India
| | - Anupama Chaudhary
- Orinin-BioSystems, LE-52, Lotus Road 4, CHD City, Karnal, Haryana 132001, India
| | - Jaspreet Kaur Dhanjal
- Department of Computational Biology, Indraprastha Institute of Information Technology Delhi (IIIT-D), Okhla Industrial Estate, Phase III, New Delhi 110020, India
| | - Saikat Dewanjee
- Advanced Pharmacognosy Research Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Jayalakshmi Vallamkondu
- Department of Physics, National Institute of Technology-Warangal, Warangal, Telangana 506004, India
| | - José M. Pérez de la Lastra
- Biotechnology of Macromolecules Research Group, Instituto de Productos Naturales y Agrobiología, IPNA-CSIC, San Cristóbal de La Laguna 38206, Tenerife, Spain
| |
Collapse
|
7
|
Belloni S, Arrigoni C, Baroni I, Conte G, Dellafiore F, Ghizzardi G, Magon A, Villa G, Caruso R. Non-pharmacologic interventions for improving cancer-related fatigue (CRF): A systematic review of systematic reviews and pooled meta-analysis. Semin Oncol 2023:S0093-7754(23)00035-0. [PMID: 36973125 DOI: 10.1053/j.seminoncol.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/29/2023]
Abstract
INTRODUCTION Literature encloses numerous systematic reviews (SRs) on nonpharmacologic interventions for improving cancer-related fatigue (CRF). The effect of these interventions remains controversial, and the available SRs have not been synthesized yet. We conducted a systematic synthesis of SRs and meta-analysis to determine the effect of nonpharmacologic interventions on CRF in adults. MATERIAL AND METHODS We systematically searched 4 databases. The effect sizes (standard mean difference) were quantitatively pooled using a random-effects model. Chi-squared (Q) and I-square statistics (I²) tested the heterogeneity. RESULTS We selected 28 SRs, including 35 eligible meta-analyses. The pooled effect size (standard mean difference, 95% CI) was -0.67 (-1.16, -0.18). The subgroup analysis by types of interventions showed a significant effect in all the investigated approaches (complementary integrative medicine, physical exercise, self-management/e-health interventions). CONCLUSIONS There is evidence that nonpharmacologic interventions are associated with CRF reduction. Future research should focus on testing these interventions on specific population clusters and trajectories. PROSPERO REGISTRATION CRD42020194258.
Collapse
Affiliation(s)
- Silvia Belloni
- IRCCS Humanitas Research Hospital, Educational and Research Unit, Rozzano, Italy.
| | - Cristina Arrigoni
- Department of Public Health, Experimental and Forensic Medicine, Section of Hygiene, University of Pavia, Pavia, Italy
| | - Irene Baroni
- Health Professions Research and Development Unit, IRCCS Policlinico San Donato, Milan, Italy
| | - Gianluca Conte
- Health Professions Research and Development Unit, IRCCS Policlinico San Donato, Milan, Italy
| | - Federica Dellafiore
- Department of Public Health, Experimental and Forensic Medicine, Section of Hygiene, University of Pavia, Pavia, Italy
| | - Greta Ghizzardi
- Health Professions Directorate, Bachelor in Nursing Course, ASST Lodi, Lodi, Italy
| | - Arianna Magon
- Health Professions Research and Development Unit, IRCCS Policlinico San Donato, Milan, Italy
| | - Giulia Villa
- Center for Nursing Research and Innovation, Vita-Salute San Raffaele University, Milan, Italy
| | - Rosario Caruso
- Health Professions Research and Development Unit, IRCCS Policlinico San Donato, Milan, Italy
| |
Collapse
|
8
|
Derbal Y. Cell Adaptive Fitness and Cancer Evolutionary Dynamics. Cancer Inform 2023; 22:11769351231154679. [PMID: 36860424 PMCID: PMC9969436 DOI: 10.1177/11769351231154679] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/17/2023] [Indexed: 02/26/2023] Open
Abstract
Genome instability of cancer cells translates into increased entropy and lower information processing capacity, leading to metabolic reprograming toward higher energy states, presumed to be aligned with a cancer growth imperative. Dubbed as the cell adaptive fitness, the proposition postulates that the coupling between cell signaling and metabolism constrains cancer evolutionary dynamics along trajectories privileged by the maintenance of metabolic sufficiency for survival. In particular, the conjecture postulates that clonal expansion becomes restricted when genetic alterations induce a sufficiently high level of disorder, that is, high entropy, in the regulatory signaling network, abrogating as a result the ability of cancer cells to successfully replicate, leading to a stage of clonal stagnation. The proposition is analyzed in the context of an in-silico model of tumor evolutionary dynamics to illustrate how cell-inherent adaptive fitness may predictably constrain clonal evolution of tumors, which would have significant implications for the design of adaptive cancer therapies.
Collapse
Affiliation(s)
- Youcef Derbal
- Youcef Derbal, Ted Rogers School of
Information Technology Management, Toronto Metropolitan University, 350 Victoria
Street, Toronto, ON M5B 2K3, Canada.
| |
Collapse
|
9
|
Antitumoral Activity of Leptocarpha rivularis Flower Extracts against Gastric Cancer Cells. Int J Mol Sci 2023; 24:ijms24021439. [PMID: 36674960 PMCID: PMC9862749 DOI: 10.3390/ijms24021439] [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: 11/28/2022] [Revised: 12/17/2022] [Accepted: 12/27/2022] [Indexed: 01/13/2023] Open
Abstract
Leptocarpha rivularis is a native South American plant used ancestrally by Mapuche people to treat gastrointestinal ailments. L. rivularis flower extracts are rich in molecules with therapeutic potential, including the sesquiterpene lactone leptocarpin, which displays cytotoxic effects against various cancer types in vitro. However, the combination of active molecules in these extracts could offer a hitherto unexplored potential for targeting cancer. In this study, we investigated the effect of L. rivularis flower extracts on the proliferation, survival, and spread parameters of gastric cancer cells in vitro. Gastric cancer (AGS and MKN-45) and normal immortalized (GES-1) cell lines were treated with different concentrations of L. rivularis flower extracts (DCM, Hex, EtOAc, and EtOH) and we determined the changes in proliferation (MTS assay, cell cycle analysis), cell viability/cytotoxicity (trypan blue exclusion assay, DEVDase activity, mitochondrial membrane potential MMP, and clonogenic ability), senescence (β-galactosidase activity) and spread potential (invasion and migration assays using the Boyden chamber approach) in all these cells. The results showed that the DCM, EtOAc, and Hex extracts display a selective antitumoral effect in gastric cancer cells by affecting all the cancer parameters tested. These findings reveal an attractive antitumoral potential of L. rivularis flower extracts by targeting several acquired capabilities of cancer cells.
Collapse
|
10
|
Ray SK, Mukherjee S. Hypoxia-Inducible Factors-Based Single Nucleotide Polymorphism in Breast Cancer with More Cancer Susceptibility. Curr Mol Med 2023; 23:285-288. [PMID: 35570541 DOI: 10.2174/1566524022666220513124853] [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: 03/08/2022] [Revised: 03/10/2022] [Accepted: 03/17/2022] [Indexed: 11/22/2022]
Abstract
Hypoxia-inducible factors (HIFs) are a collection of transcriptional factors that engage in the regulation of oxygen homeostasis. They are hypoxia-responsive stress factors whose expression is linked to tumor growth and angiogenesis. HIF is a crucial player in the progression of breast cancer. Patients with high levels of hypoxia-inducible HIFs in their primary tumor biopsies had a higher chance of metastasis, the leading cause of breast cancer-related death. HIF polymorphisms have been shown in several epidemiological studies to influence breast cancer susceptibility. In the oxygendependent degradation domain, several short nucleotide polymorphisms (SNPs) of the HIF gene have been connected with higher HIF activity. To find SNP that make up the genetic diversity that underpins the phenotypic difference found between individuals in their susceptibility to cancer and the course of their disease, researchers used a variety of potential pathway-based approaches.
Collapse
Affiliation(s)
- Suman Kumar Ray
- Independent Researcher, Bhopal, Madhya Pradesh-462020, India
| | - Sukhes Mukherjee
- Department of Biochemistry, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh-462020. India
| |
Collapse
|
11
|
Keller RB, Mazor T, Sholl L, Aguirre AJ, Singh H, Sethi N, Bass A, Nagaraja AK, Brais LK, Hill E, Hennessey C, Cusick M, Del Vecchio Fitz C, Zwiesler Z, Siegel E, Ovalle A, Trukhanov P, Hansel J, Shapiro GI, Abrams TA, Biller LH, Chan JA, Cleary JM, Corsello SM, Enzinger AC, Enzinger PC, Mayer RJ, McCleary NJ, Meyerhardt JA, Ng K, Patel AK, Perez KJ, Rahma OE, Rubinson DA, Wisch JS, Yurgelun MB, Hassett MJ, MacConaill L, Schrag D, Cerami E, Wolpin BM, Nowak JA, Giannakis M. Programmatic Precision Oncology Decision Support for Patients With Gastrointestinal Cancer. JCO Precis Oncol 2023; 7:e2200342. [PMID: 36634297 PMCID: PMC9929103 DOI: 10.1200/po.22.00342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/30/2022] [Accepted: 11/22/2022] [Indexed: 01/13/2023] Open
Abstract
PURPOSE With the growing number of available targeted therapeutics and molecular biomarkers, the optimal care of patients with cancer now depends on a comprehensive understanding of the rapidly evolving landscape of precision oncology, which can be challenging for oncologists to navigate alone. METHODS We developed and implemented a precision oncology decision support system, GI TARGET, (Gastrointestinal Treatment Assistance Regarding Genomic Evaluation of Tumors) within the Gastrointestinal Cancer Center at the Dana-Farber Cancer Institute. With a multidisciplinary team, we systematically reviewed tumor molecular profiling for GI tumors and provided molecularly informed clinical recommendations, which included identifying appropriate clinical trials aided by the computational matching platform MatchMiner, suggesting targeted therapy options on or off the US Food and Drug Administration-approved label, and consideration of additional or orthogonal molecular testing. RESULTS We reviewed genomic data and provided clinical recommendations for 506 patients with GI cancer who underwent tumor molecular profiling between January and June 2019 and determined follow-up using the electronic health record. Summary reports were provided to 19 medical oncologists for patients with colorectal (n = 198, 39%), pancreatic (n = 124, 24%), esophagogastric (n = 67, 13%), biliary (n = 40, 8%), and other GI cancers. We recommended ≥ 1 precision medicine clinical trial for 80% (406 of 506) of patients, leading to 24 enrollments. We recommended on-label and off-label targeted therapies for 6% (28 of 506) and 25% (125 of 506) of patients, respectively. Recommendations for additional or orthogonal testing were made for 42% (211 of 506) of patients. CONCLUSION The integration of precision medicine in routine cancer care through a dedicated multidisciplinary molecular tumor board is scalable and sustainable, and implementation of precision oncology recommendations has clinical utility for patients with cancer.
Collapse
Affiliation(s)
- Rachel B. Keller
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Tali Mazor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Lynette Sholl
- Center for Advanced Molecular Diagnostics, Brigham & Women's Hospital & Harvard Medical School, Boston, MA
| | - Andrew J. Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - Harshabad Singh
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Nilay Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Adam Bass
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Ankur K. Nagaraja
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Lauren K. Brais
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Emma Hill
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Connor Hennessey
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Margaret Cusick
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | | | - Zachary Zwiesler
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Ethan Siegel
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Andrea Ovalle
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Pavel Trukhanov
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Jason Hansel
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Geoffrey I. Shapiro
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Thomas A. Abrams
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Leah H. Biller
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Jennifer A. Chan
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - James M. Cleary
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Steven M. Corsello
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Andrea C. Enzinger
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Peter C. Enzinger
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Robert J. Mayer
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Nadine J. McCleary
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Jeffrey A. Meyerhardt
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Kimmie Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Anuj K. Patel
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Kimberley J. Perez
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Osama E. Rahma
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Douglas A. Rubinson
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Jeffrey S. Wisch
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Matthew B. Yurgelun
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Michael J. Hassett
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Laura MacConaill
- Center for Advanced Molecular Diagnostics, Brigham & Women's Hospital & Harvard Medical School, Boston, MA
| | - Deborah Schrag
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Ethan Cerami
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Brian M. Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
| | - Jonathan A. Nowak
- Center for Advanced Molecular Diagnostics, Brigham & Women's Hospital & Harvard Medical School, Boston, MA
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
| |
Collapse
|
12
|
Fedorov II, Lineva VI, Tarasova IA, Gorshkov MV. Mass Spectrometry-Based Chemical Proteomics for Drug Target Discoveries. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:983-994. [PMID: 36180990 DOI: 10.1134/s0006297922090103] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 06/16/2023]
Abstract
Chemical proteomics, emerging rapidly in recent years, has become a main approach to identifying interactions between the small molecules and proteins in the cells on a proteome scale and mapping the signaling and/or metabolic pathways activated and regulated by these interactions. The methods of chemical proteomics allow not only identifying proteins targeted by drugs, characterizing their toxicity and discovering possible off-target proteins, but also elucidation of the fundamental mechanisms of cell functioning under conditions of drug exposure or due to the changes in physiological state of the organism itself. Solving these problems is essential for both basic research in biology and clinical practice, including approaches to early diagnosis of various forms of serious diseases or prediction of the effectiveness of therapeutic treatment. At the same time, recent developments in high-resolution mass spectrometry have provided the technology for searching the drug targets across the whole cell proteomes. This review provides a concise description of the main objectives and problems of mass spectrometry-based chemical proteomics, the methods and approaches to their solution, and examples of implementation of these methods in biomedical research.
Collapse
Affiliation(s)
- Ivan I Fedorov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
- Moscow Institute of Physics and Technology (National University), Dolgoprudny, Moscow Region, 141700, Russia
| | - Victoria I Lineva
- Moscow Institute of Physics and Technology (National University), Dolgoprudny, Moscow Region, 141700, Russia
| | - Irina A Tarasova
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Mikhail V Gorshkov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia.
| |
Collapse
|
13
|
Zhang L, Zheng L, Yang Q, Sun J. The Evolution of BRAF Activation in Non-Small-Cell Lung Cancer. Front Oncol 2022; 12:882940. [PMID: 35912223 PMCID: PMC9326470 DOI: 10.3389/fonc.2022.882940] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 05/05/2022] [Indexed: 12/12/2022] Open
Abstract
Non-small-cell lung cancer (NSCLC) is the most common subtype of lung cancer, of which approximate 4% had BRAF activation, with an option for targeted therapy. BRAF activation comprises of V600 and non-V600 mutations, fusion, rearrangement, in-frame deletions, insertions, and co-mutations. In addition, BRAF primary activation and secondary activation presents with different biological phenotypes, medical senses and subsequent treatments. BRAF primary activation plays a critical role in proliferation and metastasis as a driver gene of NSCLC, while secondary activation mediates acquired resistance to other targeted therapy, especially for epidermal growth factor tyrosine kinase inhibitor (EGFR-TKI). Treatment options for different activation of BRAF are diverse. Targeted therapy, especially two-drug combination therapy, is an important option. Besides, immune checkpoint inhibitors (ICIs) would be another option since BRAF activation would be a positive biomarker of tumor response of ICIs therapy. To date, no high level evidences support targeted therapy or immunotherapy as prioritized recommendation. After targeted therapy, the evolution of BRAF includes the activation of the upstream, downstream and bypass pathways of BRAF. In this review, therapeutic modalities and post-therapeutic evolutionary pathways of BRAF are discussed, and future research directions are also provided.
Collapse
Affiliation(s)
- Longyao Zhang
- Cancer Institute, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Linpeng Zheng
- Cancer Institute, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Qiao Yang
- Department of Ultrasound, The 941Hospital of the Chinese People's Liberation Army (PLA) Joint Logistic Support Force, Xining, China
| | - Jianguo Sun
- Cancer Institute, Xinqiao Hospital, Army Medical University, Chongqing, China
| |
Collapse
|
14
|
Seo SH, Shin JH, Ham DW, Shin EH. PTEN/AKT signaling pathway related to hTERT downregulation and telomere shortening induced in Toxoplasma GRA16-expressing colorectal cancer cells. Biomed Pharmacother 2022; 153:113366. [PMID: 35810694 DOI: 10.1016/j.biopha.2022.113366] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/30/2022] Open
Abstract
This study investigated whether the molecular mechanism of granule protein 16 (GRA16), a dense granule protein of Toxoplasma gondii (T. gondii) that induces cancer cell apoptosis, results in telomere shortening in cancer cells. The molecular mechanism of GRA16 responsible for regulating telomerase reverse transcriptase (hTERT) activity and telomere shortening was investigated using GRA16-transferred HCT116 human colorectal cancer cells (GRA16-stable cells). GRA16 directly decreased hTERT expression by downregulating the expression and phosphorylation of hTERT transcriptional factors accompanied by decreased expression of shelterin complex molecules. Moreover, GRA16 resulted in cancer cell death through reduction of telomerase activity which leads to telomere shortening (decreased relative ratio of telomeric repeat-amplified sequence to that of a single-copy gene) (T/S ratio)), and at the same time gamma-H2A histone family member X (γ-H2A.X) stained nucleus was increased in the cells. The molecular mechanism between GRA16 and hTERT inactivation was revealed using inhibitors for phosphatase and tensin homolog (PTEN) and protein phosphatase 2A (PP2A) as well as siRNAs against PTEN and PP2A. hTERT dephosphorylation was induced effectively by the signaling pathway of HAUSP/PTEN/p-AKT(S473) but not by PP2A-B55/p-AKT(T308). Inhibition of the PTEN signaling pathway increased mRNA expressions in hTERT transcriptional factors, cell cycle activating factors, and apoptosis-inhibiting factors. When HCT116 cells were infected with T. gondii, the number of γ-H2A.X-stained nuclei also increased and p-hTERT/hTERT decreased as in GRA16-stable cells. Altogether, our results emphasize that GRA16 is a novel promising telomerase inhibitor that causes telomere shortening through telomerase inactivation by inducing the activation of the tumor suppressor PTEN.
Collapse
Affiliation(s)
- Seung-Hwan Seo
- Department of Tropical Medicine and Parasitology, Seoul National University College of Medicine, and Institute of Endemic Diseases, Seoul 03080, Republic of Korea
| | - Ji-Hun Shin
- Department of Tropical Medicine and Parasitology, Seoul National University College of Medicine, and Institute of Endemic Diseases, Seoul 03080, Republic of Korea
| | - Do-Won Ham
- Department of Tropical Medicine and Parasitology, Seoul National University College of Medicine, and Institute of Endemic Diseases, Seoul 03080, Republic of Korea
| | - Eun-Hee Shin
- Department of Tropical Medicine and Parasitology, Seoul National University College of Medicine, and Institute of Endemic Diseases, Seoul 03080, Republic of Korea; Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea.
| |
Collapse
|
15
|
Russo I, Sartor E, Fagotto L, Colombo A, Tiso N, Alaibac M. The Zebrafish model in dermatology: an update for clinicians. Discov Oncol 2022; 13:48. [PMID: 35713744 PMCID: PMC9206045 DOI: 10.1007/s12672-022-00511-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/08/2022] [Indexed: 11/04/2022] Open
Abstract
Recently, the zebrafish has been established as one of the most important model organisms for medical research. Several studies have proved that there is a high level of similarity between human and zebrafish genomes, which encourages the use of zebrafish as a model for understanding human genetic disorders, including cancer. Interestingly, zebrafish skin shows several similarities to human skin, suggesting that this model organism is particularly suitable for the study of neoplastic and inflammatory skin disorders. This paper appraises the specific characteristics of zebrafish skin and describes the major applications of the zebrafish model in dermatological research.
Collapse
Affiliation(s)
- Irene Russo
- Unit of Dermatology, University of Padua, Via Gallucci 4, 35128, Padua, Italy
| | - Emma Sartor
- Unit of Dermatology, University of Padua, Via Gallucci 4, 35128, Padua, Italy
| | - Laura Fagotto
- Unit of Dermatology, University of Padua, Via Gallucci 4, 35128, Padua, Italy
| | - Anna Colombo
- Unit of Dermatology, University of Padua, Via Gallucci 4, 35128, Padua, Italy
| | - Natascia Tiso
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Mauro Alaibac
- Unit of Dermatology, University of Padua, Via Gallucci 4, 35128, Padua, Italy.
| |
Collapse
|
16
|
Iwaya K, Arai H, Takatou N, Morita Y, Ozeki R, Nakaoka H, Sakamoto M, Kouno T, Soma M. A sheet pocket to prevent cross-contamination of formalin-fixed paraffin-embedded block for application in next generation sequencing. PLoS One 2022; 17:e0266947. [PMID: 35507545 PMCID: PMC9067696 DOI: 10.1371/journal.pone.0266947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 03/31/2022] [Indexed: 11/23/2022] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) blocks are used as biomaterials for next-generation sequencing of cancer panels. Cross-contamination is detected in approximately 5% of the DNA extracted from FFPE samples, which reduces the detection rate of genetic abnormalities. There are no effective methods available for processing FFPE blocks that prevent cells from mixing with other specimens. The present study evaluated 897 sheets that could potentially prevent cell transmission but allow for the movement of various solvents used in FFPE blocks. According to the International Organization for Standardization and Japanese Industrial Standards, six requirements were established for the screening of packing sheets: 1) filter opening ≤5 μm, 2) thickness ≤100 μm, 3) chemical resistance, 4) permeability ≥1.0 × 10−3 cm/s, 5) water retention rate <200%, and 6) cell transit test (≤2 cells/10 high-power fields). Polyamide, polyethylene terephthalate, and polypropylene/polyethylene composite sheets met all criteria. A pocket, which was designed to wrap the tissue uniformly, was made of these sheets and was found to effectively block the entry of all cell types during FFPE block processing. Using a sheet pocket, no single cell from the cell pellet could pass through the outer layer. The presence or absence of the sheet pocket did not affect hematoxylin and eosin staining. When processing FFPE blocks as a biomaterial for next-generation sequencing, the sheet pocket was effective in preventing cross-contamination. This technology will in part support the precise translation of histopathological data into genome sequencing data in general pathology laboratories.
Collapse
Affiliation(s)
- Keiichi Iwaya
- Department of Pathology, SASAKI Institute, Kyoundo Hospital, Chiyoda-ku, Tokyo, Japan
- * E-mail:
| | - Hisae Arai
- Department of Pathology, SASAKI Institute, Kyoundo Hospital, Chiyoda-ku, Tokyo, Japan
| | - Nanao Takatou
- Department of Pathology, SASAKI Institute, Kyoundo Hospital, Chiyoda-ku, Tokyo, Japan
| | - Yuka Morita
- Department of Pathology, SASAKI Institute, Kyoundo Hospital, Chiyoda-ku, Tokyo, Japan
| | - Rinko Ozeki
- Department of Pathology, SASAKI Institute, Kyoundo Hospital, Chiyoda-ku, Tokyo, Japan
| | - Hirofumi Nakaoka
- Department of Cancer Genome Research, SASAKI Institute, Chiyoda-ku, Tokyo, Japan
| | - Masaru Sakamoto
- Department of Gynecology, SASAKI Institute, Kyoundo Hospital, Chiyoda-ku, Tokyo, Japan
| | - Tsutomu Kouno
- Department of Medical Oncology, SASAKI Institute, Kyoundo Hospital, Chiyoda-ku, Tokyo, Japan
| | - Masayoshi Soma
- Department of Internal Medicine, SASAKI Institute, Kyoundo Hospital, Chiyoda-ku, Tokyo, Japan
| |
Collapse
|
17
|
Cani AK, Dolce EM, Darga EP, Hu K, Liu C, Pierce J, Bradbury K, Kilgour E, Aung K, Schiavon G, Carroll D, Carr TH, Klinowska T, Lindemann J, Marshall G, Rowlands V, Harrington EA, Barrett JC, Sathiyayogan N, Morrow C, Sero V, Armstrong AC, Baird R, Hamilton E, Im S, Jhaveri K, Patel MR, Dive C, Tomlins SA, Udager AM, Hayes DF, Paoletti C. Serial monitoring of genomic alterations in circulating tumor cells of ER-positive/HER2-negative advanced breast cancer: feasibility of precision oncology biomarker detection. Mol Oncol 2022; 16:1969-1985. [PMID: 34866317 PMCID: PMC9120891 DOI: 10.1002/1878-0261.13150] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/02/2021] [Accepted: 12/01/2021] [Indexed: 12/18/2022] Open
Abstract
Nearly all estrogen receptor (ER)-positive (POS) metastatic breast cancers become refractory to endocrine (ET) and other therapies, leading to lethal disease presumably due to evolving genomic alterations. Timely monitoring of the molecular events associated with response/progression by serial tissue biopsies is logistically difficult. Use of liquid biopsies, including circulating tumor cells (CTC) and circulating tumor DNA (ctDNA), might provide highly informative, yet easily obtainable, evidence for better precision oncology care. Although ctDNA profiling has been well investigated, the CTC precision oncology genomic landscape and the advantages it may offer over ctDNA in ER-POS breast cancer remain largely unexplored. Whole-blood (WB) specimens were collected at serial time points from patients with advanced ER-POS/HER2-negative (NEG) advanced breast cancer in a phase I trial of AZD9496, an oral selective ER degrader (SERD) ET. Individual CTC were isolated from WB using tandem CellSearch® /DEPArray™ technologies and genomically profiled by targeted single-cell DNA next-generation sequencing (scNGS). High-quality CTC (n = 123) from 12 patients profiled by scNGS showed 100% concordance with ctDNA detection of driver estrogen receptor α (ESR1) mutations. We developed a novel CTC-based framework for precision medicine actionability reporting (MI-CTCseq) that incorporates novel features, such as clonal predominance and zygosity of targetable alterations, both unambiguously identifiable in CTC compared to ctDNA. Thus, we nominated opportunities for targeted therapies in 73% of patients, directed at alterations in phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA), fibroblast growth factor receptor 2 (FGFR2), and KIT proto-oncogene, receptor tyrosine kinase (KIT). Intrapatient, inter-CTC genomic heterogeneity was observed, at times between time points, in subclonal alterations. Our analysis suggests that serial monitoring of the CTC genome is feasible and should enable real-time tracking of tumor evolution during progression, permitting more combination precision medicine interventions.
Collapse
|
18
|
Gogleva A, Polychronopoulos D, Pfeifer M, Poroshin V, Ughetto M, Martin MJ, Thorpe H, Bornot A, Smith PD, Sidders B, Dry JR, Ahdesmäki M, McDermott U, Papa E, Bulusu KC. Knowledge graph-based recommendation framework identifies drivers of resistance in EGFR mutant non-small cell lung cancer. Nat Commun 2022; 13:1667. [PMID: 35351890 PMCID: PMC8964738 DOI: 10.1038/s41467-022-29292-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 03/09/2022] [Indexed: 12/25/2022] Open
Abstract
Resistance to EGFR inhibitors (EGFRi) presents a major obstacle in treating non-small cell lung cancer (NSCLC). One of the most exciting new ways to find potential resistance markers involves running functional genetic screens, such as CRISPR, followed by manual triage of significantly enriched genes. This triage process to identify ‘high value’ hits resulting from the CRISPR screen involves manual curation that requires specialized knowledge and can take even experts several months to comprehensively complete. To find key drivers of resistance faster we build a recommendation system on top of a heterogeneous biomedical knowledge graph integrating pre-clinical, clinical, and literature evidence. The recommender system ranks genes based on trade-offs between diverse types of evidence linking them to potential mechanisms of EGFRi resistance. This unbiased approach identifies 57 resistance markers from >3,000 genes, reducing hit identification time from months to minutes. In addition to reproducing known resistance markers, our method identifies previously unexplored resistance mechanisms that we prospectively validate. Resistance to EGFR inhibitors presents a major obstacle in treating non-small cell lung cancer. Here, the authors develop a recommender system ranking genes based on trade-offs between diverse types of evidence linking them to potential mechanisms of EGFRi resistance.
Collapse
|
19
|
O’Connor JD, Overton IM, McMahon SJ. RadSigBench: a framework for benchmarking functional genomics signatures of cancer cell radiosensitivity. Brief Bioinform 2022; 23:6513903. [PMID: 35066588 PMCID: PMC8921666 DOI: 10.1093/bib/bbab561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 11/20/2022] Open
Abstract
Multiple transcriptomic predictors of tumour cell radiosensitivity (RS) have been proposed, but they have not been benchmarked against one another or to control models. To address this, we present RadSigBench, a comprehensive benchmarking framework for RS signatures. The approach compares candidate models to those developed from randomly resampled control signatures and from cellular processes integral to the radiation response. Robust evaluation of signature accuracy, both overall and for individual tissues, is performed. The NCI60 and Cancer Cell Line Encyclopaedia datasets are integrated into our workflow. Prediction of two measures of RS is assessed: survival fraction after 2 Gy and mean inactivation dose. We apply the RadSigBench framework to seven prominent published signatures of radiation sensitivity and test for equivalence to control signatures. The mean out-of-sample R2 for the published models on test data was very poor at 0.01 (range: −0.05 to 0.09) for Cancer Cell Line Encyclopedia and 0.00 (range: −0.19 to 0.19) in the NCI60 data. The accuracy of both published and cellular process signatures investigated was equivalent to the resampled controls, suggesting that these signatures contain limited radiation-specific information. Enhanced modelling strategies are needed for effective prediction of intrinsic RS to inform clinical treatment regimes. We make recommendations for methodological improvements, for example the inclusion of perturbation data, multiomics, advanced machine learning and mechanistic modelling. Our validation framework provides for robust performance assessment of ongoing developments in intrinsic RS prediction.
Collapse
Affiliation(s)
- John D O’Connor
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, BT9 7AE, United Kingdom
| | - Ian M Overton
- Corresponding authors: Ian M. Overton, Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast BT9 7AE, UK. Tel.: +44(0)2890972802; E-mail: ; Stephen J. McMahon, Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast BT9 7AE, UK. Tel.: +44(0)2890972620; E-mail:
| | - Stephen J McMahon
- Corresponding authors: Ian M. Overton, Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast BT9 7AE, UK. Tel.: +44(0)2890972802; E-mail: ; Stephen J. McMahon, Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast BT9 7AE, UK. Tel.: +44(0)2890972620; E-mail:
| |
Collapse
|
20
|
Kanwar N, Balde Z, Nair R, Dawe M, Chen S, Maganti M, Atenafu EG, Manolescu S, Wei C, Mao A, Fu F, Wang D, Cheung A, Yerofeyeva Y, Peters R, Liu K, Desmedt C, Sotiriou C, Szekely B, Kulka J, McKee TD, Hirano N, Bartlett JMS, Yaffe MJ, Bedard PL, McCready D, Done SJ. Heterogeneity of Circulating Tumor Cell-Associated Genomic Gains in Breast Cancer and Its Association with the Host Immune Response. Cancer Res 2021; 81:6196-6206. [PMID: 34711609 PMCID: PMC9397625 DOI: 10.1158/0008-5472.can-21-1079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/10/2021] [Accepted: 10/25/2021] [Indexed: 01/07/2023]
Abstract
Tumor cells that preferentially enter circulation include the precursors of metastatic cancer. Previously, we characterized circulating tumor cells (CTC) from patients with breast cancer and identified a signature of genomic regions with recurrent copy-number gains. Through FISH, we now show that these CTC-associated regions are detected within the matched untreated primary tumors of these patients (21% to 69%, median 55.5%, n = 19). Furthermore, they are more prevalent in the metastases of patients who died from breast cancer after multiple rounds of treatment (70% to 100%, median 93%, samples n = 41). Diversity indices revealed that higher spatial heterogeneity for these regions within primary tumors is associated with increased dissemination and metastasis. An identified subclone with multiple regions gained (MRG clone) was enriched in a posttreatment primary breast carcinoma as well as multiple metastatic tumors and local breast recurrences obtained at autopsy, indicative of a distinct early subclone with the capability to resist multiple lines of treatment and eventually cause death. In addition, multiplex immunofluorescence revealed that tumor heterogeneity is significantly associated with the degree of infiltration of B lymphocytes in triple-negative breast cancer, a subtype with a large immune component. Collectively, these data reveal the functional potential of genetic subclones that comprise heterogeneous primary breast carcinomas and are selected for in CTCs and posttreatment breast cancer metastases. In addition, they uncover a relationship between tumor heterogeneity and host immune response in the tumor microenvironment. SIGNIFICANCE: As breast cancers progress, they become more heterogeneous for multiple regions amplified in circulating tumor cells, and intratumoral spatial heterogeneity is associated with the immune landscape.
Collapse
MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/genetics
- Combined Modality Therapy
- Female
- Follow-Up Studies
- Gene Expression Regulation, Neoplastic
- Humans
- Immunity
- Lung Neoplasms/genetics
- Lung Neoplasms/immunology
- Lung Neoplasms/secondary
- Lung Neoplasms/therapy
- Lymphocytes, Tumor-Infiltrating/immunology
- Middle Aged
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/immunology
- Neoplasm Recurrence, Local/pathology
- Neoplasm Recurrence, Local/therapy
- Neoplastic Cells, Circulating/pathology
- Prognosis
- Prospective Studies
- Survival Rate
- Triple Negative Breast Neoplasms/genetics
- Triple Negative Breast Neoplasms/immunology
- Triple Negative Breast Neoplasms/pathology
- Triple Negative Breast Neoplasms/therapy
- Tumor Cells, Cultured
- Tumor Microenvironment
Collapse
Affiliation(s)
- Nisha Kanwar
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Zaldy Balde
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Ranju Nair
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Melanie Dawe
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Shiyi Chen
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada
| | - Manjula Maganti
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Eshetu G Atenafu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Sabrina Manolescu
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Carrie Wei
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Amanda Mao
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Fred Fu
- STTARR Innovation Centre, University Health Network, Toronto, Canada
| | - Dan Wang
- Biomarker Imaging Research Laboratory, Sunnybrook Research Institute, Toronto, Canada
| | - Alison Cheung
- Biomarker Imaging Research Laboratory, Sunnybrook Research Institute, Toronto, Canada
| | - Yulia Yerofeyeva
- Biomarker Imaging Research Laboratory, Sunnybrook Research Institute, Toronto, Canada
| | - Rachel Peters
- Biomarker Imaging Research Laboratory, Sunnybrook Research Institute, Toronto, Canada
| | - Kela Liu
- Biomarker Imaging Research Laboratory, Sunnybrook Research Institute, Toronto, Canada
| | - Christine Desmedt
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Christos Sotiriou
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Borbala Szekely
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Janina Kulka
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Trevor D McKee
- STTARR Innovation Centre, University Health Network, Toronto, Canada
| | - Naoto Hirano
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Immunology, University of Toronto, Toronto, Canada
| | - John M S Bartlett
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Martin J Yaffe
- Biomarker Imaging Research Laboratory, Sunnybrook Research Institute, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Philippe L Bedard
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - David McCready
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Susan J Done
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Laboratory Medicine Program, University Health Network, Toronto, Canada
| |
Collapse
|
21
|
Belloni S, Arrigoni C, Caruso R. Effects from physical exercise on reduced cancer-related fatigue: a systematic review of systematic reviews and meta-analysis. Acta Oncol 2021; 60:1678-1687. [PMID: 34396915 DOI: 10.1080/0284186x.2021.1962543] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Cancer-related fatigue is one of the most prevalent and distressing symptoms among cancer patients, resulting in a great cancer research challenge. Numerous systematic reviews of physical training interventions have been conducted to find the most effective approach. However, evidence remains fragmented, and in which cancer population physical training is more effective than other populations is still unclear. Thus, this study critically appraised systematic reviews and meta-analyses on physical training to reduce adults' cancer-related fatigue. METHODS A systematic review of systematic reviews and meta-analysis (PROSPERO: CRD42020189049), assessing the efficacy of exercise training for reducing cancer-related fatigue in adults, was conducted in PubMed, CINAHL, Cochrane Database of Systematic Reviews, and the Database of Abstracts of Reviews of Effects, and Pedro. The selected studies (standardized mean difference, SMD; 95%CI), was quantitatively pooled using a random-effects model. Heterogeneity was tested using chi-squared (Q) and I-square statistics (I2). RESULTS Of 1438 identified articles, 11 met the inclusion criteria, and ten were meta-analyzed. The results yielded a positive effect of physical training on fatigue in all cancer populations, SMD = -0.33 (-0.43, -0.23). Subgroup analysis based on tumor localization showed a slightly higher physical training effect on fatigue in adults with breast cancer, SMD = -0.36 (-0.57, -0.15), and prostate cancer SMD = -0.34 (-0.45, -.0.22). CONCLUSIONS Our analysis demonstrated some potential improvement in cancer-related fatigue in adult patients undergoing physical training during and after cancer treatments, particularly in patients with breast or prostate cancer.
Collapse
Affiliation(s)
- Silvia Belloni
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Cristina Arrigoni
- Department of Public Health, Experimental and Forensic Medicine, Section of Hygiene, University of Pavia, Pavia, Italy
| | - Rosario Caruso
- Health Professions Research and Development Unit, IRCCS Policlinico San Donato, Milan, Italy
| |
Collapse
|
22
|
Abstract
Integration of ecological and evolutionary features has begun to understand the interplay of tumor heterogeneity, microenvironment, and metastatic potential. Developing a theoretical framework is intrinsic to deciphering tumors' tremendous spatial and longitudinal genetic variation patterns in patients. Here, we propose that tumors can be considered evolutionary island-like ecosystems, that is, isolated systems that undergo evolutionary and spatiotemporal dynamic processes that shape tumor microenvironments and drive the migration of cancer cells. We examine attributes of insular systems and causes of insularity, such as physical distance and connectivity. These properties modulate migration rates of cancer cells through processes causing spatial and temporal isolation of the organs and tissues functioning as a supply of cancer cells for new colonizations. We discuss hypotheses, predictions, and limitations of tumors as islands analogy. We present emerging evidence of tumor insularity in different cancer types and discuss their relevance to the islands model. We suggest that the engagement of tumor insularity into conceptual and mathematical models holds promise to illuminate cancer evolution, tumor heterogeneity, and metastatic potential of cells.
Collapse
Affiliation(s)
- Antonia Chroni
- Institute for Genomics and Evolutionary Medicine, Temple University, USA
- Department of Biology, Temple University, USA
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, USA
- Department of Biology, Temple University, USA
- Center for Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
23
|
Upadhyay A. Natural compounds in the regulation of proteostatic pathways: An invincible artillery against stress, ageing, and diseases. Acta Pharm Sin B 2021; 11:2995-3014. [PMID: 34729300 PMCID: PMC8546668 DOI: 10.1016/j.apsb.2021.01.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/12/2020] [Accepted: 11/03/2020] [Indexed: 01/13/2023] Open
Abstract
Cells have different sets of molecules for performing an array of physiological functions. Nucleic acids have stored and carried the information throughout evolution, whereas proteins have been attributed to performing most of the cellular functions. To perform these functions, proteins need to have a unique conformation and a definite lifespan. These attributes are achieved by a highly coordinated protein quality control (PQC) system comprising chaperones to fold the proteins in a proper three-dimensional structure, ubiquitin-proteasome system for selective degradation of proteins, and autophagy for bulk clearance of cell debris. Many kinds of stresses and perturbations may lead to the weakening of these protective cellular machinery, leading to the unfolding and aggregation of cellular proteins and the occurrence of numerous pathological conditions. However, modulating the expression and functional efficiency of molecular chaperones, E3 ubiquitin ligases, and autophagic proteins may diminish cellular proteotoxic load and mitigate various pathological effects. Natural medicine and small molecule-based therapies have been well-documented for their effectiveness in modulating these pathways and reestablishing the lost proteostasis inside the cells to combat disease conditions. The present article summarizes various similar reports and highlights the importance of the molecules obtained from natural sources in disease therapeutics.
Collapse
Key Words
- 17-AAG, 17-allylamino-geldanamycin
- APC, anaphase-promoting complex
- Ageing
- Autophagy
- BAG, BCL2-associated athanogene
- CAP, chaperone-assisted proteasomal degradation
- CASA, chaperone-assisted selective autophagy
- CHIP, carboxy-terminus of HSC70 interacting protein
- CMA, chaperone-mediated autophagy
- Cancer
- Chaperones
- DUBs, deubiquitinases
- Drug discovery
- EGCG, epigallocatechin-3-gallate
- ESCRT, endosomal sorting complexes required for transport
- HECT, homologous to the E6-AP carboxyl terminus
- HSC70, heat shock cognate 70
- HSF1, heat shock factor 1
- HSP, heat shock protein
- KFERQ, lysine-phenylalanine-glutamate-arginine-glutamine
- LAMP2a, lysosome-associated membrane protein 2a
- LC3, light chain 3
- NBR1, next to BRCA1 gene 1
- Natural molecules
- Neurodegeneration
- PQC, protein quality control
- Proteinopathies
- Proteostasis
- RING, really interesting new gene
- UPS, ubiquitin–proteasome system
- Ub, ubiquitin
- Ubiquitin proteasome system
Collapse
Affiliation(s)
- Arun Upadhyay
- Department of Biochemistry, Central University of Rajasthan, Bandar Sindari, Kishangarh, Ajmer, Rajasthan 305817, India
| |
Collapse
|
24
|
Upadhyay A. Cancer: An unknown territory; rethinking before going ahead. Genes Dis 2021; 8:655-661. [PMID: 34291136 PMCID: PMC8278524 DOI: 10.1016/j.gendis.2020.09.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/01/2020] [Accepted: 09/12/2020] [Indexed: 01/13/2023] Open
Abstract
Cancer is a disease of altered signaling and metabolism, causing uncontrolled division and survival of transformed cells. A host of molecules, factors, and conditions have been designated as underlying causes for the inception and progression of the disease. An enormous amount of data is available, system-wide interaction networks of the genes and proteins are generated over the years and have now reached up to a level of saturation, where we need to shift our focus to the more advanced and comprehensive methods and approaches of data analysis and visualization. Even with the availability of enormous literature on this one of the most pressing pathological conditions, a successful cure of the disease seems to be obscure. New treatment plans, like immunotherapy and precision medicine, are being employed for different studies. Nevertheless, their actual benefits to the patients would be known only after the evaluation of clinical data over the next few years. Therefore, we need to look at few fundamental challenges that should be addressed in more depth before we could devise better, rigorous, and comprehensive treatment plans and may successfully reach a possible cure of the disease. This article aims at bringing attention towards some fundamental gaps in our approach towards the disease that leads to failure in devising successful therapeutics.
Collapse
Affiliation(s)
- Arun Upadhyay
- Department of Biochemistry, Central University of Rajasthan, Rajasthan, 305817, India
| |
Collapse
|
25
|
Sugara M, Chowdappa R, Kumar KVV, Gawari R, Swamy SN, Kumar SS. Aberrant Promoter Hypermethylation of p16 and RASSF1a Genes in Colorectal Cancer - Significance in Young Patients. Indian J Surg Oncol 2021; 12:454-459. [PMID: 34658570 PMCID: PMC8490567 DOI: 10.1007/s13193-021-01325-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 04/15/2021] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVE The clinical profile of colorectal cancers (CRC) in India is different from that described in western countries. Microsatellite instability and APC mutation explain the molecular biology of up to 50% of colorectal cancers. Global genome hypermethylation may be the cause in at least 20% of cases. Few studies from India have examined the epigenetic profile of colorectal cancers. This study was designed to study aberrant promoter hypermethylation of two select tumour suppressor genes (p16, RASSF1a) in patients with colorectal cancer and their association with clinicopathologic features. METHODS A total of 41 samples including controls were collected from colorectal cancer patients. DNA was isolated from tumour tissue, and methylation-specific PCR was performed for the 2 genes. RESULTS p16 and RASSF1a promoter hypermethylation was found in 26% and 48% of CRC cases, respectively. RASSF1a promoter hypermethylation was more often seen in young CRC patients aged 40 years or less, and this was found to be statistically significant (p value = 0.037). CONCLUSION RASSF1a hypermethylation is peculiar to rectal cancers and left-sided colonic tumours in young patients. Large-scale population-based studies with extensive genetic and epigenetic characterization are required for a better understanding and further validation of our findings. For individuals diagnosed with sporadic CRC, these studies on specimen might help predict prognosis and response to therapy.
Collapse
Affiliation(s)
- Medha Sugara
- Department of Surgical oncology, St. John’s Medical College, Bengaluru, Karnataka 560034 India
| | - Ramachandra Chowdappa
- Department of Surgical Oncology, Kidwai Memorial Institute of Oncology, Bengaluru, Karnataka 560029 India
| | - K. V. Veerendra Kumar
- Department of Surgical Oncology, Jawaharlal Nehru Medical College, Belgaum, Karnataka 590010 India
| | - Ramesh Gawari
- Department of Biochemistry, Kidwai Memorial Institute of Oncology, Bengaluru, Karnataka 560029 India
| | - Shalini N. Swamy
- Department of Biochemistry, Kidwai Memorial Institute of Oncology, Bengaluru, Karnataka 560029 India
| | - Sandeep S. Kumar
- Department of Biochemistry, Kidwai Memorial Institute of Oncology, Bengaluru, Karnataka 560029 India
| |
Collapse
|
26
|
Kandimalla R, Xu J, Link A, Matsuyama T, Yamamura K, Parker MI, Uetake H, Balaguer F, Borazanci E, Tsai S, Evans D, Meltzer SJ, Baba H, Brand R, Von Hoff D, Li W, Goel A. EpiPanGI Dx: A Cell-free DNA Methylation Fingerprint for the Early Detection of Gastrointestinal Cancers. Clin Cancer Res 2021; 27:6135-6144. [PMID: 34465601 DOI: 10.1158/1078-0432.ccr-21-1982] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/24/2021] [Accepted: 08/26/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE DNA methylation alterations have emerged as front-runners in cell-free DNA (cfDNA) biomarker development. However, much effort to date has focused on single cancers. In this context, gastrointestinal (GI) cancers constitute the second leading cause of cancer-related deaths worldwide; yet there is no blood-based assay for the early detection and population screening of GI cancers. EXPERIMENTAL DESIGN Herein, we performed a genome-wide DNA methylation analysis of multiple GI cancers to develop a pan-GI diagnostic assay. By analyzing DNA methylation data from 1,781 tumor and adjacent normal tissues, we first identified differentially methylated regions (DMR) between individual GI cancers and adjacent normal, as well as across GI cancers. We next prioritized a list of 67,832 tissue DMRs by incorporating all significant DMRs across various GI cancers to design a custom, targeted bisulfite sequencing platform. We subsequently validated these tissue-specific DMRs in 300 cfDNA specimens and applied machine learning algorithms to develop three distinct categories of DMR panels RESULTS: We identified three distinct DMR panels: (i) cancer-specific biomarker panels with AUC values of 0.98 (colorectal cancer), 0.98 (hepatocellular carcinoma), 0.94 (esophageal squamous cell carcinoma), 0.90 (gastric cancer), 0.90 (esophageal adenocarcinoma), and 0.85 (pancreatic ductal adenocarcinoma); (ii) a pan-GI panel that detected all GI cancers with an AUC of 0.88; and (iii) a multi-cancer (tissue of origin) prediction panel, EpiPanGI Dx, with a prediction accuracy of 0.85-0.95 for most GI cancers. CONCLUSIONS Using a novel biomarker discovery approach, we provide the first evidence for a cfDNA methylation assay that offers robust diagnostic accuracy for GI cancers.
Collapse
Affiliation(s)
- Raju Kandimalla
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute, Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas
| | - Jianfeng Xu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas.,Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California
| | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Hospital, Magdeburg, Germany
| | - Takatoshi Matsuyama
- Department of Gastrointestinal Surgery, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo, Japan
| | - Kensuke Yamamura
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - M Iqbal Parker
- Division of Medical Biochemistry and Structural Biology, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Hiroyuki Uetake
- Department of Specialized Surgery, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo, Japan
| | - Francesc Balaguer
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | | | - Susan Tsai
- Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Douglas Evans
- Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Stephen J Meltzer
- Department of Medicine, Division of Gastroenterology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Randall Brand
- Department of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Daniel Von Hoff
- HonorHealth Research Institute, Scottsdale, Arizona.,Translational Genomics Research Institute, an Affiliate of City of Hope, Phoenix, Arizona
| | - Wei Li
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas. .,Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California
| | - Ajay Goel
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute, Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas. .,Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Monrovia, California.,City of Hope Comprehensive Cancer Center, Duarte, California
| |
Collapse
|
27
|
Nanocarriers as a Tool for the Treatment of Colorectal Cancer. Pharmaceutics 2021; 13:pharmaceutics13081321. [PMID: 34452282 PMCID: PMC8399070 DOI: 10.3390/pharmaceutics13081321] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/13/2021] [Accepted: 07/20/2021] [Indexed: 12/13/2022] Open
Abstract
Nanotechnology is a promising tool for the treatment of cancer. In the past decades, major steps have been made to bring nanotechnology into the clinic in the form of nanoparticle-based drug delivery systems. The great hope of drug delivery systems is to reduce the side effects of chemotherapeutics while simultaneously increasing the efficiency of the therapy. An increased treatment efficiency would greatly benefit the quality of life as well as the life expectancy of cancer patients. However, besides its many advantages, nanomedicines have to face several challenges and hurdles before they can be used for the effective treatment of tumors. Here, we give an overview of the hallmarks of cancer, especially colorectal cancer, and discuss biological barriers as well as how drug delivery systems can be utilized for the effective treatment of tumors and metastases.
Collapse
|
28
|
Patel KB, Mroz EA, Faquin WC, Rocco JW. A combination of intra-tumor genetic heterogeneity, estrogen receptor alpha and human papillomavirus status predicts outcomes in head and neck squamous cell carcinoma following chemoradiotherapy. Oral Oncol 2021; 120:105421. [PMID: 34198234 DOI: 10.1016/j.oraloncology.2021.105421] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/19/2021] [Accepted: 06/21/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Previous work indicates that mutant-allele tumor heterogeneity (MATH), estrogen receptor alpha (ERα) expression, and human papillomavirus (HPV) status provide prognostic utility in head and neck squamous cell carcinoma (HNSCC). We sought to assess whether the combination of these three objective biomarkers could provide better prognostication for patients who receive chemoradiotherapy (CRT). METHODS 156 patients (75 oral cavity, 44 oropharyngeal and 37 laryngeal squamous cell carcinoma cancer patients) who received CRT as primary therapy or adjuvant to surgery were identified from The Cancer Genome Atlas (TCGA). MATH values were calculated from TCGA whole exome sequencing data, HPV status was determined by mapping RNA-seq reads, and ERα expression was determined from ESR1 mRNA expression data. Relationships among clinical characteristics were assessed by Fisher exact tests. Relationships of clinical characteristics and MATH, ERα and HPV to overall survival were evaluated with Cox proportional hazard analysis. RESULTS The combination of poor-prognosis values for all 3 biomarkers (high MATH, low ERα and HPV-negative status) has a predicted hazard ratio of 28.2 (95% CI: 5.4-148, p = 0.0001) versus the combination of their good-prognosis values (low MATH, high ERα and HPV-positive status). Addition of N classification to the combination of these three biomarkers added further prognostic value. CONCLUSIONS A combination of these three biomarkers, readily determined on pretreatment biopsy specimens, can stratify patients into prognostic groups. Their application potentially offers numerous opportunities to optimize treatment or explore de-intensification strategies in the clinical trial setting.
Collapse
Affiliation(s)
- Krupal B Patel
- Head and Neck and Endocrine Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Edmund A Mroz
- Department of Otolaryngology-Head and Neck Surgery and the James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, OH, United States
| | - William C Faquin
- Department of Pathology, Massachusetts Eye and Ear, Massachusetts General Hospital, Boston, MA, United States
| | - James W Rocco
- Department of Otolaryngology-Head and Neck Surgery and the James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, OH, United States.
| |
Collapse
|
29
|
Ghaderi F, Jokar N, Gholamrezanezhad A, Assadi M, Ahmadzadehfar H. Toward radiotheranostics in cancer stem cells: a promising initial step for tumour eradication. Clin Transl Imaging 2021. [DOI: 10.1007/s40336-021-00444-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
30
|
Schrank TP, Lenze N, Landess LP, Hoyle A, Parker J, Lal A, Sheth S, Chera BS, Patel SN, Hackman TG, Major MB, Issaeva N, Yarbrough WG. Genomic heterogeneity and copy number variant burden are associated with poor recurrence-free survival and 11q loss in human papillomavirus-positive squamous cell carcinoma of the oropharynx. Cancer 2021; 127:2788-2800. [PMID: 33819343 DOI: 10.1002/cncr.33504] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 01/15/2021] [Accepted: 01/23/2021] [Indexed: 11/09/2022]
Abstract
BACKGROUND Human papillomavirus-positive (HPV+) squamous cell carcinoma of the oropharynx (OPSCC) is the most prevalent HPV-associated malignancy in the United States. Favorable treatment outcomes have led to increased interest in treatment de-escalation to reduce treatment morbidity as well as the development of prognostic markers to identify appropriately low-risk patients. Intratumoral genomic heterogeneity and copy number alteration burden have been demonstrated to be predictive of poor outcomes in many other cancers; therefore, we sought to determine whether intratumor heterogeneity and genomic instability are associated with poor outcomes in HPV+ OPSCC. METHODS Tumor heterogeneity estimates were made based on targeted exome sequencing of 45 patients with HPV+ OPSCC tumors. Analysis of an additional cohort of HPV+ OPSCC tumors lacking matched normal sequencing allowed copy number analysis of 99 patient tumors. RESULTS High intratumorally genomic heterogeneity and high numbers of copy number alterations were strongly associated with worse recurrence-free survival. Tumors with higher heterogeneity and frequent copy number alterations were associated with loss of distal 11q, which encodes key genes related to double-strand break repair, including ATM and MRE11A. CONCLUSIONS Both intratumor genomic heterogeneity and high-burden copy number alterations are strongly associated with poor recurrence-free survival in patients with HPV+ OPSCC. The drivers of genomic instability and heterogeneity in these tumors remains to be elucidated. However, 11q loss and defective DNA double-strand break repair have been associated with genomic instability in other solid tumors. Copy number alteration burden and intratumoral heterogeneity represent promising avenues for risk stratification of patients with HPV+OPSCC.
Collapse
Affiliation(s)
- Travis P Schrank
- Department of Otolaryngology-Head and Neck Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Linberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Nicholas Lenze
- Department of Otolaryngology-Head and Neck Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Lee P Landess
- Department of Otolaryngology-Head and Neck Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Alan Hoyle
- Linberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Joel Parker
- Linberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Asim Lal
- Department of Otolaryngology-Head and Neck Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Siddharth Sheth
- Division of Hematology and Oncology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Bhishamjit S Chera
- Department of Radiation Oncology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Samip N Patel
- Department of Otolaryngology-Head and Neck Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Trevor G Hackman
- Department of Otolaryngology-Head and Neck Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - M Ben Major
- Linberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, Missouri.,Institute for Informatics, School of Medicine, Washington University in St. Louis, St. Louis, Missouri.,Department of Otolaryngology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Natalia Issaeva
- Department of Otolaryngology-Head and Neck Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Linberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Pathology and Lab Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Wendell G Yarbrough
- Department of Otolaryngology-Head and Neck Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Linberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Pathology and Lab Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| |
Collapse
|
31
|
Beloni S, Arrigoni C, Dellafiore F, Diamanti O, Piredda A, Caruso R. Symptom clusters in cancer patients: An Italian survey to validate and describe unwarranted clinical variation, inequality in access to healthcare, knowledge, and risk of malpractice. ACTA BIO-MEDICA : ATENEI PARMENSIS 2021; 92:e2021015. [PMID: 33855990 PMCID: PMC8138803 DOI: 10.23750/abm.v92is2.11331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/04/2021] [Indexed: 12/09/2022]
Abstract
Background and aims: The perceptions of professionals involved in cancer care regarding the importance of their symptoms-specific knowledge, unwarranted clinical variation (UCV), and inequalities in access to healthcare are still underdescribed. This study aims to confirm the construct validity of a previously initially developed questionnaire and describe nurses’ perceptions about the relevance of their knowledge referred to cancer symptoms management, the UCV, the inequalities in access to healthcare, and malpractice risk. Method: A cross-sectional pan-national study was conducted using a convenience sample, collecting data through a previously initially validated questionnaire. Construct validity was corroborated through confirmatory factor analysis, and descriptive statistics were employed for summarizing the questionnaire’s scores. The scores between the nurses working in accredited cancer centers and nurses employed in general hospitals were inferentially compared. Results: The sample comprised 810 nurses, 480 were nurses working in accredited cancer centers, and 330 were nurses working in general hospitals. The questionnaire showed adequate construct validity and reliability. Nurses perceived the cluster of psychosocial symptoms with a greater risk of UCV and inequalities in access to cancer services than the cluster of physical symptoms. Discussion and conclusions: A paradigm shift aimed at integrating psychosocial cancer symptoms in the care paths emerged as pivotal for improving cancer care in Italy.
Collapse
Affiliation(s)
- Silvia Beloni
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy.
| | - Cristina Arrigoni
- Department of Public Health, Experimental and Forensic Medicine, Section of Hygiene, University of Pavia, Pavia, Italy .
| | - Federica Dellafiore
- Health Professions Research and Development Unit, IRCCS Policlinico San Donato, San Donato Milanese, Italy.
| | - Orejeta Diamanti
- Research Nursing Centre, IRCCS Istituto Oncologico Veneto, Padova, Italy .
| | - Alessio Piredda
- Italian Association of Cancer Nurses, European Institute of Oncology, Milan, Italy .
| | - Rosario Caruso
- Health Professions Research and Development Unit, IRCCS Policlinico San Donato, San Donato Milanese, Italy.
| |
Collapse
|
32
|
Shi C, Zhou Z, Lin H, Gao J. Imaging Beyond Seeing: Early Prognosis of Cancer Treatment. SMALL METHODS 2021; 5:e2001025. [PMID: 34927817 DOI: 10.1002/smtd.202001025] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/24/2020] [Indexed: 06/14/2023]
Abstract
Assessing cancer response to therapeutic interventions has been realized as an important course to early predict curative efficacy and treatment outcomes due to tumor heterogeneity. Compared to the traditional invasive tissue biopsy method, molecular imaging techniques have fundamentally revolutionized the ability to evaluate cancer response in a spatiotemporal manner. The past few years has witnessed a paradigm shift on the efforts from manufacturing functional molecular imaging probes for seeing a tumor to a vantage stage of interpreting the tumor response during different treatments. This review is to stand by the current development of advanced imaging technologies aiming to predict the treatment response in cancer therapy. Special interest is placed on the systems that are able to provide rapid and noninvasive assessment of pharmacokinetic drug fates (e.g., drug distribution, release, and activation) and tumor microenvironment heterogeneity (e.g., tumor cells, macrophages, dendritic cells (DCs), T cells, and inflammatory cells). The current status, practical significance, and future challenges of the emerging artificial intelligence (AI) technology and machine learning in the applications of medical imaging fields is overviewed. Ultimately, the authors hope that this review is timely to spur research interest in molecular imaging and precision medicine.
Collapse
Affiliation(s)
- Changrong Shi
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics and Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Zijian Zhou
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics and Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Hongyu Lin
- State Key Laboratory of Physical Chemistry of Solid Surfaces, The Key Laboratory for Chemical Biology of Fujian Province and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Jinhao Gao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, The Key Laboratory for Chemical Biology of Fujian Province and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| |
Collapse
|
33
|
Abstract
Glioblastoma remains incurable despite advances in surgery, radiation, and chemotherapy, underscoring the need for new therapies. The genetic heterogenicity, presence of redundant molecular pathways, and the blood-brain barrier have limited the applicability of molecularly targeted agents. The therapeutic benefit seen with a small subset of patients suggests, however, that patient selection is critical. Recent investigations show that molecularly targeted synthetic lethality is a promising complementary approach. The article provides an overview of the challenges of molecularly targeted therapy in adults with glioblastoma, including current trials and future therapeutic directions.
Collapse
Affiliation(s)
- Matthew A Smith-Cohn
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Building 37, Room 1016, Bethesda, MD 20892, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Orieta Celiku
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Building 37, Room 1142, Bethesda, MD 20892, USA
| | - Mark R Gilbert
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
34
|
Reovirus and the Host Integrated Stress Response: On the Frontlines of the Battle to Survive. Viruses 2021; 13:v13020200. [PMID: 33525628 PMCID: PMC7910986 DOI: 10.3390/v13020200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 12/17/2022] Open
Abstract
Cells are continually exposed to stressful events, which are overcome by the activation of a number of genetic pathways. The integrated stress response (ISR) is a large component of the overall cellular response to stress, which ultimately functions through the phosphorylation of the alpha subunit of eukaryotic initiation factor-2 (eIF2α) to inhibit the energy-taxing process of translation. This response is instrumental in the inhibition of viral infection and contributes to evolution in viruses. Mammalian orthoreovirus (MRV), an oncolytic virus that has shown promise in over 30 phase I–III clinical trials, has been shown to induce multiple arms within the ISR pathway, but it successfully evades, modulates, or subverts each cellular attempt to inhibit viral translation. MRV has not yet received Food and Drug Administration (FDA) approval for general use in the clinic; therefore, researchers continue to study virus interactions with host cells to identify circumstances where MRV effectiveness in tumor killing can be improved. In this review, we will discuss the ISR, MRV modulation of the ISR, and discuss ways in which MRV interaction with the ISR may increase the effectiveness of cancer therapeutics whose modes of action are altered by the ISR.
Collapse
|
35
|
Phycocyanin from Arthrospira platensis as Potential Anti-Cancer Drug: Review of In Vitro and In Vivo Studies. Life (Basel) 2021; 11:life11020091. [PMID: 33513794 PMCID: PMC7911896 DOI: 10.3390/life11020091] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/18/2022] Open
Abstract
The application of cytostatic drugs or natural substances to inhibit cancer growth and progression is an important and evolving subject of cancer research. There has been a surge of interest in marine bioresources, particularly algae, as well as cyanobacteria and their bioactive ingredients. Dried biomass products of Arthrospira and Chlorella have been categorized as “generally recognized as safe” (GRAS) by the US Food and Drug Administration (FDA). Of particular importance is an ingredient of Arthrospira: phycocyanin, a blue-red fluorescent, water-soluble and non-toxic biliprotein pigment. It is reported to be the main active ingredient of Arthrospira and was shown to have therapeutic properties, including anti-oxidant, anti-inflammatory, immune-modulatory and anti-cancer activities. In the present review, in vitro and in vivo data on the effects of phycocyanin on various tumor cells and on cells from healthy tissues are summarized. The existing knowledge of underlying molecular mechanisms, and strategies to improve the efficiency of potential phycocyanin-based anti-cancer therapies are discussed.
Collapse
|
36
|
Kim AA, Rachid Zaim S, Subbian V. Assessing reproducibility and veracity across machine learning techniques in biomedicine: A case study using TCGA data. Int J Med Inform 2020; 141:104148. [DOI: 10.1016/j.ijmedinf.2020.104148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 03/22/2020] [Accepted: 04/16/2020] [Indexed: 11/28/2022]
|
37
|
Mroz EA, Patel KB, Rocco JW. Intratumor heterogeneity could inform the use and type of postoperative adjuvant therapy in patients with head and neck squamous cell carcinoma. Cancer 2020; 126:1895-1904. [PMID: 32083741 DOI: 10.1002/cncr.32742] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 11/06/2022]
Abstract
BACKGROUND After surgery for head and neck squamous cell carcinoma (HNSCC), decisions regarding adjuvant radiotherapy (RT) or chemoradiotherapy (CRT) are based on staging and the presence of high-risk pathology. Because higher mutant allele tumor heterogeneity (MATH; a measure of intratumor genetic heterogeneity) is associated with shorter overall survival (OS) in patients with HNSCC, the authors sought to determine whether MATH analysis might further inform these decisions. METHODS Adjuvant therapy-associated relationships between MATH and OS were analyzed for 389 patients with HNSCC who were treated surgically. Data were obtained from The Cancer Genome Atlas and analyzed with Cox proportional hazards multiple regression accounting for 7 other patient characteristics. RESULTS The relationship between MATH and OS differed with adjuvant therapy in a way that could inform therapy decisions. Adjuvant RT alone was found to provide substantial benefit for patients having high-MATH tumors (RT vs no adjuvant therapy: hazard ratio, 0.29 [95% CI, 0.17-0.51]) but no benefit for those having low-MATH tumors. In contrast, adjuvant CRT provided no benefit beyond that of adjuvant RT for patients with high-MATH tumors but substantially improved OS among patients with low-MATH tumors (CRT vs no adjuvant therapy: hazard ratio, 0.34 [95% CI, 0.15-0.78]). CONCLUSIONS The results of the current analysis suggested that patients with HNSCC with high-MATH tumors who underwent surgical treatment could benefit from adjuvant RT, even when current clinical guidelines indicate otherwise. The addition of adjuvant chemotherapy for patients with high-MATH tumors would not be indicated. Adding chemotherapy might be necessary to radiosensitize low-MATH tumors to adjuvant RT. This potential predictive role of tumor MATH analysis should be evaluated in prospective clinical trials.
Collapse
Affiliation(s)
- Edmund A Mroz
- Department of Otolaryngology-Head and Neck Surgery, James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Krupal B Patel
- Department of Otolaryngology-Head and Neck Surgery, James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - James W Rocco
- Department of Otolaryngology-Head and Neck Surgery, James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| |
Collapse
|
38
|
Tomaselli D, Lucidi A, Rotili D, Mai A. Epigenetic polypharmacology: A new frontier for epi-drug discovery. Med Res Rev 2020; 40:190-244. [PMID: 31218726 PMCID: PMC6917854 DOI: 10.1002/med.21600] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 05/10/2019] [Accepted: 05/14/2019] [Indexed: 12/11/2022]
Abstract
Recently, despite the great success achieved by the so-called "magic bullets" in the treatment of different diseases through a marked and specific interaction with the target of interest, the pharmacological research is moving toward the development of "molecular network active compounds," embracing the related polypharmacology approach. This strategy was born to overcome the main limitations of the single target therapy leading to a superior therapeutic effect, a decrease of adverse reactions, and a reduction of potential mechanism(s) of drug resistance caused by robustness and redundancy of biological pathways. It has become clear that multifactorial diseases such as cancer, neurological, and inflammatory disorders, may require more complex therapeutic approaches hitting a certain biological system as a whole. Concerning epigenetics, the goal of the multi-epi-target approach consists in the development of small molecules able to simultaneously and (often) reversibly bind different specific epi-targets. To date, two dual histone deacetylase/kinase inhibitors (CUDC-101 and CUDC-907) are in an advanced stage of clinical trials. In the last years, the growing interest in polypharmacology encouraged the publication of high-quality reviews on combination therapy and hybrid molecules. Hence, to update the state-of-the-art of these therapeutic approaches avoiding redundancy, herein we focused only on multiple medication therapies and multitargeting compounds exploiting epigenetic plus nonepigenetic drugs reported in the literature in 2018. In addition, all the multi-epi-target inhibitors known in literature so far, hitting two or more epigenetic targets, have been included.
Collapse
Affiliation(s)
- Daniela Tomaselli
- Department of Chemistry and Technologies of Drugs,
“Sapienza” University of Rome, P.le A. Moro 5, 00185 Roma, Italy
| | - Alessia Lucidi
- Department of Chemistry and Technologies of Drugs,
“Sapienza” University of Rome, P.le A. Moro 5, 00185 Roma, Italy
| | - Dante Rotili
- Department of Chemistry and Technologies of Drugs,
“Sapienza” University of Rome, P.le A. Moro 5, 00185 Roma, Italy
| | - Antonello Mai
- Department of Chemistry and Technologies of Drugs,
“Sapienza” University of Rome, P.le A. Moro 5, 00185 Roma, Italy
- Pasteur Institute - Cenci Bolognetti Foundation, Viale
Regina Elena 291, 00161 Roma, Italy
| |
Collapse
|
39
|
Hason M, Bartůněk P. Zebrafish Models of Cancer-New Insights on Modeling Human Cancer in a Non-Mammalian Vertebrate. Genes (Basel) 2019; 10:genes10110935. [PMID: 31731811 PMCID: PMC6896156 DOI: 10.3390/genes10110935] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/11/2019] [Accepted: 11/11/2019] [Indexed: 12/26/2022] Open
Abstract
Zebrafish (Danio rerio) is a valuable non-mammalian vertebrate model widely used to study development and disease, including more recently cancer. The evolutionary conservation of cancer-related programs between human and zebrafish is striking and allows extrapolation of research outcomes obtained in fish back to humans. Zebrafish has gained attention as a robust model for cancer research mainly because of its high fecundity, cost-effective maintenance, dynamic visualization of tumor growth in vivo, and the possibility of chemical screening in large numbers of animals at reasonable costs. Novel approaches in modeling tumor growth, such as using transgene electroporation in adult zebrafish, could improve our knowledge about the spatial and temporal control of cancer formation and progression in vivo. Looking at genetic as well as epigenetic alterations could be important to explain the pathogenesis of a disease as complex as cancer. In this review, we highlight classic genetic and transplantation models of cancer in zebrafish as well as provide new insights on advances in cancer modeling. Recent progress in zebrafish xenotransplantation studies and drug screening has shown that zebrafish is a reliable model to study human cancer and could be suitable for evaluating patient-derived xenograft cell invasiveness. Rapid, large-scale evaluation of in vivo drug responses and kinetics in zebrafish could undoubtedly lead to new applications in personalized medicine and combination therapy. For all of the above-mentioned reasons, zebrafish is approaching a future of being a pre-clinical cancer model, alongside the mouse. However, the mouse will continue to be valuable in the last steps of pre-clinical drug screening, mostly because of the highly conserved mammalian genome and biological processes.
Collapse
|
40
|
Ravikumar S, Devanapally S, Jose AM. Gene silencing by double-stranded RNA from C. elegans neurons reveals functional mosaicism of RNA interference. Nucleic Acids Res 2019; 47:10059-10071. [PMID: 31501873 PMCID: PMC6821342 DOI: 10.1093/nar/gkz748] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/12/2019] [Accepted: 08/20/2019] [Indexed: 12/12/2022] Open
Abstract
Delivery of double-stranded RNA (dsRNA) into animals can silence genes of matching sequence in diverse cell types through mechanisms that have been collectively called RNA interference. In the nematode Caenorhabditis elegans, dsRNA from multiple sources can trigger the amplification of silencing signals. Amplification occurs through the production of small RNAs by two RNA-dependent RNA polymerases (RdRPs) that are thought to be tissue-specific - EGO-1 in the germline and RRF-1 in somatic cells. Here we demonstrate that EGO-1 can compensate for the lack of RRF-1 when dsRNA from neurons is used to silence genes in intestinal cells. However, the lineal origins of cells that can use EGO-1 varies. This variability could be because random sets of cells can either receive different amounts of dsRNA from the same source or use different RdRPs to perform the same function. Variability is masked in wild-type animals, which show extensive silencing by neuronal dsRNA. As a result, cells appear similarly functional despite underlying differences that vary from animal to animal. This functional mosaicism cautions against inferring uniformity of mechanism based on uniformity of outcome. We speculate that functional mosaicism could contribute to escape from targeted therapies and could allow developmental systems to drift over evolutionary time.
Collapse
Affiliation(s)
- Snusha Ravikumar
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Sindhuja Devanapally
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Antony M Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| |
Collapse
|
41
|
Li HN, He T, Zha YJ, Du F, Liu J, Lin HR, Yang WZ. HIF-1α rs11549465 C>T polymorphism contributes to increased cancer susceptibility: Evidence from 49 studies. J Cancer 2019; 10:5955-5963. [PMID: 31762805 PMCID: PMC6856573 DOI: 10.7150/jca.35716] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 08/20/2019] [Indexed: 12/21/2022] Open
Abstract
HIF-1α (hypoxia-inducible factor-1α) is a transcriptional factor that participates in the regulation of oxygen homeostasis. Despites numbers of case-control studies working on this area, the actual relationship of HIF-1α gene generic variant rs11549465 C>T imposing on cancer susceptibility remains unveiled. To get a better understanding of such relationship, this meta-analysis was carried out by incorporating all eligible case-control studies. Qualified articles were acquired from PubMed, CNKI, EMBASE, PMC, and Wanfang database update to April 2019. Odds ratios (ORs) and their corresponding 95% confidence intervals (CIs) were employed to estimate the relationship of interest. Heterogeneity tests, sensitivity analyses and publication bias assessments were also carried out to ensure the strength of our conclusion. A total of 46 articles with 49 studies including 12920 cases and 13363 controls were included. The results indicated that HIF-1α rs11549465 C>T was significantly related to the increased risk of overall cancer under four genetic models (TT vs. CC: OR=2.06, 95% CI=1.34-3.16; TT vs. CC/CT: OR=2.42, 95% CI=1.60-3.65; CT/TT vs. CC: OR=1.21, 95% CI=1.04-1.40; T vs. C: OR=1.29, 95% CI=1.12-1.48). Furthermore, enhanced cancer risk was detected after stratification by cancer type, ethnicity, the source of controls and HWE. These results suggest that HIF-1α rs11549465 C>T polymorphism may predispose to cancer susceptibility.
Collapse
Affiliation(s)
- Hu-Nian Li
- Emergency and Critical Care Center, Renmin Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Ting He
- Department of Neurology, Renmin Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Yong-Jiu Zha
- Emergency and Critical Care Center, Renmin Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Fang Du
- Emergency and Critical Care Center, Renmin Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Jie Liu
- Emergency and Critical Care Center, Renmin Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Hui-Ran Lin
- Animal Experimental Management Center, Public Technology Service Platform, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, Guangdong, China
| | - Wen-Zi Yang
- Emergency and Critical Care Center, Renmin Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| |
Collapse
|
42
|
Abstract
Next-generation sequencing (NGS) data have been central to the development of targeted therapy and immunotherapy for precision oncology. In targeted therapy, drugs directly attack cancer, by altering the expression of critical cancer genes identified with cancer genome profiling. Immunotherapy drugs indirectly attack cancer, by inducing the immune system to attack and treat cancer. Harnessing genomic data for deployment and development of immunotherapy comprises the field of immunogenomics. The discovery of a link between cancer cells escaping immune destruction and cancer progression, led to extensive research into this mechanism and drug development. In the past few years, FDA has granted accelerated approval to several immunotherapy cancer treatment drugs, pembrolizumab, nivolumab, and atezolizumab, belonging to the class of checkpoint inhibitors. Utilization of pretreatment genomic cancer screening to identify patients most likely to respond to immunotherapy and to customize immunotherapy for a given patient, promises to improve cancer treatment outcomes. Recent advances in molecular profiling, high-throughput sequencing, and computational efficiency has made immunogenomics the major tenet of precision medicine in cancer treatment. This review provides a brief overview on the state of art of immunogenomics in precision cancer medicine.
Collapse
|
43
|
Milo I, Bedora-Faure M, Garcia Z, Thibaut R, Périé L, Shakhar G, Deriano L, Bousso P. The immune system profoundly restricts intratumor genetic heterogeneity. Sci Immunol 2019; 3:3/29/eaat1435. [PMID: 30470696 DOI: 10.1126/sciimmunol.aat1435] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 08/03/2018] [Accepted: 10/18/2018] [Indexed: 12/14/2022]
Abstract
Tumors develop under the selective pressure of the immune system. However, it remains critical to establish how the immune system affects the clonal heterogeneity of tumors that often display cell-to-cell variation in genetic alterations and antigenic expression. To address these questions, we introduced a multicolor barcoding strategy to study the growth of a MYC-driven B cell lymphoma harboring a large degree of intratumor genetic diversity. Using intravital imaging, we visualized that lymphoma subclones grow as patches of sessile cells in the bone marrow, creating a spatially compartmentalized architecture for tumor diversity. Using multicolor barcoding and whole-exome sequencing, we demonstrated that immune responses strongly restrict intratumor genomic diversity and favor clonal dominance, a process mediated by the selective elimination of more immunogenic cells and amplified by epitope spreading. Anti-PD-1 treatment also narrowed intratumor diversity. Our results provide direct evidence that immune pressure shapes the level of intratumor genetic heterogeneity and have important implications for the design of therapeutic strategies.
Collapse
Affiliation(s)
- Idan Milo
- Dynamics of Immune Responses Unit, Equipe Labellisée Ligue Contre le Cancer, Institut Pasteur, 75015 Paris, France.,INSERM U1223, 75015 Paris, France
| | - Marie Bedora-Faure
- Genome Integrity, Immunity and Cancer Unit, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Zacarias Garcia
- Dynamics of Immune Responses Unit, Equipe Labellisée Ligue Contre le Cancer, Institut Pasteur, 75015 Paris, France.,INSERM U1223, 75015 Paris, France
| | - Ronan Thibaut
- Dynamics of Immune Responses Unit, Equipe Labellisée Ligue Contre le Cancer, Institut Pasteur, 75015 Paris, France.,INSERM U1223, 75015 Paris, France.,University Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, rue du Dr Roux, 75015 Paris, France
| | - Leïla Périé
- Institut Curie, PSL Research University, CNRS UMR168, 11 rue Pierre et Marie Curie, 75005 Paris, France.,Sorbonne Universités, UPMC University Paris 06, 4 place Jussieu, 75005 Paris, France
| | - Guy Shakhar
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ludovic Deriano
- Genome Integrity, Immunity and Cancer Unit, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Philippe Bousso
- Dynamics of Immune Responses Unit, Equipe Labellisée Ligue Contre le Cancer, Institut Pasteur, 75015 Paris, France. .,INSERM U1223, 75015 Paris, France
| |
Collapse
|
44
|
Newton R, Wernisch L. A meta-analysis of multiple matched aCGH/expression cancer datasets reveals regulatory relationships and pathway enrichment of potential oncogenes. PLoS One 2019; 14:e0213221. [PMID: 31335867 PMCID: PMC6650054 DOI: 10.1371/journal.pone.0213221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 07/05/2019] [Indexed: 12/12/2022] Open
Abstract
The copy numbers of genes in cancer samples are often highly disrupted and form a natural amplification/deletion experiment encompassing multiple genes. Matched array comparative genomics and transcriptomics datasets from such samples can be used to predict inter-chromosomal gene regulatory relationships. Previously we published the database METAMATCHED, comprising the results from such an analysis of a large number of publically available cancer datasets. Here we investigate genes in the database which are unusual in that their copy number exhibits consistent heterogeneous disruption in a high proportion of the cancer datasets. We assess the potential relevance of these genes to the pathology of the cancer samples, in light of their predicted regulatory relationships and enriched biological pathways. A network-based method was used to identify enriched pathways from the genes’ inferred targets. The analysis predicts both known and new regulator-target interactions and pathway memberships. We examine examples in detail, in particular the gene POGZ, which is disrupted in many of the cancer datasets and has an unusually large number of predicted targets, from which the network analysis predicts membership of cancer related pathways. The results suggest close involvement in known cancer pathways of genes exhibiting consistent heterogeneous copy number disruption. Further experimental work would clarify their relevance to tumor biology. The results of the analysis presented in the database METAMATCHED, and included here as an R archive file, constitute a large number of predicted regulatory relationships and pathway memberships which we anticipate will be useful in informing such experiments.
Collapse
Affiliation(s)
- Richard Newton
- MRC Biostatistics Unit, Cambridge University, Cambridge, United Kingdom
- * E-mail:
| | - Lorenz Wernisch
- MRC Biostatistics Unit, Cambridge University, Cambridge, United Kingdom
| |
Collapse
|
45
|
Sultana N, Rahman M, Myti S, Islam J, Mustafa MG, Nag K. A novel knowledge-derived data potentizing method revealed unique liver cancer-associated genetic variants. Hum Genomics 2019; 13:30. [PMID: 31272500 PMCID: PMC6610914 DOI: 10.1186/s40246-019-0213-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 06/13/2019] [Indexed: 01/28/2023] Open
Abstract
Background Next-generation sequencing (NGS) has been advancing the progress of detection of disease-associated genetic variants and genome-wide profiling of expressed sequences over the past decade. NGS enables the analyses of multiple regions of a genome in a single reaction format and has been shown to be a cost-effective and efficient tool for root-cause analysis of disease and optimization of treatment. NGS has been leading global efforts to device personalized and precision medicine (PM) in clinical practice. The effectiveness of NGS for the aforementioned applications has been proven unequivocal for multifactorial diseases like cancer. However, definitive prediction of cancer markers for all types of diseases and for global populations still remains highly rewarding because of the diversity of cancer types and genetic variants in human. Results We performed exome sequencing of four samples in quest of critical genetic factor/s associated with liver cancer. By imposing knowledge-based filter chains, we have revealed a panel of genetic variants, which are unrecognized by current major genomics data repositories. Total 20 MNV-induced, 5 INDEL-induced, and 31 SNV-induced neoplasm-exclusive genes were revealed through NGS data acquisition followed by data curing with the application of quality filter chains. Liver-specific expression profile of the identified gene pool is directed to the selection of 17 genes which could be the as likely causative genetic factors for liver cancer. Further study on expression level and relevant functional significance enables us to identify and conclude the following four novel variants, viz., c.416T>C (p.Phe139Ser) in SORD, c.1048_1049delGCinsCG (p.Ala350Arg) in KRT6A, c.1159G>T (p.Gly387Cys) in SVEP1, and c.430G>C (p.Gly144Arg) in MRPL38 as a critical genetic factor for liver cancer. Conclusion By applying a novel data prioritizing rationale, we explored a panel of previously unaddressed liver cancer-associated variants. These findings may have an opportunity for early prediction of neoplasm/cancer in liver and designing of relevant personalized/precision liver cancer therapeutics in clinical practice. Since NGS protocol is associated with tons of non-specific mutations due to the variation in background genetic makeup of subjects, therefore, our method of data curing could be applicable for more effective screening of global genetic variants related to disease onset, progression, and remission. Electronic supplementary material The online version of this article (10.1186/s40246-019-0213-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Naznin Sultana
- Globe Biotech Limited, Plot No # 3/KA, Tejgaon Industrial Area, Dhaka, 1208, Bangladesh.
| | - Mijanur Rahman
- Globe Biotech Limited, Plot No # 3/KA, Tejgaon Industrial Area, Dhaka, 1208, Bangladesh
| | - Sanat Myti
- Globe Biotech Limited, Plot No # 3/KA, Tejgaon Industrial Area, Dhaka, 1208, Bangladesh
| | - Jikrul Islam
- Globe Biotech Limited, Plot No # 3/KA, Tejgaon Industrial Area, Dhaka, 1208, Bangladesh
| | - Md G Mustafa
- Bangabandhu Sheikh Mujib Medical University, Shahbagh, Dhaka, 1000, Bangladesh
| | - Kakon Nag
- Globe Biotech Limited, Plot No # 3/KA, Tejgaon Industrial Area, Dhaka, 1208, Bangladesh.
| |
Collapse
|
46
|
DuRoss AN, Neufeld MJ, Landry MR, Rosch JG, Eaton CT, Sahay G, Thomas CR, Sun C. Micellar Formulation of Talazoparib and Buparlisib for Enhanced DNA Damage in Breast Cancer Chemoradiotherapy. ACS APPLIED MATERIALS & INTERFACES 2019; 11:12342-12356. [PMID: 30860347 PMCID: PMC7213279 DOI: 10.1021/acsami.9b02408] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Chemoradiation is an effective combined modality therapeutic approach that utilizes principles of spatial cooperation to combat the adaptability associated with cancer and to potentially expand the therapeutic window. Optimal therapeutic efficacy requires intelligent selection and refinement of radiosynergistic pharmaceutical agents, enhanced delivery methods, and temporal consideration. Here, a monodisperse sub-20 nm mixed poloxamer micelle (MPM) system was developed to deliver hydrophobic drugs intravenously, in tandem with ionizing radiation. This report demonstrates in vitro synergy and enhanced radiosensitivity when two molecularly targeted DNA repair inhibitors, talazoparib and buparlisib, are encapsulated and combined with radiation in a 4T1 murine breast cancer model. Evaluation of in vivo biodistribution and toxicity exhibited no reduction in particle accumulation upon radiation and a lack of both acute and chronic toxicities. In vivo efficacy studies suggested the promise of combining talazoparib, buparlisib, and radiation to enhance survival and control tumor growth. Tissue analysis suggests enhanced DNA damage leading to apoptosis, thus increasing efficacy. These findings highlight the challenges associated with utilizing clinically relevant inclusion criteria and treatment protocols because complete tumor regression and extended survival were masked by an aggressively metastasizing model. As with clinical treatment regimens, the findings here establish a need for further optimization of this multimodal platform.
Collapse
Affiliation(s)
- Allison N. DuRoss
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR 97201, USA
| | - Megan J. Neufeld
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR 97201, USA
| | - Madeleine R. Landry
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR 97201, USA
| | - Justin G. Rosch
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR 97201, USA
| | - Colin T. Eaton
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR 97201, USA
| | - Gaurav Sahay
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR 97201, USA
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, OR 97201, USA
| | - Charles R. Thomas
- Department of Radiation Medicine, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Conroy Sun
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR 97201, USA
- Department of Radiation Medicine, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
- Corresponding author: (C. Sun)
| |
Collapse
|
47
|
Toratani S, Ogawa I, Sasahara H, Yoshioka Y, Kanda T, Tani R, Okamoto T. Pathological factors involved in local failure in squamous cell carcinoma of the oral cavity: retrospective study and proposal of a new clinical classification. Int J Oral Maxillofac Surg 2019; 48:143-151. [DOI: 10.1016/j.ijom.2018.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 04/03/2018] [Accepted: 07/06/2018] [Indexed: 01/28/2023]
|
48
|
The Coherence Problem: Finding Meaning in GWAS Complexity. Behav Genet 2018; 49:187-195. [DOI: 10.1007/s10519-018-9935-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 10/17/2018] [Indexed: 12/15/2022]
|
49
|
Zhang Z, Yu W, Chen S, Chen Y, Chen L, Zhang S. Methylation of the claudin‑3 promoter predicts the prognosis of advanced gastric adenocarcinoma. Oncol Rep 2018; 40:49-60. [PMID: 29749528 PMCID: PMC6059754 DOI: 10.3892/or.2018.6411] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 04/13/2018] [Indexed: 02/07/2023] Open
Abstract
Claudin-3 expression is associated with gastric cancer progression, but the role of epigenetic modifications remains unclear. We investigated methylation of the claudin-3 promoter and expression profiles in gastric adenocarcinoma and their associations with clinicopathological characteristics and prognosis of the patients. A total of 122 patients with advanced gastric cancer [stage IIB-IV, with lymph node (LN) metastasis] were enrolled. Each patient provided 4 tissue samples: normal gastric epithelium, intestinal metaplasia, primary tumor and metastatic LN. Claudin-3 protein expression was examined by immunohistochemistry. Claudin-3 promoter methylation was determined by methylation-specific PCR and verified by bisulfite sequencing PCR. Claudin-3 mRNA expression was measured by real-time PCR in a subset of cases, and its correlation with protein expression was analyzed using Spearman correlation. Kaplan-Meier survival analysis was performed (log-rank test). Factors associated with survival were identified by Cox regression. The strong expression rate of claudin-3 in intestinal metaplasia, primary tumor, metastatic LN and normal gastric epithelium was 91.8, 58.2, 30.3 and 13.9%, respectively. The promoter hypermethylation rate in intestinal metaplasia, primary tumor, normal gastric epithelium and metastatic LN was 5.7, 27.9, 36.9 and 49.2%, respectively. Claudin-3 mRNA and protein expression were positively correlated (P<0.001) with normal gastric epithelium (rs=0.745), intestinal metaplasia (rs=0.876), primary gastric adenocarcinoma (rs=0.915) and metastatic LN (rs=0.819). Claudin-3 mRNA expression was negatively correlated with claudin-3 promoter methylation. Median patient survival was 38, 22 and 11 months in the hypomethylated, partially methylated and hypermethylated groups, respectively (P<0.001). Claudin-3 promoter methylation status (HR: 5.67; 95% CI: 2.27–14.17) but not claudin-3 expression was an independent predictor of survival. Claudin-3 promoter hypermethylation reduces claudin-3 expression and independently predicts poor prognosis.
Collapse
Affiliation(s)
- Zhenzhen Zhang
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou 350005, P.R. China
| | - Weixing Yu
- Institute of Translational Medicine, Fujian Medical University, Fujian, Fuzhou 350122, P.R. China
| | - Shuqin Chen
- Department of Pathology, Fujian Medical University, Fujian, Fuzhou 350122, P.R. China
| | - Yupeng Chen
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou 350005, P.R. China
| | - Linying Chen
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou 350005, P.R. China
| | - Sheng Zhang
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fujian, Fuzhou 350005, P.R. China
| |
Collapse
|
50
|
Gomez K, Miura S, Huuki LA, Spell BS, Townsend JP, Kumar S. Somatic evolutionary timings of driver mutations. BMC Cancer 2018; 18:85. [PMID: 29347918 PMCID: PMC5774140 DOI: 10.1186/s12885-017-3977-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 12/21/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND A unified analysis of DNA sequences from hundreds of tumors concluded that the driver mutations primarily occur in the earliest stages of cancer formation, with relatively few driver mutation events detected in the late-arising subclones. However, emerging evidence from the sequencing of multiple tumors and tumor regions per individual suggests that late-arising subclones with additional driver mutations are underestimated in single-sample analyses. METHODS To test whether driver mutations generally map to early tumor development, we examined multi-regional tumor sequencing data from 101 individuals reported in 11 published studies. Following previous studies, we annotated mutations as early-arising when all tumors/regions had those mutations (ubiquitous). We then inferred the fraction of mutations occurring early and compared it with late-arising mutations that were found in only single tumors/regions. RESULTS While a large fraction of driver mutations in tumors occurred relatively early in cancers, later driver mutations occurred at least as frequently as the early drivers in a substantial number of patients. This result was robust to many different approaches to annotate driver mutations. The relative frequency of early and late driver mutations varied among patients of the same cancer type and in different cancer types. We found that previous reports of the preponderance of early driver mutations were primarily informed by analysis of single tumor variant allele profiles, with which it is challenging to clearly distinguish between early and late drivers. CONCLUSIONS The origin and preponderance of new driver mutations are not limited to early stages of tumor evolution, with different tumors and regions showing distinct driver mutations and, consequently, distinct characteristics. Therefore, tumors with extensive intratumor heterogeneity appear to have many newly acquired drivers.
Collapse
Affiliation(s)
- Karen Gomez
- Institute for Genomics and Evolutionary Medicine, Sudhir Kumar, SERC 602A, 1925 N. 12th Street, Philadelphia, PA 19122 USA
- Department of Biology, Temple University, Philadelphia, PA 19122 USA
| | - Sayaka Miura
- Institute for Genomics and Evolutionary Medicine, Sudhir Kumar, SERC 602A, 1925 N. 12th Street, Philadelphia, PA 19122 USA
- Department of Biology, Temple University, Philadelphia, PA 19122 USA
| | - Louise A. Huuki
- Institute for Genomics and Evolutionary Medicine, Sudhir Kumar, SERC 602A, 1925 N. 12th Street, Philadelphia, PA 19122 USA
| | - Brianna S. Spell
- Institute for Genomics and Evolutionary Medicine, Sudhir Kumar, SERC 602A, 1925 N. 12th Street, Philadelphia, PA 19122 USA
- Department of Biology, Temple University, Philadelphia, PA 19122 USA
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut 06510 USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511 USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511 USA
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Sudhir Kumar, SERC 602A, 1925 N. 12th Street, Philadelphia, PA 19122 USA
- Department of Biology, Temple University, Philadelphia, PA 19122 USA
- Center for Genomic Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|