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Vose JM, Fu K, Wang L, Mansoor A, Stewart D, Cheng H, Smith L, Yuan J, Qureishi HN, Link BK, Cessna MH, Barr PM, Kahl BS, Mckinney MS, Khan N, Advani RH, Martin P, Goy AH, Phillips TJ, Mehta A, Kamdar M, Crump M, Pro B, Flowers CR, Jacobson CA, Smith SM, Stephens DM, Bachanova V, Jin Z, Wu S, Hernandez-Ilizaliturri F, Torka P, Anampa-Guzmán A, Kashef F, Li X, Sharma S, Greiner TC, Armitage JO, Lunning M, Weisenburger DD, Bociek RG, Iqbal J, Yu G, Bi C. Integrative analysis of clinicopathological features defines novel prognostic models for mantle cell lymphoma in the immunochemotherapy era: a report from The North American Mantle Cell Lymphoma Consortium. J Hematol Oncol 2023; 16:122. [PMID: 38104096 PMCID: PMC10725579 DOI: 10.1186/s13045-023-01520-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023] Open
Abstract
BACKGROUND Patients with mantle cell lymphoma (MCL) exhibit a wide variation in clinical presentation and outcome. However, the commonly used prognostic models are outdated and inadequate to address the needs of the current multidisciplinary management of this disease. This study aims to investigate the clinical and pathological features of MCL in the immunochemotherapy era and improve the prognostic models for a more accurate prediction of patient outcomes. METHODS The North American Mantle Cell Lymphoma Project is a multi-institutional collaboration of 23 institutions across North America to evaluate and refine prognosticators for front-line therapy. A total of 586 MCL cases diagnosed between 2000 and 2012 are included in this study. A comprehensive retrospective analysis was performed on the clinicopathological features, treatment approaches, and outcomes of these cases. The establishment of novel prognostic models was based on in-depth examination of baseline parameters, and subsequent validation in an independent cohort of MCL cases. RESULTS In front-line strategies, the use of hematopoietic stem cell transplantation was the most significant parameter affecting outcomes, for both overall survival (OS, p < 0.0001) and progression-free survival (PFS, p < 0.0001). P53 positive expression was the most significant pathological parameter correlating with inferior outcomes (p < 0.0001 for OS and p = 0.0021 for PFS). Based on the baseline risk factor profile, we developed a set of prognostic models incorporating clinical, laboratory, and pathological parameters that are specifically tailored for various applications. These models, when tested in the validation cohort, exhibited strong predictive power for survival and showed a stratification resembling the training cohort. CONCLUSIONS The outcome of patients with MCL has markedly improved over the past two decades, and further enhancement is anticipated with the evolution of clinical management. The innovative prognostic models developed in this study would serve as a valuable tool to guide the selection of more suitable treatment strategies for patients with MCL.
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Affiliation(s)
- Julie M Vose
- Division of Oncology and Hematology, Department of Internal Medicine, University of Nebraska Medical Center, Nebraska Medicine Fred and Pamela Buffett Cancer Center, 505 S 45Th St, Omaha, NE, 68105, USA
| | - Kai Fu
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Lu Wang
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Yantai University, Yantai, China
| | - Adnan Mansoor
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Canada
| | - Douglas Stewart
- Departments of Oncology and Medicine, University of Calgary, Calgary, Canada
| | - Hongxia Cheng
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong Province, China
| | - Lynette Smith
- Department of Biostatistics, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ji Yuan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Hina Naushad Qureishi
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Brian K Link
- Department of Internal Medicine, University of Iowa Hospitals & Clinics, Iowa City, Iowa, USA
| | - Melissa H Cessna
- Department of Pathology, Intermountain Medical Center, Murray, UT, USA
| | - Paul M Barr
- Department of Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Brad S Kahl
- Department of Medicine, Oncology Division, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Matthew S Mckinney
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Nadia Khan
- Department of Hematology/Oncology, Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Ranjana H Advani
- Division of Oncology, Stanford Cancer Institute, Stanford, CA, USA
| | - Peter Martin
- Division of Hematology and Oncology, Weill Cornell Medical College, New York, NY, USA
| | - Andre H Goy
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, USA
| | - Tycel J Phillips
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Amitkumar Mehta
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Manali Kamdar
- Division of Hematology, University of Colorado, Denver, CO, USA
| | - Michael Crump
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre - University Health Network, Toronto, ON, Canada
| | - Barbara Pro
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, USA
| | - Christopher R Flowers
- Division of Cancer Medicine, Department of Lymphoma-Myeloma, MD Anderson Cancer Center, Houston, TX, USA
| | - Caron A Jacobson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Sonali M Smith
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Deborah M Stephens
- Huntsman Cancer Institute at University of Utah, Salt Lake City, UT, USA
| | - Veronika Bachanova
- Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Zhaohui Jin
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Shishou Wu
- Department of Pathology, Affiliated Yantai Yuhuangding Hospital, Qingdao University, No.20 Yuhuangding East Road, Yantai, 264000, China
| | | | - Pallawi Torka
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrea Anampa-Guzmán
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Farshid Kashef
- Department of Pathology, University at Buffalo, Buffalo, NY, USA
| | - Xing Li
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Sunandini Sharma
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Timothy C Greiner
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - James O Armitage
- Division of Oncology and Hematology, Department of Internal Medicine, University of Nebraska Medical Center, Nebraska Medicine Fred and Pamela Buffett Cancer Center, 505 S 45Th St, Omaha, NE, 68105, USA
| | - Matthew Lunning
- Division of Oncology and Hematology, Department of Internal Medicine, University of Nebraska Medical Center, Nebraska Medicine Fred and Pamela Buffett Cancer Center, 505 S 45Th St, Omaha, NE, 68105, USA
| | - Dennis D Weisenburger
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Robert G Bociek
- Division of Oncology and Hematology, Department of Internal Medicine, University of Nebraska Medical Center, Nebraska Medicine Fred and Pamela Buffett Cancer Center, 505 S 45Th St, Omaha, NE, 68105, USA
| | - Javeed Iqbal
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Guohua Yu
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA.
- Department of Pathology, Affiliated Yantai Yuhuangding Hospital, Qingdao University, No.20 Yuhuangding East Road, Yantai, 264000, China.
| | - Chengfeng Bi
- Division of Oncology and Hematology, Department of Internal Medicine, University of Nebraska Medical Center, Nebraska Medicine Fred and Pamela Buffett Cancer Center, 505 S 45Th St, Omaha, NE, 68105, USA.
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Abdelmoaty MM, Lu E, Kadry R, Foster EG, Bhattarai S, Mosley RL, Gendelman HE. Clinical biomarkers for Lewy body diseases. Cell Biosci 2023; 13:209. [PMID: 37964309 PMCID: PMC10644566 DOI: 10.1186/s13578-023-01152-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023] Open
Abstract
Synucleinopathies are a group of neurodegenerative disorders characterized by pathologic aggregates of neural and glial α-synuclein (α-syn) in the form of Lewy bodies (LBs), Lewy neurites, and cytoplasmic inclusions in both neurons and glia. Two major classes of synucleinopathies are LB disease and multiple system atrophy. LB diseases include Parkinson's disease (PD), PD with dementia, and dementia with LBs. All are increasing in prevalence. Effective diagnostics, disease-modifying therapies, and therapeutic monitoring are urgently needed. Diagnostics capable of differentiating LB diseases are based on signs and symptoms which might overlap. To date, no specific diagnostic test exists despite disease-specific pathologies. Diagnostics are aided by brain imaging and cerebrospinal fluid evaluations, but more accessible biomarkers remain in need. Mechanisms of α-syn evolution to pathologic oligomers and insoluble fibrils can provide one of a spectrum of biomarkers to link complex neural pathways to effective therapies. With these in mind, we review promising biomarkers linked to effective disease-modifying interventions.
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Affiliation(s)
- Mai M Abdelmoaty
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Eugene Lu
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Rana Kadry
- Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Emma G Foster
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Shaurav Bhattarai
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - R Lee Mosley
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Howard E Gendelman
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
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Gutzmann DJ, Kramer JJ, Toomey BM, Boone CHT, Atkin AL, Nickerson KW. Transcriptional regulation of the synthesis and secretion of farnesol in the fungus Candida albicans: examination of the Homann transcription regulator knockout collection. G3 (Bethesda) 2023; 13:jkad172. [PMID: 37522561 PMCID: PMC10542173 DOI: 10.1093/g3journal/jkad172] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 08/01/2023]
Abstract
Candida albicans is an efficient colonizer of human gastrointestinal tracts and skin and is an opportunistic pathogen. C. albicans exhibits morphological plasticity, and the ability to switch between yeast and filamentous morphologies is associated with virulence. One regulator of this switch is the quorum sensing molecule farnesol that is produced by C. albicans throughout growth. However, the synthesis, secretion, regulation, and turnover of farnesol are not fully understood. To address this, we used our improved farnesol assay to screen a transcription regulator knockout library for differences in farnesol accumulation in whole cultures, pellets, and supernatants. All screened mutants produced farnesol and they averaged 9.2× more farnesol in the pellet than the supernatant. Nineteen mutants had significant differences with ten mutants producing more farnesol than their SN152+ wild-type control strain while nine produced less. Seven mutants exhibited greater secretion of farnesol while two exhibited less. We examined the time course for farnesol accumulation in six mutants with the greatest accumulation differences and found that those differences persisted throughout growth and they were not time dependent. Significantly, two high-accumulating mutants did not exhibit the decay in farnesol levels during stationary phase characteristic of wild-type C. albicans, suggesting that a farnesol modification/degradation mechanism is absent in these mutants. Identifying these transcriptional regulators provides new insight into farnesol's physiological functions regarding cell cycle progression, white-opaque switching, yeast-mycelial dimorphism, and response to cellular stress.
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Affiliation(s)
- Daniel J Gutzmann
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
| | - Jaxon J Kramer
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
| | - Brigid M Toomey
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
| | - Cory H T Boone
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
| | - Audrey L Atkin
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
| | - Kenneth W Nickerson
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
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Bessell B, Loecker J, Zhao Z, Aghamiri SS, Mohanty S, Amin R, Helikar T, Puniya BL. COMO: a pipeline for multi-omics data integration in metabolic modeling and drug discovery. Brief Bioinform 2023; 24:bbad387. [PMID: 37930022 PMCID: PMC10627799 DOI: 10.1093/bib/bbad387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/04/2023] [Accepted: 10/05/2023] [Indexed: 11/07/2023] Open
Abstract
Identifying potential drug targets using metabolic modeling requires integrating multiple modeling methods and heterogeneous biological datasets, which can be challenging without efficient tools. We developed Constraint-based Optimization of Metabolic Objectives (COMO), a user-friendly pipeline that integrates multi-omics data processing, context-specific metabolic model development, simulations, drug databases and disease data to aid drug discovery. COMO can be installed as a Docker Image or with Conda and includes intuitive instructions within a Jupyter Lab environment. It provides a comprehensive solution for the integration of bulk and single-cell RNA-seq, microarrays and proteomics outputs to develop context-specific metabolic models. Using public databases, open-source solutions for model construction and a streamlined approach for predicting repurposable drugs, COMO enables researchers to investigate low-cost alternatives and novel disease treatments. As a case study, we used the pipeline to construct metabolic models of B cells, which simulate and analyze them to predict metabolic drug targets for rheumatoid arthritis and systemic lupus erythematosus, respectively. COMO can be used to construct models for any cell or tissue type and identify drugs for any human disease where metabolic inhibition is relevant. The pipeline has the potential to improve the health of the global community cost-effectively by providing high-confidence targets to pursue in preclinical and clinical studies. The source code of the COMO pipeline is available at https://github.com/HelikarLab/COMO. The Docker image can be pulled at https://github.com/HelikarLab/COMO/pkgs/container/como.
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Affiliation(s)
- Brandt Bessell
- Department of Biochemistry, University of Nebraska-Lincoln, NE, USA
| | - Josh Loecker
- Department of Biochemistry, University of Nebraska-Lincoln, NE, USA
| | - Zhongyuan Zhao
- Department of Biochemistry, University of Nebraska-Lincoln, NE, USA
| | | | | | - Rada Amin
- Department of Biochemistry, University of Nebraska-Lincoln, NE, USA
| | - Tomáš Helikar
- Department of Biochemistry, University of Nebraska-Lincoln, NE, USA
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Sahay S, Grzybowski M, Schnable JC, Głowacka K. Genetic control of photoprotection and photosystem II operating efficiency in plants. New Phytol 2023. [PMID: 37212042 DOI: 10.1111/nph.18980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/22/2023] [Indexed: 05/23/2023]
Abstract
Photoprotection against excess light via nonphotochemical quenching (NPQ) is indispensable for plant survival. However, slow NPQ relaxation under low light conditions can decrease yield of field-grown crops up to 40%. Using semi-high-throughput assay, we quantified the kinetics of NPQ and photosystem II operating efficiency (ΦPSII) in a replicated field trial of more than 700 maize (Zea mays) genotypes across 2 yr. Parametrized kinetics data were used to conduct genome-wide association studies. For six candidate genes involved in NPQ and ΦPSII kinetics in maize the loss of function alleles of orthologous genes in Arabidopsis (Arabidopsis thaliana) were characterized: two thioredoxin genes, and genes encoding a transporter in the chloroplast envelope, an initiator of chloroplast movement, a putative regulator of cell elongation and stomatal patterning, and a protein involved in plant energy homeostasis. Since maize and Arabidopsis are distantly related, we propose that genes involved in photoprotection and PSII function are conserved across vascular plants. The genes and naturally occurring functional alleles identified here considerably expand the toolbox to achieving a sustainable increase in crop productivity.
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Affiliation(s)
- Seema Sahay
- Department of Biochemistry, Beadle Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Marcin Grzybowski
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
- Department of Plant Molecular Ecophysiology, Faculty of Biology, Institute of Plant Experimental Biology and Biotechnology, University of Warsaw, 02-096, Warsaw, Poland
| | - James C Schnable
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Katarzyna Głowacka
- Department of Biochemistry, Beadle Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Institute of Plant Genetics, Polish Academy of Sciences, 60-479, Poznań, Poland
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