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Abashkin DA, Karpov DS, Kurishev AO, Marilovtseva EV, Golimbet VE. ASCL1 Is Involved in the Pathogenesis of Schizophrenia by Regulation of Genes Related to Cell Proliferation, Neuronal Signature Formation, and Neuroplasticity. Int J Mol Sci 2023; 24:15746. [PMID: 37958729 PMCID: PMC10648210 DOI: 10.3390/ijms242115746] [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: 09/08/2023] [Revised: 10/25/2023] [Accepted: 10/28/2023] [Indexed: 11/15/2023] Open
Abstract
Schizophrenia (SZ) is a common psychiatric neurodevelopmental disorder with a complex genetic architecture. Genome-wide association studies indicate the involvement of several transcription factors, including ASCL1, in the pathogenesis of SZ. We aimed to identify ASCL1-dependent cellular and molecular mechanisms associated with SZ. We used Capture-C, CRISPR/Cas9 systems and RNA-seq analysis to confirm the involvement of ASCL1 in SZ-associated pathogenesis, establish a mutant SH-SY5Y line with a functional ASCL1 knockout (ASCL1-del) and elucidate differentially expressed genes that may underlie ASCL1-dependent pathogenic mechanisms. Capture-C confirmed the spatial interaction of the ASCL1 promoter with SZ-associated loci. Transcriptome analysis showed that ASCL1 regulation may be through a negative feedback mechanism. ASCL1 dysfunction affects the expression of genes associated with the pathogenesis of SZ, as well as bipolar and depressive disorders. Genes differentially expressed in ASCL1-del are involved in cell mitosis, neuronal projection, neuropeptide signaling, and the formation of intercellular contacts, including the synapse. After retinoic acid (RA)-induced differentiation, ASCL1 activity is restricted to a small subset of genes involved in neuroplasticity. These data suggest that ASCL1 dysfunction promotes SZ development predominantly before the onset of neuronal differentiation by slowing cell proliferation and impeding the formation of neuronal signatures.
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Affiliation(s)
| | - Dmitry S. Karpov
- Mental Health Research Center, Kashirskoe Sh., 34, Moscow 115522, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow 119991, Russia
| | | | | | - Vera E. Golimbet
- Mental Health Research Center, Kashirskoe Sh., 34, Moscow 115522, Russia
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Gall-Duncan T, Luo J, Jurkovic CM, Fischer LA, Fujita K, Deshmukh AL, Harding RJ, Tran S, Mehkary M, Li V, Leib DE, Chen R, Tanaka H, Mason AG, Lévesque D, Khan M, Razzaghi M, Prasolava T, Lanni S, Sato N, Caron MC, Panigrahi GB, Wang P, Lau R, Castel AL, Masson JY, Tippett L, Turner C, Spies M, La Spada AR, Campos EI, Curtis MA, Boisvert FM, Faull RLM, Davidson BL, Nakamori M, Okazawa H, Wold MS, Pearson CE. Antagonistic roles of canonical and Alternative-RPA in disease-associated tandem CAG repeat instability. Cell 2023; 186:4898-4919.e25. [PMID: 37827155 DOI: 10.1016/j.cell.2023.09.008] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 06/30/2023] [Accepted: 09/09/2023] [Indexed: 10/14/2023]
Abstract
Expansions of repeat DNA tracts cause >70 diseases, and ongoing expansions in brains exacerbate disease. During expansion mutations, single-stranded DNAs (ssDNAs) form slipped-DNAs. We find the ssDNA-binding complexes canonical replication protein A (RPA1, RPA2, and RPA3) and Alternative-RPA (RPA1, RPA3, and primate-specific RPA4) are upregulated in Huntington disease and spinocerebellar ataxia type 1 (SCA1) patient brains. Protein interactomes of RPA and Alt-RPA reveal unique and shared partners, including modifiers of CAG instability and disease presentation. RPA enhances in vitro melting, FAN1 excision, and repair of slipped-CAGs and protects against CAG expansions in human cells. RPA overexpression in SCA1 mouse brains ablates expansions, coincident with decreased ATXN1 aggregation, reduced brain DNA damage, improved neuron morphology, and rescued motor phenotypes. In contrast, Alt-RPA inhibits melting, FAN1 excision, and repair of slipped-CAGs and promotes CAG expansions. These findings suggest a functional interplay between the two RPAs where Alt-RPA may antagonistically offset RPA's suppression of disease-associated repeat expansions, which may extend to other DNA processes.
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Affiliation(s)
- Terence Gall-Duncan
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jennifer Luo
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | - Laura A Fischer
- Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kyota Fujita
- Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Amit L Deshmukh
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rachel J Harding
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Stephanie Tran
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Mustafa Mehkary
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Vanessa Li
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - David E Leib
- Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19146, USA
| | - Ran Chen
- Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hikari Tanaka
- Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Amanda G Mason
- Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Dominique Lévesque
- Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Mahreen Khan
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Mortezaali Razzaghi
- Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Tanya Prasolava
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stella Lanni
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Nozomu Sato
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Marie-Christine Caron
- CHU de Québec-Université Laval, Oncology Division, Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, Québec, QC, Canada
| | - Gagan B Panigrahi
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Peixiang Wang
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rachel Lau
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Jean-Yves Masson
- CHU de Québec-Université Laval, Oncology Division, Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, Québec, QC, Canada
| | - Lynette Tippett
- School of Psychology, University of Auckland, Auckland, New Zealand; University Research Centre for Brain Research, University of Auckland, Auckland, New Zealand
| | - Clinton Turner
- Anatomical Pathology, LabPlus, Auckland City Hospital, Auckland, New Zealand
| | - Maria Spies
- Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Albert R La Spada
- Pathology & Laboratory Medicine, Neurology, and Biological Chemistry, University of California, Irvine School of Medicine, Irvine, CA, USA; Neurobiology & Behavior, University of California, Irvine, Irvine, CA, USA; Center for Neurotherapeutics, University of California, Irvine, Irvine, CA 92697, USA
| | - Eric I Campos
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Maurice A Curtis
- University Research Centre for Brain Research, University of Auckland, Auckland, New Zealand; Anatomy and Medical Imaging, University of Auckland, Auckland, New Zealand
| | | | - Richard L M Faull
- University Research Centre for Brain Research, University of Auckland, Auckland, New Zealand; Anatomy and Medical Imaging, University of Auckland, Auckland, New Zealand
| | - Beverly L Davidson
- Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19146, USA
| | - Masayuki Nakamori
- Neurology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Hitoshi Okazawa
- Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Marc S Wold
- Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Christopher E Pearson
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada.
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103
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Daiß JL, Griesenbeck J, Tschochner H, Engel C. Synthesis of the ribosomal RNA precursor in human cells: mechanisms, factors and regulation. Biol Chem 2023; 404:1003-1023. [PMID: 37454246 DOI: 10.1515/hsz-2023-0214] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023]
Abstract
The ribosomal RNA precursor (pre-rRNA) comprises three of the four ribosomal RNAs and is synthesized by RNA polymerase (Pol) I. Here, we describe the mechanisms of Pol I transcription in human cells with a focus on recent insights gained from structure-function analyses. The comparison of Pol I-specific structural and functional features with those of other Pols and with the excessively studied yeast system distinguishes organism-specific from general traits. We explain the organization of the genomic rDNA loci in human cells, describe the Pol I transcription cycle regarding structural changes in the enzyme and the roles of human Pol I subunits, and depict human rDNA transcription factors and their function on a mechanistic level. We disentangle information gained by direct investigation from what had apparently been deduced from studies of the yeast enzymes. Finally, we provide information about how Pol I mutations may contribute to developmental diseases, and why Pol I is a target for new cancer treatment strategies, since increased rRNA synthesis was correlated with rapidly expanding cell populations.
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Affiliation(s)
- Julia L Daiß
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Joachim Griesenbeck
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Herbert Tschochner
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Christoph Engel
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
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104
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Bollier N, Micol-Ponce R, Dakdaki A, Maza E, Zouine M, Djari A, Bouzayen M, Chevalier C, Delmas F, Gonzalez N, Hernould M. Various tomato cultivars display contrasting morphological and molecular responses to a chronic heat stress. Front Plant Sci 2023; 14:1278608. [PMID: 37965003 PMCID: PMC10642206 DOI: 10.3389/fpls.2023.1278608] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/06/2023] [Indexed: 11/16/2023]
Abstract
Climate change is one of the biggest threats that human society currently needs to face. Heat waves associated with global warming negatively affect plant growth and development and will increase in intensity and frequency in the coming years. Tomato is one of the most produced and consumed fruit in the world but remarkable yield losses occur every year due to the sensitivity of many cultivars to heat stress (HS). New insights into how tomato plants are responding to HS will contribute to the development of cultivars with high yields under harsh temperature conditions. In this study, the analysis of microsporogenesis and pollen germination rate of eleven tomato cultivars after exposure to a chronic HS revealed differences between genotypes. Pollen development was either delayed and/or desynchronized by HS depending on the cultivar considered. In addition, except for two, pollen germination was abolished by HS in all cultivars. The transcriptome of floral buds at two developmental stages (tetrad and pollen floral buds) of five cultivars revealed common and specific molecular responses implemented by tomato cultivars to cope with chronic HS. These data provide valuable insights into the diversity of the genetic response of floral buds from different cultivars to HS and may contribute to the development of future climate resilient tomato varieties.
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Affiliation(s)
- N. Bollier
- INRAE, Université de Bordeaux, BFP, Bordeaux, France
| | | | - A. Dakdaki
- INRAE, Université de Bordeaux, BFP, Bordeaux, France
| | - E. Maza
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Toulouse, France
| | - M. Zouine
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Toulouse, France
| | - A. Djari
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Toulouse, France
| | - M. Bouzayen
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Toulouse, France
| | - C. Chevalier
- INRAE, Université de Bordeaux, BFP, Bordeaux, France
| | - F. Delmas
- INRAE, Université de Bordeaux, BFP, Bordeaux, France
| | - N. Gonzalez
- INRAE, Université de Bordeaux, BFP, Bordeaux, France
| | - M. Hernould
- INRAE, Université de Bordeaux, BFP, Bordeaux, France
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105
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Le HH, Hagen MW, Louey S, Tavori H, Thornburg KL, Giraud GD, Hinds MT, Barnes AP. Development of a novel Guinea Pig model producing transgenerational endothelial transcriptional changes driven by maternal food restriction and a second metabolic insult of high fat diet. Front Physiol 2023; 14:1266444. [PMID: 37942229 PMCID: PMC10628814 DOI: 10.3389/fphys.2023.1266444] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/26/2023] [Indexed: 11/10/2023] Open
Abstract
Developmental programming of chronic adverse cardiovascular health outcomes has been studied both using numerous human populations and an array of animal models. However, the mechanisms that produce transgenerational effects have been difficult to study due to a lack of developmentally relevant models. As such, how increased disease risk is carried to the second generation has been poorly studied. We hypothesized that the endothelium which mediates many acute and chronic vascular inflammatory responses is a key player in these effects, and epidemiological studies implicate transgenerational nutritional effects on endothelial health. To study the mutigenerational effects of maternal undernutrition on offspring endothelial health, we developed a model of transgenerational nutritional stress in guinea pigs, a translationally relevant precocial species with a relatively short lifespan. First- and second-generation offspring were subjected to a high fat diet in adolescence to exacerbate negative cardiovascular health. To assess transcriptional changes, we performed bulk RNA-sequencing in carotid artery endothelial cells, with groups stratified as prenatal control or food restricted, and postnatal control or high fat diet. We detected statistically significant gene alterations for each dietary permutation, some of which were unique to treatments and other transcriptional signatures shared by multiple or all conditions. These findings highlight a core group of genes altered by high fat diet that is shared by all cohorts and a divergence of transgenerational effects between the prenatal ad libitum and dietary restriction groups. This study establishes the groundwork for this model to be used to better understand the interplay of prenatal stress and genetic reprogramming.
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Affiliation(s)
- Hillary H. Le
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, United States
| | - Matthew W. Hagen
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, United States
| | - Samantha Louey
- Center for Developmental Health, Portland, OR, United States
- Knight Cardiovascular Institute, Portland, OR, United States
| | - Hagai Tavori
- Knight Cardiovascular Institute, Portland, OR, United States
| | - Kent L. Thornburg
- Center for Developmental Health, Portland, OR, United States
- Knight Cardiovascular Institute, Portland, OR, United States
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, United States
| | - George D. Giraud
- Center for Developmental Health, Portland, OR, United States
- Knight Cardiovascular Institute, Portland, OR, United States
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, United States
- VA Portland Health Care System, Portland, OR, United States
| | - Monica T. Hinds
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, United States
- Center for Developmental Health, Portland, OR, United States
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106
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Orlic-Milacic M, Rothfels K, Matthews L, Wright A, Jassal B, Shamovsky V, Trinh Q, Gillespie M, Sevilla C, Tiwari K, Ragueneau E, Gong C, Stephan R, May B, Haw R, Weiser J, Beavers D, Conley P, Hermjakob H, Stein LD, D'Eustachio P, Wu G. Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes. bioRxiv 2023:2023.10.18.562964. [PMID: 37904913 PMCID: PMC10614924 DOI: 10.1101/2023.10.18.562964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Disease variant annotation in the context of biological reactions and pathways can provide a standardized overview of molecular phenotypes of pathogenic mutations that is amenable to computational mining and mathematical modeling. Reactome, an open source, manually curated, peer-reviewed database of human biological pathways, provides annotations for over 4000 disease variants of close to 400 genes in the context of ∼800 disease reactions constituting ∼400 disease pathways. Functional annotation of disease variants proceeds from normal gene functions, through disease variants whose divergence from normal molecular behaviors has been experimentally verified, to extrapolation from molecular phenotypes of characterized variants to variants of unknown significance using criteria of the American College of Medical Genetics and Genomics (ACMG). Reactome's pathway-based, reaction-specific disease variant dataset and data model provide a platform to infer pathway output impacts of numerous human disease variants and model organism orthologs, complementing computational predictions of variant pathogenicity.
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107
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Zeballos C MA, Moore HJ, Smith TJ, Powell JE, Ahsan NS, Zhang S, Gaj T. Mitigating a TDP-43 proteinopathy by targeting ataxin-2 using RNA-targeting CRISPR effector proteins. Nat Commun 2023; 14:6492. [PMID: 37838698 PMCID: PMC10576788 DOI: 10.1038/s41467-023-42147-z] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 10/02/2023] [Indexed: 10/16/2023] Open
Abstract
The TDP-43 proteinopathies, which include amyotrophic lateral sclerosis and frontotemporal dementia, are a devastating group of neurodegenerative disorders that are characterized by the mislocalization and aggregation of TDP-43. Here we demonstrate that RNA-targeting CRISPR effector proteins, a programmable class of gene silencing agents that includes the Cas13 family of enzymes and Cas7-11, can be used to mitigate TDP-43 pathology when programmed to target ataxin-2, a modifier of TDP-43-associated toxicity. In addition to inhibiting the aggregation and transit of TDP-43 to stress granules, we find that the in vivo delivery of an ataxin-2-targeting Cas13 system to a mouse model of TDP-43 proteinopathy improved functional deficits, extended survival, and reduced the severity of neuropathological hallmarks. Further, we benchmark RNA-targeting CRISPR platforms against ataxin-2 and find that high-fidelity forms of Cas13 possess improved transcriptome-wide specificity compared to Cas7-11 and a first-generation effector. Our results demonstrate the potential of CRISPR technology for TDP-43 proteinopathies.
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Affiliation(s)
- M Alejandra Zeballos C
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Hayden J Moore
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Tyler J Smith
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jackson E Powell
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Najah S Ahsan
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sijia Zhang
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Thomas Gaj
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
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108
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Jayakumar MN, Muhammad JS, Dutta M, Donakonda S. Comprehensive In silico analysis of chaperones identifies CRYAB and P4HA2 as potential therapeutic targets and their small-molecule inhibitors for the treatment of cholangiocarcinoma. Comput Biol Med 2023; 166:107572. [PMID: 37844407 DOI: 10.1016/j.compbiomed.2023.107572] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/29/2023] [Accepted: 10/11/2023] [Indexed: 10/18/2023]
Abstract
Cholangiocarcinoma (CCA) is a subtype of liver cancer with increasing incidence, poor prognosis, and limited treatment modalities. It is, therefore, imperative to identify novel therapeutic targets for better management of the disease. Chaperones are known to be significant regulators of carcinogenesis, however, their role in CCA remains unclear. This study aims to screen chaperones involved in CCA pathogenesis and identify drugs targeting key chaperones to improve the therapeutic response to the disease. To achieve this, first we mined the literature to create an atlas of human chaperone proteins. Next, their expression in CCA was determined by publicly available datasets of patients at mRNA and protein levels. In addition, our analysis involving protein-protein interaction and pathway analysis of eight key dysregulated chaperones revealed that they control crucial cancer-related pathways. Furthermore, topology analysis of the CCA network identified crystallin alpha-B protein (CRYAB) and prolyl-4-hydroxylase subunit 2 (P4HA2) as novel therapeutic targets for the disease. Finally, drug repurposing of 286 clinically approved anti-cancer drugs against these two chaperones performed by molecular docking and molecular dynamics simulations showed that tucatinib and regorafenib had a modulatory effect on them and could be potential inhibitors of CRYAB and P4HA2, respectively. Overall, our study, for the first time, provides insights into the pan-chaperone expression in CCA and explains the pathways that might drive CCA pathogenesis. Further, our identification of potential therapeutic targets and their inhibitors could provide new and complementary approaches to CCA treatment.
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Affiliation(s)
- Manju Nidagodu Jayakumar
- Department of Biotechnology, Birla Institute of Technology and Science (BITS) Pilani Dubai Campus, Academic City, Dubai, 345055, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Jibran Sualeh Muhammad
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates; Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates.
| | - Mainak Dutta
- Department of Biotechnology, Birla Institute of Technology and Science (BITS) Pilani Dubai Campus, Academic City, Dubai, 345055, United Arab Emirates.
| | - Sainitin Donakonda
- Institute of Molecular Immunology and Experimental Oncology, Klinikum rechts der Isar, Technical University Munich, 81675, Germany.
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109
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Sigurjonsdottir G, De Marchi T, Ehinger A, Hartman J, Bosch A, Staaf J, Killander F, Niméus E. Comparison of SP142 and 22C3 PD-L1 assays in a population-based cohort of triple-negative breast cancer patients in the context of their clinically established scoring algorithms. Breast Cancer Res 2023; 25:123. [PMID: 37817263 PMCID: PMC10566164 DOI: 10.1186/s13058-023-01724-2] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/02/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND Immunohistochemical (IHC) PD-L1 expression is commonly employed as predictive biomarker for checkpoint inhibitors in triple-negative breast cancer (TNBC). However, IHC evaluation methods are non-uniform and further studies are needed to optimize clinical utility. METHODS We compared the concordance, prognostic value and gene expression between PD-L1 IHC expression by SP142 immune cell (IC) score and 22C3 combined positive score (CPS; companion IHC diagnostic assays for atezolizumab and pembrolizumab, respectively) in a population-based cohort of 232 early-stage TNBC patients. RESULTS The expression rates of PD-L1 for SP142 IC ≥ 1%, 22C3 CPS ≥ 10, 22C3 CPS ≥ 1 and 22C3 IC ≥ 1% were 50.9%, 27.2%, 53.9% and 41.8%, respectively. The analytical concordance (kappa values) between SP142 IC+ and these three different 22C3 scorings were 73.7% (0.48, weak agreement), 81.5% (0.63) and 86.6% (0.73), respectively. The SP142 assay was better at identifying 22C3 positive tumors than the 22C3 assay was at detecting SP142 positive tumors. PD-L1 (CD274) gene expression (mRNA) showed a strong positive association with all two-categorical IHC scorings of the PD-L1 expression, irrespective of antibody and cut-off (Spearman Rho ranged from 0.59 to 0.62; all p-values < 0.001). PD-L1 IHC positivity and abundance of tumor infiltrating lymphocytes were of positive prognostic value in univariable regression analyses in patients treated with (neo)adjuvant chemotherapy, where it was strongest for 22C3 CPS ≥ 10 and distant relapse-free interval (HR = 0.18, p = 0.019). However, PD-L1 status was not independently prognostic when adjusting for abundance of tumor infiltrating lymphocytes in multivariable analyses. CONCLUSION Our findings support that the SP142 and 22C3 IHC assays, with their respective clinically applied scoring algorithms, are not analytically equivalent where they identify partially non-overlapping subpopulations of TNBC patients and cannot be substituted with one another regarding PD-L1 detection. Trial registration The Swedish Cancerome Analysis Network - Breast (SCAN-B) study, retrospectively registered 2nd Dec 2014 at ClinicalTrials.gov; ID NCT02306096.
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Affiliation(s)
- Gudbjörg Sigurjonsdottir
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Department of Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Tommaso De Marchi
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Anna Ehinger
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Laboratory Medicine, Region Skåne, Lund, Sweden
| | - Johan Hartman
- Department of Oncology and Pathology, Karolinska Institute and University Hospital, Stockholm, Sweden
| | - Ana Bosch
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Department of Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Johan Staaf
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon Village, Lund, Sweden
| | - Fredrika Killander
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Department of Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Emma Niméus
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.
- Divison of Surgery, Department of Clinical Sciences Lund, Lund University, Sölvegatan 19 - BMC I12, 22184, Lund, Sweden.
- Department of Surgery, Skåne University Hospital, Malmö, Sweden.
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Siddiqui TR, Hoque MR, Roy BC, Anisuzzaman, Alam MZ, Khatun MS, Dey AR. Morphological and phylogenetic analysis of Raillietina spp. in indigenous chickens ( Gallus gallus domesticus) in Bangladesh. Saudi J Biol Sci 2023; 30:103784. [PMID: 37680979 PMCID: PMC10480643 DOI: 10.1016/j.sjbs.2023.103784] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 09/09/2023] Open
Abstract
Raillietina spp. (Cestoda: Davaineidae), the most common cestodes in indigenous chickens, cause a substantial production loss in poultry industry in Bangladesh. Here, we estimated the prevalence, confirmed the species and determined the genetic pattern of species of Raillietina using molecular tools. We collected and examined 375 chickens randomly from household of different villages of Mymensingh sadar and Gouripur upazila, Mymensingh district and adult parasites were isolated and identified. Genomic DNA was extracted from collected parasites, amplified ITS-2 and ND-1 genes, sequenced and analyzed. Out of 375 samples, 270 (72.0%) were found positive with Raillietina species and mean worm burden was 10.46 ± 0.56. Microscopically, three species of Raillietina, such as R. cesticillus (37.9%), R. echinobothrida (41.1%) and R. tetragona (52.8%) were detected on the basis of their morphological features. The total length, length and width of scolex, sucker and rostellum were also measured. Among different factors, age, farming nature and flock size of chickens were significantly (p < 0.05) influenced Raillietina infections. For further validation, the sequences of ITS-2 gene generated in this study were matched with reference sequences of R. cesticillus, R. echinobothrida and R. tetragona and found 99.63% - 100% similarity. The phylogenetic analyses of ITS-2 and ND-1 sequences were clustered together with the reference sequences of R. cesticillus, R. echinobothrida and R. tetragona confirming microscopic identification. This is the first confirmation of species of Raillietina along with the prevalence of the species, which will be helpful for the formulation of a control strategy and provide basic information for further molecular study.
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Affiliation(s)
- Tanbin Rubaiya Siddiqui
- Department of Parasitology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Md. Razibul Hoque
- Department of Parasitology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Babul Chandra Roy
- Department of Parasitology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Anisuzzaman
- Department of Parasitology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Mohammad Zahangir Alam
- Department of Parasitology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Mst. Sawda Khatun
- Department of Parasitology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Anita Rani Dey
- Department of Parasitology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
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111
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Bisoyi P, Ratna D, Kumar G, Mallick BN, Goswami SK. In the Rat Midbrain, SG2NA and DJ-1 have Common Interactome, Including Mitochondrial Electron Transporters that are Comodulated Under Oxidative Stress. Cell Mol Neurobiol 2023; 43:3061-3080. [PMID: 37165139 DOI: 10.1007/s10571-023-01356-2] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 04/26/2023] [Indexed: 05/12/2023]
Abstract
Scaffold proteins Striatin and SG2NA assemble kinases and phosphatases into the signalling complexes called STRIPAK. Dysfunctional STRIPAKs cause cancer, cerebral cavernous malformations, etc. DJ-1, a sensor for oxidative stress, has long been associated with the Parkinson's disease, cancer, and immune disorders. SG2NA interacts with DJ-1 and Akt providing neuroprotection under oxidative stress. To dissect the role of SG2NA and DJ-1 in neuronal pathobiology, rat midbrain extracts were immunoprecipitated with SG2NA and sixty-three interacting proteins were identified. BN-PAGE followed by the LC-MS/MS showed 1030 comigrating proteins as the potential constituents of the multimeric complexes formed by SG2NA. Forty-three proteins were common between those identified by co-immunoprecipitation and the BN-PAGE. Co-immunoprecipitation with DJ-1 identified 179 interacting partners, of which forty-one also interact with SG2NA. Among those forty-one proteins immunoprecipitated with both SG2NA and DJ-1, thirty-nine comigrated with SG2NA in the BN-PAGE, and thus are bonafide constituents of the supramolecular assemblies comprising both DJ-1 and SG2NA. Among those thirty-nine proteins, seven are involved in mitochondrial oxidative phosphorylation. In rotenone-treated rats having Parkinson's like symptoms, the levels of both SG2NA and DJ-1 increased in the mitochondria; and the association of SG2NA with the electron transport complexes enhanced. In the hemi-Parkinson's model, where the rats were injected with 6-OHDA into the midbrain, the occupancy of SG2NA and DJ-1 in the mitochondrial complexes also increased. Our study thus reveals a new family of potential STRIPAK assemblies involving both SG2NA and DJ-1, with key roles in protecting midbrain from the oxidative stress.
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Affiliation(s)
- Padmini Bisoyi
- School of Life Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, India
| | - Deshdeepak Ratna
- School of Life Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, India
| | - Gaurav Kumar
- Department of Life Sciences and Biotechnology, CSJM University, Kanpur, Uttar Pradesh, 208024, India
| | - Birendra Nath Mallick
- School of Life Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, India
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, 201313, India
| | - Shyamal K Goswami
- School of Life Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, India.
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Mehmood A, Song S, Du X, Yan H, Wang X, Guo L, Li B. mRNA expression profile reveals differentially expressed genes in splenocytes of experimental autoimmune encephalomyelitis model. Int J Exp Pathol 2023; 104:247-257. [PMID: 37427716 PMCID: PMC10500171 DOI: 10.1111/iep.12488] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/04/2023] [Accepted: 06/18/2023] [Indexed: 07/11/2023] Open
Abstract
Experimental autoimmune encephalomyelitis (EAE) is a mouse model that can be used to investigate aetiology, pathogenesis, and treatment approaches for multiple sclerosis (MS). A novel integrated bioinformatics approach was used to understand the involvement of differentially expressed genes (DEGs) in the spleen of EAE mice through data mining of existing microarray and RNA-seq datasets. We screened differentially expressed mRNAs using mRNA expression profile data of EAE spleens taken from Gene Expression Omnibus (GEO). Functional and pathway enrichment analyses of DEGs were performed by Database for Annotation, Visualization, and Integrated Discovery (DAVID). Subsequently, the DEGs-encoded protein-protein interaction (PPI) network was constructed. The 784 DEGs in GSE99300 A.SW PP-EAE mice spleen mRNA profiles, 859 DEGs in GSE151701 EAE mice spleen mRNA profiles, and 646 DEGs in GSE99300 SJL/J PP-EAE mice spleen mRNA profiles were explored. Functional enrichment of 55 common DEGs among 3 sub-datasets revealed several immune-related terms, such as neutrophil extravasation, leucocyte migration, antimicrobial humoral immune response mediated by an antimicrobial peptide, toll-like receptor 4 bindings, IL-17 signalling pathway, and TGF-beta signalling pathway. In the screening of 10 hub genes, including MPO, ELANE, CTSG, LTF, LCN2, SELP, CAMP, S100A9, ITGA2B, and PRTN3, and in choosing and validating the 5 DEGs, including ANK1, MBOAT2, SLC25A21, SLC43A1, and SOX6, the results showed that SLC43A1 and SOX6 were significantly decreased in EAE mice spleen. Thus this study offers a list of genes expressed in the spleen that might play a key role in the pathogenesis of EAE.
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Affiliation(s)
- Arshad Mehmood
- Department of NeurologyThe Second Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
- Key Laboratory of Neurology of Hebei ProvinceShijiazhuangHebeiChina
| | - Shuang Song
- Department of NeurologyThe Second Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
- Key Laboratory of Neurology of Hebei ProvinceShijiazhuangHebeiChina
| | - Xiaochen Du
- Department of NeurologyThe Second Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
- Key Laboratory of Neurology of Hebei ProvinceShijiazhuangHebeiChina
| | - Hongjing Yan
- Department of NeurologyThe Second Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
- Key Laboratory of Neurology of Hebei ProvinceShijiazhuangHebeiChina
| | - Xuan Wang
- Department of NeurologyThe Second Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
- Key Laboratory of Neurology of Hebei ProvinceShijiazhuangHebeiChina
| | - Li Guo
- Department of NeurologyThe Second Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
- Key Laboratory of Neurology of Hebei ProvinceShijiazhuangHebeiChina
| | - Bin Li
- Department of NeurologyThe Second Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
- Key Laboratory of Neurology of Hebei ProvinceShijiazhuangHebeiChina
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Faraj KS, Kaufman SR, Herrel LA, Oerline MK, Maganty A, Shahinian VB, Hollenbeck BK. Association between urology practice use of multiparametric MRI and genomic testing and treatment of men with newly diagnosed prostate cancer. Urol Oncol 2023; 41:430.e17-430.e23. [PMID: 37580226 PMCID: PMC10836888 DOI: 10.1016/j.urolonc.2023.08.002] [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: 05/24/2023] [Revised: 07/12/2023] [Accepted: 08/02/2023] [Indexed: 08/16/2023]
Abstract
INTRODUCTION Biomarkers for prostate cancer, such as multiparametric MRI (mpMRI) and tissue-based genomics, are increasingly used for treatment decision-making. Using biomarkers indiscriminately and thus ignoring competing risks of mortality may lead to treatment in some men who derive little clinical benefit. We assessed the relationship between urology practice use of biomarkers and subsequent treatment in men with newly diagnosed prostate cancer. METHODS We used a 20% random sample of national Medicare data to perform a retrospective cohort study of men with newly diagnosed prostate cancer diagnosed from 2015 through 2019. Urology practice-level use of biomarkers was characterized based on urology practice propensity to use either biomarker after diagnosis (never, below median, above the median). Noncancer mortality risk within 10 years of diagnosis was calculated for all men. Multilevel models were used to assess the relationship between practice-level biomarker use and treatment by noncancer mortality risk. RESULTS Between 2015 and 2019, 1,764 (65%) urology practices used mpMRI and 897 (33%) used genomic testing for prostate cancer. Compared with urology practices never using each biomarker, those using mpMRI above the median (56% vs. 47%, P = 0.003) and tissue-based genomics below the median (56% vs. 50%, P = 0.03) were more likely to treat men with >75% risk of noncancer mortality. Additionally, compared with urology practices never using either biomarker, use of mpMRI (72% vs. 69%, P = 0.07) or tissue-based genomics (71% vs. 70%, P = 0.65) did not impact treatment in the healthiest group (i.e., those with <25% risk of noncancer mortality). CONCLUSIONS Compared to practices that do not use each biomarker in men with newly diagnosed prostate cancer, urology practices using mpMRI, and tissue-based genomics to a lesser extent, are more likely to treat men at very high risk of dying from competing risks of mortality within 10 years of prostate cancer diagnosis.
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Affiliation(s)
- Kassem S Faraj
- Dow Division of Health Services Research, Department of Urology, University of Michigan, Ann Arbor, MI.
| | - Samuel R Kaufman
- Dow Division of Health Services Research, Department of Urology, University of Michigan, Ann Arbor, MI
| | - Lindsey A Herrel
- Dow Division of Health Services Research, Department of Urology, University of Michigan, Ann Arbor, MI
| | - Mary K Oerline
- Dow Division of Health Services Research, Department of Urology, University of Michigan, Ann Arbor, MI
| | - Avinash Maganty
- Dow Division of Health Services Research, Department of Urology, University of Michigan, Ann Arbor, MI
| | - Vahakn B Shahinian
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
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Bech CB, Svendsen JA, Knudsen AW, Munk T, Beck AM. The association between malnutrition and dehydration in older adults admitted to a geriatric unit: An observational study. Clin Nutr ESPEN 2023; 57:598-605. [PMID: 37739711 DOI: 10.1016/j.clnesp.2023.08.011] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 08/10/2023] [Indexed: 09/24/2023]
Abstract
BACKGROUND AND AIM There is an overlap between the risk factors causing low intake of water and low intake of nutrients, respectively. This study aims to explore the agreement between the assessment of malnutrition and the outcome of low-intake dehydration in a population of older hospitalized patients. METHODS Patients ≥65 years old and hospitalized at the geriatric hospital ward were screened for eligibility within 96 h of admission. Dehydration was assessed with the calculated serum osmolarity ≥295 mmol/L (1.86 × (Na+ + K+) + 1.15 × glucose + urea + 14), and (risk of) malnutrition was assessed with NRS-2002 ≥ 3 points, MNA-SF ≤ 7 points, MNA-LF < 17, MUST ≥ 2 points, and GLIM after screening with NRS-2002 and MNA-LF. Follow-up data regarding exercise rehabilitation, readmissions, and mortality was collected 30 days after discharge. Statistics used were the Chi-squared test, Fishers-exact test, and Wilcoxon signed rank test. RESULTS A total of 114 patients (57% females) were included. Median age 85.5 (IQR 80; 89.25) years. A total of 49 (43%) were dehydrated. Fewer females were dehydrated (F: 42.9% vs. M: 67.7%, p = 0.013). The patients with osmolarity ≥295 mmol/L had a higher median weight (68.3 (IQR 58.5; 78.4) vs. 62 (IQR 51.8; 72.1), p = 0.021) and mid-up-arm circumference (27 (IQR 26; 30) vs. 25.5 (IQR 22.9; 28.3), p = 0.004). No significant difference was found in the prevalence of malnutrition between those with or without dehydration (NRS-2002; 70% vs. 81%, p = 0.174; MNA-SF: 23.1 vs. 23.2%, p = 1.0; MNA-LF: 37.1 vs. 30.2%, p = 0.644; MUST: 24.5 vs. 33.8%, p = 0.308; GLIM after screening with NRS-2002: 84.4 vs. 74.5%, p = 0.405, GLIM after screening with MNA-LF: 74.1 vs. 75.6%, p = 0.438). Kappa values varied around 0 and reflected low agreement. There were no differences in the follow-up data, between those who were normohydrated and those who were dehydrated. CONCLUSION We found low agreement between the assessment of malnutrition and low-intake dehydration in a population of older hospitalized patients. All geriatric patients should therefore be assessed for both conditions.
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Affiliation(s)
- Camilla Balle Bech
- Dietetic and Nutritional Research Unit, EATEN, Copenhagen University Hospital - Herlev Gentofte, Denmark
| | | | - Anne Wilkens Knudsen
- Dietetic and Nutritional Research Unit, EATEN, Copenhagen University Hospital - Herlev Gentofte, Denmark
| | - Tina Munk
- Dietetic and Nutritional Research Unit, EATEN, Copenhagen University Hospital - Herlev Gentofte, Denmark
| | - Anne Marie Beck
- Dietetic and Nutritional Research Unit, EATEN, Copenhagen University Hospital - Herlev Gentofte, Denmark.
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115
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Fehr A, Arvidsson G, Nordlund J, Lönnerholm G, Stenman G, Andersson MK. Increased MYB alternative promoter usage is associated with relapse in acute lymphoblastic leukemia. Genes Chromosomes Cancer 2023; 62:597-606. [PMID: 37218648 DOI: 10.1002/gcc.23151] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/09/2023] [Accepted: 05/09/2023] [Indexed: 05/24/2023] Open
Abstract
Therapy-resistant disease is a major cause of death in patients with acute lymphoblastic leukemia (ALL). Activation of the MYB oncogene is associated with ALL and leads to uncontrolled neoplastic cell proliferation and blocked differentiation. Here, we used RNA-seq to study the clinical significance of MYB expression and MYB alternative promoter (TSS2) usage in 133 pediatric ALLs. RNA-seq revealed that all cases analyzed overexpressed MYB and demonstrated MYB TSS2 activity. qPCR analyses confirmed the expression of the alternative MYB promoter also in seven ALL cell lines. Notably, high MYB TSS2 activity was significantly associated with relapse (p = 0.007). Moreover, cases with high MYB TSS2 usage showed evidence of therapy-resistant disease with increased expression of ABC multidrug resistance transporter genes (e.g., ABCA2, ABCB5, and ABCC10) and enzymes catalyzing drug degradation (e.g., CYP1A2, CYP2C9, and CYP3A5). Elevated MYB TSS2 activity was further associated with augmented KRAS signaling (p < 0.05) and decreased methylation of the conventional MYB promoter (p < 0.01). Taken together, our results suggest that MYB alternative promoter usage is a novel potential prognostic biomarker for relapse and therapy resistance in pediatric ALL.
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Affiliation(s)
- André Fehr
- Sahlgrenska Center for Cancer Research, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
| | - Gustav Arvidsson
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Gudmar Lönnerholm
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Göran Stenman
- Sahlgrenska Center for Cancer Research, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
| | - Mattias K Andersson
- Sahlgrenska Center for Cancer Research, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
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Luis TC, Barkas N, Carrelha J, Giustacchini A, Mazzi S, Norfo R, Wu B, Aliouat A, Guerrero JA, Rodriguez-Meira A, Bouriez-Jones T, Macaulay IC, Jasztal M, Zhu G, Ni H, Robson MJ, Blakely RD, Mead AJ, Nerlov C, Ghevaert C, Jacobsen SEW. Perivascular niche cells sense thrombocytopenia and activate hematopoietic stem cells in an IL-1 dependent manner. Nat Commun 2023; 14:6062. [PMID: 37770432 PMCID: PMC10539537 DOI: 10.1038/s41467-023-41691-y] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 09/11/2023] [Indexed: 09/30/2023] Open
Abstract
Hematopoietic stem cells (HSCs) residing in specialized niches in the bone marrow are responsible for the balanced output of multiple short-lived blood cell lineages in steady-state and in response to different challenges. However, feedback mechanisms by which HSCs, through their niches, sense acute losses of specific blood cell lineages remain to be established. While all HSCs replenish platelets, previous studies have shown that a large fraction of HSCs are molecularly primed for the megakaryocyte-platelet lineage and are rapidly recruited into proliferation upon platelet depletion. Platelets normally turnover in an activation-dependent manner, herein mimicked by antibodies inducing platelet activation and depletion. Antibody-mediated platelet activation upregulates expression of Interleukin-1 (IL-1) in platelets, and in bone marrow extracellular fluid in vivo. Genetic experiments demonstrate that rather than IL-1 directly activating HSCs, activation of bone marrow Lepr+ perivascular niche cells expressing IL-1 receptor is critical for the optimal activation of quiescent HSCs upon platelet activation and depletion. These findings identify a feedback mechanism by which activation-induced depletion of a mature blood cell lineage leads to a niche-dependent activation of HSCs to reinstate its homeostasis.
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Affiliation(s)
- Tiago C Luis
- Haematopoietic Stem Cell Biology Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK.
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK.
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, W12 0NN, London, UK.
- Department of Life Sciences, Imperial College London, SW7 2AZ, London, UK.
| | - Nikolaos Barkas
- Haematopoietic Stem Cell Biology Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Joana Carrelha
- Haematopoietic Stem Cell Biology Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Alice Giustacchini
- Haematopoietic Stem Cell Biology Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
- Molecular and Cellular Immunology Section, UCL Great Ormond Street Institute of Child Health, London, UK
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Stefania Mazzi
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, SE-141 86, Stockholm, Sweden
| | - Ruggiero Norfo
- Haematopoietic Stem Cell Biology Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Bishan Wu
- Haematopoietic Stem Cell Biology Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Affaf Aliouat
- Haematopoietic Stem Cell Biology Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Jose A Guerrero
- Department of Haematology, University of Cambridge, Cambridge, UK
- National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
| | - Alba Rodriguez-Meira
- Haematopoietic Stem Cell Biology Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Tiphaine Bouriez-Jones
- Haematopoietic Stem Cell Biology Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Iain C Macaulay
- Haematopoietic Stem Cell Biology Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
- Earlham Institute, Norwich Research Park, NR4 7UZ, Norwich, UK
| | - Maria Jasztal
- Department of Haematology, University of Cambridge, Cambridge, UK
- National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
| | - Guangheng Zhu
- Toronto Platelet Immunobiology Group and Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, M5B 1W8, Canada
- CCOA Therapeutics Inc, Toronto, ON, M5B 1T8, Canada
| | - Heyu Ni
- Toronto Platelet Immunobiology Group and Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, M5B 1W8, Canada
- CCOA Therapeutics Inc, Toronto, ON, M5B 1T8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A1, Canada
- Canadian Blood Services Centre for Innovation, Toronto, ON, M5B 1W8, Canada
| | - Matthew J Robson
- Department of Biomedical Science, Charles E. Schmidt College of Medicine and Stiles-Nicholson Brain Institute, Florida Atlantic University, Jupiter, FL, 33458, USA
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Randy D Blakely
- Department of Biomedical Science, Charles E. Schmidt College of Medicine and Stiles-Nicholson Brain Institute, Florida Atlantic University, Jupiter, FL, 33458, USA
| | - Adam J Mead
- Haematopoietic Stem Cell Biology Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Claus Nerlov
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Cedric Ghevaert
- Department of Haematology, University of Cambridge, Cambridge, UK
- National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
| | - Sten Eirik W Jacobsen
- Haematopoietic Stem Cell Biology Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK.
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK.
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, SE-141 86, Stockholm, Sweden.
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77, Stockholm, Sweden.
- Department of Hematology, Karolinska University Hospital, Stockholm, Sweden.
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Sokol-Borrelli SL, Reilly SM, Holmes MJ, Orchanian SB, Massmann MD, Sharp KG, Cabo LF, Alrubaye HS, Martorelli Di Genova B, Lodoen MB, Sullivan WJ, Boyle JP. A transcriptional network required for bradyzoite development in Toxoplasma gondii is dispensable for recrudescent disease. Nat Commun 2023; 14:6078. [PMID: 37770433 PMCID: PMC10539341 DOI: 10.1038/s41467-023-40948-w] [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: 02/23/2023] [Accepted: 08/16/2023] [Indexed: 09/30/2023] Open
Abstract
Identification of regulators of Toxoplasma gondii bradyzoite development and cyst formation is the most direct way to address the importance of parasite development in long-term persistence and reactivation of this parasite. Here we show that a T. gondii gene (named Regulator of Cystogenesis 1; ROCY1) is sufficient for T. gondii bradyzoite formation in vitro and in vivo. ROCY1 encodes an RNA binding protein that has a preference for 3' regulatory regions of hundreds of T. gondii transcripts, and its RNA-binding domains are required to mediate bradyzoite development. Female mice infected with ΔROCY1 parasites have reduced (>90%) cyst burden. While viable parasites can be cultivated from brain tissue for up to 6 months post-infection, chronic brain-resident ΔROCY1 parasites have reduced oral infectivity compared to wild type. Despite clear defects in bradyzoite formation and oral infectivity, ΔROCY1 parasites were able to reactivate with similar timing and magnitude as wild type parasites for up to 5 months post-infection. Therefore while ROCY1 is a critical regulator of the bradyzoite developmental pathway, it is not required for parasite reactivation, raising new questions about the persisting life stage responsible for causing recrudescent disease.
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Affiliation(s)
- Sarah L Sokol-Borrelli
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sarah M Reilly
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael J Holmes
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, IN, 462022, USA
| | - Stephanie B Orchanian
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, USA
| | - Mackenzie D Massmann
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Katherine G Sharp
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Leah F Cabo
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hisham S Alrubaye
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bruno Martorelli Di Genova
- Department of Microbiology and Molecular Genetics, University of Vermont Larner College of Medicine, Burlington, VT, USA
| | - Melissa B Lodoen
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, USA
| | - William J Sullivan
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, IN, 462022, USA
| | - Jon P Boyle
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
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Kwak MJ, Wang Q, Onyebeke C, Holder T, Goyal P, Aparasu R, Dhoble A, Holmes HM. How do we define high and low dose intensity of heart failure medications: a scoping review. BMC Cardiovasc Disord 2023; 23:478. [PMID: 37759279 PMCID: PMC10523693 DOI: 10.1186/s12872-023-03514-2] [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: 03/04/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Older adults with heart failure often experience adverse drug events with high doses of heart failure medications. Recognizing whether a patient is on a high or low dose intensity heart failure medication can be helpful for daily practice, since it could potentially guide the physician on which symptoms to look for, whether from overdosing or underdosing. However, the current guideline does not provide sufficient information about the dose intensity below the target dose. Furthermore, the definition of high or low-intensity heart failure medication is unclear, and there is no consensus. METHODS To close the knowledge gap, we conducted a scoping review of the current literature to identify the most frequently used definition of high versus low doses of heart failure medications. We searched Pubmed, Embase, CINAHL, and Cochrane Library using comprehensive search terms that can capture the intensity of heart failure medications. RESULTS We reviewed 464 articles, including 144 articles that had information about beta-blockers (BB), 179 articles about angiotensin-converting enzyme inhibitors (ACEi), 75 articles about angiotensin receptor blockers (ARB), 80 articles about diuretics, 37 articles about mineralocorticoid receptor antagonists (MRA), and 33 articles about angiotensin receptor-neprilysin inhibitor (ARNI). For hydralazine with isosorbide dinitrate or ivabradine, we could not identify any eligible articles. We identified 40 medications with most frequently used definitions of dose intensity. Four medications (nadolol, pindolol, cilazapril, and torsemide) did not reach consensus in definitions. Most of the BBs, ACEis, or ARBs used the definition of low being < 50% of the target dose and high being ≥ 50% of the target dose from the guideline. However, for lisinopril and losartan, the most commonly used definitions of high or low were from pivotal clinical trials with a pre-defined definition of high or low. CONCLUSION Our comprehensive scoping review studies identified the most frequently used definition of dose intensity for 40 medications but could not identify the definitions for 4 medications. The results of the current scoping review will be helpful for clinicians to have awareness whether the currently prescribed dose is considered high - requiring close monitoring of side effects, or low - requiring more aggressive up-titration.
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Affiliation(s)
- Min Ji Kwak
- The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX, 77030, USA.
| | - Qian Wang
- The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX, 77030, USA
| | | | - Travis Holder
- Texas Medical Center Library, Houston Academy of Medicine, Texas Medical Center, Houston, TX, USA
| | - Parag Goyal
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Rajender Aparasu
- Department of Pharmaceutical Health Outcomes and Policy, University of Houston, Houston, TX, USA
| | - Abhjeet Dhoble
- The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX, 77030, USA
| | - Holly M Holmes
- The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX, 77030, USA
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Reay DP, Tabib T, Wang Y, Oriss TB, Young NA, Lafyatis RA, Jarjour WN, Clemens PR, Ascherman DP. Antigen-driven T cell-macrophage interactions mediate the interface between innate and adaptive immunity in histidyl-tRNA synthetase-induced myositis. Front Immunol 2023; 14:1238221. [PMID: 37809058 PMCID: PMC10556668 DOI: 10.3389/fimmu.2023.1238221] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction Previous work in humans has demonstrated that both innate and adaptive immune signaling pathways contribute to the pathogenesis of idiopathic inflammatory myopathy (IIM), a systemic autoimmune disease targeting muscle as well as extra-muscular organs. To better define interactive signaling networks in IIM, we characterized the cellular phenotype and transcriptomic profiles of muscle-infiltrating cells in our established murine model of histidyl-tRNA synthetase (HRS)-induced myositis. Methods Myositis was induced in wild type (WT) and various congenic/mutant strains of C57BL/6 mice through intramuscular immunization with recombinant HRS. Histopathological, immunohistochemical, flow cytometric, and transcriptomic assessments were used to characterize the functional relationship between muscle-infiltrating cell populations in these strains lacking different components of innate and/or adaptive immune signaling. Results RAG1 KO mice developed markedly reduced muscle inflammation relative to WT mice, demonstrating a key requirement for T cells in driving HRS-induced myositis. While the reduction of mononuclear cell infiltrates in CD4-Cre.MyD88fl/fl conditional knockout mice and OT-II TCR transgenic mice highlighted roles for both innate and TCR-mediated/adaptive immune signaling in T cells, diminished inflammation in Lyz2-Cre.MyD88fl/fl conditional knockout mice underscored the importance of macrophage/myeloid cell populations in supporting T cell infiltration. Single cell RNA sequencing-based clustering of muscle-infiltrating subpopulations and associated pathway analyses showed that perturbations of T cell signaling/function alter the distribution and phenotype of macrophages, fibroblasts, and other non-lymphoid cell populations contributing to HRS-induced myositis. Discussion Overall, HRS-induced myositis reflects the complex interplay between multiple cell types that collectively drive a TH1-predominant, pro-inflammatory tissue phenotype requiring antigen-mediated activation of both MyD88- and TCR-dependent T cell signaling pathways.
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Affiliation(s)
- Daniel P Reay
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Tracy Tabib
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Ying Wang
- Department of Medicine, University of Miami School of Medicine, Miami, FL, United States
| | - Timothy B Oriss
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Nicholas A Young
- Department of Medicine, Ohio State University School of Medicine, Columbus, OH, United States
| | - Robert A Lafyatis
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Wael N Jarjour
- Department of Medicine, Ohio State University School of Medicine, Columbus, OH, United States
| | - Paula R Clemens
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Dana P Ascherman
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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He M, Cao Y, Chi C, Zhao J, Chong E, Chin KXC, Tan NZV, Dmitry K, Yang G, Yang X, Hu K, Enikeev M. Unleashing novel horizons in advanced prostate cancer treatment: investigating the potential of prostate specific membrane antigen-targeted nanomedicine-based combination therapy. Front Immunol 2023; 14:1265751. [PMID: 37795091 PMCID: PMC10545965 DOI: 10.3389/fimmu.2023.1265751] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/04/2023] [Indexed: 10/06/2023] Open
Abstract
Prostate cancer (PCa) is a prevalent malignancy with increasing incidence in middle-aged and older men. Despite various treatment options, advanced metastatic PCa remains challenging with poor prognosis and limited effective therapies. Nanomedicine, with its targeted drug delivery capabilities, has emerged as a promising approach to enhance treatment efficacy and reduce adverse effects. Prostate-specific membrane antigen (PSMA) stands as one of the most distinctive and highly selective biomarkers for PCa, exhibiting robust expression in PCa cells. In this review, we explore the applications of PSMA-targeted nanomedicines in advanced PCa management. Our primary objective is to bridge the gap between cutting-edge nanomedicine research and clinical practice, making it accessible to the medical community. We discuss mainstream treatment strategies for advanced PCa, including chemotherapy, radiotherapy, and immunotherapy, in the context of PSMA-targeted nanomedicines. Additionally, we elucidate novel treatment concepts such as photodynamic and photothermal therapies, along with nano-theragnostics. We present the content in a clear and accessible manner, appealing to general physicians, including those with limited backgrounds in biochemistry and bioengineering. The review emphasizes the potential benefits of PSMA-targeted nanomedicines in enhancing treatment efficiency and improving patient outcomes. While the use of PSMA-targeted nano-drug delivery has demonstrated promising results, further investigation is required to comprehend the precise mechanisms of action, pharmacotoxicity, and long-term outcomes. By meticulous optimization of the combination of nanomedicines and PSMA ligands, a novel horizon of PSMA-targeted nanomedicine-based combination therapy could bring renewed hope for patients with advanced PCa.
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Affiliation(s)
- Mingze He
- Institute for Urology and Reproductive Health, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Yu Cao
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Changliang Chi
- Department of Urology, First Hospital of Jilin University, Changchun, China
| | - Jiang Zhao
- Department of Urology, Xi’an First Hospital, Xi’an, China
| | - Eunice Chong
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Ke Xin Casey Chin
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Nicole Zian Vi Tan
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Korolev Dmitry
- Institute for Urology and Reproductive Health, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Guodong Yang
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Xinyi Yang
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Kebang Hu
- Department of Urology, First Hospital of Jilin University, Changchun, China
| | - Mikhail Enikeev
- Institute for Urology and Reproductive Health, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
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Raycheva R, Kostadinov K, Mitova E, Bogoeva N, Iskrov G, Stefanov G, Stefanov R. Challenges in mapping European rare disease databases, relevant for ML-based screening technologies in terms of organizational, FAIR and legal principles: scoping review. Front Public Health 2023; 11:1214766. [PMID: 37780450 PMCID: PMC10540868 DOI: 10.3389/fpubh.2023.1214766] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/30/2023] [Indexed: 10/03/2023] Open
Abstract
Background Given the increased availability of data sources such as hospital information systems, electronic health records, and health-related registries, a novel approach is required to develop artificial intelligence-based decision support that can assist clinicians in their diagnostic decision-making and shorten rare disease patients' diagnostic odyssey. The aim is to identify key challenges in the process of mapping European rare disease databases, relevant to ML-based screening technologies in terms of organizational, FAIR and legal principles. Methods A scoping review was conducted based on the PRISMA-ScR checklist. The primary article search was conducted in three electronic databases (MEDLINE/Pubmed, Scopus, and Web of Science) and a secondary search was performed in Google scholar and on the organizations' websites. Each step of this review was carried out independently by two researchers. A charting form for relevant study analysis was developed and used to categorize data and identify data items in three domains - organizational, FAIR and legal. Results At the end of the screening process, 73 studies were eligible for review based on inclusion and exclusion criteria with more than 60% (n = 46) of the research published in the last 5 years and originated only from EU/EEA countries. Over the ten-year period (2013-2022), there is a clear cycling trend in the publications, with a peak of challenges reporting every four years. Within this trend, the following dynamic was identified: except for 2016, organizational challenges dominated the articles published up to 2018; legal challenges were the most frequently discussed topic from 2018 to 2022. The following distribution of the data items by domains was observed - (1) organizational (n = 36): data accessibility and sharing (20.2%); long-term sustainability (18.2%); governance, planning and design (17.2%); lack of harmonization and standardization (17.2%); quality of data collection (16.2%); and privacy risks and small sample size (11.1%); (2) FAIR (n = 15): findable (17.9%); accessible sustainability (25.0%); interoperable (39.3%); and reusable (17.9%); and (3) legal (n = 33): data protection by all means (34.4%); data management and ownership (22.9%); research under GDPR and member state law (20.8%); trust and transparency (13.5%); and digitalization of health (8.3%). We observed a specific pattern repeated in all domains during the process of data charting and data item identification - in addition to the outlined challenges, good practices, guidelines, and recommendations were also discussed. The proportion of publications addressing only good practices, guidelines, and recommendations for overcoming challenges when mapping RD databases in at least one domain was calculated to be 47.9% (n = 35). Conclusion Despite the opportunities provided by innovation - automation, electronic health records, hospital-based information systems, biobanks, rare disease registries and European Reference Networks - the results of the current scoping review demonstrate a diversity of the challenges that must still be addressed, with immediate actions on ensuring better governance of rare disease registries, implementing FAIR principles, and enhancing the EU legal framework.
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Affiliation(s)
- Ralitsa Raycheva
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, Plovdiv, Bulgaria
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
| | - Kostadin Kostadinov
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, Plovdiv, Bulgaria
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
| | - Elena Mitova
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
| | - Nataliya Bogoeva
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
| | - Georgi Iskrov
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, Plovdiv, Bulgaria
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
| | - Georgi Stefanov
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
| | - Rumen Stefanov
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, Plovdiv, Bulgaria
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
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Norman JE, Nuthikattu S, Milenkovic D, Villablanca AC. Sex Modifies the Impact of Type 2 Diabetes Mellitus on the Murine Whole Brain Metabolome. Metabolites 2023; 13:1012. [PMID: 37755291 PMCID: PMC10536706 DOI: 10.3390/metabo13091012] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 09/28/2023] Open
Abstract
Type 2 diabetes mellitus (T2DM) leads to the development of cardiovascular diseases, cognitive impairment, and dementia. There are sex differences in the presentation of T2DM and its associated complications. We sought to determine the impact of sex and T2DM on the brain metabolome to gain insights into the underlying mechanisms of T2DM-associated cognitive complications. Untargeted metabolomic analysis was performed, using liquid chromatography-mass spectrometry, on whole brain tissue from adult male and female db/db mice (a T2DM model) compared to wild-type (WT) C57Bl6/J mice. Regardless of sex, T2DM increased free fatty acids and decreased acylcarnitines in the brain. Sex impacted the number (103 versus 65 in males and females, respectively), and types of metabolites shifted by T2DM. Many choline-containing phospholipids were decreased by T2DM in males. Female-specific T2DM effects included changes in neuromodulatory metabolites (γ-aminobutyric acid, 2-linoleoyl glycerol, N-methylaspartic acid, and taurine). Further, there were more significantly different metabolites between sexes in the T2DM condition as compared to the WT controls (54 vs. 15 in T2DM and WT, respectively). T2DM alters the murine brain metabolome in both sex-independent and sex-dependent manners. This work extends our understanding of brain metabolic sex differences in T2DM, cognitive implications, and potential sex-specific metabolic therapeutic targets.
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Affiliation(s)
- Jennifer E. Norman
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis. 1 Shields Ave, Davis, CA 95616, USA; (S.N.); (A.C.V.)
| | - Saivageethi Nuthikattu
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis. 1 Shields Ave, Davis, CA 95616, USA; (S.N.); (A.C.V.)
| | - Dragan Milenkovic
- Department of Nutrition, University of California, Davis. 1 Shields Ave, Davis, CA 95616, USA;
| | - Amparo C. Villablanca
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis. 1 Shields Ave, Davis, CA 95616, USA; (S.N.); (A.C.V.)
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Yousef A, Yousef M, Zeineddine M, More A, Chowdhury S, Knafl M, Edelkamp P, Ito I, Gu Y, Pattalachinti V, Naini ZA, Zeineddine F, Peterson J, Alfaro K, Foo WC, Jin J, Bhutiani N, Higbie V, Scally C, Kee B, Kopetz S, Goldstein D, Uppal A, White MG, Helmink B, Fournier K, Raghav K, Taggart M, Overman MJ, Shen JP. The Clinical Significance of CEA, CA19-9, and CA125 in Management of Appendiceal Adenocarcinoma. medRxiv 2023:2023.09.10.23295319. [PMID: 37745596 PMCID: PMC10516068 DOI: 10.1101/2023.09.10.23295319] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Importance Serum tumor markers CEA, CA19-9, & CA125 have been useful in the management of gastrointestinal and gynecological cancers, however there is limited information regarding their utility in patients with appendiceal adenocarcinoma. Objective Assessing the association of serum tumor markers (CEA, CA19-9, and CA125) with clinical outcomes, pathologic, and molecular features in patients with appendiceal adenocarcinoma. Design This is a retrospective study with results reported in 2023. The median follow-up time was 43 months. Setting Single tertiary care comprehensive cancer center. Participants Under an approved Institutional Review Board protocol, the Palantir Foundry software system was used to query the MD Anderson internal patient database to identify patients with a diagnosis of appendiceal adenocarcinoma and at least one tumor marker measured at MD Anderson between 2016 and 2023. Results A total of 1,338 patients with appendiceal adenocarcinoma were included, with a median age of 56.5 years. The majority of the patients had metastatic disease (80.7%). CEA was elevated in more than half of the patients tested (56%), while CA19-9 and CA125 were elevated in 34% and 27%, respectively. Individually, elevation of CEA, CA19-9, or CA125 were associated with worse 5-year survival; 82% vs 95%, 84% vs 92%, and 69% vs 93% elevated vs normal for CEA, CA19-9, and CA125 respectively (all p<0.0001). Quantitative evaluation of tumor markers increased prognostic ability. Patients with highly elevated (top 10th percentile) CEA, CA19-9 or CA125 had markedly worse survival with 5-year survival rates of 59%, 64%, and 57%, respectively (HR vs. normal : 9.8, 6.0, 7.6, all p<0.0001). Although metastatic tumors had higher levels of all tumor markers, when restricting survival analysis to 1080 patients with metastatic disease elevated CEA, CA19-9 or CA125 were all still associated worse survival (HR vs. normal : 3.4, 1.8, 3.9, p<0.0001 for CEA and CA125, p=0.0019 for CA19-9). Interestingly tumor grade was not associated with CEA or CA19-9 level, while CA-125 was slightly higher in high relative to low-grade tumors (18.3 vs. 15.0, p=0.0009). Multivariable analysis identified an incremental increase in the risk of death with an increase in the number of elevated tumor markers, with a 11-fold increased risk of death in patients with all three tumor markers elevated relative to those with none elevated. Mutation in KRAS and GNAS were associated with significantly higher levels of CEA and CA19-9. Conclusions These findings demonstrate the utility of measuring CEA, CA19-9, and CA125 in the management of appendiceal adenocarcinoma. Given their prognostic value, all three biomarkers should be included in the initial workup of patients diagnosed with appendiceal adenocarcinoma.
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Affiliation(s)
- Abdelrahman Yousef
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mahmoud Yousef
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mohammad Zeineddine
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Aditya More
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Saikat Chowdhury
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mark Knafl
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paul Edelkamp
- Department of Data Engineering & Analytics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ichiaki Ito
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yue Gu
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vinay Pattalachinti
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zahra Alavi Naini
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fadl Zeineddine
- Department of Internal Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Jennifer Peterson
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kristin Alfaro
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wai Chin Foo
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jeff Jin
- Department of Enterprise Dev & Integration, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Neal Bhutiani
- Department of Colon and Rectal Surgery, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Victoria Higbie
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher Scally
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bryan Kee
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Abhineet Uppal
- Department of Colon and Rectal Surgery, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael G. White
- Department of Colon and Rectal Surgery, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Beth Helmink
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Keith Fournier
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kanwal Raghav
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Melissa Taggart
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael J. Overman
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John Paul Shen
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Hogenhout R, Remmers S, van Slooten-Midderigh ME, de Vos II, Roobol MJ. From Screening to Mortality Reduction: An Overview of Empirical Data on the Patient Journey in European Randomized Study of Screening for Prostate Cancer Rotterdam After 21 Years of Follow-up and a Reflection on Quality of Life. Eur Urol Oncol 2023:S2588-9311(23)00172-4. [PMID: 37690917 DOI: 10.1016/j.euo.2023.08.011] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/13/2023] [Accepted: 08/23/2023] [Indexed: 09/12/2023]
Abstract
BACKGROUND Previous research quantified the effect of prostate-specific antigen (PSA)-based prostate cancer (PCa) screening on quality-adjusted life years using 11-yr follow-up data from the European Randomized Study of Screening for Prostate Cancer (ERSPC) extrapolated by the Microsimulation Screening Analysis (MISCAN). ERSPC data now matured to 21 yr of follow-up. OBJECTIVE To provide an overview of the effect of PSA-based screening on tumour characteristics and PCa treatment using long-term, detailed, empirical ERSPC data. DESIGN, SETTING, AND PARTICIPANTS Men were included from the ERSPC Rotterdam who were randomised to a PSA-based screening (S) or control (C) arm. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS We assessed the effects of PSA-based screening on the number of PCa diagnoses, tumour characteristics, treatments, and cumulative incidence of disease progression. We also evaluated the changes in tumour characteristics and treatments over time for both study arms. RESULTS AND LIMITATIONS Among PCa patients in the S-arm, fewer patients were diagnosed with advanced tumour stages (T3/T4: 12% vs 23%; relative risk [RR] = 0.50; 95% confidence interval [CI] 0.44-0.57), less disease progression was observed, and less secondary treatment (30% vs 48%; RR = 0.61; 95% CI 0.57-0.66; p < 0.001) and less palliative treatment were needed (21% vs 55%; RR = 0.38; 95% CI 0.35-0.42) than among those in the C-arm. This was at the cost of overdiagnosis and increased local treatments (eg, radical prostatectomy: 32% vs 14%; RR = 2.18; 95% CI 1.92-2.48). Over time, the number of local treatments decreased, whereas expectant management strategies increased. The RRs of treatments were slightly different from those of the MISCAN. CONCLUSIONS After 21 yr of follow-up, empirical data of the ERSPC showed that PSA-based screening reduces advanced PCa stages, disease progression, and extensive treatments at the cost of more overdiagnosis and probably more overtreatment. Our data showed reduced local treatments and increased expectant management strategies over time. PATIENT SUMMARY Prostate-specific antigen-based screening reduces the number of invasive prostate cancer treatments needed, however, at the cost of more overdiagnosis and probably more overtreatment. Limiting these costs remains crucial to benefit optimally from prostate cancer screening.
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Affiliation(s)
- Renée Hogenhout
- Department of Urology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
| | - Sebastiaan Remmers
- Department of Urology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | | | - Ivo I de Vos
- Department of Urology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Monique J Roobol
- Department of Urology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
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Ninivaggi A, Guzzi F, Degennaro A, Ricapito A, Bettocchi C, Busetto GM, Sanguedolce F, Milillo P, Selvaggio O, Cormio L, Carrieri G, Falagario UG. External Validation of the IMPROD-MRI Volumetric Model to Predict the Utility of Systematic Biopsies at the Time of Targeted Biopsy. J Clin Med 2023; 12:5748. [PMID: 37685815 PMCID: PMC10488903 DOI: 10.3390/jcm12175748] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/26/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023] Open
Abstract
Background: The aim of this study was to validate externally a nomogram that relies on MRI volumetric parameters and clinical data to determine the need for a standard biopsy in addition to a target biopsy for men with suspicious prostate MRI findings. Methods: We conducted a retrospective analysis of a prospectively maintained database of 469 biopsy-naïve men who underwent prostate biopsies. These biopsies were guided by pre-biopsy multiparametric Magnetic Resonance Imaging (mpMRI) and were performed at two different institutions. We included men with a PIRADSsv 2.1 score from 3 to 5. Each patient underwent both an MRI-ultrasound fusion biopsy of identified MRI-suspicious lesions and a systematic biopsy according to our protocol. The lesion volume percentage was determined as the proportion of cancer volume on MRI relative to the entire prostate volume. The study's outcomes were iPCa (Gleason Grade Group 1) and csPCa (Gleason Grade Group > 1). We evaluated the model's performance using AUC decision curve analyses and a systematic analysis of model-derived probability cut-offs in terms of the potential to avoid diagnosing iPCa and to accurately diagnose csPCa. Results: The nomogram includes age, PSA value, prostate volume, PIRADSsv 2.1 score, percentage of MRI-suspicious lesion volume, and lesion location. AUC was determined to be 0.73. By using various nomogram cut-off thresholds (ranging from 5% to 30%), it was observed that 19% to 58% of men could potentially avoid undergoing standard biopsies. In this scenario, the model might miss 0% to 10% of diagnosis of csPCa and could prevent identifying 6% to 31% of iPCa cases. These results are in line with findings from the multi-institutional external validation study based on the IMPROD trial (n = 122) and the MULTI-IMPROD trial (n = 262). According to DCA, the use of this nomogram led to an increased overall net clinical benefit when the threshold probability exceeded 10%. Conclusions: This study supports the potential value of a model relying on MRI volumetric measurements for selecting individuals with clinical suspicion of prostate cancer who would benefit from undergoing a standard biopsy in addition to a targeted biopsy.
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Affiliation(s)
- Antonella Ninivaggi
- Department of Urology and Organ Transplantation, University of Foggia, 71122 Foggia, Italy (U.G.F.)
| | - Francesco Guzzi
- Department of Urology and Organ Transplantation, University of Foggia, 71122 Foggia, Italy (U.G.F.)
| | - Alessio Degennaro
- Department of Urology and Organ Transplantation, University of Foggia, 71122 Foggia, Italy (U.G.F.)
- Department of Urology, Bonomo Teaching Hospital, 76123 Andria, Italy
| | - Anna Ricapito
- Department of Urology and Organ Transplantation, University of Foggia, 71122 Foggia, Italy (U.G.F.)
| | - Carlo Bettocchi
- Department of Urology and Organ Transplantation, University of Foggia, 71122 Foggia, Italy (U.G.F.)
- Andrology Unit, Department of Urology, University of Foggia, 71122 Foggia, Italy
| | - Gian Maria Busetto
- Department of Urology and Organ Transplantation, University of Foggia, 71122 Foggia, Italy (U.G.F.)
| | | | - Paola Milillo
- Department of Radiology, University of Foggia, 71122 Foggia, Italy
| | - Oscar Selvaggio
- Department of Urology and Organ Transplantation, University of Foggia, 71122 Foggia, Italy (U.G.F.)
| | - Luigi Cormio
- Department of Urology and Organ Transplantation, University of Foggia, 71122 Foggia, Italy (U.G.F.)
- Department of Urology, Bonomo Teaching Hospital, 76123 Andria, Italy
| | - Giuseppe Carrieri
- Department of Urology and Organ Transplantation, University of Foggia, 71122 Foggia, Italy (U.G.F.)
| | - Ugo Giovanni Falagario
- Department of Urology and Organ Transplantation, University of Foggia, 71122 Foggia, Italy (U.G.F.)
- Department of Molecular Medicine and Surgery, (Solna), Karolinska Institutet, 17177 Stockholm, Sweden
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Ersoy B, Herzog ML, Pan W, Schilling S, Endres M, Göttert R, Kronenberg GD, Gertz K. The atypical antidepressant tianeptine confers neuroprotection against oxygen-glucose deprivation. Eur Arch Psychiatry Clin Neurosci 2023:10.1007/s00406-023-01685-9. [PMID: 37653354 DOI: 10.1007/s00406-023-01685-9] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 08/14/2023] [Indexed: 09/02/2023]
Abstract
Proregenerative and neuroprotective effects of antidepressants are an important topic of inquiry in neuropsychiatric research. Oxygen-glucose deprivation (OGD) mimics key aspects of ischemic injury in vitro. Here, we studied the effects of 24-h pretreatment with serotonin (5-HT), citalopram (CIT), fluoxetine (FLU), and tianeptine (TIA) on primary mouse cortical neurons subjected to transient OGD. 5-HT (50 μM) significantly enhanced neuron viability as measured by MTT assay and reduced cell death and LDH release. CIT (10 μM) and FLU (1 μM) did not increase the effects of 5-HT and neither antidepressant conferred neuroprotection in the absence of supplemental 5-HT in serum-free cell culture medium. By contrast, pre-treatment with TIA (10 μM) resulted in robust neuroprotection, even in the absence of 5-HT. Furthermore, TIA inhibited mRNA transcription of candidate genes related to cell death and hypoxia and attenuated lipid peroxidation, a hallmark of neuronal injury. Finally, deep RNA sequencing of primary neurons subjected to OGD demonstrated that OGD induces many pathways relating to cell survival, the inflammation-immune response, synaptic dysregulation and apoptosis, and that TIA pretreatment counteracted these effects of OGD. In conclusion, this study highlights the comparative strength of the 5-HT independent neuroprotective effects of TIA and identifies the molecular pathways involved.
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Affiliation(s)
- Burcu Ersoy
- Department of Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Center for Stroke Research Berlin, Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin-Brandenburg School for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Marie-Louise Herzog
- Department of Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Center for Stroke Research Berlin, Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- DZHK (German Center for Cardiovascular Research), Partner site, Berlin, Germany
| | - Wen Pan
- Department of Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Center for Stroke Research Berlin, Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- DZHK (German Center for Cardiovascular Research), Partner site, Berlin, Germany
| | - Simone Schilling
- Department of Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Center for Stroke Research Berlin, Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- DZHK (German Center for Cardiovascular Research), Partner site, Berlin, Germany
- Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Endres
- Department of Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Center for Stroke Research Berlin, Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- DZHK (German Center for Cardiovascular Research), Partner site, Berlin, Germany
- Einstein Center for Neurosciences, Charité-Universitätsmedizin Berlin, Berlin, Germany
- DZNE (German Center for Neurodegenerative Diseases), Partner site, Berlin, Germany
- DZPG (German Center for Mental Health), Partner site, Berlin, Germany
| | - Ria Göttert
- Department of Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Center for Stroke Research Berlin, Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- DZHK (German Center for Cardiovascular Research), Partner site, Berlin, Germany
| | - Golo D Kronenberg
- Department of Psychiatry, Psychotherapy and Psychosomatics, University Hospital of Psychiatry Zürich, Lenggstrasse 31, P.O. Box 363, 8032, Zurich, Switzerland
| | - Karen Gertz
- Department of Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- Center for Stroke Research Berlin, Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- DZHK (German Center for Cardiovascular Research), Partner site, Berlin, Germany.
- Einstein Center for Neurosciences, Charité-Universitätsmedizin Berlin, Berlin, Germany.
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127
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Sens JP, Hofford RS, Kiraly DD. Effect of germ-free status on transcriptional profiles in the nucleus accumbens and transcriptomic response to chronic morphine. Mol Cell Neurosci 2023; 126:103874. [PMID: 37315877 PMCID: PMC10921993 DOI: 10.1016/j.mcn.2023.103874] [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: 01/14/2023] [Revised: 05/01/2023] [Accepted: 06/07/2023] [Indexed: 06/16/2023] Open
Abstract
Opioid use disorder is a public health crisis that causes tremendous suffering for patients as well as substantial social and economic costs for society. There are currently available treatments for patients with opioid use disorder, but they remain intolerable or ineffective for many. Thus the need to develop new avenues for therapeutics development in this space is great. Substantial work in models of substance use disorders, including opioid use disorder, demonstrates that prolonged exposure to drugs of abuse leads to marked transcriptional and epigenetic dysregulation in limbic substructures. It is widely believed that these changes in gene regulation in response to drugs are a key driving factor in the perpetuation of drug taking and seeking behaviors. Thus, development of interventions that could shape transcriptional regulation in response to drugs of abuse would be of high value. Over the past decade there has been a surge in research demonstrating that the resident bacteria of the gastrointestinal tract, collectively the gut microbiome, can have tremendous influence on neurobiological and behavioral plasticity. Previous work from our group and others has demonstrated that alterations in the gut microbiome can alter behavioral responses to opioids in multiple paradigms. Additionally, we have previously reported that depletion of the gut microbiome with antibiotics markedly shifts the transcriptome of the nucleus accumbens following prolonged morphine exposure. In this manuscript we present a comprehensive analysis of the effects of the gut microbiome on transcriptional regulation of the nucleus accumbens following morphine by utilizing germ-free, antibiotic treated, and control mice. This allows for detailed understanding of the role of the microbiome in regulating baseline transcriptomic control, as well as response to morphine. We find that germ-free status leads to a marked gene dysregulation in a manner distinct to adult mice treated with antibiotics, and that altered gene pathways are highly related to cellular metabolic processes. These data provide additional insight into the role of the gut microbiome in modulating brain function and lay a foundation for further study in this area.
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Affiliation(s)
- Jonathon P Sens
- Department of Physiology & Pharmacology, Wake Forest University School of Medicine, Atrium Wake Forest Baptist Health, Winston-Salem, NC 27101, United States
| | - Rebecca S Hofford
- Department of Physiology & Pharmacology, Wake Forest University School of Medicine, Atrium Wake Forest Baptist Health, Winston-Salem, NC 27101, United States; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Drew D Kiraly
- Department of Physiology & Pharmacology, Wake Forest University School of Medicine, Atrium Wake Forest Baptist Health, Winston-Salem, NC 27101, United States; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Psychiatry, Wake Forest University School of Medicine, Atrium Wake Forest Baptist Health, Winston-Salem, NC 27101, United States.
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128
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Yang H, Ulge UY, Quijano-Rubio A, Bernstein ZJ, Maestas DR, Chun JH, Wang W, Lin JX, Jude KM, Singh S, Orcutt-Jahns BT, Li P, Mou J, Chung L, Kuo YH, Ali YH, Meyer AS, Grayson WL, Heller NM, Garcia KC, Leonard WJ, Silva DA, Elisseeff JH, Baker D, Spangler JB. Design of cell-type-specific hyperstable IL-4 mimetics via modular de novo scaffolds. Nat Chem Biol 2023; 19:1127-1137. [PMID: 37024727 PMCID: PMC10697138 DOI: 10.1038/s41589-023-01313-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 08/23/2022] [Accepted: 03/10/2023] [Indexed: 04/08/2023]
Abstract
The interleukin-4 (IL-4) cytokine plays a critical role in modulating immune homeostasis. Although there is great interest in harnessing this cytokine as a therapeutic in natural or engineered formats, the clinical potential of native IL-4 is limited by its instability and pleiotropic actions. Here, we design IL-4 cytokine mimetics (denoted Neo-4) based on a de novo engineered IL-2 mimetic scaffold and demonstrate that these cytokines can recapitulate physiological functions of IL-4 in cellular and animal models. In contrast with natural IL-4, Neo-4 is hyperstable and signals exclusively through the type I IL-4 receptor complex, providing previously inaccessible insights into differential IL-4 signaling through type I versus type II receptors. Because of their hyperstability, our computationally designed mimetics can directly incorporate into sophisticated biomaterials that require heat processing, such as three-dimensional-printed scaffolds. Neo-4 should be broadly useful for interrogating IL-4 biology, and the design workflow will inform targeted cytokine therapeutic development.
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Affiliation(s)
- Huilin Yang
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Umut Y Ulge
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Alfredo Quijano-Rubio
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Zachary J Bernstein
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David R Maestas
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jung-Ho Chun
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA
| | - Wentao Wang
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jian-Xin Lin
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kevin M Jude
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Srujan Singh
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Peng Li
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jody Mou
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Liam Chung
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD, USA
| | - Yun-Huai Kuo
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yasmin H Ali
- College of Medicine, Florida State University, Tallahassee, FL, USA
| | - Aaron S Meyer
- Department of Bioengineering, University of California, Los Angeles, CA, USA
- Department of Bioinformatics, University of California, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
| | - Warren L Grayson
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD, USA
- Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD, USA
| | - Nicola M Heller
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
- Allergy and Clinical Immunology, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - K Christopher Garcia
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Warren J Leonard
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Daniel-Adriano Silva
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jennifer H Elisseeff
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David Baker
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
| | - Jamie B Spangler
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD, USA.
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Sidney Kimmel Cancer Center, The Johns Hopkins University, Baltimore, MD, USA.
- Department of Ophthalmology, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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129
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Cabrera-Cabrera F, Tull H, Capuana R, Kasvandik S, Timmusk T, Koppel I. Cell type-specific labeling of newly synthesized proteins by puromycin inactivation. J Biol Chem 2023; 299:105129. [PMID: 37543363 PMCID: PMC10497999 DOI: 10.1016/j.jbc.2023.105129] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/07/2023] Open
Abstract
Puromycin and its derivative O-propargyl puromycin (OPP) have recently found widespread use in detecting nascent proteins. Use of these metabolic labels in complex mixtures of cells leads to indiscriminate tagging of nascent proteomes independent of cell type. Here, we show how a widely used mammalian selection marker, puromycin N-acetyltransferase, can be repurposed for cell-specific metabolic labeling. This approach, which we named puromycin inactivation for cell-selective proteome labeling (PICSL), is based on efficient inactivation of puromycin or OPP in cells expressing puromycin N-acetyltransferase and detection of translation in other cell types. Using cocultures of neurons and glial cells from the rat brain cortex, we show the application of PICSL for puromycin immunostaining, Western blot, and mass spectrometric identification of nascent proteins. By combining PICSL and OPP-mediated proteomics, cell type-enriched proteins can be identified based on reduced OPP labeling in the cell type of interest.
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Affiliation(s)
| | - Helena Tull
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Roberta Capuana
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Sergo Kasvandik
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Tõnis Timmusk
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia; Protobios Llc, Tallinn, Estonia
| | - Indrek Koppel
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia.
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130
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Jiang S, Wang T, Zhang KH. Data-driven decision-making for precision diagnosis of digestive diseases. Biomed Eng Online 2023; 22:87. [PMID: 37658345 PMCID: PMC10472739 DOI: 10.1186/s12938-023-01148-1] [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: 01/14/2023] [Accepted: 08/15/2023] [Indexed: 09/03/2023] Open
Abstract
Modern omics technologies can generate massive amounts of biomedical data, providing unprecedented opportunities for individualized precision medicine. However, traditional statistical methods cannot effectively process and utilize such big data. To meet this new challenge, machine learning algorithms have been developed and applied rapidly in recent years, which are capable of reducing dimensionality, extracting features, organizing data and forming automatable data-driven clinical decision systems. Data-driven clinical decision-making have promising applications in precision medicine and has been studied in digestive diseases, including early diagnosis and screening, molecular typing, staging and stratification of digestive malignancies, as well as precise diagnosis of Crohn's disease, auxiliary diagnosis of imaging and endoscopy, differential diagnosis of cystic lesions, etiology discrimination of acute abdominal pain, stratification of upper gastrointestinal bleeding (UGIB), and real-time diagnosis of esophageal motility function, showing good application prospects. Herein, we reviewed the recent progress of data-driven clinical decision making in precision diagnosis of digestive diseases and discussed the limitations of data-driven decision making after a brief introduction of methods for data-driven decision making.
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Affiliation(s)
- Song Jiang
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, No. 17, Yongwai Zheng Street, Nanchang, 330006 China
- Jiangxi Institute of Gastroenterology and Hepatology, Nanchang, 330006 China
| | - Ting Wang
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, No. 17, Yongwai Zheng Street, Nanchang, 330006 China
- Jiangxi Institute of Gastroenterology and Hepatology, Nanchang, 330006 China
| | - Kun-He Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, No. 17, Yongwai Zheng Street, Nanchang, 330006 China
- Jiangxi Institute of Gastroenterology and Hepatology, Nanchang, 330006 China
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131
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Tam RW, Keung AJ. Profiling transcriptomic responses of human stem cell-derived medium spiny neuron-like cells to exogenous phasic and tonic neurotransmitters. Mol Cell Neurosci 2023; 126:103876. [PMID: 37385515 PMCID: PMC10528483 DOI: 10.1016/j.mcn.2023.103876] [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: 01/17/2023] [Revised: 06/06/2023] [Accepted: 06/24/2023] [Indexed: 07/01/2023] Open
Abstract
Transcriptomic responses to neurotransmitters contribute to the complex processes driving memory and addiction. Advances in both measurement methods and experimental models continue to improve our understanding of this regulatory layer. Here we focus on the experimental potential of stem cell derived neurons, currently the only ethical model that can be used in reductionist and experimentally perturbable studies of human cells. Prior work has focused on generating distinct cell types from human stem cells, and has also shown their utility in modeling development and cellular phenotypes related to neurodegeneration. Here we seek an understanding of how stem cell derived neural cultures respond to perturbations experienced during development and disease progression. This work profiles transcriptomic responses of human medium spiny neuron-like cells with three specific goals. We first characterize transcriptomic responses to dopamine and dopamine receptor agonists and antagonists presented in dosing patterns mimicking acute, chronic, and withdrawal regimens. We also assess transcriptomic responses to low and persistent tonic levels of dopamine, acetylcholine, and glutamate to better mimic the in vivo environment. Finally, we identify similar and distinct responses between hMSN-like cells derived from H9 and H1 stem cell lines, providing some context for the extent of variability these types of systems will likely pose for experimentalists. The results here suggest future optimizations of human stem cell derived neurons to increase their in vivo relevance and the biological insights that can be garnered from these models.
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Affiliation(s)
- Ryan W Tam
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27606, United States of America
| | - Albert J Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27606, United States of America.
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132
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Chinchankar MN, Taylor WB, Ko SH, Apple EC, Rodriguez KA, Chen L, Fisher AL. A novel endoplasmic reticulum adaptation is critical for the long-lived Caenorhabditis elegans rpn-10 proteasomal mutant. Biochim Biophys Acta Gene Regul Mech 2023; 1866:194957. [PMID: 37355092 PMCID: PMC10528105 DOI: 10.1016/j.bbagrm.2023.194957] [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] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/24/2023] [Accepted: 06/14/2023] [Indexed: 06/26/2023]
Abstract
The loss of proteostasis due to reduced efficiency of protein degradation pathways plays a key role in multiple age-related diseases and is a hallmark of the aging process. Paradoxically, we have previously reported that the Caenorhabditis elegans rpn-10(ok1865) mutant, which lacks the RPN-10/RPN10/PSMD4 subunit of the 19S regulatory particle of the 26S proteasome, exhibits enhanced cytosolic proteostasis, elevated stress resistance and extended lifespan, despite possessing reduced proteasome function. However, the response of this mutant against threats to endoplasmic reticulum (ER) homeostasis and proteostasis was unknown. Here, we find that the rpn-10 mutant is highly ER stress resistant compared to the wildtype. Under unstressed conditions, the ER unfolded protein response (UPR) is activated in the rpn-10 mutant as signified by increased xbp-1 splicing. This primed response appears to alter ER homeostasis through the upregulated expression of genes involved in ER protein quality control (ERQC), including those in the ER-associated protein degradation (ERAD) pathway. Pertinently, we find that ERQC is critical for the rpn-10 mutant longevity. These changes also alter ER proteostasis, as studied using the C. elegans alpha-1 antitrypsin (AAT) deficiency model, which comprises an intestinal ER-localised transgenic reporter of an aggregation-prone form of AAT called ATZ. The rpn-10 mutant shows a significant reduction in the accumulation of the ATZ reporter, thus indicating that its ER proteostasis is augmented. Via a genetic screen for suppressors of decreased ATZ aggregation in the rpn-10 mutant, we then identified ecps-2/H04D03.3, a novel ortholog of the proteasome-associated adaptor and scaffold protein ECM29/ECPAS. We further show that ecps-2 is required for improved ER proteostasis as well as lifespan extension of the rpn-10 mutant. Thus, we propose that ECPS-2-proteasome functional interactions, alongside additional putative molecular processes, contribute to a novel ERQC adaptation which underlies the superior proteostasis and longevity of the rpn-10 mutant.
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Affiliation(s)
- Meghna N Chinchankar
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio (UTHSCSA), SA, TX, United States of America; Department of Cell Systems and Anatomy, UTHSCSA, SA, TX, United States of America
| | - William B Taylor
- Division of Geriatrics, Gerontology, and Palliative Medicine, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Su-Hyuk Ko
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio (UTHSCSA), SA, TX, United States of America; Department of Cell Systems and Anatomy, UTHSCSA, SA, TX, United States of America
| | - Ellen C Apple
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio (UTHSCSA), SA, TX, United States of America; Department of Cell Systems and Anatomy, UTHSCSA, SA, TX, United States of America
| | - Karl A Rodriguez
- Department of Cell Systems and Anatomy, UTHSCSA, SA, TX, United States of America
| | - Lizhen Chen
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio (UTHSCSA), SA, TX, United States of America; Department of Cell Systems and Anatomy, UTHSCSA, SA, TX, United States of America
| | - Alfred L Fisher
- Division of Geriatrics, Gerontology, and Palliative Medicine, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, United States of America.
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133
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Morris E, Abreu A, Scordilis SP. Effect of Tamoxifen on Proteome Expression during In Vitro Myogenesis in Murine Skeletal Muscle C 2C 12 Cells. J Proteome Res 2023; 22:3040-3053. [PMID: 37552804 PMCID: PMC10476267 DOI: 10.1021/acs.jproteome.3c00340] [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: 06/08/2023] [Indexed: 08/10/2023]
Abstract
Tamoxifen (TMX), a selective estrogen receptor modulator, is commonly used in the treatment of hormone-responsive cancers. However, the effects of TMX in anabolic tissues harboring estrogen receptors, such as skeletal muscle, are poorly understood. We report a tandem mass-tag approach to TMX-treated myogenesis in C2C12 cells, a well-characterized model of in vitro murine skeletal muscle differentiation. A longitudinal analysis of >10,000 proteins identified in untreated C2C12 myogenesis revealed a novel subset of 1,062 myogenically regulated proteins. These proteins clustered into five distinct longitudinal expression trends which significantly overlap those obtained in similar analyses performed in human myocytes. We document a specific functional enrichment for adiponectin-signaling unique to TMX-treated myogenesis, as well as a subset of 198 proteins that are differentially expressed in TMX-treated cells relative to controls at one or more stages of myogenesis, the majority of which were involved in steroid and lipid metabolism. Further analysis highlights metallothionein-1 as a novel target of TMX treatment at each stage of C2C12 myogenesis. Finally, we present a powerful, self-validating pipeline for analyzing the total proteomic response to in vitro treatment across every stage of muscle cell development which can be easily adapted to study the effects of other drugs on myogenesis.
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Affiliation(s)
- Emily
A. Morris
- Department
of Microbiology and Immunology, Geisel School
of Medicine at Dartmouth, Borwell Building 644E, Lebanon, New Hampshire 03756, United States
| | - Ahlenne Abreu
- Department
of Cancer Biology, Perelman School of Medicine,
University of Pennsylvania Medical School, 421 Curie Blvd. Room 612 BRB II/III, Philadelphia, Pennsylvania 19104, United States
| | - Stylianos P. Scordilis
- Department
of Biological Sciences, Smith College, Ford Hall 202 B, Northampton, Massachusetts 01063, United States
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Flint AC, Mitchell DK, Angus SP, Smith AE, Bessler W, Jiang L, Mang H, Li X, Lu Q, Rodriguez B, Sandusky GE, Masters AR, Zhang C, Dang P, Koenig J, Johnson GL, Shen W, Liu J, Aggarwal A, Donoho GP, Willard MD, Bhagwat SV, Clapp DW, Rhodes SD. Combined CDK4/6 and ERK1/2 Inhibition Enhances Antitumor Activity in NF1-Associated Plexiform Neurofibroma. Clin Cancer Res 2023; 29:3438-3456. [PMID: 37406085 DOI: 10.1158/1078-0432.ccr-22-2854] [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: 10/17/2022] [Revised: 04/06/2023] [Accepted: 06/29/2023] [Indexed: 07/07/2023]
Abstract
PURPOSE Plexiform neurofibromas (PNF) are peripheral nerve sheath tumors that cause significant morbidity in persons with neurofibromatosis type 1 (NF1), yet treatment options remain limited. To identify novel therapeutic targets for PNF, we applied an integrated multi-omic approach to quantitatively profile kinome enrichment in a mouse model that has predicted therapeutic responses in clinical trials for NF1-associated PNF with high fidelity. EXPERIMENTAL DESIGN Utilizing RNA sequencing combined with chemical proteomic profiling of the functionally enriched kinome using multiplexed inhibitor beads coupled with mass spectrometry, we identified molecular signatures predictive of response to CDK4/6 and RAS/MAPK pathway inhibition in PNF. Informed by these results, we evaluated the efficacy of the CDK4/6 inhibitor, abemaciclib, and the ERK1/2 inhibitor, LY3214996, alone and in combination in reducing PNF tumor burden in Nf1flox/flox;PostnCre mice. RESULTS Converging signatures of CDK4/6 and RAS/MAPK pathway activation were identified within the transcriptome and kinome that were conserved in both murine and human PNF. We observed robust additivity of the CDK4/6 inhibitor, abemaciclib, in combination with the ERK1/2 inhibitor, LY3214996, in murine and human NF1(Nf1) mutant Schwann cells. Consistent with these findings, the combination of abemaciclib (CDK4/6i) and LY3214996 (ERK1/2i) synergized to suppress molecular signatures of MAPK activation and exhibited enhanced antitumor activity in Nf1flox/flox;PostnCre mice in vivo. CONCLUSIONS These findings provide rationale for the clinical translation of CDK4/6 inhibitors alone and in combination with therapies targeting the RAS/MAPK pathway for the treatment of PNF and other peripheral nerve sheath tumors in persons with NF1.
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Affiliation(s)
- Alyssa C Flint
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana
| | - Dana K Mitchell
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana
| | - Steven P Angus
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana
| | - Abbi E Smith
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana
| | - Waylan Bessler
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana
| | - Li Jiang
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana
| | - Henry Mang
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana
| | - Xiaohong Li
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana
| | - Qingbo Lu
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana
| | - Brooke Rodriguez
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana
| | - George E Sandusky
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Andi R Masters
- Clinical Pharmacology Analytical Core, Indiana University School of Medicine, Indianapolis, Indiana
| | - Chi Zhang
- Center for Computational Biology and Bioinformatics and Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Pengtao Dang
- Center for Computational Biology and Bioinformatics and Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Jenna Koenig
- Medical Scientist Training Program, Indiana University School of Medicine, Indianapolis, Indiana
| | - Gary L Johnson
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Weihua Shen
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Jiangang Liu
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Amit Aggarwal
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Gregory P Donoho
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Melinda D Willard
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Shripad V Bhagwat
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - D Wade Clapp
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana
| | - Steven D Rhodes
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana
- Division of Pediatric Hematology-Oncology, Indiana University School of Medicine, Indianapolis, Indiana
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135
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Tohi Y, Kato T, Sugimoto M. Aggressive Prostate Cancer in Patients Treated with Active Surveillance. Cancers (Basel) 2023; 15:4270. [PMID: 37686546 PMCID: PMC10486407 DOI: 10.3390/cancers15174270] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
Active surveillance has emerged as a promising approach for managing low-risk and favorable intermediate-risk prostate cancer (PC), with the aim of minimizing overtreatment and maintaining the quality of life. However, concerns remain about identifying "aggressive prostate cancer" within the active surveillance cohort, which refers to cancers with a higher potential for progression. Previous studies are predictors of aggressive PC during active surveillance. To address this, a personalized risk-based follow-up approach that integrates clinical data, biomarkers, and genetic factors using risk calculators was proposed. This approach enables an efficient risk assessment and the early detection of disease progression, minimizes unnecessary interventions, and improves patient management and outcomes. As active surveillance indications expand, the importance of identifying aggressive PC through a personalized risk-based follow-up is expected to increase.
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Affiliation(s)
- Yoichiro Tohi
- Department of Urology, Faculty of Medicine, Kagawa University, Kagawa 761-0793, Japan
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136
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Dubey P, Kumar S. Advancing prostate cancer detection: a comparative analysis of PCLDA-SVM and PCLDA-KNN classifiers for enhanced diagnostic accuracy. Sci Rep 2023; 13:13745. [PMID: 37612436 PMCID: PMC10447543 DOI: 10.1038/s41598-023-40906-y] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/18/2023] [Indexed: 08/25/2023] Open
Abstract
This investigation aimed to assess the effectiveness of different classification models in diagnosing prostate cancer using a screening dataset obtained from the National Cancer Institute's Cancer Data Access System. The dataset was first reduced using the PCLDA method, which combines Principal Component Analysis and Linear Discriminant Analysis. Two classifiers, Support Vector Machine (SVM) and k-Nearest Neighbour (KNN), were then applied to compare their performance. The results showed that the PCLDA-SVM model achieved an impressive accuracy rate of 97.99%, with a precision of 0.92, sensitivity of 92.83%, specificity of 97.65%, and F1 score of 0.93. Additionally, it demonstrated a low error rate of 0.016 and a Matthews Correlation Coefficient (MCC) and Kappa coefficient of 0.946. On the other hand, the PCLDA-KNN model also performed well, achieving an accuracy of 97.8%, precision of 0.93, sensitivity of 93.39%, specificity of 97.86%, an F1 score of 0.92, a high MCC and Kappa coefficient of 0.98, and an error rate of 0.006. In conclusion, the PCLDA-SVM method exhibited improved efficacy in diagnosing prostate cancer compared to the PCLDA-KNN model. Both models, however, showed promising results, suggesting the potential of these classifiers in prostate cancer diagnosis.
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Affiliation(s)
- Priya Dubey
- Electrical and Electronics Engineering, Birla Institute of Technology, Ranchi, Jharkhand, 835215, India.
| | - Surendra Kumar
- Electrical and Electronics Engineering, Birla Institute of Technology, Ranchi, Jharkhand, 835215, India
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137
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Naplekov D, Jadeja S, Fučíková AM, Švec F, Sklenářová H, Lenčo J. Easy, Robust, and Repeatable Online Acid Cleavage of Proteins in Mobile Phase for Fast Quantitative LC-MS Bottom-Up Protein Analysis─Application for Ricin Detection. Anal Chem 2023; 95:12339-12348. [PMID: 37565982 PMCID: PMC10448442 DOI: 10.1021/acs.analchem.3c01772] [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: 04/24/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023]
Abstract
Sample preparation involving the cleavage of proteins into peptides is the first critical step for successful bottom-up proteomics and protein analyses. Time- and labor-intensiveness are among the bottlenecks of the commonly used methods for protein sample preparation. Here, we report a fast online method for postinjection acid cleavage of proteins directly in the mobile phase typically used for LC-MS analyses in proteomics. The chemical cleavage is achieved in 0.1% formic acid within 35 s in a capillary heated to 195 °C installed upstream of the analytical column, enabling the generated peptides to be separated. The peptides generated by the optimized method covered the entire sequence except for one amino acid of trastuzumab used for the method development. The qualitative results are extraordinarily stable, even over a long period of time. Moreover, the method is also suitable for accurate and repeatable quantification. The procedure requires only one manual step, significantly decreasing sample transfer losses. To demonstrate its practical utility, we tested the method for the fast detection of ricin. Ricin can be unambiguously identified from an injection of 10 ng, and the results can be obtained within 7-8 min after receiving a suspicious sample. Because no sophisticated accessories and no additional reagents are needed, the method can be seamlessly transferred to any laboratory for high-throughput proteomic workflows.
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Affiliation(s)
- Denis
K. Naplekov
- Department
of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Siddharth Jadeja
- Department
of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Alena Myslivcová Fučíková
- Department
of Biology, Faculty of Science, University
of Hradec Králové, Hradecká 1285, 500 03 Hradec Králové, Czech Republic
| | - František Švec
- Department
of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Hana Sklenářová
- Department
of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Juraj Lenčo
- Department
of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
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138
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Castillo-Castrejon M, Sankofi BM, Murguia SJ, Udeme AA, Cen HH, Xia YH, Thomas NS, Berry WL, Jones KL, Richard VR, Zahedi RP, Borchers CH, Johnson JD, Wellberg EA. FGF1 supports glycolytic metabolism through the estrogen receptor in endocrine-resistant and obesity-associated breast cancer. Breast Cancer Res 2023; 25:99. [PMID: 37608351 PMCID: PMC10463730 DOI: 10.1186/s13058-023-01699-0] [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: 05/24/2023] [Accepted: 08/16/2023] [Indexed: 08/24/2023] Open
Abstract
BACKGROUND Obesity increases breast cancer risk and breast cancer-specific mortality, particularly for people with estrogen receptor (ER)-positive tumors. Body mass index (BMI) is used to define obesity, but it may not be the best predictor of breast cancer risk or prognosis on an individual level. Adult weight gain is an independent indicator of breast cancer risk. Our previous work described a murine model of obesity, ER-positive breast cancer, and weight gain and identified fibroblast growth factor receptor (FGFR) as a potential driver of tumor progression. During adipose tissue expansion, the FGF1 ligand is produced by hypertrophic adipocytes as a stimulus to stromal preadipocytes that proliferate and differentiate to provide additional lipid storage capacity. In breast adipose tissue, FGF1 production may stimulate cancer cell proliferation and tumor progression. METHODS We explored the effects of FGF1 on ER-positive endocrine-sensitive and resistant breast cancer and compared that to the effects of the canonical ER ligand, estradiol. We used untargeted proteomics, specific immunoblot assays, gene expression profiling, and functional metabolic assessments of breast cancer cells. The results were validated in tumors from obese mice and breast cancer datasets from women with obesity. RESULTS FGF1 stimulated ER phosphorylation independently of estradiol in cells that grow in obese female mice after estrogen deprivation treatment. Phospho- and total proteomic, genomic, and functional analyses of endocrine-sensitive and resistant breast cancer cells show that FGF1 promoted a cellular phenotype characterized by glycolytic metabolism. In endocrine-sensitive but not endocrine-resistant breast cancer cells, mitochondrial metabolism was also regulated by FGF1. Comparison of gene expression profiles indicated that tumors from women with obesity shared hallmarks with endocrine-resistant breast cancer cells. CONCLUSIONS Collectively, our data suggest that one mechanism by which obesity and weight gain promote breast cancer progression is through estrogen-independent ER activation and cancer cell metabolic reprogramming, partly driven by FGF/FGFR. The first-line treatment for many patients with ER-positive breast cancer is inhibition of estrogen synthesis using aromatase inhibitors. In women with obesity who are experiencing weight gain, locally produced FGF1 may activate ER to promote cancer cell metabolic reprogramming and tumor progression independently of estrogen.
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Affiliation(s)
- Marisol Castillo-Castrejon
- Department of Pathology, University of Oklahoma Health Sciences Center, 975 NE 10th Street BRC 309, Oklahoma City, OK, 73104, USA
| | - Barbara Mensah Sankofi
- Department of Pathology, University of Oklahoma Health Sciences Center, 975 NE 10th Street BRC 309, Oklahoma City, OK, 73104, USA
| | - Stevi Johnson Murguia
- Department of Pathology, University of Oklahoma Health Sciences Center, 975 NE 10th Street BRC 309, Oklahoma City, OK, 73104, USA
| | - Abasi-Ama Udeme
- Department of Pathology, University of Oklahoma Health Sciences Center, 975 NE 10th Street BRC 309, Oklahoma City, OK, 73104, USA
| | - Hoaning Howard Cen
- Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Yi Han Xia
- Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Nisha S Thomas
- Department of Pathology, University of Oklahoma Health Sciences Center, 975 NE 10th Street BRC 309, Oklahoma City, OK, 73104, USA
| | - William L Berry
- Department of Pathology, University of Oklahoma Health Sciences Center, 975 NE 10th Street BRC 309, Oklahoma City, OK, 73104, USA
| | - Kenneth L Jones
- Department of Pathology, University of Oklahoma Health Sciences Center, 975 NE 10th Street BRC 309, Oklahoma City, OK, 73104, USA
| | - Vincent R Richard
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital and McGill University, Montreal, QC, Canada
| | - Rene P Zahedi
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg, MB, R3E 3P4, Canada
- Department of Internal Medicine, University of Manitoba, Winnipeg, MB, R3E 3P4, Canada
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada
- CancerCare Manitoba Research Institute, Winnipeg, MB, R3E 0V9, Canada
| | - Christoph H Borchers
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg, MB, R3E 3P4, Canada
- Gerald Bronfman Department of Oncology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, H3T 1E2, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, H4A 3J1, Canada
- Department of Pathology, McGill University, Montreal, QC, H3A 2B4, Canada
| | - James D Johnson
- Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Elizabeth A Wellberg
- Department of Pathology, University of Oklahoma Health Sciences Center, 975 NE 10th Street BRC 309, Oklahoma City, OK, 73104, USA.
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139
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Ribarski-Chorev I, Schudy G, Strauss C, Schlesinger S. Short heat shock has a long-term effect on mesenchymal stem cells' transcriptome. iScience 2023; 26:107305. [PMID: 37529103 PMCID: PMC10387575 DOI: 10.1016/j.isci.2023.107305] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/23/2023] [Accepted: 07/03/2023] [Indexed: 08/03/2023] Open
Abstract
The adverse effects of heat stress (HS) on physiological systems are well documented, yet the underlying molecular mechanisms behind it remain poorly understood. To address this knowledge gap, we conducted a comprehensive investigation into the impact of HS on mesenchymal stem cells (MSCs), focusing on their morphology, phenotype, proliferative capacity, and fate determination. Our in-depth analysis of the MSCs' transcriptome revealed a significant influence of HS on the transcriptional landscape. Notably, even after a short period of stress, we observed a persistent alteration in cell identity, potentially mediated by the activation of bivalent genes. Furthermore, by comparing the differentially expressed genes following short HS with their transcriptional state after recovery, we identified the transient upregulation of MLL and other histone modifiers, providing a potential mechanistic explanation for the stable activation of bivalent genes. This could be used to predict and modify the long-term effect of HS on cell identity.
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Affiliation(s)
- Ivana Ribarski-Chorev
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Gisele Schudy
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Carmit Strauss
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Sharon Schlesinger
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
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140
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Mirzadeh Azad F, Struys EA, Wingert V, Hannibal L, Mills K, Jansen JH, Longley DB, Stunnenberg HG, Atlasi Y. Spic regulates one-carbon metabolism and histone methylation in ground-state pluripotency. Sci Adv 2023; 9:eadg7997. [PMID: 37595034 DOI: 10.1126/sciadv.adg7997] [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] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 07/20/2023] [Indexed: 08/20/2023]
Abstract
Understanding mechanisms of epigenetic regulation in embryonic stem cells (ESCs) is of fundamental importance for stem cell and developmental biology. Here, we identify Spic, a member of the ETS family of transcription factors (TFs), as a marker of ground state pluripotency. We show that Spic is rapidly induced in ground state ESCs and in response to extracellular signal-regulated kinase (ERK) inhibition. We find that SPIC binds to enhancer elements and stabilizes NANOG binding to chromatin, particularly at genes involved in choline/one-carbon (1C) metabolism such as Bhmt, Bhmt2, and Dmgdh. Gain-of-function and loss-of-function experiments revealed that Spic controls 1C metabolism and the flux of S-adenosyl methionine to S-adenosyl-L-homocysteine (SAM-to-SAH), thereby, modulating the levels of H3R17me2 and H3K4me3 histone marks in ESCs. Our findings highlight betaine-dependent 1C metabolism as a hallmark of ground state pluripotency primarily activated by SPIC. These findings underscore the role of uncharacterized auxiliary TFs in linking cellular metabolism to epigenetic regulation in ESCs.
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Affiliation(s)
- Fatemeh Mirzadeh Azad
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Eduard A Struys
- Department of Clinical Chemistry, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Victoria Wingert
- Laboratory of Clinical Biochemistry and Metabolism, Department of General Pediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Luciana Hannibal
- Laboratory of Clinical Biochemistry and Metabolism, Department of General Pediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Ken Mills
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Joop H Jansen
- Department of Laboratory Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
| | - Daniel B Longley
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen, Netherlands
- Princess Maxima Centre for Pediatric Oncology, Utrecht, Netherlands
| | - Yaser Atlasi
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
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Tuladhar S, Mwamelo K, Manyama C, Obuobi D, Antunes M, Gashaw M, Vogel M, Shrinivasan H, Mugambwa KA, Korley I, Froeschl G, Hoffaeller L, Scholze S. Proceedings from the CIHLMU 2022 Symposium: "Availability of and Access to Quality Data in Health". BMC Proc 2023; 17:21. [PMID: 37587461 PMCID: PMC10433535 DOI: 10.1186/s12919-023-00270-1] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2023] [Indexed: 08/18/2023] Open
Abstract
Data is an essential tool for valid and reliable healthcare management. Access to high-quality data is critical to ensuring the early identification of problems, the design of appropriate interventions, and the effective implementation and evaluation of health intervention outcomes. During the COVID-19 pandemic, the need for strong information systems and the value of producing high-quality data for timely response and tracking resources and progress have been very evident across countries. The availability of and access to high-quality data at all levels of the health systems of low and middle-income countries is a challenge, which is exacerbated by multiple parallels and poorly integrated data sources, a lack of data-sharing standards and policy frameworks, their weak enforcement, and inadequate skills among those handling data. Completeness, accuracy, integrity, validity, and timeliness are challenges to data availability and use. "Big Data" is a necessity and a challenge in the current complexities of health systems. In transitioning to digital systems with proper data standards and policy frameworks for privacy protection, data literacy, ownership, and data use at all levels of the health system, skill enhancement of the staff is critical. Adequate funding for strengthening routine information systems and periodic surveys and research, and reciprocal partnerships between high-income countries and low- and middle-income countries in data generation and use, should be prioritized by the low- and middle-income countries to foster evidence-based healthcare practices.
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Affiliation(s)
- Sabita Tuladhar
- Teaching & Training Unit, Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU, Munich, Germany.
- Center for International Health, Ludwig-Maximilians-Universität, Munich, Germany.
| | - Kimothy Mwamelo
- Teaching & Training Unit, Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU, Munich, Germany
- Center for International Health, Ludwig-Maximilians-Universität, Munich, Germany
| | - Christina Manyama
- Teaching & Training Unit, Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU, Munich, Germany
- Center for International Health, Ludwig-Maximilians-Universität, Munich, Germany
| | - Dorothy Obuobi
- Teaching & Training Unit, Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU, Munich, Germany
- Center for International Health, Ludwig-Maximilians-Universität, Munich, Germany
| | - Mario Antunes
- Teaching & Training Unit, Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU, Munich, Germany
- Center for International Health, Ludwig-Maximilians-Universität, Munich, Germany
| | - Mulatu Gashaw
- Teaching & Training Unit, Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU, Munich, Germany
- Center for International Health, Ludwig-Maximilians-Universität, Munich, Germany
| | - Monica Vogel
- Teaching & Training Unit, Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU, Munich, Germany
- Center for International Health, Ludwig-Maximilians-Universität, Munich, Germany
| | - Harinee Shrinivasan
- Teaching & Training Unit, Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU, Munich, Germany
- Center for International Health, Ludwig-Maximilians-Universität, Munich, Germany
| | - Kashung Annie Mugambwa
- Teaching & Training Unit, Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU, Munich, Germany
- Center for International Health, Ludwig-Maximilians-Universität, Munich, Germany
| | - Isabella Korley
- Teaching & Training Unit, Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU, Munich, Germany
- Center for International Health, Ludwig-Maximilians-Universität, Munich, Germany
| | - Guenter Froeschl
- Teaching & Training Unit, Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU, Munich, Germany
- Center for International Health, Ludwig-Maximilians-Universität, Munich, Germany
| | - Lisa Hoffaeller
- Teaching & Training Unit, Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU, Munich, Germany
- Center for International Health, Ludwig-Maximilians-Universität, Munich, Germany
| | - Sarah Scholze
- Teaching & Training Unit, Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU, Munich, Germany
- Center for International Health, Ludwig-Maximilians-Universität, Munich, Germany
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142
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Alomair L, Abolfotouh MA. Awareness and Predictors of the Use of Bioinformatics in Genome Research in Saudi Arabia. Int J Gen Med 2023; 16:3413-3425. [PMID: 37587979 PMCID: PMC10426440 DOI: 10.2147/ijgm.s421815] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/03/2023] [Indexed: 08/18/2023] Open
Abstract
Background With the advances in genomics research, many countries still need more bioinformatics skills. This study aimed to assess the levels of awareness of bioinformatics and predictors of its use in genomics research among scientists in Saudi Arabia. Methods In a cross-sectional survey, 309 scientists of different biological and biomedical specialties were subjected to a previously validated e-questionnaire to collect data on (1) Knowledge about bioinformatics programming languages and tools, (2) Attitude toward acceptance of bioinformatics resources in genome-related research, and (3) The pattern of information-seeking to online bioinformatics resources. Logistic regression analysis was applied to identify the predictors of using bioinformatics in research. Significance was set at p<0.05. Results More than one-half (248, 56.4%) of all scientists reported a lack of bioinformatics knowledge. Most participants had a neutral attitude toward bioinformatics (295, 95.4%). The barriers facing acceptance of bioinformatics tools reported were; lack of training (210, 67.9%), insufficient support (180, 58.2%), and complexity of software (138, 44.6%). The limited experience was reported in; having one or more bioinformatics tools (98, 31.7%), using a supercomputer in their research inside (44, 14.2%) and outside Saudi Arabia (55, 17.8%), the need for developing a program to solve a biological problem (129, 41.7%), working in one or more fields of bioinformatics (93, 30.1%), using web applications (112, 36.2%), and using programming languages (102, 33.0%). Significant predictors of conducting genomics research were; younger scientists (p=0.039), Ph.D. education (p=0.003), more than five years of experience (p<0.05), previous training (p<0.001), and higher bioinformatics knowledge scores (p<0.001). Conclusion The study revealed a short knowledge, a neutral attitude, a lack of resources, and limited use of bioinformatics resources in genomics research. Education and training during each education level and during the job is recommended. Cloud-based resources may help scientists do research using publicly available Omics data. Further studies are necessary to evaluate collaboration among bioinformatics software developers and biologists.
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Affiliation(s)
- Lamya Alomair
- AI and Bioinformatics Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
- King Saud Bin-Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Mostafa A Abolfotouh
- King Saud Bin-Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
- Research Training and Development Section, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
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Mayo KR, Basford MA, Carroll RJ, Dillon M, Fullen H, Leung J, Master H, Rura S, Sulieman L, Kennedy N, Banks E, Bernick D, Gauchan A, Lichtenstein L, Mapes BM, Marginean K, Nyemba SL, Ramirez A, Rotundo C, Wolfe K, Xia W, Azuine RE, Cronin RM, Denny JC, Kho A, Lunt C, Malin B, Natarajan K, Wilkins CH, Xu H, Hripcsak G, Roden DM, Philippakis AA, Glazer D, Harris PA. The All of Us Data and Research Center: Creating a Secure, Scalable, and Sustainable Ecosystem for Biomedical Research. Annu Rev Biomed Data Sci 2023; 6:443-464. [PMID: 37561600 DOI: 10.1146/annurev-biodatasci-122120-104825] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
The All of Us Research Program's Data and Research Center (DRC) was established to help acquire, curate, and provide access to one of the world's largest and most diverse datasets for precision medicine research. Already, over 500,000 participants are enrolled in All of Us, 80% of whom are underrepresented in biomedical research, and data are being analyzed by a community of over 2,300 researchers. The DRC created this thriving data ecosystem by collaborating with engaged participants, innovative program partners, and empowered researchers. In this review, we first describe how the DRC is organized to meet the needs of this broad group of stakeholders. We then outline guiding principles, common challenges, and innovative approaches used to build the All of Us data ecosystem. Finally, we share lessons learned to help others navigate important decisions and trade-offs in building a modern biomedical data platform.
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Affiliation(s)
- Kelsey R Mayo
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Melissa A Basford
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Robert J Carroll
- Deparment of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
| | - Moira Dillon
- Verily Life Sciences, South San Francisco, California, USA
| | - Heather Fullen
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jesse Leung
- Verily Life Sciences, South San Francisco, California, USA
| | - Hiral Master
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Shimon Rura
- Verily Life Sciences, South San Francisco, California, USA
| | - Lina Sulieman
- Deparment of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
| | - Nan Kennedy
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Eric Banks
- Data Sciences Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - David Bernick
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Asmita Gauchan
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Lee Lichtenstein
- Data Sciences Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Brandy M Mapes
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kayla Marginean
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Steve L Nyemba
- Deparment of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
| | - Andrea Ramirez
- The All of Us Research Program, National Institutes of Health, Bethesda, Maryland, USA
| | - Charissa Rotundo
- Vanderbilt University Medical Center Enterprise Cybersecurity, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Keri Wolfe
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Weiyi Xia
- Deparment of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
| | - Romuladus E Azuine
- The All of Us Research Program, National Institutes of Health, Bethesda, Maryland, USA
| | - Robert M Cronin
- Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Joshua C Denny
- The All of Us Research Program, National Institutes of Health, Bethesda, Maryland, USA
| | - Abel Kho
- Department of Medicine and Institute for Augmented Intelligence in Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Christopher Lunt
- The All of Us Research Program, National Institutes of Health, Bethesda, Maryland, USA
| | - Bradley Malin
- Deparment of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
| | - Karthik Natarajan
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Consuelo H Wilkins
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Hua Xu
- Section of Biomedical Informatics and Data Science, School of Medicine, Yale University, New Haven, Connecticut, USA
| | - George Hripcsak
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Dan M Roden
- Deparment of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - David Glazer
- Verily Life Sciences, South San Francisco, California, USA
| | - Paul A Harris
- Deparment of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
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Bustamante Eduardo M, Keller I, Schuster N, Aebi S, Jaggi R. Molecular characterization of breast cancer cell pools with normal or reduced ability to respond to progesterone: a study based on RNA-seq. J Genet Eng Biotechnol 2023; 21:81. [PMID: 37550554 PMCID: PMC10406740 DOI: 10.1186/s43141-023-00541-6] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/31/2023] [Indexed: 08/09/2023]
Abstract
BACKGROUND About one-third of patients with estrogen receptor alpha (ERα)-positive breast cancer have tumors which are progesterone receptor (PR) negative. PR is an important prognostic factor in breast cancer. Patients with ERα-positive/PR-negative tumors have shorter disease-free and overall survival than patients with ERα-positive/PR-positive tumors. New evidence has shown that progesterone (P4) has an anti-proliferative effect in ERα-positive breast cancer cells. However, the role of PR in breast cancer is only poorly understood. METHODS We disrupted the PR gene (PGR) in ERα-positive/PR-positive T-47D cells using the CRISPR/Cas9 system. This resulted in cell pools we termed PR-low as P4 mediated effects were inhibited or blocked compared to control T-47D cells. We analyzed the gene expression profiles of PR-low and control T-47D cells in the absence of hormone and upon treatment with P4 alone or P4 together with estradiol (E2). Differentially expressed (DE) genes between experimental groups were characterized based on RNA-seq and Gene Ontology (GO) enrichment analyses. RESULTS The overall gene expression pattern was very similar between untreated PR-low and untreated control T-47D cells. More than 6000 genes were DE in control T-47D cells upon stimulation with P4 or P4 plus E2. When PR-low pools were subjected to the same hormonal treatment, up- or downregulation was either blocked/absent or consistently lower. We identified more than 3000 genes that were DE between hormone-treated PR-low and control T-47D cells. GO analysis revealed seven significantly enriched biological processes affected by PR and associated with G protein-coupled receptor (GPCR) pathways which have been described to support growth, invasiveness, and metastasis in breast cancer cells. CONCLUSIONS The present study provides new insights into the complex role of PR in ERα-positive/PR-positive breast cancer cells. Many of the genes affected by PR are part of central biological processes of tumorigenesis.
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Affiliation(s)
- Mariana Bustamante Eduardo
- Department for BioMedical Research, University of Bern, Bern, Switzerland.
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, USA.
| | - Irene Keller
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nathalie Schuster
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Stefan Aebi
- Department of Medical Oncology, Cantonal Hospital, Lucerne, Switzerland
| | - Rolf Jaggi
- Department for BioMedical Research, University of Bern, Bern, Switzerland
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Connors TJ, Matsumoto R, Verma S, Szabo PA, Guyer R, Gray J, Wang Z, Thapa P, Dogra P, Poon MML, Rybkina K, Bradley MC, Idzikowski E, McNichols J, Kubota M, Pethe K, Shen Y, Atkinson MA, Brusko M, Brusko TM, Yates AJ, Sims PA, Farber DL. Site-specific development and progressive maturation of human tissue-resident memory T cells over infancy and childhood. Immunity 2023; 56:1894-1909.e5. [PMID: 37421943 PMCID: PMC10527943 DOI: 10.1016/j.immuni.2023.06.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [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: 10/24/2022] [Revised: 03/23/2023] [Accepted: 06/13/2023] [Indexed: 07/10/2023]
Abstract
Infancy and childhood are critical life stages for generating immune memory to protect against pathogens; however, the timing, location, and pathways for memory development in humans remain elusive. Here, we investigated T cells in mucosal sites, lymphoid tissues, and blood from 96 pediatric donors aged 0-10 years using phenotypic, functional, and transcriptomic profiling. Our results revealed that memory T cells preferentially localized in the intestines and lungs during infancy and accumulated more rapidly in mucosal sites compared with blood and lymphoid organs, consistent with site-specific antigen exposure. Early life mucosal memory T cells exhibit distinct functional capacities and stem-like transcriptional profiles. In later childhood, they progressively adopt proinflammatory functions and tissue-resident signatures, coincident with increased T cell receptor (TCR) clonal expansion in mucosal and lymphoid sites. Together, our findings identify staged development of memory T cells targeted to tissues during the formative years, informing how we might promote and monitor immunity in children.
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Affiliation(s)
- Thomas J Connors
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Rei Matsumoto
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Shivali Verma
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Peter A Szabo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Rebecca Guyer
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Joshua Gray
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Zicheng Wang
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Puspa Thapa
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Pranay Dogra
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Maya M L Poon
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ksenia Rybkina
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Marissa C Bradley
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Emma Idzikowski
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - James McNichols
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Masaru Kubota
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Kalpana Pethe
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Mark A Atkinson
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Maigan Brusko
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Todd M Brusko
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Andrew J Yates
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Donna L Farber
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA.
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Schliep KC, Ghabayen L, Shaaban M, Hughes FR, Pollack AZ, Stanford JB, Brady KA, Kiser A, Peterson CM. Examining the co-occurrence of endometriosis and polycystic ovarian syndrome. AJOG Glob Rep 2023; 3:100259. [PMID: 37663310 PMCID: PMC10472311 DOI: 10.1016/j.xagr.2023.100259] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023] Open
Abstract
BACKGROUND Polycystic ovarian syndrome and endometriosis are 2 of the most common reproductive disorders among women but are thought to be unrelated. OBJECTIVE This study aimed to examine the overlap and common symptoms of polycystic ovarian syndrome and endometriosis. STUDY DESIGN The study population included the Endometriosis, Natural History, Diagnosis, and Outcomes Study (2007-2009) operative cohort: 473 women, aged 18 to 44 years, who underwent a diagnostic and/or therapeutic laparoscopy or laparotomy at 1 of 14 surgical centers located in Salt Lake City, Utah, or San Francisco, California, in addition to a population cohort composed of 127 women from the surgical centers' catchment areas. Age and site-adjusted multinomial regression models were used to estimate adjusted prevalence ratios and 95% confidence intervals of reproductive history characteristics among women with endometriosis only, women with polycystic ovarian syndrome only, and women with both endometriosis and polycystic ovarian syndrome. RESULTS Among the operative cohort, 35% had endometriosis only, 9% had polycystic ovarian syndrome only, and 5% had endometriosis and polycystic ovarian syndrome. Among the population cohort, 10% had endometriosis only, 8% had polycystic ovarian syndrome only, and 2% had endometriosis and polycystic ovarian syndrome. In the operative cohort, a history of subfertility was associated with a higher adjusted probability of having both conditions (adjusted prevalence ratio, 10.33; 95% confidence interval, 3.94-27.08), followed by having endometriosis only (adjusted prevalence ratio, 2.45; 95% confidence interval, 1.56-3.84) or polycystic ovarian syndrome only (adjusted prevalence ratio, 1.15; 95% confidence interval, 0.51-2.61), than having neither condition. In addition, experiencing chronic pelvic pain within the past 12 months was associated with a higher probability of having both conditions (adjusted prevalence ratio, 2.53; 95% confidence interval, 1.07-6.00) than having neither condition. CONCLUSION Among a cohort of women undergoing gynecologic laparoscopy or laparotomy, our study found that nearly 1 in 20 women had both an incident endometriosis diagnosis and symptoms consistent with polycystic ovarian syndrome. Among a population cohort of women not seeking gynecologic care, polycystic ovarian syndrome and endometriosis overlap prevalence was approximately 1 in 50 women.
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Affiliation(s)
- Karen C. Schliep
- Department of Family and Preventive Medicine, University of Utah, Salt Lake City, UT (Dr Schliep, Mses Ghabayen, Shaaban, and Hughes, and Dr Stanford)
| | - Lina Ghabayen
- Department of Family and Preventive Medicine, University of Utah, Salt Lake City, UT (Dr Schliep, Mses Ghabayen, Shaaban, and Hughes, and Dr Stanford)
| | - May Shaaban
- Department of Family and Preventive Medicine, University of Utah, Salt Lake City, UT (Dr Schliep, Mses Ghabayen, Shaaban, and Hughes, and Dr Stanford)
| | - Felicity R. Hughes
- Department of Family and Preventive Medicine, University of Utah, Salt Lake City, UT (Dr Schliep, Mses Ghabayen, Shaaban, and Hughes, and Dr Stanford)
| | - Anna Z. Pollack
- College of Health and Human Services, George Mason University, Fairfax, VA (Dr Pollack)
| | - Joseph B. Stanford
- Department of Family and Preventive Medicine, University of Utah, Salt Lake City, UT (Dr Schliep, Mses Ghabayen, Shaaban, and Hughes, and Dr Stanford)
| | - Kristy Allen Brady
- Department of Internal Medicine, University of Utah, Salt Lake City, UT (Dr Allen Brady)
| | - Amber Kiser
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT (Ms Kiser)
| | - C. Matthew Peterson
- Department of Obstetrics and Gynecology, University of Utah, Salt Lake City, UT (Dr Peterson)
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McNamar R, Freeman E, Baylor KN, Fakhouri AM, Huang S, Knutson BA, Rothblum LI. PAF49: An RNA Polymerase I subunit essential for rDNA transcription and stabilization of PAF53. J Biol Chem 2023; 299:104951. [PMID: 37356716 PMCID: PMC10365956 DOI: 10.1016/j.jbc.2023.104951] [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: 04/04/2023] [Revised: 05/30/2023] [Accepted: 06/09/2023] [Indexed: 06/27/2023] Open
Abstract
The application of genetic and biochemical techniques in yeast has informed our knowledge of transcription in mammalian cells. Such systems have allowed investigators to determine whether a gene was essential and to determine its function in rDNA transcription. However, there are significant differences in the nature of the transcription factors essential for transcription by Pol I in yeast and mammalian cells, and yeast RNA polymerase I contains 14 subunits while mammalian polymerase contains 13 subunits. We previously reported the adaptation of the auxin-dependent degron that enabled a combination of a "genetics-like" approach and biochemistry to study mammalian rDNA transcription. Using this system, we studied the mammalian orthologue of yeast RPA34.5, PAF49, and found that it is essential for rDNA transcription and cell division. The auxin-induced degradation of PAF49 induced nucleolar stress and the accumulation of P53. Interestingly, the auxin-induced degradation of AID-tagged PAF49 led to the degradation of its binding partner, PAF53, but not vice versa. A similar pattern of co-dependent expression was also found when we studied the non-essential, yeast orthologues. An analysis of the domains of PAF49 that are essential for rDNA transcription demonstrated a requirement for both the dimerization domain and an "arm" of PAF49 that interacts with PolR1B. Further, we demonstrate this interaction can be disrupted to inhibit Pol I transcription in normal and cancer cells which leads to the arrest of normal cells and cancer cell death. In summary, we have shown that both PAF53 and PAF49 are necessary for rDNA transcription and cell growth.
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Affiliation(s)
- Rachel McNamar
- Department of Cell Biology, University of Oklahoma College of Medicine, Oklahoma City, Oklahoma, USA
| | - Emma Freeman
- Department of Cell and Development Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Kairo N Baylor
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Aula M Fakhouri
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Sui Huang
- Department of Cell and Development Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Bruce A Knutson
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Lawrence I Rothblum
- Department of Cell Biology, University of Oklahoma College of Medicine, Oklahoma City, Oklahoma, USA.
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148
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Potter A, Hangas A, Goffart S, Huynen MA, Cabrera-Orefice A, Spelbrink JN. Uncharacterized protein C17orf80 - a novel interactor of human mitochondrial nucleoids. J Cell Sci 2023; 136:jcs260822. [PMID: 37401363 PMCID: PMC10445727 DOI: 10.1242/jcs.260822] [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: 11/23/2022] [Accepted: 06/26/2023] [Indexed: 07/05/2023] Open
Abstract
Molecular functions of many human proteins remain unstudied, despite the demonstrated association with diseases or pivotal molecular structures, such as mitochondrial DNA (mtDNA). This small genome is crucial for the proper functioning of mitochondria, the energy-converting organelles. In mammals, mtDNA is arranged into macromolecular complexes called nucleoids that serve as functional stations for its maintenance and expression. Here, we aimed to explore an uncharacterized protein C17orf80, which was previously detected close to the nucleoid components by proximity labelling mass spectrometry. To investigate the subcellular localization and function of C17orf80, we took advantage of immunofluorescence microscopy, interaction proteomics and several biochemical assays. We demonstrate that C17orf80 is a mitochondrial membrane-associated protein that interacts with nucleoids even when mtDNA replication is inhibited. In addition, we show that C17orf80 is not essential for mtDNA maintenance and mitochondrial gene expression in cultured human cells. These results provide a basis for uncovering the molecular function of C17orf80 and the nature of its association with nucleoids, possibly leading to new insights about mtDNA and its expression.
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Affiliation(s)
- Alisa Potter
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Anu Hangas
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, 80101, Finland
| | - Steffi Goffart
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, 80101, Finland
| | - Martijn A. Huynen
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Alfredo Cabrera-Orefice
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Johannes N. Spelbrink
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
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149
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Anker J, Pal SK, Kim-Schulze S, Wang H, Halperin R, Uzilov A, Imai N, Eikawa S, Saito T, Sebra R, Hahn NM, Patel M, Qi J, Xie H, Bhardwaj N, Gnjatic S, Galsky MD. Antitumor immunity as the basis for durable disease-free treatment-free survival in patients with metastatic urothelial cancer. J Immunother Cancer 2023; 11:e007613. [PMID: 37607770 PMCID: PMC10445357 DOI: 10.1136/jitc-2023-007613] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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] [Accepted: 08/04/2023] [Indexed: 08/24/2023] Open
Abstract
Cisplatin-based chemotherapy has been associated with durable disease control in a small subset of patients with metastatic urothelial cancer. However, the mechanistic basis for this phenomenon has remained elusive. Antitumor immunity may underlie these exceptional responders. In a phase II trial evaluating a phased schedule of gemcitabine and cisplatin followed by gemcitabine and cisplatin with ipilimumab for metastatic urothelial cancer, 4 of 36 patients achieved durable disease-free treatment-free survival (DDFTFS) and remain in remission over 5 years after enrolment on the study. We sought to identify the genomic and immunological mechanisms associated with functional cures of such patients. Whole exome sequencing was performed on pretreatment archival tumor tissue. Neoantigen prediction and ranking were performed using a novel pipeline. For a subset of patients with available biospecimens, selected peptides were tested for neoantigen-specific T cell reactivity in peripheral blood CD4+ and CD8+ T cells cultured with autologous antigen-presenting cells at baseline, postchemotherapy, and postchemotherapy and ipilimumab timepoints. Multiplex assays of serum protein analytes were also assessed at each time point. Serum proteomic analysis revealed that pretreatment, patients achieving DDFTFS demonstrated an immune activated phenotype with elevations in TH1 adaptive immunity, costimulatory molecules, and immune checkpoint markers. After combination cisplatin-based chemotherapy and ipilimumab treatment, DDFTFS patients again displayed enrichment for markers of adaptive immunity, as well as T cell cytotoxicity. CD27 was uniquely enriched in DDFTFS patients at all timepoints. Neoantigen reactivity was not detected in any patient at baseline or post two cycles of chemotherapy. Both CD4+ and CD8+ neoantigen-specific T cell reactivity was detected in two of two DDFTFS patients in comparison to zero of five non-DDFTFS patients after combination cisplatin-based chemotherapy and ipilimumab treatment. Antitumor immunity may underlie functional cures achieved in patients with metastatic urothelial cancer treated with cisplatin-based chemotherapy and immune checkpoint blockade. Probing the mechanistic basis for DDFTFS may facilitate the identification of biomarkers, therapeutic components, and optimal treatment sequences necessary to extend this ultimate goal to a larger subset of patients.
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Affiliation(s)
- Jonathan Anker
- Department of Hematology and Medical Oncology, Mount Sinai School of Medicine, New York, New York, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sumanta K Pal
- Department of Hematology and Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, California, USA
| | - Seunghee Kim-Schulze
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | | | - Naoko Imai
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Shingo Eikawa
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Takuro Saito
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Osaka University School of Medicine Graduate School of Medicine, Suita, Osaka, Japan
| | - Robert Sebra
- Sema4, Branford, Connecticut, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Noah M Hahn
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Manishkumar Patel
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jingjing Qi
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Hui Xie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nina Bhardwaj
- Department of Hematology and Medical Oncology, Mount Sinai School of Medicine, New York, New York, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sacha Gnjatic
- Department of Hematology and Medical Oncology, Mount Sinai School of Medicine, New York, New York, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Matthew D Galsky
- Department of Hematology and Medical Oncology, Mount Sinai School of Medicine, New York, New York, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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150
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Bar-Oz M, Martini MC, Alonso MN, Meir M, Lore NI, Miotto P, Riva C, Angala SK, Xiao J, Masiello CS, Misiakou MA, Sun H, Moy JK, Jackson M, Johansen HK, Cirillo DM, Shell SS, Barkan D. The small non-coding RNA B11 regulates multiple facets of Mycobacterium abscessus virulence. PLoS Pathog 2023; 19:e1011575. [PMID: 37603560 PMCID: PMC10470900 DOI: 10.1371/journal.ppat.1011575] [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: 01/11/2023] [Revised: 08/31/2023] [Accepted: 07/24/2023] [Indexed: 08/23/2023] Open
Abstract
Mycobacterium abscessus causes severe disease in patients with cystic fibrosis. Little is known in M. abscessus about the roles of small regulatory RNAs (sRNA) in gene regulation. We show that the sRNA B11 controls gene expression and virulence-associated phenotypes in this pathogen. B11 deletion from the smooth strain ATCC_19977 produced a rough strain, increased pro-inflammatory signaling and virulence in multiple infection models, and increased resistance to antibiotics. Examination of clinical isolate cohorts identified isolates with B11 mutations or reduced expression. We used RNAseq and proteomics to investigate the effects of B11 on gene expression and test the impact of mutations found in clinical isolates. Over 200 genes were differentially expressed in the deletion mutant. Strains with the clinical B11 mutations showed expression trends similar to the deletion mutant, suggesting partial loss of function. Among genes upregulated in the B11 mutant, there was a strong enrichment for genes with B11-complementary sequences in their predicted ribosome binding sites (RBS), consistent with B11 functioning as a negative regulator that represses translation via base-pairing to RBSs. Comparing the proteomes similarly revealed that upregulated proteins were strongly enriched for B11-complementary sequences. Intriguingly, genes upregulated in the absence of B11 included components of the ESX-4 secretion system, critical for M. abscessus virulence. Many of these genes had B11-complementary sequences at their RBSs, which we show is sufficient to mediate repression by B11 through direct binding. Altogether, our data show that B11 acts as a direct negative regulator and mediates (likely indirect) positive regulation with pleiotropic effects on gene expression and clinically important phenotypes in M. abscessus. The presence of hypomorphic B11 mutations in clinical strains is consistent with the idea that lower B11 activity may be advantageous for M. abscessus in some clinical contexts. This is the first report on an sRNA role in M. abscessus.
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Affiliation(s)
- Michal Bar-Oz
- Koret School of Veterinary Medicine, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Maria Carla Martini
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Maria Natalia Alonso
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | | | | | - Paolo Miotto
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Camilla Riva
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Shiva K Angala
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Junpei Xiao
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Catherine S Masiello
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Maria-Anna Misiakou
- Center for Genomic Medicine, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | - Huaming Sun
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Justin K Moy
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | | | | | - Scarlet S Shell
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Daniel Barkan
- Koret School of Veterinary Medicine, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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