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Tafavvoghi M, Bongo LA, Shvetsov N, Busund LTR, Møllersen K. Publicly available datasets of breast histopathology H&E whole-slide images: A scoping review. J Pathol Inform 2024; 15:100363. [PMID: 38405160 PMCID: PMC10884505 DOI: 10.1016/j.jpi.2024.100363] [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: 09/14/2023] [Revised: 11/24/2023] [Accepted: 01/23/2024] [Indexed: 02/27/2024] Open
Abstract
Advancements in digital pathology and computing resources have made a significant impact in the field of computational pathology for breast cancer diagnosis and treatment. However, access to high-quality labeled histopathological images of breast cancer is a big challenge that limits the development of accurate and robust deep learning models. In this scoping review, we identified the publicly available datasets of breast H&E-stained whole-slide images (WSIs) that can be used to develop deep learning algorithms. We systematically searched 9 scientific literature databases and 9 research data repositories and found 17 publicly available datasets containing 10 385 H&E WSIs of breast cancer. Moreover, we reported image metadata and characteristics for each dataset to assist researchers in selecting proper datasets for specific tasks in breast cancer computational pathology. In addition, we compiled 2 lists of breast H&E patches and private datasets as supplementary resources for researchers. Notably, only 28% of the included articles utilized multiple datasets, and only 14% used an external validation set, suggesting that the performance of other developed models may be susceptible to overestimation. The TCGA-BRCA was used in 52% of the selected studies. This dataset has a considerable selection bias that can impact the robustness and generalizability of the trained algorithms. There is also a lack of consistent metadata reporting of breast WSI datasets that can be an issue in developing accurate deep learning models, indicating the necessity of establishing explicit guidelines for documenting breast WSI dataset characteristics and metadata.
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Affiliation(s)
- Masoud Tafavvoghi
- Department of Community Medicine, Uit The Arctic University of Norway, Tromsø, Norway
| | - Lars Ailo Bongo
- Department of Computer Science, Uit The Arctic University of Norway, Tromsø, Norway
| | - Nikita Shvetsov
- Department of Computer Science, Uit The Arctic University of Norway, Tromsø, Norway
| | | | - Kajsa Møllersen
- Department of Community Medicine, Uit The Arctic University of Norway, Tromsø, Norway
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2
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Mazzone E, Gandaglia G, Robesti D, Rajwa P, Gomez Rivas J, Ibáñez L, Soeterik TFW, Bianchi L, Afferi L, Kesch C, Darr C, Guo H, Zhuang J, Zattoni F, Fendler WP, Amparore D, Huebner NA, Giesen A, Joniau S, Schiavina R, Brunocilla E, Mattei A, Dal Moro F, Moreno Sierra J, Porpiglia F, Picchio M, Chiti A, van den Bergh R, Shariat SF, Montorsi F, Briganti A. Which Patients with Prostate Cancer and Lymph Node Uptake at Preoperative Prostate-specific Membrane Antigen Positron Emission Tomography/Computerized Tomography Scan Are at a Higher Risk of Prostate-specific Antigen Persistence After Radical Prostatectomy? Identifying Indicators of Systemic Disease by Integrating Clinical, Magnetic Resonance Imaging, and Functional Imaging Parameters. Eur Urol Oncol 2024; 7:231-240. [PMID: 37689506 DOI: 10.1016/j.euo.2023.08.010] [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: 05/22/2023] [Revised: 08/11/2023] [Accepted: 08/23/2023] [Indexed: 09/11/2023]
Abstract
BACKGROUND The role of local therapies including radical prostatectomy (RP) in prostate cancer (PCa) patients with clinical lymphadenopathies on prostate-specific membrane antigen (PSMA) positron emission tomography/computerized tomography (PET/CT) has scarcely been explored. Limited data are available to identify men who would benefit from RP; on the contrary, those more likely to benefit already have systemic disease. OBJECTIVE We aimed to assess the predictors of prostate-specific antigen (PSA) persistence in surgically managed PCa patients with lymphadenopathies on a PSMA PET/CT scan by integrating clinical, magnetic resonance imaging (MRI), and PSMA PET/CT parameters. DESIGN, SETTING, AND PARTICIPANTS We identified 519 patients treated with RP and extended lymph node dissection, and who received preoperative PSMA PET between 2017 and 2022 in nine referral centers. Among them, we selected 88 patients with nodal uptake at preoperative PSMA PET (miTxN1M0). OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS The outcome was PSA persistence, defined as a PSA value of ≥0.1 ng/ml at the first measurement after surgery. Multivariable logistic regression models tested the predictors of PSA persistence. Covariates consisted of biopsy International Society of Urological Pathology (ISUP) grade group, clinical stage at MRI, and number of positive spots at a PET/CT scan. A regression tree analysis stratified patients into risk groups based on preoperative characteristics. RESULTS AND LIMITATIONS Overall, lymph node invasion (LNI) was detected in 63 patients (72%) and 32 (36%) experienced PSA persistence after RP. At multivariable analyses, having more than two lymph nodal positive findings at PSMA PET, seminal vesicle invasion (SVI) at MRI, and ISUP grade group >3 at biopsy were independent predictors of PSA persistence (all p < 0.05). At the regression tree analysis, patients were stratified in four risk groups according to biopsy ISUP grade, number of positive findings at PET/CT, and clinical stage at MRI. The model depicted good discrimination at internal validation (area under the curve 78%). CONCLUSIONS One out of three miN1M0 patients showed PSA persistence after surgery. Patients with ISUP grade 2-3, as well as patients with organ-confined disease at MRI and a single or two positive nodal findings at PET are those in whom RP may achieve the best oncological outcomes in the context of a multimodal approach. Conversely, patients with a high ISUP grade and extracapsular extension or SVI or more than two spots at PSMA PET should be considered as potentially affected by systemic disease upfront. PATIENT SUMMARY Our novel and straightforward risk classification integrates currently available preoperative risk tools and should, therefore, assist physician in preoperative counseling of men candidates for radical treatment for prostate cancer with positive lymph node uptake at prostate-specific membrane antigen positron emission tomography.
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Affiliation(s)
- Elio Mazzone
- Unit of Urology/Division of Oncology, Gianfranco Soldera Prostate Cancer Laboratory, IRCCS San Raffaele Scientific Institute, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy.
| | - Giorgio Gandaglia
- Unit of Urology/Division of Oncology, Gianfranco Soldera Prostate Cancer Laboratory, IRCCS San Raffaele Scientific Institute, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
| | - Daniele Robesti
- Unit of Urology/Division of Oncology, Gianfranco Soldera Prostate Cancer Laboratory, IRCCS San Raffaele Scientific Institute, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
| | - Pawel Rajwa
- Department of Urology, Medical University of Vienna, Vienna, Austria; Department of Urology, Medical University of Silesia, Zabrze, Poland
| | - Juan Gomez Rivas
- Department of Urology, Hospital Clinico San Carlos, Madrid, Spain
| | - Laura Ibáñez
- Department of Urology, Hospital Clinico San Carlos, Madrid, Spain
| | - Timo F W Soeterik
- Department of Urology, St Antonius Hospital, Utrecht, The Netherlands; Department of Radiation Oncology, University Medical Center Utrecht, The Netherlands
| | - Lorenzo Bianchi
- Division of Urology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Luca Afferi
- Department of Urology, Luzerner Kantonsspital, Luzern, Switzerland
| | - Claudia Kesch
- Department of Urology, West German Cancer Center, University of Duisburg, Essen, Germany; German Cancer Consortium, University Hospital Essen, Essen, Germany
| | - Christopher Darr
- Department of Urology, West German Cancer Center, University of Duisburg, Essen, Germany; German Cancer Consortium, University Hospital Essen, Essen, Germany
| | - Hongqian Guo
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of Urology, Nanjing University, Jiangsu, China
| | - Junlong Zhuang
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of Urology, Nanjing University, Jiangsu, China
| | - Fabio Zattoni
- Department Surgery, Oncology and Gastroenterology, Urologic Unit, University of Padova, Padua, Italy
| | - Wolfgang P Fendler
- German Cancer Consortium, University Hospital Essen, Essen, Germany; Department of Nuclear Medicine, University of Duisburg, Essen, Germany
| | - Daniele Amparore
- Department of Oncology, Division of Urology, San Luigi Gonzaga Hospital, Turin, Italy
| | - Nicolai A Huebner
- Department of Urology, Medical University of Vienna, Vienna, Austria
| | - Alexander Giesen
- Department of Urology, University Hospitals Leuven, Leuven, Belgium
| | - Steven Joniau
- Department of Urology, University Hospitals Leuven, Leuven, Belgium
| | - Riccardo Schiavina
- Division of Urology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Eugenio Brunocilla
- Division of Urology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Agostino Mattei
- Department of Urology, Luzerner Kantonsspital, Luzern, Switzerland
| | - Fabrizio Dal Moro
- Department Surgery, Oncology and Gastroenterology, Urologic Unit, University of Padova, Padua, Italy
| | | | - Francesco Porpiglia
- Department of Oncology, Division of Urology, San Luigi Gonzaga Hospital, Turin, Italy
| | - Maria Picchio
- Vita-Salute San Raffaele University, Milan, Italy; Department of Nuclear Medicine, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Arturo Chiti
- Vita-Salute San Raffaele University, Milan, Italy; Department of Nuclear Medicine, IRCCS Ospedale San Raffaele, Milan, Italy
| | | | - Shahrokh F Shariat
- Department of Urology, Medical University of Vienna, Vienna, Austria; Department of Urology, Weill Cornell Medical College, New York, NY, USA; Department of Urology, Second Faculty of Medicine, Charles University, Prague, Czech Republic; Department of Urology, University of Texas Southwestern, Dallas, TX, USA; Division of Urology, Department of Special Surgery, The University of Jordan, Amman, Jordan
| | - Francesco Montorsi
- Unit of Urology/Division of Oncology, Gianfranco Soldera Prostate Cancer Laboratory, IRCCS San Raffaele Scientific Institute, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
| | - Alberto Briganti
- Unit of Urology/Division of Oncology, Gianfranco Soldera Prostate Cancer Laboratory, IRCCS San Raffaele Scientific Institute, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
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3
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Singh N, Chérin E, Roa CF, Soenjaya Y, Wodlinger B, Zheng G, Wilson BC, Foster FS, Demore CEM. Adaptation of a Clinical High-Frequency Transrectal Ultrasound System for Prostate Photoacoustic Imaging: Implementation and Pre-clinical Demonstration. Ultrasound Med Biol 2024; 50:457-466. [PMID: 38238200 DOI: 10.1016/j.ultrasmedbio.2023.11.010] [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] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 11/06/2023] [Accepted: 11/19/2023] [Indexed: 02/17/2024]
Abstract
OBJECTIVE High-frequency, high-resolution transrectal micro-ultrasound (micro-US: ≥15 MHz) imaging of the prostate is emerging as a beneficial tool for scoring disease risk and accurately targeting biopsies. Adding photoacoustic (PA) imaging to visualize abnormal vascularization and accumulation of contrast agents in tumors has potential for guiding focal therapies. In this work, we describe a new imaging platform that combines a transrectal micro-US system with transurethral light delivery for PA imaging. METHODS A clinical transrectal micro-US system was adapted to acquire PA images synchronous to a tunable laser pulse. A transurethral side-firing optical fiber was developed for light delivery. A polyvinyl chloride (PVC)-plastisol phantom was developed and characterized to image PA contrast agents in wall-less channels. After resolution measurement in water, PA imaging was demonstrated in phantom channels with dyes and biodegradable nanoparticle contrast agents called porphysomes. In vivo imaging of a tumor model was performed, with porphysomes administered intravenously. RESULTS Photoacoustic imaging data were acquired at 5 Hz, and image reconstruction was performed offline. PA image resolution at a 14-mm depth was 74 and 261 μm in the axial and lateral directions, respectively. The speed of sound in PVC-plastisol was 1383 m/s, and the attenuation was 4 dB/mm at 20 MHz. PA signal from porphysomes was spectrally unmixed from blood signals in the tumor, and a signal increase was observed 3 h after porphysome injection. CONCLUSION A combined transrectal micro-US and PA imaging system was developed and characterized, and in vivo imaging demonstrated. High-resolution PA imaging may provide valuable additional information for diagnostic and therapeutic applications in the prostate.
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Affiliation(s)
- Nidhi Singh
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Sunnybrook Research Institute, Toronto, ON, Canada.
| | | | - Carlos-Felipe Roa
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Sunnybrook Research Institute, Toronto, ON, Canada
| | | | | | - Gang Zheng
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Princess Margret Cancer Center, Toronto, ON, Canada
| | - Brian C Wilson
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Princess Margret Cancer Center, Toronto, ON, Canada
| | - F Stuart Foster
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Sunnybrook Research Institute, Toronto, ON, Canada
| | - Christine E M Demore
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Sunnybrook Research Institute, Toronto, ON, Canada
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Paul S, McCourt PM, Le LTM, Ryu J, Czaja W, Bode AM, Contreras-Galindo R, Dong Z. Fyn-mediated phosphorylation of Menin disrupts telomere maintenance in stem cells. bioRxiv 2024:2023.10.04.560876. [PMID: 37873235 PMCID: PMC10592958 DOI: 10.1101/2023.10.04.560876] [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] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Telomeres protect chromosome ends and determine the replication potential of dividing cells. The canonical telomere sequence TTAGGG is synthesized by telomerase holoenzyme, which maintains telomere length in proliferative stem cells. Although the core components of telomerase are well-defined, mechanisms of telomerase regulation are still under investigation. We report a novel role for the Src family kinase Fyn, which disrupts telomere maintenance in stem cells by phosphorylating the scaffold protein Menin. We found that Fyn knockdown prevented telomere erosion in human and mouse stem cells, validating the results with four telomere measurement techniques. We show that Fyn phosphorylates Menin at tyrosine 603 (Y603), which increases Menin's SUMO1 modification, C-terminal stability, and importantly, its association with the telomerase RNA component (TR). Using mass spectrometry, immunoprecipitation, and immunofluorescence experiments we found that SUMO1-Menin decreases TR's association with telomerase subunit Dyskerin, suggesting that Fyn's phosphorylation of Menin induces telomerase subunit mislocalization and may compromise telomerase function at telomeres. Importantly, we find that Fyn inhibition reduces accelerated telomere shortening in human iPSCs harboring mutations for dyskeratosis congenita.
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Affiliation(s)
- Souren Paul
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN 55912, USA
| | - Preston M. McCourt
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN 55912, USA
| | - Le Thi My Le
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN 55912, USA
| | - Joohyun Ryu
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN 55912, USA
- Department of Laboratory Medicine and Pathology, University of Minnesota School of Medicine, Minneapolis, MN, USA
| | - Wioletta Czaja
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN 55912, USA
- Department of Genetics, University of Alabama, Birmingham, AL 35294, USA
| | - Ann M. Bode
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN 55912, USA
| | - Rafael Contreras-Galindo
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN 55912, USA
- Department of Genetics, University of Alabama, Birmingham, AL 35294, USA
| | - Zigang Dong
- Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University, Henan, China 450001
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5
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Emerson FJ, Chiu C, Lin LY, Riedel CG, Zhu M, Lee SS. The chromatin factors SET-26 and HCF-1 oppose the histone deacetylase HDA-1 in longevity and gene regulation in C. elegans. Nat Commun 2024; 15:2320. [PMID: 38485937 PMCID: PMC10940595 DOI: 10.1038/s41467-024-46510-6] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 02/28/2024] [Indexed: 03/18/2024] Open
Abstract
SET-26, HCF-1, and HDA-1 are highly conserved chromatin factors with key roles in development and aging. Here we present mechanistic insights into how these factors regulate gene expression and modulate longevity in C. elegans. We show that SET-26 and HCF-1 cooperate to regulate a common set of genes, and both antagonize the histone deacetylase HDA-1 to limit longevity. HCF-1 localization at chromatin is largely dependent on functional SET-26, whereas SET-26 is only minorly affected by loss of HCF-1, suggesting that SET-26 could recruit HCF-1 to chromatin. HDA-1 opposes SET-26 and HCF-1 on the regulation of a subset of their common target genes and in longevity. Our findings suggest that SET-26, HCF-1, and HDA-1 comprise a mechanism to fine-tune gene expression and longevity and likely have important implications for the mechanistic understanding of how these factors function in diverse organisms, particularly in aging biology.
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Affiliation(s)
- Felicity J Emerson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Caitlin Chiu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Laura Y Lin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Christian G Riedel
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Ming Zhu
- National Institute of Biological Sciences, Beijing, China
| | - Siu Sylvia Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
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6
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Mitsi V, Ruiz A, Polizu C, Farzinpour Z, Ramakrishnan A, Serafini RA, Parise EM, Floodstrand M, Sial OK, Gaspari S, Tang CY, Nestler EJ, Schmidt EF, Shen L, Zachariou V. RGS4 Actions in Mouse Prefrontal Cortex Modulate Behavioral and Transcriptomic Responses to Chronic Stress and Ketamine. Mol Pharmacol 2024; 105:272-285. [PMID: 38351270 PMCID: PMC10949159 DOI: 10.1124/molpharm.123.000753] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 01/16/2024] [Indexed: 03/16/2024] Open
Abstract
The signal transduction protein, regulator of G protein signaling 4 (RGS4), plays a prominent role in physiologic and pharmacological responses by controlling multiple intracellular pathways. Our earlier work identified the dynamic but distinct roles of RGS4 in the efficacy of monoamine-targeting versus fast-acting antidepressants. Using a modified chronic variable stress (CVS) paradigm in mice, we demonstrate that stress-induced behavioral abnormalities are associated with the downregulation of RGS4 in the medial prefrontal cortex (mPFC). Knockout of RGS4 (RGS4KO) increases susceptibility to CVS, as mutant mice develop behavioral abnormalities as early as 2 weeks after CVS resting-state functional magnetic resonance imaging I (rs-fMRI) experiments indicate that stress susceptibility in RGS4KO mice is associated with changes in connectivity between the mediodorsal thalamus (MD-THL) and the mPFC. Notably, RGS4KO also paradoxically enhances the antidepressant efficacy of ketamine in the CVS paradigm. RNA-sequencing analysis of naive and CVS samples obtained from mPFC reveals that RGS4KO triggers unique gene expression signatures and affects several intracellular pathways associated with human major depressive disorder. Our analysis suggests that ketamine treatment in the RGS4KO group triggers changes in pathways implicated in synaptic activity and responses to stress, including pathways associated with axonal guidance and myelination. Overall, we show that reducing RGS4 activity triggers unique gene expression adaptations that contribute to chronic stress disorders and that RGS4 is a negative modulator of ketamine actions. SIGNIFICANCE STATEMENT: Chronic stress promotes robust maladaptation in the brain, but the exact intracellular pathways contributing to stress vulnerability and mood disorders have not been thoroughly investigated. In this study, the authors used murine models of chronic stress and multiple methodologies to demonstrate the critical role of the signal transduction modulator regulator of G protein signaling 4 in the medial prefrontal cortex in vulnerability to chronic stress and the efficacy of the fast-acting antidepressant ketamine.
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Affiliation(s)
- Vasiliki Mitsi
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Anne Ruiz
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Claire Polizu
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Zahra Farzinpour
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Aarthi Ramakrishnan
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Randal A Serafini
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Eric M Parise
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Madeline Floodstrand
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Omar K Sial
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Sevasti Gaspari
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Cheuk Y Tang
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Eric J Nestler
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Eric F Schmidt
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Li Shen
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Venetia Zachariou
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
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7
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van Harten MJ, Roobol MJ, van Leeuwen PJ, Willemse PPM, van den Bergh RCN. Evolution of European prostate cancer screening protocols and summary of ongoing trials. BJU Int 2024. [PMID: 38469728 DOI: 10.1111/bju.16311] [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] [Indexed: 03/13/2024]
Abstract
Population-based organised repeated screening for prostate cancer has been found to reduce disease-specific mortality, but with substantial overdiagnosis leading to overtreatment. Although only very few countries have implemented a screening programme on a national level, individual prostate-specific antigen (PSA) testing is common. This opportunistic testing may have little favourable impact, while stressing the side-effects. The classic early detection protocols as were state-of-the-art in the 1990s applied a PSA and digital rectal examination threshold for sextant systematic prostate biopsy, with a fixed interval for re-testing, and limited indication for expectant management. In the three decades since these trials were started, different important improvements have become available in the cascade of screening, indication for biopsy, and treatment. The main developed aspects include: better identification of individuals at risk (using early/baseline PSA, family history, and/or genetic profile), individualised re-testing interval, optimised and individualised starting and stopping age, with gradual invitation at a fixed age rather than invitation of a wider range of age groups, risk stratification for biopsy (using PSA density, risk calculator, magnetic resonance imaging, serum and urine biomarkers, or combinations/sequences), targeted biopsy, transperineal biopsy approach, active surveillance for low-risk prostate cancer, and improved staging of disease. All these developments are suggested to decrease the side-effects of screening, while at least maintaining the advantages, but Level 1 evidence is lacking. The knowledge gained and new developments on early detection are being tested in different prospective screening trials throughout Europe. In addition, the European Union-funded PRostate cancer Awareness and Initiative for Screening in the European Union (PRAISE-U) project will compare and evaluate different screening pilots throughout Europe. Implementation and sustainability will also be addressed. Modern screening approaches may reduce the burden of the second most frequent cause of cancer-related death in European males, while minimising side-effects. Also, less efficacious opportunistic early detection may be indirectly reduced.
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Affiliation(s)
- Meike J van Harten
- Cancer Center, Department of Urology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Monique J Roobol
- Cancer Institute, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | | | - Peter-Paul M Willemse
- Cancer Center, Department of Urology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Roderick C N van den Bergh
- Cancer Institute, Erasmus University Medical Centre, Rotterdam, The Netherlands
- St Antonius Hospital, Utrecht, The Netherlands
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8
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Mathies LD, Kim AC, Soukup EM, Thomas AE, Bettinger JC. PBRM-1/PBAF-regulated genes in a multipotent progenitor in Caenorhabditis elegans. G3 (Bethesda) 2024; 14:jkad297. [PMID: 38150396 PMCID: PMC10917506 DOI: 10.1093/g3journal/jkad297] [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: 10/15/2023] [Revised: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 12/29/2023]
Abstract
The Caenorhabditis elegans somatic gonadal precursors (SGPs) are multipotent progenitors that generate all somatic cells of the adult reproductive system. The 2 SGPs originate in the mesodermal layer and are born through a division that produces one SGP and one head mesodermal cell (hmc). One hmc terminally differentiates, and the other dies by programmed cell death. The polybromo-associated BAF (PBAF) chromatin remodeling complex promotes the multipotent SGP fate. The complete loss of PBAF causes lethality, so we used a combination of Cre/lox recombination and GFP nanobody-directed protein degradation to eliminate PBRM-1, the signature subunit of the PBAF complex, from 83 mesodermal cells, including SGPs, body muscles, and the hmc. We used RNA sequencing to identify genes acting downstream of PBAF in these cells and identified 1,955 transcripts that were significantly differentially expressed between pbrm-1(-) and pbrm-1(+) in the mesoderm of L1 larvae. We found that genes involved in muscle cell function were overrepresented; most of these genes had lower expression in the absence of PBRM-1, suggesting that PBAF promotes muscle differentiation. Among the differentially expressed genes were 125 that are normally expressed at higher levels in SGP vs hmc and positively regulated by pbrm-1 and 53 that are normally expressed at higher levels in hmc vs SGP and are negatively regulated by pbrm-1; these are candidate regulators of the SGP/hmc fate decision. We validated one candidate gene using a fluorescent reporter; the hsp-12.3 reporter was derepressed in SGPs in pbrm-1 mutants, suggesting that hsp-12.3 expression is normally repressed by pbrm-1 in SGPs.
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Affiliation(s)
- Laura D Mathies
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Andrew C Kim
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Evan M Soukup
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Alan’da E Thomas
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Jill C Bettinger
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
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9
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Gnanapragasam V. Shifting the paradigm in the management of early prostate cancer. Br J Cancer 2024:10.1038/s41416-024-02641-7. [PMID: 38448750 DOI: 10.1038/s41416-024-02641-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/08/2024] Open
Abstract
Outcomes from active surveillance have clearly shown that it is the optimal method of managing many early prostate cancers. Yet, clinician training and healthcare systems are still primarily focused on the "need to treat". This comment explores the challenges and resource issues in future implementation of high-quality surveillance programmes.
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Affiliation(s)
- Vincent Gnanapragasam
- Cambridge Urology Translational Research and Clinical Trials Office, Cambridge, UK.
- Division of Urology, Department of Surgery, University of Cambridge, Cambridge, UK.
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10
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Tripathi A, Waqas A, Venkatesan K, Yilmaz Y, Rasool G. Building Flexible, Scalable, and Machine Learning-Ready Multimodal Oncology Datasets. Sensors (Basel) 2024; 24:1634. [PMID: 38475170 DOI: 10.3390/s24051634] [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] [Received: 12/10/2023] [Revised: 01/25/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024]
Abstract
The advancements in data acquisition, storage, and processing techniques have resulted in the rapid growth of heterogeneous medical data. Integrating radiological scans, histopathology images, and molecular information with clinical data is essential for developing a holistic understanding of the disease and optimizing treatment. The need for integrating data from multiple sources is further pronounced in complex diseases such as cancer for enabling precision medicine and personalized treatments. This work proposes Multimodal Integration of Oncology Data System (MINDS)-a flexible, scalable, and cost-effective metadata framework for efficiently fusing disparate data from public sources such as the Cancer Research Data Commons (CRDC) into an interconnected, patient-centric framework. MINDS consolidates over 41,000 cases from across repositories while achieving a high compression ratio relative to the 3.78 PB source data size. It offers sub-5-s query response times for interactive exploration. MINDS offers an interface for exploring relationships across data types and building cohorts for developing large-scale multimodal machine learning models. By harmonizing multimodal data, MINDS aims to potentially empower researchers with greater analytical ability to uncover diagnostic and prognostic insights and enable evidence-based personalized care. MINDS tracks granular end-to-end data provenance, ensuring reproducibility and transparency. The cloud-native architecture of MINDS can handle exponential data growth in a secure, cost-optimized manner while ensuring substantial storage optimization, replication avoidance, and dynamic access capabilities. Auto-scaling, access controls, and other mechanisms guarantee pipelines' scalability and security. MINDS overcomes the limitations of existing biomedical data silos via an interoperable metadata-driven approach that represents a pivotal step toward the future of oncology data integration.
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Affiliation(s)
- Aakash Tripathi
- Department of Machine Learning, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
- Department of Electrical Engineering, University of South Florida, Tampa, FL 33620, USA
| | - Asim Waqas
- Department of Machine Learning, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
- Department of Electrical Engineering, University of South Florida, Tampa, FL 33620, USA
| | - Kavya Venkatesan
- Department of Machine Learning, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Yasin Yilmaz
- Department of Electrical Engineering, University of South Florida, Tampa, FL 33620, USA
| | - Ghulam Rasool
- Department of Machine Learning, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
- Department of Electrical Engineering, University of South Florida, Tampa, FL 33620, USA
- Department of Neuro-Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
- Department of Oncologic Sciences, University of South Florida, Tampa, FL 33612, USA
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11
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Taniguchi R, Moriya Y, Dohmae N, Suzuki T, Nakahara K, Kubota S, Takasugi N, Uehara T. Attenuation of protein arginine dimethylation via S-nitrosylation of protein arginine methyltransferase 1. J Pharmacol Sci 2024; 154:209-217. [PMID: 38395522 DOI: 10.1016/j.jphs.2023.12.012] [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: 11/01/2023] [Revised: 12/14/2023] [Accepted: 12/27/2023] [Indexed: 02/25/2024] Open
Abstract
Upregulation of nitric oxide (NO) production contributes to the pathogenesis of numerous diseases via S-nitrosylation, a post-translational modification of proteins. This process occurs due to the oxidative reaction between NO and a cysteine thiol group; however, the extent of this reaction remains unknown. S-Nitrosylation of PRMT1, a major asymmetric arginine methyltransferase of histones and numerous RNA metabolic proteins, was induced by NO donor treatment. We found that nitrosative stress leads to S-nitrosylation of cysteine 119, located near the active site, and attenuates the enzymatic activity of PRMT1. Interestingly, RNA sequencing analysis revealed similarities in the changes in expression elicited by NO and PRMT1 inhibitors or knockdown. A comprehensive search for PRMT1 substrates using the proximity-dependent biotin identification method highlighted many known and new substrates, including RNA-metabolizing enzymes. To validate this result, we selected the RNA helicase DDX3 and demonstrated that arginine methylation of DDX3 is induced by PRMT1 and attenuated by NO treatment. Our results suggest the existence of a novel regulatory system associated with transcription and RNA metabolism via protein S-nitrosylation.
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Affiliation(s)
- Rikako Taniguchi
- Department of Medicinal Pharmacology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Yuto Moriya
- Department of Medicinal Pharmacology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Kengo Nakahara
- Department of Medicinal Pharmacology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Sho Kubota
- Department of Medicinal Pharmacology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Nobumasa Takasugi
- Department of Medicinal Pharmacology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Takashi Uehara
- Department of Medicinal Pharmacology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan.
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12
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Lehto TPK, Pylväläinen J, Sandeman K, Kenttämies A, Nordling S, Mills IG, Tang J, Mirtti T, Rannikko A. Histomic and transcriptomic features of MRI-visible and invisible clinically significant prostate cancers are associated with prognosis. Int J Cancer 2024; 154:926-939. [PMID: 37767987 DOI: 10.1002/ijc.34743] [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: 04/03/2023] [Revised: 08/27/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023]
Abstract
Magnetic resonance imaging (MRI) is increasingly used to triage patients for prostate biopsy. However, 9% to 24% of clinically significant (cs) prostate cancers (PCas) are not visible in MRI. We aimed to identify histomic and transcriptomic determinants of MRI visibility and their association to metastasis, and PCa-specific death (PCSD). We studied 45 radical prostatectomy-treated patients with csPCa (grade group [GG]2-3), including 30 with MRI-visible and 15 with MRI-invisible lesions, and 18 men without PCa. First, histological composition was quantified. Next, transcriptomic profiling was performed using NanoString technology. MRI visibility-associated differentially expressed genes (DEGs) and Reactome pathways were identified. MRI visibility was classified using publicly available genes in MSK-IMPACT and Decipher, Oncotype DX, and Prolaris. Finally, DEGs and clinical parameters were used to classify metastasis and PCSD in an external cohort, which included 76 patients with metastatic GG2-4 PCa, and 84 baseline-matched controls without progression. Luminal area was lower in MRI-visible than invisible lesions and low luminal area was associated with short metastasis-free and PCa-specific survival. We identified 67 DEGs, eight of which were associated with survival. Cell division, inflammation and transcriptional regulation pathways were upregulated in MRI-visible csPCas. Genes in Decipher, Oncotype DX and MSK-IMPACT performed well in classifying MRI visibility (AUC = 0.86-0.94). DEGs improved classification of metastasis (AUC = 0.69) and PCSD (AUC = 0.68) over clinical parameters. Our data reveals that MRI-visible csPCas harbor more aggressive histomic and transcriptomic features than MRI-invisible csPCas. Thus, targeted biopsy of visible lesions may be sufficient for risk stratification in patients with a positive MRI.
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Affiliation(s)
- Timo-Pekka K Lehto
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Urology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Juho Pylväläinen
- Department of Radiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | | | - Anu Kenttämies
- Department of Radiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Stig Nordling
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Ian G Mills
- Nuffield Department of Surgical Sciences, University of Oxford, Oxfordshire, UK
- Patrik G Johnston Centre for Cancer Research, Queen's University of Belfast, Belfast, UK
| | - Jing Tang
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland
| | - Tuomas Mirtti
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Biomedical Engineering, School of Medicine, Emory University, Atlanta, Georgia, USA
- iCAN-Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Antti Rannikko
- Department of Urology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN-Digital Precision Cancer Medicine Flagship, Helsinki, Finland
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13
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Novara G, Zattoni F, Zecchini G, Aceti A, Pellizzari A, Ferraioli G, Cobacchini C, Taverna A, Sattin F, Carletti F, La Bombarda G, Lacognata CS, Lauro A, Gardiman M, Morlacco A, Betto G, Dal Moro F. Role of targeted biopsy, perilesional biopsy, random biopsy, and their combination in the detection of clinically significant prostate cancer by mpMRI/transrectal ultrasonography fusion biopsy in confirmatory biopsy during active surveillance program. Prostate Cancer Prostatic Dis 2024; 27:129-135. [PMID: 37828151 DOI: 10.1038/s41391-023-00733-8] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/07/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023]
Abstract
BACKGROUND Based on the findings of different trials in biopsy naïve patients, target biopsy (TB) plus random biopsy (RB) during mpMRI-guided transrectal ultrasound fusion biopsy (FB) are often also adopted for the biopsy performed during active surveillance (AS) programs. At the moment, a clear consensus on the extent and modalities of the procedure is lacking. OBJECTIVE To evaluate the increase in diagnostic accuracy achieved by perilesional biopsy (PL) and different RB schemes during FB performed in AS protocol. DESIGN, SETTING, AND PARTICIPANTS We collected prospectively the data of 112 consecutive patients with low- or very-low-risk prostate cancer; positive mpMRI underwent biopsy at a single academic institution in the context of an AS protocol. INTERVENTION(S) mpMRI/transrectal US FB with Hitachi RVS system with 3 TB and concurrent transrectal 24-core RB. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS The diagnostic yield of the different possible biopsy schemes (TB only; TB + 4 perilesional (PL) cores; TB + 12-core RB; TB + 24-core RB) was compared by the McNemar test. Univariable and multivariable regression analyses were adopted to identify predictors of any cancer, Gleason grade group (GGG) ≥2 cancers, and the presence of GGG≥2 cancers in the larger schemes only. RESULTS AND LIMITATIONS The detection rate of GGG ≥2 cancers increased to 30%, 39%, and 49% by adding 4 PL cores, 14, and 24 RB cores, respectively, to TB cores (all p values <0.01). On the whole, TB alone, 14-core RB, and 24-core-RB identified 38%, 47%, and 56% of all the GGG ≥2 cancers. Such figures increased to 62% by adding to TB 4 PL cores, and to 80% by adding 14 RB cores. Most of the differences were observed in PI-RADS 4 lesions. CONCLUSIONS We found that PL biopsy increased the detection rate of GGG ≥2 cancers as compared with TB alone. However, the combination of those cores missed a large percentage of the CS cancers identified with larger RB cores, including a 20% of CS cancers diagnosed only by the combination of TB plus 24-core RB.
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Affiliation(s)
- Giacomo Novara
- Department of Surgery, Oncology, and Gastroenterology - Urology Clinic, University of Padua, Padua, Italy.
| | - Fabio Zattoni
- Department of Surgery, Oncology, and Gastroenterology - Urology Clinic, University of Padua, Padua, Italy
| | - Giovanni Zecchini
- Department of Surgery, Oncology, and Gastroenterology - Urology Clinic, University of Padua, Padua, Italy
| | - Alberto Aceti
- Department of Surgery, Oncology, and Gastroenterology - Urology Clinic, University of Padua, Padua, Italy
| | - Anna Pellizzari
- Department of Surgery, Oncology, and Gastroenterology - Urology Clinic, University of Padua, Padua, Italy
| | - Giordana Ferraioli
- Department of Surgery, Oncology, and Gastroenterology - Urology Clinic, University of Padua, Padua, Italy
| | - Claudia Cobacchini
- Department of Surgery, Oncology, and Gastroenterology - Urology Clinic, University of Padua, Padua, Italy
| | - Alessandra Taverna
- Department of Surgery, Oncology, and Gastroenterology - Urology Clinic, University of Padua, Padua, Italy
| | - Francesca Sattin
- Department of Surgery, Oncology, and Gastroenterology - Urology Clinic, University of Padua, Padua, Italy
| | - Filippo Carletti
- Department of Surgery, Oncology, and Gastroenterology - Urology Clinic, University of Padua, Padua, Italy
| | - Giulia La Bombarda
- Department of Surgery, Oncology, and Gastroenterology - Urology Clinic, University of Padua, Padua, Italy
| | | | - Alberto Lauro
- Radiology Unit, University Hospital of Padua, Padua, Italy
| | - Marina Gardiman
- Surgical Pathology Unit, Department of Medicine, University Hospital of Padua, Padua, Italy
| | - Alessandro Morlacco
- Department of Surgery, Oncology, and Gastroenterology - Urology Clinic, University of Padua, Padua, Italy
| | - Giovanni Betto
- Department of Surgery, Oncology, and Gastroenterology - Urology Clinic, University of Padua, Padua, Italy
| | - Fabrizio Dal Moro
- Department of Surgery, Oncology, and Gastroenterology - Urology Clinic, University of Padua, Padua, Italy
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14
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Suda K, Moriyama Y, Razali N, Chiu Y, Masukagami Y, Nishimura K, Barbee H, Takase H, Sugiyama S, Yamazaki Y, Sato Y, Higashiyama T, Johmura Y, Nakanishi M, Kono K. Plasma membrane damage limits replicative lifespan in yeast and induces premature senescence in human fibroblasts. Nat Aging 2024; 4:319-335. [PMID: 38388781 PMCID: PMC10950784 DOI: 10.1038/s43587-024-00575-6] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/26/2024] [Indexed: 02/24/2024]
Abstract
Plasma membrane damage (PMD) occurs in all cell types due to environmental perturbation and cell-autonomous activities. However, cellular outcomes of PMD remain largely unknown except for recovery or death. In this study, using budding yeast and normal human fibroblasts, we found that cellular senescence-stable cell cycle arrest contributing to organismal aging-is the long-term outcome of PMD. Our genetic screening using budding yeast unexpectedly identified a close genetic association between PMD response and replicative lifespan regulations. Furthermore, PMD limits replicative lifespan in budding yeast; upregulation of membrane repair factors ESCRT-III (SNF7) and AAA-ATPase (VPS4) extends it. In normal human fibroblasts, PMD induces premature senescence via the Ca2+-p53 axis but not the major senescence pathway, DNA damage response pathway. Transient upregulation of ESCRT-III (CHMP4B) suppressed PMD-dependent senescence. Together with mRNA sequencing results, our study highlights an underappreciated but ubiquitous senescent cell subtype: PMD-dependent senescent cells.
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Affiliation(s)
- Kojiro Suda
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Yohsuke Moriyama
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Nurhanani Razali
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Yatzu Chiu
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Yumiko Masukagami
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Koutarou Nishimura
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Hyogo, Japan
| | - Hunter Barbee
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Hiroshi Takase
- Core Laboratory, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
| | - Shinju Sugiyama
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Yuta Yamazaki
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Yoshikatsu Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
- Department of Biological Science, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Yoshikazu Johmura
- Division of Cancer Cell Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Keiko Kono
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
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15
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Eng SE, Basasie B, Lam A, John Semmes O, Troyer DA, Clarke GD, Sunnapwar AG, Leach RJ, Johnson-Pais TL, Sokoll LJ, Chan DW, Tosoian JJ, Siddiqui J, Chinnaiyan AM, Thompson IM, Boutros PC, Liss MA. Prospective comparison of restriction spectrum imaging and non-invasive biomarkers to predict upgrading on active surveillance prostate biopsy. Prostate Cancer Prostatic Dis 2024; 27:65-72. [PMID: 36097168 DOI: 10.1038/s41391-022-00591-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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/10/2022] [Accepted: 08/24/2022] [Indexed: 11/08/2022]
Abstract
BACKGROUND Protocol-based active surveillance (AS) biopsies have led to poor compliance. To move to risk-based protocols, more accurate imaging biomarkers are needed to predict upgrading on AS prostate biopsy. We compared restriction spectrum imaging (RSI-MRI) generated signal maps as a biomarker to other available non-invasive biomarkers to predict upgrading or reclassification on an AS biopsy. METHODS We prospectively enrolled men on prostate cancer AS undergoing repeat biopsy from January 2016 to June 2019 to obtain an MRI and biomarkers to predict upgrading. Subjects underwent a prostate multiparametric MRI and a short duration, diffusion-weighted enhanced MRI called RSI to generate a restricted signal map along with evaluation of 30 biomarkers (14 clinico-epidemiologic features, 9 molecular biomarkers, and 7 radiologic-associated features). Our primary outcome was upgrading or reclassification on subsequent AS prostate biopsy. Statistical analysis included operating characteristic improvement using AUROC and AUPRC. RESULTS The individual biomarker with the highest area under the receiver operator characteristic curve (AUC) was RSI-MRI (AUC = 0.84; 95% CI: 0.71-0.96). The best non-imaging biomarker was prostate volume-corrected Prostate Health Index density (PHI, AUC = 0.68; 95% CI: 0.53-0.82). Non-imaging biomarkers had a negligible effect on predicting upgrading at the next biopsy but did improve predictions of overall time to progression in AS. CONCLUSIONS RSI-MRI, PIRADS, and PHI could improve the predictive ability to detect upgrading in AS. The strongest predictor of clinically significant prostate cancer on AS biopsy was RSI-MRI signal output.
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Affiliation(s)
- Stefan E Eng
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA
- Institute for Precision Health, UCLA, Los Angeles, CA, USA
- Department of Urology, UCLA, Los Angeles, CA, USA
| | - Benjamin Basasie
- Department of Urology, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Alfonso Lam
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA
- Institute for Precision Health, UCLA, Los Angeles, CA, USA
- Department of Urology, UCLA, Los Angeles, CA, USA
| | - O John Semmes
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Dean A Troyer
- Department of Pathology, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Geoffrey D Clarke
- Research Imaging Institute, University of Texas Health San Antonio, San Antonio, TX, USA
- Department of Radiology, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Abhijit G Sunnapwar
- Department of Radiology, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Robin J Leach
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX, USA
| | | | - Lori J Sokoll
- Department of Pathology, Division of Clinical Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Daniel W Chan
- Department of Pathology, Division of Clinical Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | | | - Javed Siddiqui
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Paul C Boutros
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA.
- Institute for Precision Health, UCLA, Los Angeles, CA, USA.
- Department of Urology, UCLA, Los Angeles, CA, USA.
- Department of Human Genetics, UCLA, Los Angeles, CA, USA.
- Broad Stem Cell Research Center, UCLA, Los Angeles, CA, USA.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
| | - Michael A Liss
- Department of Urology, University of Texas Health San Antonio, San Antonio, TX, USA.
- Research Imaging Institute, University of Texas Health San Antonio, San Antonio, TX, USA.
- College of Pharmacy, University of Texas Austin, Austin, TX, USA.
- Department of Urology, South Texas Veterans Healthcare System, San Antonio, TX, USA.
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16
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Yang Z, Heijnsdijk EAM, Newcomb LF, Rizopoulos D, Erler NS. Exploring the relation of active surveillance schedules and prostate cancer mortality. Cancer Med 2024; 13:e6977. [PMID: 38491826 PMCID: PMC10943374 DOI: 10.1002/cam4.6977] [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: 09/14/2023] [Revised: 01/11/2024] [Accepted: 01/18/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Active surveillance (AS), where treatment is deferred until cancer progression is detected by a biopsy, is acknowledged as a way to reduce overtreatment in prostate cancer. However, a consensus on the frequency of taking biopsies while in AS is lacking. In former studies to optimize biopsy schedules, the delay in progression detection was taken as an evaluation indicator and believed to be associated with the long-term outcome, prostate cancer mortality. Nevertheless, this relation was never investigated in empirical data. Here, we use simulated data from a microsimulation model to fill this knowledge gap. METHODS In this study, the established MIcrosimulation SCreening Analysis model was extended with functionality to simulate the AS procedures. The biopsy sensitivity in the model was calibrated on the Canary Prostate Cancer Active Surveillance Study (PASS) data, and four (tri-yearly, bi-yearly, PASS, and yearly) AS programs were simulated. The relation between detection delay and prostate cancer mortality was investigated by Cox models. RESULTS The biopsy sensitivity of progression detection was found to be 50%. The Cox models show a positive relation between a longer detection delay and a higher risk of prostate cancer death. A 2-year delay resulted in a prostate cancer death risk of 2.46%-2.69% 5 years after progression detection and a 10-year risk of 5.75%-5.91%. A 4-year delay led to an approximately 8% greater 5-year risk and an approximately 25% greater 10-year risk. CONCLUSION The detection delay is confirmed as a surrogate for prostate cancer mortality. A cut-off for a "safe" detection delay could not be identified.
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Affiliation(s)
- Zhenwei Yang
- Department of BiostatisticsErasmus University Medical CenterRotterdamthe Netherlands
- Department of EpidemiologyErasmus University Medical CenterRotterdamthe Netherlands
| | | | - Lisa F. Newcomb
- Cancer Prevention Program, Public Health Sciences, Fred Hutchinson Cancer CenterSeattleWashingtonUSA
| | - Dimitris Rizopoulos
- Department of BiostatisticsErasmus University Medical CenterRotterdamthe Netherlands
- Department of EpidemiologyErasmus University Medical CenterRotterdamthe Netherlands
| | - Nicole S. Erler
- Department of BiostatisticsErasmus University Medical CenterRotterdamthe Netherlands
- Department of EpidemiologyErasmus University Medical CenterRotterdamthe Netherlands
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17
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Niu B, Pang J, Lundholm N, Liang C, Teng ST, Zheng Q, Guo X, Li Y. A Pseudo-nitzschia metabarcoding approach with a calibrated ITS1 reference sequence database applied in the Taiwan Strait. Harmful Algae 2024; 133:102602. [PMID: 38485439 DOI: 10.1016/j.hal.2024.102602] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 01/28/2024] [Accepted: 02/05/2024] [Indexed: 03/19/2024]
Abstract
Pseudo-nitzschia is a cosmopolitan phytoplankton genus of which some species can form blooms and produce the neurotoxin domoic acid (DA). Identification of Pseudo-nitzschia is generally based on field material or strains followed by morphological and/or molecular characterization. However, this process is time-consuming and laborious, and can not obtain a relatively complete and reliable profile of the Pseudo-nitzschia community, because species with low abundance in the field or potentially unavailable for culturing may easily be overlooked. In the present study, specific ITS primer sets were designed and evaluated using in silico matching. The primer set ITS-84F/456R involving the complete ITS1 region was found optimal. Based on matching with a Pseudo-nitzschia ITS1 reference sequence database carefully-calibrated in this study, a metabarcoding approach using annotated amplicon sequence variants (ASV) was applied in the Taiwan Strait of the East China Sea during two cruises in the spring and summer of 2019. In total, 48 Pseudo-nitzschia species/phylotypes including 36 known and 12 novel were uncovered, and verified by haplotype networks, ITS2 secondary structure comparisons and divergence analyses. Correlation analyses revealed that temperature was a key factor affecting the seasonal variation of the Pseudo-nitzschia community. This study provides an overview of the Pseudo-nitzschia community in the Taiwan Strait, with new insights into the diversity. The developed metabarcoding approach may be used elsewhere as a standard reference for accurate annotation of Pseudo-nitzschia.
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Affiliation(s)
- Biaobiao Niu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, College of Life Science, South China Normal University, West 55 of Zhongshan Avenue, Guangzhou 510631, China
| | - Jinxiu Pang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, College of Life Science, South China Normal University, West 55 of Zhongshan Avenue, Guangzhou 510631, China
| | - Nina Lundholm
- Natural History Museum of Denmark, University of Copenhagen, Øster Farimagsgade 5, 1353 Copenhagen K, Denmark
| | - Cuiwen Liang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, College of Life Science, South China Normal University, West 55 of Zhongshan Avenue, Guangzhou 510631, China
| | - Sing Tung Teng
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, Kota Samarahan 94300, Sarawak, Malaysia
| | - Qixiang Zheng
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, College of Life Science, South China Normal University, West 55 of Zhongshan Avenue, Guangzhou 510631, China
| | - Xin Guo
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, College of Life Science, South China Normal University, West 55 of Zhongshan Avenue, Guangzhou 510631, China
| | - Yang Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, College of Life Science, South China Normal University, West 55 of Zhongshan Avenue, Guangzhou 510631, China.
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18
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Rossi IV, de Almeida RF, Sabatke B, de Godoy LMF, Ramirez MI. Trypanosoma cruzi interaction with host tissues modulate the composition of large extracellular vesicles. Sci Rep 2024; 14:5000. [PMID: 38424216 PMCID: PMC10904747 DOI: 10.1038/s41598-024-55302-3] [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: 12/20/2023] [Accepted: 02/22/2024] [Indexed: 03/02/2024] Open
Abstract
Trypanosoma cruzi is the protozoan that causes Chagas disease (CD), an endemic parasitosis in Latin America distributed around the globe. If CD is not treated in acute phase, the parasite remains silent for years in the host's tissues in a chronic form, which may progress to cardiac, digestive or neurological manifestations. Recently, studies indicated that the gastrointestinal tract represents an important reservoir for T. cruzi in the chronic phase. During interaction T. cruzi and host cells release extracellular vesicles (EVs) that modulates the immune system and infection, but the dynamics of secretion of host and parasite molecules through these EVs is not understood. Now, we used two cell lines: mouse myoblast cell line C2C12, and human intestinal epithelial cell line Caco-2to simulate the environments found by the parasite in the host. We isolated large EVs (LEVs) from the interaction of T. cruzi CL Brener and Dm28c/C2C12 and Caco-2 cells upon 2 and 24 h of infection. Our data showed that at two hours there is a strong cellular response mediated by EVs, both in the number, variety and enrichment/targeting of proteins found in LEVs for diverse functions. Qualitative and quantitative analysis showed that proteins exported in LEVs of C2C12 and Caco-2 have different patterns. We found a predominance of host proteins at early infection. The parasite-host cell interaction induces a switch in the functionality of proteins carried by LEVs and a heterogeneous response depending on the tissues analyzed. Protein-protein interaction analysis showed that cytoplasmic and mitochondrial homologues of the same parasite protein, tryparedoxin peroxidase, were differentially packaged in LEVs, also impacting the interacting molecule of this protein in the host. These data provide new evidence that the interaction with T. cruzi leads to a rapid tissue response through the release of LEVs, reflecting the enrichment of some proteins that could modulate the infection environment.
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Affiliation(s)
- Izadora Volpato Rossi
- Programa de Pós-graduação em Microbiologia, Parasitologia e Patologia, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
- EVAHPI Research Group, Laboratório de Biologia Celular, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba, Paraná, Brazil
| | - Rafael Fogaça de Almeida
- Laboratório de Biologia Molecular e Sistêmica de Tripanossomatídeos, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba, Paraná, Brazil
| | - Bruna Sabatke
- Programa de Pós-graduação em Microbiologia, Parasitologia e Patologia, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
- EVAHPI Research Group, Laboratório de Biologia Celular, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba, Paraná, Brazil
| | - Lyris Martins Franco de Godoy
- Laboratório de Biologia Molecular e Sistêmica de Tripanossomatídeos, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba, Paraná, Brazil
| | - Marcel Ivan Ramirez
- EVAHPI Research Group, Laboratório de Biologia Celular, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba, Paraná, Brazil.
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19
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Zeng PYF, Prokopec SD, Lai SY, Pinto N, Chan-Seng-Yue MA, Clifton-Bligh R, Williams MD, Howlett CJ, Plantinga P, Cecchini MJ, Lam AK, Siddiqui I, Wang J, Sun RX, Watson JD, Korah R, Carling T, Agrawal N, Cipriani N, Ball D, Nelkin B, Rooper LM, Bishop JA, Garnis C, Berean K, Nicolson NG, Weinberger P, Henderson YC, Lalansingh CM, Tian M, Yamaguchi TN, Livingstone J, Salcedo A, Patel K, Vizeacoumar F, Datti A, Xi L, Nikiforov YE, Smallridge R, Copland JA, Marlow LA, Hyrcza MD, Delbridge L, Sidhu S, Sywak M, Robinson B, Fung K, Ghasemi F, Kwan K, MacNeil SD, Mendez A, Palma DA, Khan MI, Shaikh M, Ruicci KM, Wehrli B, Winquist E, Yoo J, Mymryk JS, Rocco JW, Wheeler D, Scherer S, Giordano TJ, Barrett JW, Faquin WC, Gill AJ, Clayman G, Boutros PC, Nichols AC. The genomic and evolutionary landscapes of anaplastic thyroid carcinoma. Cell Rep 2024; 43:113826. [PMID: 38412093 DOI: 10.1016/j.celrep.2024.113826] [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: 04/11/2023] [Revised: 12/04/2023] [Accepted: 02/05/2024] [Indexed: 02/29/2024] Open
Abstract
Anaplastic thyroid carcinoma is arguably the most lethal human malignancy. It often co-occurs with differentiated thyroid cancers, yet the molecular origins of its aggressivity are unknown. We sequenced tumor DNA from 329 regions of thyroid cancer, including 213 from patients with primary anaplastic thyroid carcinomas. We also whole genome sequenced 9 patients using multi-region sequencing of both differentiated and anaplastic thyroid cancer components. Using these data, we demonstrate thatanaplastic thyroid carcinomas have a higher burden of mutations than other thyroid cancers, with distinct mutational signatures and molecular subtypes. Further, different cancer driver genes are mutated in anaplastic and differentiated thyroid carcinomas, even those arising in a single patient. Finally, we unambiguously demonstrate that anaplastic thyroid carcinomas share a genomic origin with co-occurring differentiated carcinomas and emerge from a common malignant field through acquisition of characteristic clonal driver mutations.
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Affiliation(s)
- Peter Y F Zeng
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada; London Regional Cancer Program, London, ON, Canada; Lawson Health Research Institute, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada
| | - Stephenie D Prokopec
- Ontario Institute for Cancer Research, Toronto, ON, Canada; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Stephen Y Lai
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nicole Pinto
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada
| | | | - Roderick Clifton-Bligh
- Division of Endocrinology, Royal North Shore Hospital, and University of Sydney, Sydney, NSW, Australia
| | - Michelle D Williams
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Paul Plantinga
- Department of Pathology, Western University, London, ON, Canada
| | - Matthew J Cecchini
- Department of Pathology, School of Medicine, Griffith University, Gold Coast, QLD, Australia
| | - Alfred K Lam
- Department of Pathology, School of Medicine, Griffith University, Gold Coast, QLD, Australia
| | - Iram Siddiqui
- Department of Laboratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Jianxin Wang
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Ren X Sun
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - John D Watson
- Ontario Institute for Cancer Research, Toronto, ON, Canada; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Reju Korah
- Department of Surgery, Yale University, New Haven, CT, USA
| | - Tobias Carling
- Department of Surgery, Yale University, New Haven, CT, USA
| | - Nishant Agrawal
- Department of Otolaryngology - Head and Neck Surgery, University of Chicago, Chicago, IL, USA
| | - Nicole Cipriani
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Douglas Ball
- Division of Endocrinology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Barry Nelkin
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Lisa M Rooper
- Division of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Justin A Bishop
- Department of Pathology, University of Texas Southwestern, Dallas, TX, USA
| | | | | | | | - Paul Weinberger
- Department of Otolaryngology - Head and Neck Surgery, Louisiana State University Health Sciences Center, Shreveport, LA, USA; Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - Ying C Henderson
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Mao Tian
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Takafumi N Yamaguchi
- Ontario Institute for Cancer Research, Toronto, ON, Canada; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Julie Livingstone
- Ontario Institute for Cancer Research, Toronto, ON, Canada; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Adriana Salcedo
- Ontario Institute for Cancer Research, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Krupal Patel
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Alessandro Datti
- Network Biology Collaborative Centre, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada; Department of Agricultural, Food, and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Liu Xi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yuri E Nikiforov
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Robert Smallridge
- Division of Endocrinology, Department of Medicine, Mayo Clinic, Jacksonville, FL, USA
| | - John A Copland
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | - Laura A Marlow
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | - Martin D Hyrcza
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Leigh Delbridge
- Department of Surgery, Royal North Shore Hospital, Sydney, NSW, Australia; University of Sydney, Sydney, NWS, Australia
| | - Stan Sidhu
- Department of Surgery, Royal North Shore Hospital, Sydney, NSW, Australia; University of Sydney, Sydney, NWS, Australia
| | - Mark Sywak
- Department of Surgery, Royal North Shore Hospital, Sydney, NSW, Australia; University of Sydney, Sydney, NWS, Australia
| | - Bruce Robinson
- University of Sydney, Sydney, NWS, Australia; Department of Endocrinology, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Kevin Fung
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada
| | - Farhad Ghasemi
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada
| | - Keith Kwan
- Department of Pathology, Western University, London, ON, Canada
| | - S Danielle MacNeil
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada
| | - Adrian Mendez
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada
| | - David A Palma
- London Regional Cancer Program, London, ON, Canada; Lawson Health Research Institute, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada
| | - Mohammed I Khan
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada
| | - Mushfiq Shaikh
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada
| | - Kara M Ruicci
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada
| | - Bret Wehrli
- Department of Pathology, Western University, London, ON, Canada
| | - Eric Winquist
- London Regional Cancer Program, London, ON, Canada; Lawson Health Research Institute, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada
| | - John Yoo
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada
| | - Joe S Mymryk
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada; London Regional Cancer Program, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada; Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - James W Rocco
- Department of Otolaryngology - Head and Neck Surgery, Ohio State University, Columbus, OH, USA
| | - David Wheeler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Steve Scherer
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - John W Barrett
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada
| | - William C Faquin
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Anthony J Gill
- University of Sydney, Sydney, NWS, Australia; Cancer Diagnosis and Pathology Group, Kolling Institute of Medicine, Royal North Shore Hospital, Sydney, NSW, Australia; NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Gary Clayman
- The Clayman Thyroid Surgery and Thyroid Cancer Center, The Thyroid Institute, Tampa General Hospital, Tampa, FL, USA
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Anthony C Nichols
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada; London Regional Cancer Program, London, ON, Canada; Lawson Health Research Institute, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada.
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Walshe J, Elphinstone B, Nicol D, Taylor M. A systematic literature review of the 'commercialisation effect' on public attitudes towards biobank and genomic data repositories. Public Underst Sci 2024:9636625241230864. [PMID: 38389329 DOI: 10.1177/09636625241230864] [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] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Initiatives that collect and share genomic data to advance health research are widespread and accelerating. Commercial interests in these efforts, while vital, may erode public trust and willingness to provide personal genomic data, upon which these initiatives depend. Understanding public attitudes towards providing genomic data for health research in the context of commercial involvement is critical. A PRISMA-guided search of six online academic databases identified 113 quantitative and qualitative studies using primary data pertaining to public attitudes towards commercial actors in the management, collection, access, and use of biobank and genomic data. The presence of commercial interests yields interrelated public concerns around consent, privacy and data security, trust in science and scientists, benefit sharing, and the ownership and control of health data. Carefully considered regulatory and data governance and access policies are therefore required to maintain public trust and support for genomic health initiatives.
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21
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Duijn M, de Reijke TM, Barwari K, Hagens MJ, Rynja SP, Immerzeel J, Barentsz JO, Jager A. The association between patient and disease characteristics, and the risk of disease progression in patients with prostate cancer on active surveillance. World J Urol 2024; 42:87. [PMID: 38372786 DOI: 10.1007/s00345-024-04805-9] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 01/16/2024] [Indexed: 02/20/2024] Open
Abstract
PURPOSE The objective of this study was to identify and assess patient and disease characteristics associated with an increased risk of disease progression in men with prostate cancer on active surveillance. METHODS We studied patients with low-risk (ISUP GG1) or favorable intermediate-risk (ISUP GG2) PCa. All patients had at least one repeat biopsy. Disease progression was the primary outcome of this study, based on pathological upgrading. Univariate and multivariate Cox proportional hazard analyses were used to evaluate the association between covariates and disease progression. RESULTS In total, 240 men were included, of whom 198 (82.5%) were diagnosed with low-risk PCa and 42 (17.5%) with favorable intermediate-risk PCa. Disease progression was observed in 42.9% (103/240) of men. Index lesion > 10 mm (HR = 2.85; 95% CI 1.74-4.68; p < 0.001), MRI (m)T-stage 2b/2c (HR = 2.52; 95% CI 1.16-5.50; p = 0.02), highest PI-RADS score of 5 (HR 3.05; 95% CI 1.48-6.28; p = 0.002) and a higher PSA level (HR 1.06; 95% CI 1.01-1.11; p = 0.014) at baseline were associated with disease progression on univariate analysis. Multivariate analysis showed no significant baseline predictors of disease progression. CONCLUSION In AS patients with low-risk or favorable intermediate-risk PCa, diameter of index lesion, MRI (m)T-stage, height of the PI-RADS score and the PSA level at baseline are significant predictors of disease progression to first repeat biopsy.
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Affiliation(s)
- Matthijs Duijn
- Department of Urology, OLVG, PO Box 95500, 1090 HM, Amsterdam, The Netherlands.
- Andros Clinics, Arnhem, The Netherlands.
| | - Theo M de Reijke
- Andros Clinics, Arnhem, The Netherlands
- Department of Urology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Kurdo Barwari
- Andros Clinics, Arnhem, The Netherlands
- Department of Urology, Netherlands Cancer Institute (NCI), Amsterdam, The Netherlands
| | - Marias J Hagens
- Department of Urology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Department of Urology, Netherlands Cancer Institute (NCI), Amsterdam, The Netherlands
- Prostate Cancer Network the Netherlands, Amsterdam, The Netherlands
| | - Sybren P Rynja
- Department of Urology, Spaarne Gasthuis, Hoofddorp, The Netherlands
| | | | | | - Auke Jager
- Department of Urology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
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22
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Penumarthi LR, Baptista RP, Beaudry MS, Glenn TC, Kissinger JC. A new chromosome-level genome assembly and annotation of Cryptosporidium meleagridis. bioRxiv 2024:2024.02.16.580748. [PMID: 38405792 PMCID: PMC10888889 DOI: 10.1101/2024.02.16.580748] [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] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Cryptosporidium spp. are medically and scientifically relevant protozoan parasites that cause severe diarrheal illness in infants and immunosuppressed populations as well as animals. Although most human Cryptosporidium infections are caused by C. parvum and C. hominis, there are several other human-infecting species including C. meleagridis, which is commonly observed in developing countries. Here, we polished and annotated a long-read genome sequence assembly for C. meleagridis TU1867, a species which infects birds and humans. The genome sequence was generated using a combination of whole genome amplification (WGA) and long-read Oxford Nanopore Technologies sequencing. The assembly was then polished with Illumina data. The chromosome-level genome assembly is 9.2 Mbp with a contig N50 of 1.1 Mb. Annotation revealed 3,923 protein-coding genes. A BUSCO analysis indicates a completeness of 96.6% (n=446), including 430 (96.4%) single-copy and 1 (0.224%) duplicated apicomplexan conserved gene(s). The new C. meleagridis genome assembly is nearly gap-free and provides a valuable new resource for the Cryptosporidium community and future studies on evolution and host-specificity.
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Affiliation(s)
- Lasya R Penumarthi
- Institute of Bioinformatics, University of Georgia. Athens, Georgia. 30602, USA
- Center for Tropical and Emerging Global Diseases, University of Georgia. Athens, Georgia 30602, USA
| | - Rodrigo P Baptista
- Institute of Bioinformatics, University of Georgia. Athens, Georgia. 30602, USA
- Center for Tropical and Emerging Global Diseases, University of Georgia. Athens, Georgia 30602, USA
| | - Megan S Beaudry
- Department of Environmental Health Science, University of Georgia. Athens, GA, USA
| | - Travis C Glenn
- Institute of Bioinformatics, University of Georgia. Athens, Georgia. 30602, USA
- Department of Environmental Health Science, University of Georgia. Athens, GA, USA
- Department of Genetics, University of Georgia. Athens, Georgia 30602, USA
| | - Jessica C Kissinger
- Institute of Bioinformatics, University of Georgia. Athens, Georgia. 30602, USA
- Center for Tropical and Emerging Global Diseases, University of Georgia. Athens, Georgia 30602, USA
- Department of Genetics, University of Georgia. Athens, Georgia 30602, USA
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23
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Flores-Concha M, Gómez LA, Soto-Shara R, Molina RE, Coloma-Rivero RF, Montero DA, Ferrari Í, Oñate Á. Brucella abortus triggers the differential expression of immunomodulatory lncRNAs in infected murine macrophages. Front Immunol 2024; 15:1352306. [PMID: 38464511 PMCID: PMC10921354 DOI: 10.3389/fimmu.2024.1352306] [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: 12/07/2023] [Accepted: 01/30/2024] [Indexed: 03/12/2024] Open
Abstract
Introduction The lncRNAs (long non-coding RNAs) are the most diverse group of non-coding RNAs and are involved in most biological processes including the immune response. While some of them have been recognized for their influence on the regulation of inflammatory activity, little is known in the context of infection by Brucella abortus, a pathogen that presents significant challenges due to its ability to manipulate and evade the host immune system. This study focuses on characterize the expression profile of LincRNA-cox2, Lethe, lincRNA-EPS, Malat1 and Gas5 during infection of macrophages by B. abortus. Methods Using public raw RNA-seq datasets we constructed for a lncRNA expression profile in macrophages Brucella-infected. In addition, from public RNA-seq raw datasets of RAW264.7 cells infected with B. abortus we constructed a transcriptomic profile of lncRNAs in order to know the expression of the five immunomodulating lncRNAs studied here at 8 and 24 h post-infection. Finally, we performed in vitro infection assays in RAW264.7 cells and peritoneal macrophages to detect by qPCR changes in the expression of these lncRNAs at first 12 hours post infection, a key stage in the infection cycle where Brucella modulates the immune response to survive. Results Our results demonstrate that infection of macrophages with Brucella abortus, induces significant changes in the expression of LincRNA-Cox2, Lethe, LincRNA-EPS, Gas5, and Malat1. Discussion The change in the expression profile of these immunomodulatory lncRNAs in response to infection, suggest a potential involvement in the immune evasion strategy employed by Brucella to facilitate its intracellular survival.
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Affiliation(s)
| | | | | | | | | | | | | | - Ángel Oñate
- Laboratory of Molecular Immunology, Department of Microbiology, Universidad de Concepción, Concepción, Chile
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24
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Dhakal A, Salim C, Skelly M, Amichan Y, Lamm AT, Hundley HA. ADARs regulate cuticle collagen expression and promote survival to pathogen infection. BMC Biol 2024; 22:37. [PMID: 38360623 PMCID: PMC10870475 DOI: 10.1186/s12915-024-01840-1] [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: 04/05/2023] [Accepted: 02/02/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND In all organisms, the innate immune system defends against pathogens through basal expression of molecules that provide critical barriers to invasion and inducible expression of effectors that combat infection. The adenosine deaminase that act on RNA (ADAR) family of RNA-binding proteins has been reported to influence innate immunity in metazoans. However, studies on the susceptibility of ADAR mutant animals to infection are largely lacking. RESULTS Here, by analyzing adr-1 and adr-2 null mutants in well-established slow-killing assays, we find that both Caenorhabditis elegans ADARs are important for organismal survival to gram-negative and gram-positive bacteria, all of which are pathogenic to humans. Furthermore, our high-throughput sequencing and genetic analysis reveal that ADR-1 and ADR-2 function in the same pathway to regulate collagen expression. Consistent with this finding, our scanning electron microscopy studies indicate adr-1;adr-2 mutant animals also have altered cuticle morphology prior to pathogen exposure. CONCLUSIONS Our data uncover a critical role of the C. elegans ADAR family of RNA-binding proteins in promoting cuticular collagen expression, which represents a new post-transcriptional regulatory node that influences the extracellular matrix. In addition, we provide the first evidence that ADAR mutant animals have altered susceptibility to infection with several opportunistic human pathogens, suggesting a broader role of ADARs in altering physical barriers to infection to influence innate immunity.
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Affiliation(s)
- Alfa Dhakal
- Cell, Molecular and Cancer Biology Graduate Program, Indiana University School of Medicine-Bloomington, Bloomington, IN, 47405, USA
| | - Chinnu Salim
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Mary Skelly
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Yarden Amichan
- Faculty of Biology, Technion Institute of Technology, Haifa, Israel
| | - Ayelet T Lamm
- Faculty of Biology, Technion Institute of Technology, Haifa, Israel
| | - Heather A Hundley
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.
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25
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Forsyth KS, Toothacre NE, Jiwrajka N, Driscoll AM, Shallberg LA, Cunningham-Rundles C, Barmettler S, Farmer J, Verbsky J, Routes J, Beiting DP, Romberg N, May MJ, Anguera MC. NF-κB Signaling is Required for X-Chromosome Inactivation Maintenance Following T cell Activation. bioRxiv 2024:2024.02.08.579505. [PMID: 38405871 PMCID: PMC10888971 DOI: 10.1101/2024.02.08.579505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
X Chromosome Inactivation (XCI) is a female-specific process which balances X-linked gene dosage between sexes. Unstimulated T cells lack cytological enrichment of Xist RNA and heterochromatic modifications on the inactive X chromosome (Xi), and these modifications become enriched at the Xi after cell stimulation. Here, we examined allele-specific gene expression and the epigenomic profiles of the Xi following T cell stimulation. We found that the Xi in unstimulated T cells is largely dosage compensated and is enriched with the repressive H3K27me3 modification, but not the H2AK119-ubiquitin (Ub) mark, even at promoters of XCI escape genes. Upon CD3/CD28-mediated T cell stimulation, the Xi accumulates H2AK119-Ub and H3K27me3 across the Xi. Next, we examined the T cell signaling pathways responsible for Xist RNA localization to the Xi and found that T cell receptor (TCR) engagement, specifically NF-κB signaling downstream of TCR, is required. Disruption of NF-κB signaling, using inhibitors or genetic deletions, in mice and patients with immunodeficiencies prevents Xist/XIST RNA accumulation at the Xi and alters expression of some X-linked genes. Our findings reveal a novel connection between NF-κB signaling pathways which impact XCI maintenance in female T cells.
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26
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Fülle JB, de Almeida RA, Lawless C, Stockdale L, Yanes B, Lane EB, Garrod DR, Ballestrem C. Proximity Mapping of Desmosomes Reveals a Striking Shift in Their Molecular Neighborhood Associated With Maturation. Mol Cell Proteomics 2024; 23:100735. [PMID: 38342409 PMCID: PMC10943070 DOI: 10.1016/j.mcpro.2024.100735] [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: 05/04/2023] [Revised: 01/29/2024] [Accepted: 02/08/2024] [Indexed: 02/13/2024] Open
Abstract
Desmosomes are multiprotein adhesion complexes that link intermediate filaments to the plasma membrane, ensuring the mechanical integrity of cells across tissues, but how they participate in the wider signaling network to exert their full function is unclear. To investigate this, we carried out protein proximity mapping using biotinylation (BioID). The combined interactomes of the essential desmosomal proteins desmocollin 2a, plakoglobin, and plakophilin 2a (Pkp2a) in Madin-Darby canine kidney epithelial cells were mapped and their differences and commonalities characterized as desmosome matured from Ca2+ dependence to the mature, Ca2+-independent, hyper-adhesive state, which predominates in tissues. Results suggest that individual desmosomal proteins have distinct roles in connecting to cellular signaling pathways and that these roles alter substantially when cells change their adhesion state. The data provide further support for a dualistic concept of desmosomes in which the properties of Pkp2a differ from those of the other, more stable proteins. This body of data provides an invaluable resource for the analysis of desmosome function.
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Affiliation(s)
- Judith B Fülle
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester, UK
| | | | - Craig Lawless
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester, UK
| | - Liam Stockdale
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester, UK
| | - Bian Yanes
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester, UK
| | - E Birgitte Lane
- Skin Research Institute of Singapore, Agency of Science Technology and Research (A∗STAR), Singapore, Singapore
| | - David R Garrod
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester, UK.
| | - Christoph Ballestrem
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester, UK.
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27
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Begni V, Marizzoni M, Creutzberg KC, Silipo DM, Papp M, Cattaneo A, Riva MA. Transcriptomic analyses of rats exposed to chronic mild stress: Modulation by chronic treatment with the antipsychotic drug lurasidone. Prog Neuropsychopharmacol Biol Psychiatry 2024; 129:110885. [PMID: 37865392 DOI: 10.1016/j.pnpbp.2023.110885] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/09/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023]
Abstract
Exposure to stressful experiences accounts for almost half of the risk for mental disorders. Hence, stress-induced alterations represent a key target for pharmacological interventions aimed at restoring brain function in affected individuals. We have previously demonstrated that lurasidone, a multi-receptor antipsychotic drug approved for the treatment of schizophrenia and bipolar depression, can normalize the functional and molecular impairments induced by stress exposure, representing a valuable tool for the treatment of stress-induced mental illnesses. However, the mechanisms that may contribute to the therapeutic effects of lurasidone are still poorly understood. Here, we performed a transcriptomic analysis on the prefrontal cortex (PFC) of adult male rats exposed to the chronic mild stress (CMS) paradigm and we investigated the impact of chronic lurasidone treatment on such changes. We found that CMS exposure leads to an anhedonic phenotype associated with a down-regulation of different pathways associated to neuronal guidance and synaptic plasticity within the PFC. Interestingly, a significant part of these alterations (around 25%) were counteracted by lurasidone treatment. In summary, we provided new insights on the transcriptional changes relevant for the therapeutic intervention with lurasidone, which may ultimately promote resilience.
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Affiliation(s)
- Veronica Begni
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via Balzaretti 9, 20133 Milan, Italy
| | - Moira Marizzoni
- Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Via Pilastroni 4, 25125 Brescia, Italy; Lab of Neuroimaging and Alzheimer's Epidemiology, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Via Pilastroni 4, 25125 Brescia, Italy
| | - Kerstin Camile Creutzberg
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via Balzaretti 9, 20133 Milan, Italy
| | - Diana Morena Silipo
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via Balzaretti 9, 20133 Milan, Italy
| | - Mariusz Papp
- Institute of Pharmacology and Polish Academy of Sciences, Smętna Street 12, Kraków 31-343, Poland
| | - Annamaria Cattaneo
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via Balzaretti 9, 20133 Milan, Italy; Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Via Pilastroni 4, 25125 Brescia, Italy
| | - Marco Andrea Riva
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via Balzaretti 9, 20133 Milan, Italy; Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Via Pilastroni 4, 25125 Brescia, Italy.
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28
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Rebak AS, Hendriks IA, Elsborg JD, Buch-Larsen SC, Nielsen CH, Terslev L, Kirsch R, Damgaard D, Doncheva NT, Lennartsson C, Rykær M, Jensen LJ, Christophorou MA, Nielsen ML. A quantitative and site-specific atlas of the citrullinome reveals widespread existence of citrullination and insights into PADI4 substrates. Nat Struct Mol Biol 2024:10.1038/s41594-024-01214-9. [PMID: 38321148 DOI: 10.1038/s41594-024-01214-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 01/04/2024] [Indexed: 02/08/2024]
Abstract
Despite the importance of citrullination in physiology and disease, global identification of citrullinated proteins, and the precise targeted sites, has remained challenging. Here we employed quantitative-mass-spectrometry-based proteomics to generate a comprehensive atlas of citrullination sites within the HL60 leukemia cell line following differentiation into neutrophil-like cells. We identified 14,056 citrullination sites within 4,008 proteins and quantified their regulation upon inhibition of the citrullinating enzyme PADI4. With this resource, we provide quantitative and site-specific information on thousands of PADI4 substrates, including signature histone marks and transcriptional regulators. Additionally, using peptide microarrays, we demonstrate the potential clinical relevance of certain identified sites, through distinct reactivities of antibodies contained in synovial fluid from anti-CCP-positive and anti-CCP-negative people with rheumatoid arthritis. Collectively, we describe the human citrullinome at a systems-wide level, provide a resource for understanding citrullination at the mechanistic level and link the identified targeted sites to rheumatoid arthritis.
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Affiliation(s)
- Alexandra S Rebak
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ivo A Hendriks
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jonas D Elsborg
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sara C Buch-Larsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claus H Nielsen
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Lene Terslev
- Copenhagen Center for Arthritis Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Rebecca Kirsch
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dres Damgaard
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Nadezhda T Doncheva
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Caroline Lennartsson
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martin Rykær
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars J Jensen
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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29
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Bayne EF, Buck KM, Towler AG, Zhu Y, Pergande MR, Zhou T, Price S, Rossler KJ, Morales-Tirado V, Lloyd S, Wang F, He Y, Tian Y, Ge Y. High-Throughput Extracellular Matrix Proteomics of Human Lungs Enabled by Photocleavable Surfactant and diaPASEF. J Proteome Res 2024. [PMID: 38315831 DOI: 10.1021/acs.jproteome.3c00532] [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] [Indexed: 02/07/2024]
Abstract
The extracellular matrix (ECM) is a complex assembly of proteins that provide interstitial scaffolding and elastic recoil for human lungs. The pulmonary extracellular matrix is increasingly recognized as an independent bioactive entity, by creating biochemical and mechanical signals that influence disease pathogenesis, making it an attractive therapeutic target. However, the pulmonary ECM proteome ("matrisome") remains challenging to analyze by mass spectrometry due to its inherent biophysical properties and relatively low abundance. Here, we introduce a strategy designed for rapid and efficient characterization of the human pulmonary ECM using the photocleavable surfactant Azo. We coupled this approach with trapped ion mobility MS with diaPASEF to maximize the depth of matrisome coverage. Using this strategy, we identify nearly 400 unique matrisome proteins with excellent reproducibility that are known to be important in lung biology, including key core matrisome proteins.
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Affiliation(s)
- Elizabeth F Bayne
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kevin M Buck
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Anna G Towler
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Yanlong Zhu
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Melissa R Pergande
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Tianhua Zhou
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Scott Price
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Kalina J Rossler
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Vanessa Morales-Tirado
- Discovery Immunology, Pharmacology and Pathology, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Sarah Lloyd
- Discovery Immunology, Pharmacology and Pathology, AbbVie, Inc., North Chicago, Illinois 60064, United States
| | - Fei Wang
- Quantitative Translational & ADME Science, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Yupeng He
- Discovery Immunology, Pharmacology and Pathology, AbbVie, Inc., North Chicago, Illinois 60064, United States
| | - Yu Tian
- Quantitative Translational & ADME Science, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
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30
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Yousef A, Yousef M, Zeineddine MA, More A, Fanaeian M, Chowdhury S, Knafl M, Edelkamp P, Ito I, Gu Y, Pattalachinti V, Naini ZA, Zeineddine FA, Peterson J, Alfaro K, Foo WC, Jin J, Bhutiani N, Higbie V, Scally CP, Kee B, Kopetz S, Goldstein D, Strach M, Williamson A, Aziz O, Barriuso J, Uppal A, White MG, Helmink B, Fournier KF, Raghav KP, Taggart MW, Overman MJ, Shen JP. Serum Tumor Markers and Outcomes in Patients With Appendiceal Adenocarcinoma. JAMA Netw Open 2024; 7:e240260. [PMID: 38416491 PMCID: PMC10902735 DOI: 10.1001/jamanetworkopen.2024.0260] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/02/2024] [Indexed: 02/29/2024] Open
Abstract
Importance Serum tumor markers carcinoembryonic antigen (CEA), carbohydrate antigen 19-9 (CA19-9), and cancer antigen 125 (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 To assess the association of serum tumor markers (CEA, CA19-9, and CA125) with clinical outcomes and pathologic and molecular features in patients with appendiceal adenocarcinoma. Design, Setting, and Participants This is a retrospective cohort study at a single tertiary care comprehensive cancer center. The median (IQR) follow-up time was 52 (21-101) months. Software was used to query the MD Anderson internal patient database to identify patients with a diagnosis of appendiceal adenocarcinoma and at least 1 tumor marker measured at MD Anderson between March 2016 and May 2023. Data were analyzed from January to December 2023. Main Outcomes and Measures Association of serum tumor markers with survival in patients with appendiceal adenocarcinoma. Cox proportional hazards regression analyses were also performed to assess associations between clinical factors (serum tumor marker levels, demographics, and patient and disease characteristics) and patient outcomes (overall survival). Results A total of 1338 patients with appendiceal adenocarcinoma were included, with a median (range) age at diagnosis of 56.5 (22.3-89.6) years. The majority of the patients had metastatic disease (1080 patients [80.7%]). CEA was elevated in 742 of the patients tested (56%), while CA19-9 and CA125 were elevated in 381 patients (34%) and 312 patients (27%), respectively. Individually, elevation of CEA, CA19-9, or CA125 were associated with worse 5-year survival; elevated vs normal was 81% vs 95% for CEA (hazard ratio [HR], 4.0; 95% CI, 2.9-5.6), 84% vs 92% for CA19-9 (HR, 2.2; 95% CI, 1.4-3.4), and 69% vs 93% for CA125 (HR, 4.6; 95% CI, 2.7-7.8) (P < .001 for all). Quantitative evaluation of tumor markers was associated with outcomes. Patients with highly elevated (top 10th percentile) CEA, CA19-9, or CA125 had markedly worse survival, with 5-year survival rates of 59% for CEA (HR, 9.8; 95% CI, 5.3-18.0), 64% for CA19-9 (HR, 6.0; 95% CI, 3.0-11.7), and 57% for CA125 (HR, 7.6; 95% CI, 3.5-16.5) (P < .001 for all). 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 for CEA, 3.4; 95% CI, 2.5-4.8; P < .001; HR for CA19-9, 1.8; 95% CI, 1.2-2.7; P = .002; and HR for CA125, 3.9; 95% CI, 2.4-6.4; P < .001). Interestingly, tumor grade was not associated with CEA or CA19-9 level, while CA-125 was slightly higher in high-grade tumors relative to low-grade tumors (mean value, 18.3 vs 15.0; difference, 3.3; 95% CI, 0.9-3.7; P < .001). Multivariable analysis identified an incremental increase in the risk of death with an increase in the number of elevated tumor markers, with an 11-fold increased risk of death in patients with all 3 tumor markers elevated relative to those with none elevated. Somatic mutations in KRAS and GNAS were associated with significantly higher levels of CEA and CA19-9. Conclusions and Relevance In this retrospective study of serum tumor markers in patients with appendiceal adenocarcinoma, CEA, CA19-9, and CA125 were associated with overall survival in appendiceal adenocarcinoma. Given their value, all 3 biomarkers should be included in the initial workup of patients with a diagnosis of appendiceal adenocarcinoma.
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Affiliation(s)
- Abdelrahman Yousef
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Mahmoud Yousef
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Mohammad A. Zeineddine
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Aditya More
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Mohammad Fanaeian
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Saikat Chowdhury
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Mark Knafl
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston
| | - Paul Edelkamp
- Department of Data Engineering and Analytics, University of Texas MD Anderson Cancer Center, Houston
| | - Ichiaki Ito
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Yue Gu
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Vinay Pattalachinti
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Zahra Alavi Naini
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Fadl A. Zeineddine
- Department of Internal Medicine, Houston Methodist Hospital, Houston, Texas
| | - Jennifer Peterson
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Kristin Alfaro
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Wai Chin Foo
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston
| | - Jeff Jin
- Department of Enterprise Development and Integration, University of Texas MD Anderson Cancer Center, Houston
| | - Neal Bhutiani
- Department of Colon and Rectal Surgery, University of Texas MD Anderson Cancer Center, Houston
| | - Victoria Higbie
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Christopher P. Scally
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Bryan Kee
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | | | - Madeleine Strach
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, United Kingdom
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, School of Medical Sciences, University of Manchester, Manchester, United Kingdom
- Faculty of Medicine and Health, The University of Sydney, Darlington, Victoria, Australia
| | - Andrew Williamson
- Department of Medical Oncology, The Christie National Health Service Foundation Trust, Manchester, United Kingdom
| | - Omer Aziz
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, United Kingdom
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, School of Medical Sciences, University of Manchester, Manchester, United Kingdom
| | - Jorge Barriuso
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, United Kingdom
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, School of Medical Sciences, University of Manchester, Manchester, United Kingdom
| | - Abhineet Uppal
- Department of Colon and Rectal Surgery, University of Texas MD Anderson Cancer Center, Houston
| | - Michael G. White
- Department of Colon and Rectal Surgery, University of Texas MD Anderson Cancer Center, Houston
| | - Beth Helmink
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Keith F. Fournier
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Kanwal P. Raghav
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Melissa W. Taggart
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston
| | - Michael J. Overman
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - John Paul Shen
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
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Chen S, Phillips CM. HRDE-2 drives small RNA specificity for the nuclear Argonaute protein HRDE-1. Nat Commun 2024; 15:957. [PMID: 38302462 PMCID: PMC10834429 DOI: 10.1038/s41467-024-45245-8] [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: 08/23/2023] [Accepted: 01/18/2024] [Indexed: 02/03/2024] Open
Abstract
RNA interference (RNAi) is a conserved gene silencing process that exists in diverse organisms to protect genome integrity and regulate gene expression. In C. elegans, the majority of RNAi pathway proteins localize to perinuclear, phase-separated germ granules, which are comprised of sub-domains referred to as P granules, Mutator foci, Z granules, and SIMR foci. However, the protein components and function of the newly discovered SIMR foci are unknown. Here we demonstrate that HRDE-2 localizes to SIMR foci and interacts with the germline nuclear Argonaute HRDE-1 in its small RNA unbound state. In the absence of HRDE-2, HRDE-1 exclusively loads CSR-class 22G-RNAs rather than WAGO-class 22G-RNAs, resulting in inappropriate H3K9me3 deposition on CSR-target genes. Thus, our study demonstrates that the recruitment of unloaded HRDE-1 to germ granules, mediated by HRDE-2, is critical to ensure that the correct small RNAs are used to guide nuclear RNA silencing in the C. elegans germline.
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Affiliation(s)
- Shihui Chen
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Carolyn M Phillips
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
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Ciceri G, Baggiolini A, Cho HS, Kshirsagar M, Benito-Kwiecinski S, Walsh RM, Aromolaran KA, Gonzalez-Hernandez AJ, Munguba H, Koo SY, Xu N, Sevilla KJ, Goldstein PA, Levitz J, Leslie CS, Koche RP, Studer L. An epigenetic barrier sets the timing of human neuronal maturation. Nature 2024; 626:881-890. [PMID: 38297124 PMCID: PMC10881400 DOI: 10.1038/s41586-023-06984-8] [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: 05/17/2022] [Accepted: 12/15/2023] [Indexed: 02/02/2024]
Abstract
The pace of human brain development is highly protracted compared with most other species1-7. The maturation of cortical neurons is particularly slow, taking months to years to develop adult functions3-5. Remarkably, such protracted timing is retained in cortical neurons derived from human pluripotent stem cells (hPSCs) during in vitro differentiation or upon transplantation into the mouse brain4,8,9. Those findings suggest the presence of a cell-intrinsic clock setting the pace of neuronal maturation, although the molecular nature of this clock remains unknown. Here we identify an epigenetic developmental programme that sets the timing of human neuronal maturation. First, we developed a hPSC-based approach to synchronize the birth of cortical neurons in vitro which enabled us to define an atlas of morphological, functional and molecular maturation. We observed a slow unfolding of maturation programmes, limited by the retention of specific epigenetic factors. Loss of function of several of those factors in cortical neurons enables precocious maturation. Transient inhibition of EZH2, EHMT1 and EHMT2 or DOT1L, at progenitor stage primes newly born neurons to rapidly acquire mature properties upon differentiation. Thus our findings reveal that the rate at which human neurons mature is set well before neurogenesis through the establishment of an epigenetic barrier in progenitor cells. Mechanistically, this barrier holds transcriptional maturation programmes in a poised state that is gradually released to ensure the prolonged timeline of human cortical neuron maturation.
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Affiliation(s)
- Gabriele Ciceri
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Arianna Baggiolini
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Institute of Oncology Research (IOR), Bellinzona Institutes of Science (BIOS+), Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
| | - Hyein S Cho
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Meghana Kshirsagar
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Microsoft AI for Good Research, Redmond, WA, USA
| | - Silvia Benito-Kwiecinski
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryan M Walsh
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Hermany Munguba
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - So Yeon Koo
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Neuroscience PhD Program, New York, NY, USA
| | - Nan Xu
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kaylin J Sevilla
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Peter A Goldstein
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - Christina S Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lorenz Studer
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Chauhan PS, Benninghoff AD, Favor OK, Wagner JG, Lewandowski RP, Rajasinghe LD, Li QZ, Harkema JR, Pestka JJ. Dietary docosahexaenoic acid supplementation inhibits acute pulmonary transcriptional and autoantibody responses to a single crystalline silica exposure in lupus-prone mice. Front Immunol 2024; 15:1275265. [PMID: 38361937 PMCID: PMC10867581 DOI: 10.3389/fimmu.2024.1275265] [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: 08/09/2023] [Accepted: 01/08/2024] [Indexed: 02/17/2024] Open
Abstract
Introduction Workplace exposure to respirable crystalline silica (cSiO2) has been epidemiologically linked to lupus. Consistent with this, repeated subchronic intranasal cSiO2 instillation in lupus-prone NZBWF1 mice induces inflammation-/autoimmune-related gene expression, ectopic lymphoid tissue (ELT), autoantibody (AAb) production in the lung within 5 to 13 wk followed systemic AAb increases and accelerated onset and progression of glomerulonephritis within 13 to 17 wk. Interestingly, dietary docosahexaenoic acid (DHA) supplementation suppresses these pathologic effects, but the underlying molecular mechanisms remain unclear. Methods This study aimed to test the hypothesis that dietary DHA supplementation impacts acute transcriptional and autoantibody responses in the lungs of female NZBWF1 mice 1 and 4 wk after a single high-dose cSiO2 challenge. Groups of mice were initially fed a control (Con) diet or a DHA-containing diet (10 g/kg). Cohorts of Con- and DHA-fed were subjected to a single intranasal instillation of 2.5 mg cSiO2 in a saline vehicle (Veh), while a Con-fed cohort was instilled with Veh only. At 1 and 4 wk post-instillation (PI), we compared cSiO2's effects on innate-/autoimmune-related gene expression and autoantibody (AAb) in lavage fluid/lungs of Con- and DHA-fed mice and related these findings to inflammatory cell profiles, histopathology, cell death, and cytokine/chemokine production. Results DHA partially alleviated cSiO2-induced alterations in total immune cell and lymphocyte counts in lung lavage fluid. cSiO2-triggered dead cell accumulation and levels of inflammation-associated cytokines and IFN-stimulated chemokines were more pronounced in Con-fed mice than DHA-fed mice. Targeted multiplex transcriptome analysis revealed substantial upregulation of genes associated with autoimmune pathways in Con-fed mice in response to cSiO2 that were suppressed in DHA-fed mice. Pathway analysis indicated that DHA inhibited cSiO2 induction of proinflammatory and IFN-regulated gene networks, affecting key upstream regulators (e.g., TNFα, IL-1β, IFNAR, and IFNγ). Finally, cSiO2-triggered AAb responses were suppressed in DHA-fed mice. Discussion Taken together, DHA mitigated cSiO2-induced upregulation of pathways associated with proinflammatory and IFN-regulated gene responses within 1 wk and reduced AAb responses by 4 wk. These findings suggest that the acute short-term model employed here holds substantial promise for efficient elucidation of the molecular mechanisms through which omega-3 PUFAs exert protective effects against cSiO2-induced autoimmunity.
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Affiliation(s)
- Preeti S. Chauhan
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI, United States
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI, United States
| | - Abby D. Benninghoff
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, United States
| | - Olivia K. Favor
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI, United States
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, MI, United States
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, United States
| | - James G. Wagner
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI, United States
- Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, MI, United States
| | - Ryan P. Lewandowski
- Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, MI, United States
| | - Lichchavi D. Rajasinghe
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI, United States
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI, United States
| | | | - Jack R. Harkema
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, United States
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, United States
- Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, MI, United States
| | - James J. Pestka
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI, United States
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, United States
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, MI, United States
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34
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Löscher W. On hidden factors and design-associated errors that may lead to data misinterpretation: An example from preclinical research on the potential seasonality of neonatal seizures. Epilepsia 2024; 65:287-292. [PMID: 38037258 DOI: 10.1111/epi.17840] [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: 10/26/2023] [Revised: 11/20/2023] [Accepted: 11/28/2023] [Indexed: 12/02/2023]
Abstract
Unintentional misinterpretation of research in published biomedical reports that is not based on statistical flaws is often underrecognized, despite its possible impact on science, clinical practice, and public health. Important causes of such misinterpretation of scientific data, resulting in either false positive or false negative conclusions, include design-associated errors and hidden (or latent) variables that are not easily recognized during data analysis. Furthermore, cognitive biases, such as the inclination to seek patterns in data whether they exist or not, may lead to misinterpretation of data. Here, we give an example of these problems from hypothesis-driven research on the potential seasonality of neonatal seizures in a rat model of birth asphyxia. This commentary aims to raise awareness among the general scientific audience about the issues related to the presence of unintentional misinterpretation in published reports.
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Affiliation(s)
- Wolfgang Löscher
- Translational Neuropharmacology Lab, NIFE, Department of Experimental Otology of the ENT Clinics, Hannover Medical School, Hannover, Germany
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35
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Amini AE, Salari K. Incorporating Genetic Risk Into Prostate Cancer Care: Implications for Early Detection and Precision Oncology. JCO Precis Oncol 2024; 8:e2300560. [PMID: 38412389 DOI: 10.1200/po.23.00560] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/12/2023] [Accepted: 01/08/2024] [Indexed: 02/29/2024] Open
Abstract
The availability and cost of germline and somatic genetic testing have dramatically improved over the past two decades, enabling precision medicine approaches in oncology, with significant implications for prostate cancer (PCa) care. Roughly 12% of individuals with advanced disease are carriers of rare pathogenic germline variants that predispose to particularly aggressive and earlier-onset disease. Several of these variants are already established as clinically actionable by modern precision oncology therapeutics, while others may come to aid the selection of active surveillance, definitive local therapies, and systemic therapies. Concurrently, the number of common variants (ie, incorporated into polygenic risk scores) associated with PCa risk has continued to grow, but with several important considerations both at the intersection of race and ancestry and for early detection of aggressive disease. Family history has historically been used as a proxy for this inherited genetic risk of PCa, but recently emerging evidence examining this relation has shifted our understanding of how best to leverage this tool in PCa care. This review seeks to clarify and contextualize the existing and emerging precision oncology paradigms that use inherited genetic risk in PCa care, for both early detection and localized disease management.
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Affiliation(s)
- Andrew E Amini
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Keyan Salari
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
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36
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Hofford RS, Meckel KR, Wiser EJ, Wang W, Sens JP, Kim M, Godino A, Lam TT, Kiraly DD. Microbiome Depletion Increases Fentanyl Self-Administration and Alters the Striatal Proteome Through Short-Chain Fatty Acids. eNeuro 2024; 11:11/2/ENEURO.0388-23.2023. [PMID: 38164564 PMCID: PMC10875718 DOI: 10.1523/eneuro.0388-23.2023] [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: 10/05/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 01/03/2024] Open
Abstract
Opioid use disorder (OUD) is a public health crisis currently being exacerbated by increased rates of use and overdose of synthetic opioids, primarily fentanyl. Therefore, the identification of novel biomarkers and treatment strategies to reduce problematic fentanyl use and relapse to fentanyl taking is critical. In recent years, there has been a growing body of work demonstrating that the gut microbiome can serve as a potent modulator of the behavioral and transcriptional responses to both stimulants and opioids. Here, we advance this work to define how manipulations of the microbiome drive fentanyl intake and fentanyl-seeking in a translationally relevant drug self-administration model. Depletion of the microbiome of male rats with broad spectrum antibiotics leads to increased drug administration on increased fixed ratio, progressive ratio, and drug seeking after abstinence. Utilizing 16S sequencing of microbiome contents from these animals, specific populations of bacteria from the gut microbiome correlate closely with levels of drug taking. Additionally, global proteomic analysis of the nucleus accumbens following microbiome manipulation and fentanyl administration to define how microbiome status alters the functional proteomic landscape in this key limbic substructure. These data demonstrate that an altered microbiome leads to marked changes in the synaptic proteome in response to repeated fentanyl treatment. Finally, behavioral effects of microbiome depletion are reversible by upplementation of the microbiome derived short-chain fatty acid metabolites. Taken together, these findings establish clear relevance for gut-brain signaling in models of OUD and lay foundations for further translational work in this space.
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Affiliation(s)
- Rebecca S Hofford
- Department of Translational Neuroscience, Wake Forest School of Medicine, Winston-Salem, NC 27101
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, NewYork, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, NewYork, NY 10029
| | - Katherine R Meckel
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, NewYork, NY 10029
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, NewYork, NY 10029
| | - Elizabeth J Wiser
- Department of Translational Neuroscience, Wake Forest School of Medicine, Winston-Salem, NC 27101
| | - Weiwei Wang
- Keck MS & Proteomics Resource, Yale University School of Medicine, New Haven, CT 06520
| | - Jonathon P Sens
- Department of Translational Neuroscience, Wake Forest School of Medicine, Winston-Salem, NC 27101
| | - Michelle Kim
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, NewYork, NY 10029
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, NewYork, NY 10029
| | - Arthur Godino
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, NewYork, NY 10029
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, NewYork, NY 10029
| | - TuKiet T Lam
- Keck MS & Proteomics Resource, Yale University School of Medicine, New Haven, CT 06520
- Yale/NIDA Neuroproteomics Center, Yale University School of Medicine, New Haven, CT 06520
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520
| | - Drew D Kiraly
- Department of Translational Neuroscience, Wake Forest School of Medicine, Winston-Salem, NC 27101
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, NewYork, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, NewYork, NY 10029
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, NewYork, NY 10029
- Department of Psychiatry, Atrium Health Wake Forest Baptist, Winston-Salem, NC 27101
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Lejeune S, Kaushik A, Parsons ES, Chinthrajah S, Snyder M, Desai M, Manohar M, Prunicki M, Contrepois K, Gosset P, Deschildre A, Nadeau K. Untargeted metabolomic profiling in children identifies novel pathways in asthma and atopy. J Allergy Clin Immunol 2024; 153:418-434. [PMID: 38344970 DOI: 10.1016/j.jaci.2023.09.040] [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: 05/06/2023] [Revised: 09/19/2023] [Accepted: 09/25/2023] [Indexed: 02/15/2024]
Abstract
BACKGROUND Asthma and other atopic disorders can present with varying clinical phenotypes marked by differential metabolomic manifestations and enriched biological pathways. OBJECTIVE We sought to identify these unique metabolomic profiles in atopy and asthma. METHODS We analyzed baseline nonfasted plasma samples from a large multisite pediatric population of 470 children aged <13 years from 3 different sites in the United States and France. Atopy positivity (At+) was defined as skin prick test result of ≥3 mm and/or specific IgE ≥ 0.35 IU/mL and/or total IgE ≥ 173 IU/mL. Asthma positivity (As+) was based on physician diagnosis. The cohort was divided into 4 groups of varying combinations of asthma and atopy, and 6 pairwise analyses were conducted to best assess the differential metabolomic profiles between groups. RESULTS Two hundred ten children were classified as At-As-, 42 as At+As-, 74 as At-As+, and 144 as At+As+. Untargeted global metabolomic profiles were generated through ultra-high-performance liquid chromatography-tandem mass spectroscopy. We applied 2 independent machine learning classifiers and short-listed 362 metabolites as discriminant features. Our analysis showed the most diverse metabolomic profile in the At+As+/At-As- comparison, followed by the At-As+/At-As- comparison, indicating that asthma is the most discriminant condition associated with metabolomic changes. At+As+ metabolomic profiles were characterized by higher levels of bile acids, sphingolipids, and phospholipids, and lower levels of polyamine, tryptophan, and gamma-glutamyl amino acids. CONCLUSION The At+As+ phenotype displays a distinct metabolomic profile suggesting underlying mechanisms such as modulation of host-pathogen and gut microbiota interactions, epigenetic changes in T-cell differentiation, and lower antioxidant properties of the airway epithelium.
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Affiliation(s)
- Stéphanie Lejeune
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; University of Lille, Pediatric Pulmonology and Allergy Department, Hôpital Jeanne de Flandre, CHU Lille, Lille, France; University of Lille, INSERM Unit 1019, CNRS UMR 9017, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France.
| | - Abhinav Kaushik
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Department of Environmental Health, T. H. Chan School of Public Health, Harvard University, Boston, Mass
| | - Ella S Parsons
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif
| | - Sharon Chinthrajah
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, Calif
| | - Manisha Desai
- Quantitative Science Unit, Department of Medicine, Stanford University School of Medicine, Stanford, Calif
| | - Monali Manohar
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif
| | - Mary Prunicki
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Department of Environmental Health, T. H. Chan School of Public Health, Harvard University, Boston, Mass
| | - Kévin Contrepois
- Department of Genetics, Stanford University School of Medicine, Stanford, Calif
| | - Philippe Gosset
- University of Lille, INSERM Unit 1019, CNRS UMR 9017, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | - Antoine Deschildre
- University of Lille, Pediatric Pulmonology and Allergy Department, Hôpital Jeanne de Flandre, CHU Lille, Lille, France; University of Lille, INSERM Unit 1019, CNRS UMR 9017, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | - Kari Nadeau
- Department of Environmental Health, T. H. Chan School of Public Health, Harvard University, Boston, Mass
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Zeng Z, Wijnands LM, Boeren S, Smid EJ, Notebaart RA, Abee T. Impact of vitamin B 12 on rhamnose metabolism, stress defense and in-vitro virulence of Listeria monocytogenes. Int J Food Microbiol 2024; 410:110486. [PMID: 37992553 DOI: 10.1016/j.ijfoodmicro.2023.110486] [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: 02/03/2023] [Revised: 07/05/2023] [Accepted: 11/11/2023] [Indexed: 11/24/2023]
Abstract
Listeria monocytogenes is a facultative anaerobe which can cause a severe food-borne infection known as listeriosis. L. monocytogenes is capable of utilizing various nutrient sources including rhamnose, a naturally occurring deoxy sugar abundant in foods. L. monocytogenes can degrade rhamnose into lactate, acetate and 1,2-propanediol. Our previous study showed that addition of vitamin B12 stimulated anaerobic growth of L. monocytogenes on rhamnose due to the activation of bacterial microcompartments for 1,2-propanediol utilization (pdu BMC) with concomitant production of propionate and propanol. Notably, anaerobic 1,2-propanediol metabolism has been linked to virulence of enteric pathogens including Salmonella spp. and L. monocytogenes. In this study we investigated the impact of B12 and BMC activation on i) aerobic and anerobic growth of L. monocytogenes on rhamnose and ii) the level of virulence. We observed B12-induced pdu BMC activation and growth stimulation only in anaerobically grown cells. Comparative Caco-2 virulence assays showed that these pdu BMC-induced cells have significantly higher translocation efficiency compared to non-induced cells (anaerobic growth without B12; aerobic growth with or without B12), while adhesion and invasion capacity is similar for all cells. Comparative proteome analysis showed specific and overlapping responses linked to metabolic shifts, activation of stress defense proteins and virulence factors, with RNA polymerase sigma factor SigL, teichoic acid export ATP-binding protein TagH, DNA repair and protection proteins, RadA and DPS, and glutathione synthase GshAB, previously linked to activation of virulence response in L. monocytogenes, uniquely upregulated in anaerobically rhamnose grown pdu-induced cells. Our results shed light on possible effects of B12 on L. monocytogenes competitive fitness and virulence activation when utilizing rhamnose in anaerobic conditions encountered during transmission and the human intestine.
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Affiliation(s)
- Zhe Zeng
- Food Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Lucas M Wijnands
- National Institute of Public Health and the Environment, Bilthoven, the Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University and Research, Wageningen, the Netherlands
| | - Eddy J Smid
- Food Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Richard A Notebaart
- Food Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Tjakko Abee
- Food Microbiology, Wageningen University and Research, Wageningen, the Netherlands.
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Wu X, Ko ICH, Hong CYL, Yee SCH, Teoh JYC, Chan SYS, Tam HM, Chan CK, Ng CF, Chiu PKF. A prospective cohort of men with localized prostate cancer on active surveillance protocol in Hong Kong, China: what did we learn? Asian J Androl 2024:00129336-990000000-00158. [PMID: 38284779 DOI: 10.4103/aja202373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 11/21/2023] [Indexed: 01/30/2024] Open
Abstract
This study aimed to report the outcomes of active surveillance (AS) in the management of low-risk prostate cancer (PCa). It recruited 87 men who were prospectively followed up according to the Prostate Cancer Research International Active Surveillance (PRIAS) protocol with local adaptation at SH Ho Urology Centre, Prince of Wales Hospital, Hong Kong, China. We investigated the predictors of disease progression and found that baseline prostate-specific antigen density (PSAD) and the presence of the highest Prostate Imaging-Reporting and Data System (PI-RADS) score 5 lesion on magnetic resonance imaging (MRI) are significantly correlated with disease progression. Moreover, men with PSAD >0.2 ng ml-2 or PI-RADS 4 or 5 lesions had significantly worse upgrading-free survival compared to those with PSAD ≤0.2 ng ml-2 and PI-RADS 2 or 3 lesions. The study concludes that AS is a safe and effective management strategy for selected patients to defer radical treatment and that most disease progression can be detected after the first repeated biopsy. The combination of PSAD >0.2 ng ml-2 and PI-RADS 4 or 5 lesions may serve as a useful predictor of early disease progression and provide a guide to optimize follow-up protocols for men in different risk groups.
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Affiliation(s)
- Xiaobo Wu
- SH Ho Urology Centre, Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
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Thi HV, Hoang TN, Le NQK, Chu DT. Application of data science and bioinformatics in RNA therapeutics. Prog Mol Biol Transl Sci 2024; 203:83-97. [PMID: 38360007 DOI: 10.1016/bs.pmbts.2023.12.019] [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] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Nowadays, information technology (IT) has been holding a significant role in daily life worldwide. The trajectory of data science and bioinformatics promises pioneering personalized therapies, reshaping medical landscapes and patient care. For RNA therapy to reach more patients, a comprehensive understanding of the application of data science and bioinformatics to this therapy is essential. Thus, this chapter has summarized the application of data science and bioinformatics in RNA therapeutics. Data science applications in RNA therapy, such as data integration and analytics, machine learning, and drug development, have been discussed. In addition, aspects of bioinformatics such as RNA design and evaluation, drug delivery system simulation, and databases for personalized medicine have also been covered in this chapter. These insights have shed light on existing evidence and opened potential future directions. From there, scientists can elevate RNA-based therapeutics into an era of tailored treatments and revolutionary healthcare.
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Affiliation(s)
- Hue Vu Thi
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam
| | - Thanh-Nhat Hoang
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Nguyen Quoc Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; AIBioMed Research Group, Taipei Medical University, Taipei, Taiwan
| | - Dinh-Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam.
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Yayan J, Franke KJ, Berger M, Windisch W, Rasche K. Adhesion, metastasis, and inhibition of cancer cells: a comprehensive review. Mol Biol Rep 2024; 51:165. [PMID: 38252369 PMCID: PMC10803487 DOI: 10.1007/s11033-023-08920-5] [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: 08/25/2023] [Accepted: 10/23/2023] [Indexed: 01/23/2024]
Abstract
This comprehensive review delves into cancer's complexity, focusing on adhesion, metastasis, and inhibition. It explores the pivotal role of these factors in disease progression and therapeutic strategies. This review covers cancer cell migration, invasion, and colonization of distant organs, emphasizing the significance of cell adhesion and the intricate metastasis process. Inhibition approaches targeting adhesion molecules, such as integrins and cadherins, are discussed. Overall, this review contributes significantly to advancing cancer research and developing targeted therapies, holding promise for improving patient outcomes worldwide. Exploring different inhibition strategies revealed promising therapeutic targets to alleviate adhesion and metastasis of cancer cells. The effectiveness of integrin-blocking antibodies, small molecule inhibitors targeting Focal adhesion kinase (FAK) and the Transforming Growth Factor β (TGF-β) pathway, and combination therapies underscores their potential to disrupt focal adhesions and control epithelial-mesenchymal transition processes. The identification of as FAK, Src, β-catenin and SMAD4 offers valuable starting points for further research and the development of targeted therapies. The complex interrelationships between adhesion and metastatic signaling networks will be relevant to the development of new treatment approaches.
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Affiliation(s)
- Josef Yayan
- Department of Internal Medicine, Division of Pulmonary, Allergy, and Sleep Medicine, Witten/Herdecke University, HELIOS Clinic Wuppertal, Heusnerstr. 40, 42283, Wuppertal, Germany.
| | - Karl-Josef Franke
- Department of Internal Medicine, Pulmonary Division, Internal Intensive Care Medicine, Infectiology, and Sleep Medicine, Märkische Clinics Health Holding Ltd, Clinic Lüdenscheid, Witten/Herdecke University, Lüdenscheid, Germany
| | - Melanie Berger
- Department of Pneumology, Cologne Merheim Hospital, Witten/Herdecke University, Cologne, Germany
| | - Wolfram Windisch
- Department of Pneumology, Cologne Merheim Hospital, Witten/Herdecke University, Cologne, Germany
| | - Kurt Rasche
- Department of Internal Medicine, Division of Pulmonary, Allergy, and Sleep Medicine, Witten/Herdecke University, HELIOS Clinic Wuppertal, Heusnerstr. 40, 42283, Wuppertal, Germany
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Xu J, Bock CH, Janisse J, Woo J, Cher ML, Ginsburg K, Yacoub R, Goodman M. Determinants of active surveillance uptake in a diverse population-based cohort of men with low-risk prostate cancer: The Treatment Options in Prostate Cancer Study (TOPCS). Cancer 2024. [PMID: 38247317 DOI: 10.1002/cncr.35190] [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: 09/17/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND Active surveillance (AS) is the preferred strategy for low-risk prostate cancer (LRPC); however, limited data on determinants of AS adoption exist, particularly among Black men. METHODS Black and White newly diagnosed (from January 2014 through June 2017) patients with LRPC ≤75 years of age were identified through metro-Detroit and Georgia population-based cancer registries and completed a survey evaluating factors influencing AS uptake. RESULTS Among 1688 study participants, 57% chose AS (51% of Black participants, 61% of White) over definitive treatment. In the unadjusted analysis, patient factors associated with initial AS uptake included older age, White race, and higher education. However, after adjusting for covariates, none of these factors was significant predictors of AS uptake. The strongest determinant of AS uptake was the AS recommendation by a urologist (adjusted prevalence ratio, 6.59, 95% CI, 4.84-8.97). Other factors associated with the decision to undergo AS included a shared patient-physician treatment decision, greater prostate cancer knowledge, and residence in metro-Detroit compared with Georgia. Conversely, men whose decision was strongly influenced by the desire to achieve "cure" or "live longer" with treatment and those who perceived their LRPC diagnosis as more serious were less likely to choose AS. CONCLUSIONS In this contemporary sample, the majority of patients with newly diagnosed LRPC chose AS. Although the input from their urologists was highly influential, several patient decisional and psychological factors were independently associated with AS uptake. These data shed new light on potentially modifiable factors that can help further increase AS uptake among patients with LRPC.
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Affiliation(s)
- Jinping Xu
- Department of Family Medicine and Public Health Sciences, School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Cathryn H Bock
- Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - James Janisse
- Department of Family Medicine and Public Health Sciences, School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Justin Woo
- Department of Family Medicine and Public Health Sciences, School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Michael L Cher
- Department of Urology, School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Kevin Ginsburg
- Department of Urology, School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Rami Yacoub
- Department of Epidemiology, School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Michael Goodman
- Department of Epidemiology, School of Public Health, Emory University, Atlanta, Georgia, USA
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Kumar R, Fu J, Ortiz BL, Cao X, Shedden K, Choi SW. Dyadic and Individual Variation in 24-Hour Heart Rates of Cancer Patients and Their Caregivers. Bioengineering (Basel) 2024; 11:95. [PMID: 38247972 PMCID: PMC10813060 DOI: 10.3390/bioengineering11010095] [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: 12/20/2023] [Revised: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 01/23/2024] Open
Abstract
BACKGROUND Twenty-four-hour heart rate (HR) integrates multiple physiological and psychological systems related to health and well-being, and can be continuously monitored in high temporal resolution over several days with wearable HR monitors. Using HR data from two independent datasets of cancer patients and their caregivers, we aimed to identify dyadic and individual patterns of 24 h HR variation and assess their relationship to demographic, environmental, psychological, and clinical variables of interest. METHODS a novel regularized approach to high-dimensional canonical correlation analysis (CCA) was used to identify factors reflecting dyadic and individual variation in the 24 h (circadian) HR trajectories of 430 people in 215 dyads, then regression analysis was used to relate these patterns to explanatory variables. RESULTS Four distinct factors of dyadic covariation in circadian HR were found, contributing approximately 7% to overall circadian HR variation. These factors, along with non-dyadic factors reflecting individual variation exhibited diverse and statistically robust patterns of association with explanatory variables of interest. CONCLUSIONS Both dyadic and individual anomalies are present in the 24 h HR patterns of cancer patients and their caregivers. These patterns are largely synchronous, and their presence robustly associates with multiple explanatory variables. One notable finding is that higher mood scores in cancer patients correspond to an earlier HR nadir in the morning and higher HR during the afternoon.
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Affiliation(s)
- Rajnish Kumar
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (R.K.); (B.L.O.); (X.C.)
| | - Junhan Fu
- Department of Statistics, College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA; (J.F.); (K.S.)
| | - Bengie L. Ortiz
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (R.K.); (B.L.O.); (X.C.)
| | - Xiao Cao
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (R.K.); (B.L.O.); (X.C.)
| | - Kerby Shedden
- Department of Statistics, College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA; (J.F.); (K.S.)
| | - Sung Won Choi
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (R.K.); (B.L.O.); (X.C.)
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Xu W, Billon C, Li H, Wilderman A, Qi L, Graves A, Rideb JRDC, Zhao Y, Hayes M, Yu K, Losby M, Hampton CS, Adeyemi CM, Hong SJ, Nasiotis E, Fu C, Oh TG, Fan W, Downes M, Welch RD, Evans RM, Milosavljevic A, Walker JK, Jensen BC, Pei L, Burris T, Zhang L. Novel Pan-ERR Agonists Ameliorate Heart Failure Through Enhancing Cardiac Fatty Acid Metabolism and Mitochondrial Function. Circulation 2024; 149:227-250. [PMID: 37961903 PMCID: PMC10842599 DOI: 10.1161/circulationaha.123.066542] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND Cardiac metabolic dysfunction is a hallmark of heart failure (HF). Estrogen-related receptors ERRα and ERRγ are essential regulators of cardiac metabolism. Therefore, activation of ERR could be a potential therapeutic intervention for HF. However, in vivo studies demonstrating the potential usefulness of ERR agonist for HF treatment are lacking, because compounds with pharmacokinetics appropriate for in vivo use have not been available. METHODS Using a structure-based design approach, we designed and synthesized 2 structurally distinct pan-ERR agonists, SLU-PP-332 and SLU-PP-915. We investigated the effect of ERR agonist on cardiac function in a pressure overload-induced HF model in vivo. We conducted comprehensive functional, multi-omics (RNA sequencing and metabolomics studies), and genetic dependency studies both in vivo and in vitro to dissect the molecular mechanism, ERR isoform dependency, and target specificity. RESULTS Both SLU-PP-332 and SLU-PP-915 significantly improved ejection fraction, ameliorated fibrosis, and increased survival associated with pressure overload-induced HF without affecting cardiac hypertrophy. A broad spectrum of metabolic genes was transcriptionally activated by ERR agonists, particularly genes involved in fatty acid metabolism and mitochondrial function. Metabolomics analysis showed substantial normalization of metabolic profiles in fatty acid/lipid and tricarboxylic acid/oxidative phosphorylation metabolites in the mouse heart with 6-week pressure overload. ERR agonists increase mitochondria oxidative capacity and fatty acid use in vitro and in vivo. Using both in vitro and in vivo genetic dependency experiments, we show that ERRγ is the main mediator of ERR agonism-induced transcriptional regulation and cardioprotection and definitively demonstrated target specificity. ERR agonism also led to downregulation of cell cycle and development pathways, which was partially mediated by E2F1 in cardiomyocytes. CONCLUSIONS ERR agonists maintain oxidative metabolism, which confers cardiac protection against pressure overload-induced HF in vivo. Our results provide direct pharmacologic evidence supporting the further development of ERR agonists as novel HF therapeutics.
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Affiliation(s)
- Weiyi Xu
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX (W.X., H.L., A.W., L.Q., A.G., J.R.D.C.R., Y.Z., K.Y., M.L., E.N., A.M., L.Z.)
| | - Cyrielle Billon
- Department of Pharmaceutical and Administrative Sciences, University of Health Sciences and Pharmacy, St Louis, MO (C.B., M.H., T.B.)
- Center for Clinical Pharmacology, St Louis College of Pharmacy, Washington University School of Medicine, St Louis, MO (C.B., M.H., T.B.)
| | - Hui Li
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX (W.X., H.L., A.W., L.Q., A.G., J.R.D.C.R., Y.Z., K.Y., M.L., E.N., A.M., L.Z.)
| | - Andrea Wilderman
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX (W.X., H.L., A.W., L.Q., A.G., J.R.D.C.R., Y.Z., K.Y., M.L., E.N., A.M., L.Z.)
| | - Lei Qi
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX (W.X., H.L., A.W., L.Q., A.G., J.R.D.C.R., Y.Z., K.Y., M.L., E.N., A.M., L.Z.)
| | - Andrea Graves
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX (W.X., H.L., A.W., L.Q., A.G., J.R.D.C.R., Y.Z., K.Y., M.L., E.N., A.M., L.Z.)
| | - Jernie Rae Dela Cruz Rideb
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX (W.X., H.L., A.W., L.Q., A.G., J.R.D.C.R., Y.Z., K.Y., M.L., E.N., A.M., L.Z.)
| | - Yuanbiao Zhao
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX (W.X., H.L., A.W., L.Q., A.G., J.R.D.C.R., Y.Z., K.Y., M.L., E.N., A.M., L.Z.)
| | - Matthew Hayes
- Department of Pharmaceutical and Administrative Sciences, University of Health Sciences and Pharmacy, St Louis, MO (C.B., M.H., T.B.)
- Center for Clinical Pharmacology, St Louis College of Pharmacy, Washington University School of Medicine, St Louis, MO (C.B., M.H., T.B.)
| | - Keyang Yu
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX (W.X., H.L., A.W., L.Q., A.G., J.R.D.C.R., Y.Z., K.Y., M.L., E.N., A.M., L.Z.)
| | - McKenna Losby
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX (W.X., H.L., A.W., L.Q., A.G., J.R.D.C.R., Y.Z., K.Y., M.L., E.N., A.M., L.Z.)
| | - Carissa S Hampton
- Department of Pharmacology and Physiology, St Louis University School of Medicine, MO (C.S.H., C.M.A., J.K.W.)
| | - Christiana M Adeyemi
- Department of Pharmacology and Physiology, St Louis University School of Medicine, MO (C.S.H., C.M.A., J.K.W.)
| | - Seok Jae Hong
- McAllister Heart Institute (S.J.H., B.C.J.), University of North Carolina, Chapel Hill
| | - Eleni Nasiotis
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX (W.X., H.L., A.W., L.Q., A.G., J.R.D.C.R., Y.Z., K.Y., M.L., E.N., A.M., L.Z.)
| | - Chen Fu
- Department of Psychiatry, University of Massachusetts Chan Medical School, Worcester, MA (C.F.)
- University Hospitals Cleveland Medical Center, OH (C.F.)
| | - Tae Gyu Oh
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA (T.G.O., W.F., M.D., R.M.E.)
| | - Weiwei Fan
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA (T.G.O., W.F., M.D., R.M.E.)
| | - Michael Downes
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA (T.G.O., W.F., M.D., R.M.E.)
| | - Ryan D Welch
- Biology and Chemistry Department, Blackburn College, Carlinville, IL (R.D.W.)
| | - Ronald M Evans
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA (T.G.O., W.F., M.D., R.M.E.)
| | - Aleksandar Milosavljevic
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX (W.X., H.L., A.W., L.Q., A.G., J.R.D.C.R., Y.Z., K.Y., M.L., E.N., A.M., L.Z.)
| | - John K Walker
- Department of Pharmacology and Physiology, St Louis University School of Medicine, MO (C.S.H., C.M.A., J.K.W.)
| | - Brian C Jensen
- McAllister Heart Institute (S.J.H., B.C.J.), University of North Carolina, Chapel Hill
- Department of Medicine, Division of Cardiology (B.C.J.), University of North Carolina, Chapel Hill
| | - Liming Pei
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, and University of Pennsylvania, Philadelphia (L.P.)
| | - Thomas Burris
- Department of Pharmaceutical and Administrative Sciences, University of Health Sciences and Pharmacy, St Louis, MO (C.B., M.H., T.B.)
- Center for Clinical Pharmacology, St Louis College of Pharmacy, Washington University School of Medicine, St Louis, MO (C.B., M.H., T.B.)
| | - Lilei Zhang
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX (W.X., H.L., A.W., L.Q., A.G., J.R.D.C.R., Y.Z., K.Y., M.L., E.N., A.M., L.Z.)
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Deschner F, Risch T, Baier C, Schlüter D, Herrmann J, Müller R. Nitroxoline resistance is associated with significant fitness loss and diminishes in vivo virulence of Escherichia coli. Microbiol Spectr 2024; 12:e0307923. [PMID: 38063385 PMCID: PMC10782962 DOI: 10.1128/spectrum.03079-23] [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: 08/11/2023] [Accepted: 11/14/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Antimicrobial resistance (AMR) poses a global threat and requires the exploration of underestimated treatment options. Nitroxoline, an effective broad-spectrum antibiotic, does not suffer from high resistance rates in the clinics but surprisingly, it is not heavily used yet. Our findings provide compelling evidence that Nitroxoline resistance renders bacteria unable to cause an infection in vivo, thereby reinvigorating the potential of Nitroxoline in combating AMR.
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Affiliation(s)
- Felix Deschner
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy Saarland University, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Braunschweig, Germany
| | - Timo Risch
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy Saarland University, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Braunschweig, Germany
| | - Claas Baier
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School (MHH), Hannover, Germany
| | - Dirk Schlüter
- German Centre for Infection Research (DZIF), Braunschweig, Germany
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School (MHH), Hannover, Germany
| | - Jennifer Herrmann
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy Saarland University, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Braunschweig, Germany
| | - Rolf Müller
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy Saarland University, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Braunschweig, Germany
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Liu J, Santucci J, Woon DTS, Catterwell R, Perera M, Murphy DG, Lawrentschuk N. A Systematic Review on Prostate-Specific Membrane Antigen Positron Emission Tomography (PSMA PET) Evaluating Localized Low- to Intermediate-Risk Prostate Cancer: A Tool to Improve Risk Stratification for Active Surveillance? Life (Basel) 2024; 14:76. [PMID: 38255691 PMCID: PMC10817570 DOI: 10.3390/life14010076] [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: 11/15/2023] [Revised: 12/28/2023] [Accepted: 01/01/2024] [Indexed: 01/24/2024] Open
Abstract
Active surveillance remains a treatment option for low- to intermediate-risk prostate cancer (PCa) patients. Prostate-specific membrane antigen positron emission tomography and computed tomography (PSMA PET/CT) has emerged as a useful modality to assess intraprostatic lesions. This systematic review aims to evaluate PSMA PET/CT in localized low- to intermediate-risk PCa to determine its role in active surveillance. Following PRISMA guidelines, a search was performed on Medline, Embase, and Scopus. Only studies evaluating PSMA PET/CT in localized low- to intermediate-risk PCa were included. Studies were excluded if patients received previous treatment, or if they included high-risk PCa. The search yielded 335 articles, of which only four publications were suitable for inclusion. One prospective study demonstrated that PSMA PET/CT-targeted biopsy has superior diagnostic accuracy when compared to mpMRI. One prospective and one retrospective study demonstrated MRI occult lesions in 12.3-29% of patients, of which up to 10% may harbor underlying unfavorable pathology. The last retrospective study demonstrated the ability of PSMA PET/CT to predict the volume of Gleason pattern 4 disease. Early evidence demonstrated the utility of PSMA PET/CT as a tool in making AS safer by detecting MRI occult lesions and patients at risk of upgrading of disease.
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Affiliation(s)
- Jianliang Liu
- EJ Whitten Prostate Cancer Research Centre, Epworth Healthcare, Melbourne, VIC 3005, Australia
- Department of Urology, The Royal Melbourne Hospital, University of Melbourne, Melbourne, VIC 3052, Australia
- Department of Surgery, University of Melbourne, Melbourne, VIC 3052, Australia;
- Department of Surgery, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Jordan Santucci
- Department of Urology, The Royal Melbourne Hospital, University of Melbourne, Melbourne, VIC 3052, Australia
- Department of Surgery, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Dixon T. S. Woon
- EJ Whitten Prostate Cancer Research Centre, Epworth Healthcare, Melbourne, VIC 3005, Australia
- Department of Surgery, University of Melbourne, Melbourne, VIC 3052, Australia;
- Department of Urology, University of Melbourne, Austin Health, Heidelberg, VIC 3084, Australia
| | - Rick Catterwell
- Department of Urology, The Queen Elizabeth Hospital, Woodville, SA 5011, Australia
- Discipline of Surgery, University of Adelaide, Adelaide, SA 5005, Australia
| | - Marlon Perera
- Department of Urology, The Royal Melbourne Hospital, University of Melbourne, Melbourne, VIC 3052, Australia
- Department of Surgery, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
- Department of Urology, University of Melbourne, Austin Health, Heidelberg, VIC 3084, Australia
| | - Declan G. Murphy
- Department of Surgery, University of Melbourne, Melbourne, VIC 3052, Australia;
- Department of Surgery, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Nathan Lawrentschuk
- EJ Whitten Prostate Cancer Research Centre, Epworth Healthcare, Melbourne, VIC 3005, Australia
- Department of Urology, The Royal Melbourne Hospital, University of Melbourne, Melbourne, VIC 3052, Australia
- Department of Surgery, University of Melbourne, Melbourne, VIC 3052, Australia;
- Department of Surgery, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
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Gómez-Brandón M, Beesigamukama D, Probst M, Klammsteiner T, Zhou Y, Zhu YG, Mbi Tanga C. Garden fruit chafer (Pachnoda sinuata L.) accelerates recycling and bioremediation of animal waste. Waste Manag 2024; 173:131-140. [PMID: 37989012 DOI: 10.1016/j.wasman.2023.11.019] [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] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 10/26/2023] [Accepted: 11/16/2023] [Indexed: 11/23/2023]
Abstract
Bioconversion of livestock wastes using insect larvae represents an emerging and effective strategy for waste management. However, knowledge on the role of the garden fruit chafer (Pachnoda sinuataL.) in waste recycling and influence on the diversity ofmicrobial community infrass fertilizeris limited. Here, we determined whether and to what extent the conversion of cattle dung into insect frass fertilizer byP. sinuatainfluences the frass' microbial community and its associated antibiotic resistance genes abundance. Pachnoda sinuata larvae were used to valorise cattle dung into frass fertilizer; samples were collected weekly to determine the composition of bacteria and fungi, and antibiotic resistant genes using molecular tools. Results revealed that bioconversion of cattle dung byP. sinuatalarvae significantly increased the richness of beneficial bacteria in the frass fertilizer by 2.5-folds within 28 days, but fungal richness did not vary during the study. Treatment of cattle dung withP. sinuatalarvae caused 2 - 3-folds decrease in the genes conferring resistance to commonly used antibiotics such as aminoglycoside, diaminopyrimidine, multidrug, sulfonamide and tetracycline within 14 days. Furthermore, the recycling cattle dung using considerably reduced the abundance of mobile genetic elements known to play critical roles in the horizontal transfer of antibiotic resistance genes between organisms. This studyhighlights the efficiency ofsaprohytic insects in recycling animal manure and suppressing manure-borne pathogens in the organic fertilizer products, opening new market opportunities for innovative and safe bio-based products and achieving efficient resource utilization in a circular and green economy.
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Affiliation(s)
- María Gómez-Brandón
- Grupo de Ecología Animal (GEA), University of Vigo, Vigo 36310, Galicia, Spain
| | - Dennis Beesigamukama
- International Centre of Insect Physiology and Ecology, P. O. Box 30772-00100, Nairobi, Kenya
| | - Maraike Probst
- Universität Innsbruck, Department of Microbiology, Technikerstraβe 25d, Innsbruck, A-6020, Austria
| | - Thomas Klammsteiner
- Universität Innsbruck, Department of Microbiology, Technikerstraβe 25d, Innsbruck, A-6020, Austria; Universität Innsbruck, Department of Ecology, Technikerstraße 25, Innsbruck, A-6020, Austria
| | - YanYan Zhou
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Chrysantus Mbi Tanga
- International Centre of Insect Physiology and Ecology, P. O. Box 30772-00100, Nairobi, Kenya.
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Maddalon A, Pierzchalski A, Krause JL, Bauer M, Finckh S, Brack W, Zenclussen AC, Marinovich M, Corsini E, Krauss M, Herberth G. Impact of chemical mixtures from wastewater treatment plant effluents on human immune cell activation: An effect-based analysis. Sci Total Environ 2024; 906:167495. [PMID: 37804965 DOI: 10.1016/j.scitotenv.2023.167495] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/09/2023]
Abstract
BACKGROUND Humans are exposed to many different chemicals on a daily basis, mostly as chemical mixtures, usually from food, consumer products and the environment. Wastewater treatment plant effluent contains mixtures of chemicals that have been discarded or excreted by humans and not removed by water treatment. These effluents contribute directly to water pollution, they are used in agriculture and may affect human health. The possible effect of such chemical mixtures on the immune system has not been characterized. OBJECTIVE The aim of this study was to investigate the effect of extracts obtained from four European wastewater treatment plant effluents on human primary immune cell activation. METHODS Immune cells were exposed to the effluent extracts and modulation of cell activation was performed by multi-parameter flow cytometry. Messenger-RNA (mRNA) expression of genes related to immune system and hormone receptors was measured by RT-PCR. RESULTS The exposure of immune cells to these extracts, containing 339 detected chemicals, significantly reduced the activation of human lymphocytes, mainly affecting T helper and mucosal-associated invariant T cells. In addition, basophil activation was also altered upon mixture exposure. Concerning mRNA expression, we observed that 12 transcripts were down-regulated by at least one extract while 11 were up-regulated. Correlation analyses between the analyzed immune parameters and the concentration of chemicals in the WWTP extracts, highlighted the most immunomodulatory chemicals. DISCUSSION Our results suggest that the mixture of chemicals present in the effluents of wastewater treatment plants could be considered as immunosuppressive, due to their ability to interfere with the activation of immune cells, a process of utmost importance for the functionality of the immune system. The combined approach of immune effect-based analysis and chemical content analysis used in our study provides a useful tool for investigating the effect of environmental mixtures on the human immune response.
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Affiliation(s)
- Ambra Maddalon
- Laboratory of Toxicology, Department of Pharmacological and Biomolecular Sciences 'Rodolfo Paoletti', Università degli Studi di Milano, Via Balzaretti 9, 20133 Milan, Italy
| | - Arkadiusz Pierzchalski
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Jannike Lea Krause
- Schwiete Laboratory for Microbiota and Inflammation, German Rheumatism Research (DRFZ), Centre-a Leibniz Institute, Berlin, Germany
| | - Mario Bauer
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Saskia Finckh
- Department of Effect-Directed Analysis, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Werner Brack
- Department of Effect-Directed Analysis, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany; Department of Evolutionary Ecology and Environmental Toxicology, Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Ana C Zenclussen
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany; Perinatal Immunology Research Group, Medical Faculty, Saxonian Incubator for Clinical Translation (SIKT), University of Leipzig, Germany
| | - Marina Marinovich
- Laboratory of Toxicology, Department of Pharmacological and Biomolecular Sciences 'Rodolfo Paoletti', Università degli Studi di Milano, Via Balzaretti 9, 20133 Milan, Italy
| | - Emanuela Corsini
- Laboratory of Toxicology, Department of Pharmacological and Biomolecular Sciences 'Rodolfo Paoletti', Università degli Studi di Milano, Via Balzaretti 9, 20133 Milan, Italy
| | - Martin Krauss
- Department of Effect-Directed Analysis, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Gunda Herberth
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.
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Dariane C, Chierigo F, Ouellet V, Delvoye N, Jammal MP, Bégin LR, Paradis JB, Mes-Masson AM, Karakiewicz PI, Saad F. Analysis of active surveillance uptake for localized prostate cancer in Quebec in 2016: A Canadian bicentric study and comparison with 2010 data. Fr J Urol 2024; 34:102544. [PMID: 37858379 DOI: 10.1016/j.purol.2023.09.031] [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] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/28/2023] [Indexed: 10/21/2023]
Abstract
INTRODUCTION Active surveillance (AS) has emerged as a primary management strategy for low-risk prostate cancer (PC) patients. We aimed to assess AS uptake over a 1-year snapshot throughout Quebec and to compare it to 2010 multicentric Canadian data. METHODS A retrospective chart review and data collection was performed in 1 academic and 2 non-academic community centres from Quebec, among men identified in 2016 with localized T1c-T2c PC on biopsy, fulfilling NCCN criteria of low-risk (LR)-PC, including very-low-risk (VLR) and non-VLR-PC, and favourable-intermediate risk (FIR)-PC. AS adherence was defined when chosen as initial strategy, without any radical treatment within 6 months. RESULTS Overall, 259 patients fulfilled the inclusion criteria with 50.2% of VLR-PC patients. At 6 months, 81% patients in the LR group and 65% in the FIR group were considered as adherent to AS, in both centres, but with an increased use of AS in the community centres compared to 2010 data. The rates of AS maintenance decreased at 12 months to respectively 69% and 58%. Among the VLR group, the rate of initiation was 98% and decreased to 85% at 12 months. CONCLUSION Our data suggest that the majority of low-risk PC patients indeed initiated an AS in 2016, with even a greater proportion of VLR-PC patients compared to 2010. This ideal strategy should be encouraged and improved at 12 months, and assessed with recent data and longer follow-up. LEVEL OF EVIDENCE: 4
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Affiliation(s)
- C Dariane
- Institut du cancer de Montréal, centre de recherche du centre hospitalier de l'université de Montréal (CRCHUM), Montréal, Canada; Department of Urology, hôpital européen Georges-Pompidou, Paris University, 20, rue Leblanc, 75015 Paris, France.
| | - F Chierigo
- Department of Surgical and Diagnostic Integrated Sciences (DISC), University of Genova, Genova, Italy; Cancer Prognostics and Health Outcomes Unit, Division of Urology, University of Montréal Health Center, Montréal, Canada
| | - V Ouellet
- Institut du cancer de Montréal, centre de recherche du centre hospitalier de l'université de Montréal (CRCHUM), Montréal, Canada
| | - N Delvoye
- Institut du cancer de Montréal, centre de recherche du centre hospitalier de l'université de Montréal (CRCHUM), Montréal, Canada
| | - M-P Jammal
- Centre de santé et des services sociaux de Laval, Laval, QC, Canada
| | - L R Bégin
- Centre intégré de santé et des services sociaux des Laurentides, St-Eustache, QC, Canada
| | - J-B Paradis
- Centre de santé et des services sociaux de Chicoutimi, Chicoutimi, QC, Canada
| | - A-M Mes-Masson
- Institut du cancer de Montréal, centre de recherche du centre hospitalier de l'université de Montréal (CRCHUM), Montréal, Canada
| | - P I Karakiewicz
- Cancer Prognostics and Health Outcomes Unit, Division of Urology, University of Montréal Health Center, Montréal, Canada
| | - F Saad
- Institut du cancer de Montréal, centre de recherche du centre hospitalier de l'université de Montréal (CRCHUM), Montréal, Canada; Department of Surgery, Division of Urology, centre hospitalier de l'université de Montréal (CHUM), Montréal, Canada
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50
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El Hindi K, Brachtendorf S, Hartel JC, Renné C, Birod K, Schilling K, Labocha S, Thomas D, Ferreirós N, Hahnefeld L, Dorochow E, Del Turco D, Deller T, Scholich K, Fuhrmann DC, Weigert A, Brüne B, Geisslinger G, Wittig I, Link KH, Grösch S. Hypoxia induced deregulation of sphingolipids in colon cancer is a prognostic marker for patient outcome. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166906. [PMID: 37802156 DOI: 10.1016/j.bbadis.2023.166906] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/08/2023]
Abstract
Sphingolipids are important for the physicochemical properties of cellular membranes and deregulated in tumors. In human colon cancer tissue ceramide synthase (CerS) 4 and CerS5 are reduced which correlates with a reduced survival probability of late-stage colon cancer patients. Both enzymes are reduced after hypoxia in advanced colorectal cancer (CRC) cells (HCT-116, SW620) but not in non-metastatic CRC cells (SW480, Caco-2). Downregulation of CerS4 or CerS5 in advanced CRC cells enhanced tumor formation in nude mice and organoid growth in vitro. This was accompanied by an enhanced proliferation rate and metabolic changes leading to a shift towards the Warburg effect. In contrast, CerS4 or CerS5 depletion in Caco-2 cells reduced tumor growth in vivo. Lipidomic and proteomic analysis of membrane fractions revealed significant changes in tumor-promoting cellular pathways and cellular transporters. This study identifies CerS4 and CerS5 as prognostic markers for advanced colon cancer patients and provides a comprehensive overview about the associated cellular metabolic changes. We propose that the expression level of CerS4 and CerS5 in colon tumors could serve as a basis for decision-making for personalized treatment of advanced colon cancer patients. Trial registration: The study was accredited by the study board of the Deutsche Krebsgesellschaft (Registration No: St-D203, 2017/06/30, retrospectively registered).
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Affiliation(s)
- Khadija El Hindi
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Sebastian Brachtendorf
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Jennifer C Hartel
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany; Goethe-University Frankfurt, Department of Life Sciences, 60590 Frankfurt, Germany
| | - Christoph Renné
- Institute of Pathology and Cytology, Group Practice Wiesbaden, Germany
| | - Kerstin Birod
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Karin Schilling
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Sandra Labocha
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Dominique Thomas
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Nerea Ferreirós
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Lisa Hahnefeld
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Erika Dorochow
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Domenico Del Turco
- Goethe-University Frankfurt, Institute of Clinical Neuroanatomy, Dr. Senckenberg Anatomy, Faculty of Medicine, Theodor Stern Kai 7, 60596 Frankfurt am Main, Germany
| | - Thomas Deller
- Goethe-University Frankfurt, Institute of Clinical Neuroanatomy, Dr. Senckenberg Anatomy, Faculty of Medicine, Theodor Stern Kai 7, 60596 Frankfurt am Main, Germany
| | - Klaus Scholich
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Dominik C Fuhrmann
- Goethe-University Frankfurt, Institute of Biochemistry I, Faculty of Medicine, Theodor-Stern-Kai 7, 60596 Frankfurt, Germany
| | - Andreas Weigert
- Goethe-University Frankfurt, Institute of Biochemistry I, Faculty of Medicine, Theodor-Stern-Kai 7, 60596 Frankfurt, Germany
| | - Bernhard Brüne
- Goethe-University Frankfurt, Institute of Biochemistry I, Faculty of Medicine, Theodor-Stern-Kai 7, 60596 Frankfurt, Germany
| | - Gerd Geisslinger
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Ilka Wittig
- Goethe-University Frankfurt, Functional Proteomics, Institute of Cardiovascular Physiology, Faculty of Medicine, Frankfurt am Main, Germany
| | - Karl-Heinrich Link
- Asklepios Tumor Center (ATC) and Surgical Center, Asklepios Paulinen Klinik, Wiesbaden 65197, Germany
| | - Sabine Grösch
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany.
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