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From castaways to discoveries: unveiling treasures in skin RNAseq using a novel multidimensional data processing workflow including infection-host dynamics

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Physiological Genomics 2025年第5期57卷 343-356页

作者： Bhargava, Disha Labadie, Alec Hanson-Rios-stutz, Rebecca L. Goodyke, Austin Moses, Ella M. Das, Akansha S. Vanderweele, Sophie Lemon, Janelle V. Cook, Taylor W. Pearson, David Redinger, Joseph M. Caulfield, Adam J. Olivero, Rosemary Foster, Kate Ashack, Kurt Rajasekaran, Surender Bupp, Caleb P. Triche, Timothy J. Krawczyk, Connie M. Chesla, Dave Sims, Matthew D. Hartog, Nicholas L. Prokop, Jeremy W. College of Human Medicine Michigan State University Grand Rapids MI United States Office of Research Corewell Health Grand Rapids MI United States Department of Biology Washington and Jefferson College Washington PA United States Department of Pharmacology and Toxicology Michigan State University East Lansing MI United States Department of Large Animal Clinical Sciences College of Veterinary Medicine Michigan State University East Lansing MI United States School for Environment and Sustainability University of Michigan Ann Arbor MI United States Regional Laboratory Corewell Health Grand Rapids MI United States Infectious Disease Helen DeVos Children’s Hospital Grand Rapids MI United States Dermatology Helen DeVos Children’s Hospital Corewell Health Grand Rapids MI United States Dermatology Associates of West Michigan Grand Rapids MI United States Pediatric Intensive Care Unit Helen DeVos Children’s Hospital Corewell Health Grand Rapids MI United States Medical Genetics Corewell Health Grand Rapids MI United States Center for Epigenetics Van Andel Research Institute Grand Rapids MI United States Department of Metabolism and Nutritional Programming Van Andel Institute Grand Rapids MI United States Section of Infectious Diseases Corewell Health Royal Oak MI United States Allergy and Immunology Corewell Health Grand Rapids MI United States

Defining physiology and methods to measure biological mechanisms is essential. Extensive datasets such as RNA sequencing are used with little analysis of the knowledge gained from the various methodologies. Within thi... 详细信息

Defining physiology and methods to measure biological mechanisms is essential. Extensive datasets such as RNA sequencing are used with little analysis of the knowledge gained from the various methodologies. Within this work, we have processed publicly available NCBI RNAseq datasets using a combination of bioinformatics tools for the largest physiological organ, the skin. In many datasets, we identify the quality of the sample, human transcript mapping, the sex of each sample, foreign RNA from bacteria/viruses/protists, and the presence of B/T-cell immune repertoire. Processing 8,274 samples from 132 different experiments for skin samples identifies common flora of skin with elevation of protists (such as Leishmania), bacteria (Staphylococcus, Cutibacterium acnes), and viruses [Human alpha-herpesvirus (HSV), Human papillomavirus (HPV)] that may be involved in physiological differences. We observed samples with the Heilongjiang tick virus, human T-cell leukemia virus type I, and equine infectious anemia virus that likely play pathological roles in physi-ology. Integrating the various biomarkers identified five ideal datasets for skin pathologies that elucidated a novel correlation between the normal skin flora bacterium Bacillus megaterium with major histocompatibility complex (MHC) regulation and the immune repertoire clonal expansion, particularly in patients with hidradenitis suppurativa. Finally, we show that in multiple independent experiments, biological sex is associated with multiple sex chromosome gene differences, highlighting the importance of future work in studying sex differences in skin. Data integrations and multidimensional data mapping are critical for physiological omics advancements, and this work highlights the exciting ability to apply these tools to skin physiology. NEW & NOTEWORTHY Complex bioinformatics mapping to skin RNA sequencing datasets can simultaneously map biological sex, skin-specific genes, bacteria, viruses, protists, and the acqui

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Deletion of a single CTCF motif at the boundary of a chromatin domain with three FGF genes disrupts gene expression and embryonic development

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Developmental Cell 2025年

作者： Chakraborty, Shreeta Wenzlitschke, Nina Anderson, Matthew J. Eraso, Ariel Baudic, Manon Thompson, Joyce J. Evans, Alicia A. Shatford-Adams, Lilly M. Chari, Raj Awasthi, Parirokh Dale, Ryan K. Lewandoski, Mark Petros, Timothy J. Rocha, Pedro P. Unit on Genome Structure and Regulation National Institute of Child Health and Human Development National Institutes of Health Bethesda 20892 MD United States Genetics of Vertebrate Development Section Cancer and Developmental Biology Laboratory National Cancer Institute National Institutes of Health Frederick 21702 MD United States Bioinformatics and Scientific Programming Core National Institute of Child Health and Human Development National Institutes of Health Bethesda 20892 MD United States Laboratory Animal Sciences Program Frederick National Laboratory for Cancer Research Frederick 21702 MD United States Unit on Cellular and Molecular Neurodevelopment National Institute of Child Health and Human Development National Institutes of Health Bethesda 20892 MD United States National Cancer Institute NIH Bethesda 20892 MD United States

Chromatin domains delimited by CTCF can restrict the range of enhancer action. However, disruption of some domain boundaries results in mild gene dysregulation and phenotypes. We tested whether perturbing a domain wit... 详细信息

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VP6-2022: Adjuvant pertuzumab and trastuzumab in patients with early HER-2 positive breast cancer in APHINITY: 8.4 years' follow-up

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Annals of Oncology 2022年第9期33卷 986-987页

作者： S. Loibl J. Jassem A. Sonnenblick D. Parlier E. Winer J. Bergh R.D. Gelber E. Restuccia Y-H. Im C. Huang F. Dalenc I. Calvo M. Procter C. Caballero E. Clark H.L. Gomez Moreno J. Bliss G. Viale J. Bines M. Piccart Medicine and Research Dept. German Breast Group (GBG) Forschungs GmbH Neu-Isenburg Germany Oncology & Radiotherapy Medical University of Gdansk Gdansk Poland Oncology Department Tel Aviv Sourasky Medical Center-(Ichilov) Tel Aviv Israel Clinical Trials Support Unit Institut Jules Bordet Brussels Belgium Yale Cancer Center Yale University School of Medicine - Yale Cancer Center New Haven CT USA Department of Oncology-Pathology Karolinska Institutet and Breast Cancer Centre Cancer Theme Karolinska University Hospital Stockholm Sweden Biostatistics Dana Farber Cancer Institute Boston MA USA Product Development Oncology F. Hoffmann-La Roche Ltd Basel Switzerland Medicine Dept. Hematology/Medical Oncology Division Samsung Medical Center (SMC) - Sungkyunkwan University School of Medicine Seoul Republic of Korea Surgery Dept. NTUH - National Taiwan University Hospital Taipei Taiwan Oncologie 1A Institut Universitaire du Cancer Toulouse - Oncopole Toulouse France Breast Cancer Unit MD Anderson Cancer Center Madrid Madrid Spain Statistics and Programming Frontier Science Scotland Kincraig UK Medical Department Breast International Group (BIG) - AISBL Brussels Belgium Data Sciences - Data & Statistical Sciences (DSS) Roche Products Limited Welwyn Garden City UK Medicine Department INEN - Instituto Nacional de Enfermedades Neoplasicas Lima Peru Clinical Trials and Statistics Unit ICR - Institute of Cancer Research London UK Department of Oncology Università degli Studi di Milano Milan Italy Medical Oncology Department Instituto Nacional de Cancer - Research Center Rio de Janeiro Brazil Institut Jules Bordet Brussels Belgium

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Correction to: Fat intake during pregnancy and risk of preeclampsia: a prospective cohort study in Denmark

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European journal of clinical nutrition 2022年第1期76卷 177-178页

作者： Mariel Arvizu Myriam C Afeiche Susanne Hansen Thorhallur F Halldorsson Sjurdur F Olsen Jorge E Chavarro Department of Nutrition Harvard T.H. Chan School of Public Health Boston MA USA. Department of Environmental Health Harvard T.H. Chan School of Public Health Boston MA USA. Centre for Fetal Programming Statens Serum Institut Copenhagen Denmark. Unit for Nutrition Research Faculty of Food Science and Nutrition School of Health Sciences University of Iceland Reykjavík Iceland. Department of Nutrition Harvard T.H. Chan School of Public Health Boston MA USA. jchavarr@hsph.harvard.edu. Department of Epidemiology Harvard T.H. Chan School of Public Health Boston MA USA. jchavarr@hsph.harvard.edu. Channing Division of Network Medicine Department of Medicine Brigham and Women's Hospital and Harvard Medical School Boston MA USA. jchavarr@hsph.harvard.edu.

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The EORTC QLQ-F17 as a shortened version of the EORTC QLQ-C30 to assess self-reported functioning in cancer patients: investigating equivalence and psychometric properties in a randomized cross-over trial

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eClinicalMedicine 2025年 84卷

作者： Florian Zeman Johannes M. Giesinger Tobias Pukrop Morten Aa Petersen Mogens Groenvold Sandra Nolte Dagmara Kuliś Sunil Shrestha Laurence Leysen Kim Cocks Corneel Coens Georgios Ioannidis Cecilia Pompili Michael Koller Center for Clinical Studies University Hospital Regensburg Regensburg Germany Bavarian Cancer Research Center (BZKF) Regensburg Germany Department of Psychiatry Psychotherapy Psychosomatics and Medical Psychology Innsbruck Medical University Innsbruck Austria Department of Internal Medicine III Hematology and Oncology University Hospital Regensburg Regensburg Germany Palliative Care Research Unit Department of Geriatrics and Palliative Medicine GP Bispebjerg and Frederiksberg Hospital University of Copenhagen Copenhagen Denmark Department of Public Health University of Copenhagen Copenhagen Denmark Person-Centred Research Eastern Health Clinical School Monash University Melbourne VIC Australia School of Health Sciences Swinburne University of Technology Melbourne VIC Australia European Organisation for Research and Treatment of Cancer (EORTC) Quality of Life Department Brussels Belgium Department of Research and Academics Kathmandu Cancer Center Tathali Bhaktapur Nepal Statistics and Programming Adelphi Values Bollington Cheshire England UK Oncology Department Nicosia General Hospital State of Health Services Organisation Nicosia Cyprus University of Hull Hull and York Medical School Hull UK

Background The EORTC QLQ-F17, a shortened version of the EORTC QLQ-C30, solely contains the items related to functioning and omits symptom scales. The QLQ-F17 is conceived an equivalent to the functional part of the Q... 详细信息

Background The EORTC QLQ-F17, a shortened version of the EORTC QLQ-C30, solely contains the items related to functioning and omits symptom scales. The QLQ-F17 is conceived an equivalent to the functional part of the QLQ-C30, but to date there is no empirical evidence to support this rationale. Methods This randomized, cross-over, multi-national, questionnaire-based study investigates the equivalence and psychometric properties of the QLQ-F17 compared to the functional scales of the QLQ-C30. Respondents had to fill in both questionnaires, the order of which was presented in a randomized and balanced manner (QLQ-C30—QLQ-F17 vs. QLQ-F17—QLQ-C30). Equivalence testing used Differential Item Functioning (DIF) and linear models. The margin of equivalence was set at ]–5, 5[ points. The study is registered with *** ( NCT05479682 ). Patients were enrolled between February 17 and March 28, 2023. Findings A total of 2672 cancer patients of all major cancer types, aged between 18 and 92 years with an equal gender distribution (50/50) from 11 countries, were recruited between 17 February and 28 March 2023. Adjusted mean differences between QLQ-C30 and QLQ-F17 ranged between −1·55 and 3·25 for all scales, and the limits of the 95%-CIs, ranging from −3·11 to 4·87, were all within the equivalence margin. All effect sizes of the DIF analyses were <0·01. For the scales of the QLQ-F17, Cronbach's Alpha ranged from 0·73 to 0·89, item–own scale correlations from 0·47 to 0·78 and item–other scale correlations from 0·19 to 0·70. Interpretation The QLQ-F17 yielded score values that are equivalent to the functional part of the QLQ-C30. Consequently, future clinical studies can employ the QLQ-F17 as a generic tool without losing comparability to studies using the QLQ-C30. Supplementing the QLQ-F17 with relevant symptom items from the EORTC Item Library allows for a time-efficient and flexible measurement strategy. Funding This research was funded by the European Organisation fo

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CHARACTERIZATION OF A NEW HUMAN NEURONAL MODEL FOR SYNGAP1 DISEASE

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IBRO Neuroscience Reports 2023年 15卷 S151-S152页

作者： Oriana Zerpa Rios Christina Au Yeung Alba Tristan-Noguero Diego Del Castillo-Berges Cristian De Quintana-Schmidt Michael Peitz Nerea Roher Oliver Brüstle Àlex Bayés Biomedical Research Institute Hospital Sant Pau Molecular Physiology Of The Synapse Barcelona Spain Universitat Autònoma de Barcelona Institut De Biotecnologia I De Biomedicina Barcelona Spain Universitat Autònoma de Barcelona Animal Physiology Unit (faculty Of Biosciences) Department Of Cellular Biology Physiology And Immunology Barcelona Spain University of Bonn School of Medicine & University Hospital Bonn Institute Of Reconstructive Neurobiology Life & Brain Center Bonn Germany Universitat de Barcelona Departament De Genètica Microbiologia I Estadística Facultat De Biologia Barcelona Spain University of Bonn School of Medicine Cell Programming Core Facility Bonn Germany Biomateriales y Nanomedicina (BBN) Ciber De Bioingenieria Barcelona Spain

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Do Not Exclude Your Observations: Negative Cortisol Awakening Responses (Car) May Be Biologically Relevant

SSRN

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SSRN 2022年

作者： Herrera-Moreno, Jose Francisco Trejo-Valdivia, Belem Tolentino, Maricruz Wright, Robert O. Baccarelli, Andrea A. Wright, Rosalind J. Niedzwieck, Megan M. Téllez-Rojo, Martha M. Tamayo-Ortiz, Marcela Department of Environmental Health Sciences Mailman School of Public Health Columbia University New YorkNY United States Centro de Investigación en Nutrición y Salud Instituto Nacional de Salud Pública Morelos Cuernavaca Mexico Department of Nutrition and Bio programming National Institute of Perinatology Mexico City11000 Mexico Department of Environmental Medicine and Public Health Icahn School of Medicine at Mount Sinai New YorkNY United States Department of Pediatrics Kravis Children's Hospital Icahn School of Medicine at Mount Sinai New YorkNY United States Department of Environmental Medicine and Public Health Icahn School of Medicine at Mount Sinai New YorkNY United States Department of Pediatrics Kravis Children's Hospital Icahn School of Medicine at Mount Sinai New YorkNY United States Institute for Exposomic Research Icahn School of Medicine at Mount Sinai New YorkNY United States Department of Environmental Medicine and Public Health Icahn School of Medicine at Mount Sinai New YorkNY United States Occupational Health Research Unit Mexican Social Security Institute Mexico City Mexico Centro de Investigación en Nutrición y Salud Instituto Nacional de Salud Pública Universidad 655 Sta. Ma. Ahuacatitlán C.P. 62100 Cuernavaca Morelos Mexico

The Cortisol Awakening Response (CAR) is one of the main stress biomarkers. Although positive CAR values are expected, negative values could be associated to health status, reflected in hematological parameters, or to... 详细信息

The Cortisol Awakening Response (CAR) is one of the main stress biomarkers. Although positive CAR values are expected, negative values could be associated to health status, reflected in hematological parameters, or to environmental exposures. For example, exposure to lead (Pb) has shown neuroendocrine effects, including altering cortisol diurnal rhythms. The aim of this study was to analyze the prevalence of negative CAR values and their association with hematological parameters and blood Pb (BPb) levels in women participating in a birth cohort. Cortisol was measured by luminescence immunoassay in two-day saliva samples from n= 900 pregnant women from the PROGRESS cohort in Mexico. CAR was estimated as the difference between the first (time of awakening) and second (45 min after) cortisol concentrations for each collection day. CAR was categorized as: both days positive (CAR-PP), either day with a negative CAR (CAR-NP/PN), and both negative (CAR-NN). A complete blood count was done using a coulter hematology analyzer. BPb was analyzed by inductively coupled plasma-mass spectrometry. Associations and estimated probabilities analyses were carried out to determine the variation in hematological variables and BPb concentrations for each CAR group. The median (25th, 75th) CAR for the first collection day was -1.0 ng/ml (-6.0, 5.3) and -1.5 ng/ml (-6.4, 4.8) for the second day;23% of the women were CAR-PP, 40% CAR-NP/PN, and 37% CAR-NN. Women with higher concentrations of leukocytes, eosinophils, basophils, and BPb were more likely to belong to CAR-NN or CAR-NP/PN groups. Compared to women with CAR-PP, those with CAR-NP/PN and CAR-NN had inverse associations for leukocyte levels and higher BPb concentrations. In this study 77% of women had at least one negative CAR value that could be an indicator of an underlying health condition or associated with lead exposure. researchers should consider not excluding negative CAR values from their analyses. © 2022, The Authors. All r

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1411P Tusamitamab ravtansine plus ramucirumab as 2L therapy or beyond in patients with metastatic NSq NSCLC and high CEACAM5 expression (CARMEN-LC04)

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Annals of Oncology 2023年 34卷 S807-S807页

作者： G.K. Dy B.C. Cho J. Oliveira M.D. Isla Casado A. Blasco Cordellat M. Zemanova J. Roubec L. Vila Martinez L. Charbonnier C. Soufflet J. de Castro Carpeño Department of Medicine Roswell Park Comprehensive Cancer Center Buffalo NY USA Division of Medical Oncology Yonsei Cancer Center Yonsei University College of Medicine Seoul Republic of Korea Medical Oncology Service Early Phase Clinical Trial Unit-IPO Porto/RISE@CI-IPOP (Health Research Network Experimental Pathology and Therapeutics Group Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network) Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Porto Portugal Medical Oncology Department Hospital Clínico Universitario Lozano Blesa Zaragoza Spain Medical Oncology Department Hospital General de Valencia Valencia Spain Department of Oncology First Faculty of Medicine Charles University and General University Hospital in Prague Prague Czech Republic Pneumooncology Nemocnice AGEL Ostrava-Vítkovice Ostrava-Vítkovice Czech Republic Oncology Department Consorci Corporació Sanitària Parc Taulí de Sabadell Sabadell Spain Biostatistics & Programming Sanofi Chilly-Mazarin France Clinical Development Sanofi Vitry-sur-Seine France Medical Oncology Service Hospital Universitario La Paz Madrid Spain

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9O Phase I/II, open-label, first-in-human study of the anti-GPC3 T cell engager SAR444200 in patients with advanced solid tumors: Updated safety and pharmacokinetic analysis

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ESMO Open 2025年 10卷 104165-104165页

作者： Almhanna, K. Hong, J.Y. Chenard-Poirier, M. Ryoo, B-Y. Lim, D.W-T. El-Khoueiry, A.B. Goh, B-C. Samol, J. Kefsi, A. Perez, R. Meng, R. Masciari, S. Abbadessa, G. Guillemin-Paveau, H. Lepine, L. Zhang, Y. Dumbrava, E.E. Medical Oncology Warren Alpert Medical School of Brown University Providence United States of America Hematology-Oncology Samsung Medical Center (SMC) Seoul Republic of Korea Gastrointestinal Cancer Unit Centre Intégré de Cancérologie - Chu de Québec Québec Canada Department of Oncology Asan Medical Center - University of Ulsan Seoul Republic of Korea Medical Oncology Department NCCS - National Cancer Centre Singapore Medical Oncology Division USC - Kenneth J. Norris Jr. Comprehensive Cancer Center Los Angeles United States of America Hematology-Oncology NCIS - National University Cancer Institute Singapore Singapore Medical Oncology Department National Healthcare Group - Tan Tock Seng Hospital Singapore Oncology Early Development Sanofi Vitry-sur-Seine France Immuno Modulatory Agents-Early Development Sanofi Bridgewater United States of America Research and Development Department Sanofi Cambridge United States of America Early Development in Oncology Sanofi Cambridge United States of America Oncology Early Development Sanofi Cambridge United States of America Pharmacokinetics/Pharmacodynamics VA Sanofi Vitry-sur-Seine France Pharmacokinetics Dynamics and Metabolism Sanofi Vitry-sur-Seine France Department of Biostatistics and Programming Sanofi Cambridge United States of America Investigational Cancer Therapeutics Department The University of Texas MD Anderson Cancer Center - Main Building Houston United States of America

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