Article
Multidisciplinary Sciences
Julia Guthrie, Sevgi Koestel Bal, Salvo Danilo Lombardo, Felix Mueller, Celine Sin, Christiane V. R. Huetter, Joerg Menche, Kaan Boztug
Summary: This study utilizes a network-based approach to integrate 186 genetic immune diseases into a comprehensive map of human immune dysregulation called AutoCore. AutoCore is divided into 19 endotypes corresponding to cohesive disease subgroups, providing a molecular mechanism-based disease classification and therapeutic targeting.
Article
Multidisciplinary Sciences
Zhongwei Xin, Mingjie Lin, Zhixing Hao, Di Chen, Yongyuan Chen, Xiaoke Chen, Xia Xu, Jinfan Li, Dang Wu, Ying Chai, Pin Wu
Summary: In this study, the developmental pattern of intra-tumoral T-cells in human thymic epithelial tumors (TET) was analyzed by single cell analysis. Three types of TETs were identified based on the characteristics of tumor cells and their effects on T-cell development. The molecular subtypes of TETs were found to determine their tumor immune microenvironment, and GNB3 and CHI3L1 might serve as predictors for the immunological behavior and prognosis of these tumors.
NATURE COMMUNICATIONS
(2022)
Article
Oncology
Mingwei Wang, Shasha Li, Wencong Guo, Lulu Wang, Jiaxin Huang, Junzhe Zhuo, Botao Lai, Chenqi Liao, Tianlan Ge, Yuxuan Nie, Su Jin, Manxiang Wang, Yanggeling Zhang, Yimeng Liu, Xiaowen Li, Huixia Zhang
Summary: The study demonstrates that CHRAC1 is highly expressed in lung cancer tissues, promoting lung cancer cell proliferation and migration when overexpressed. On the other hand, silencing CHRAC1 inhibits cell proliferation and migration. This suggests that CHRAC1 plays a critical role in promoting lung cancer tumorigenesis.
Article
Medicine, Research & Experimental
Amir Hossein Saeidian, Leila Youssefian, Charles Y. Huang, Fahimeh Palizban, Mahtab Naji, Zahra Saffarian, Hamidreza Mahmoudi, Azadeh Goodarzi, Soheila Sotoudeh, Fatemeh Vahidnezhad, Maliheh Amani, Narjes Tavakoli, Ali Ajami, Samaneh Mozafarpoor, Mehrdad Teimoorian, Saeed Dorgaleleh, Sima Shokri, Mohammad Shenagari, Nima Abedi, Sirous Zeinali, Paolo Fortina, Vivien Beziat, Emmanuelle Jouanguy, Jean-Laurent Casanova, Jouni Uitto, Hassan Vahidnezhad
Summary: This study presents a whole-transcriptome sequencing-based method that can simultaneously identify the cutaneous virome and the underlying inborn errors of immunity (IEI) genes by RNA-Seq on a single skin biopsy. The method allows for rapid and accurate diagnosis of patients with viral skin infections and potential genetic defects, providing guidance for further treatment.
Article
Microbiology
Tawanda E. Maguvu, Cornelius C. Bezuidenhout
Summary: This study utilized whole-genome-based taxonomic classification and comparative genomic analysis to reveal the genomic features of potential human pathogenic Enterobacter isolates from wastewaters, emphasizing the role of wastewaters in the dissemination of pathogenic microbes and the necessity to monitor the effectiveness of wastewater treatment.
Editorial Material
Multidisciplinary Sciences
Charles N. Rotimi, Adebowale A. Adeyemo
Summary: Over the past 20 years, the increasing diversity in genomic sequencing has provided valuable insights into our evolutionary history and health status.
Article
Immunology
Astri Frafjord, Linn Buer, Clara Hammarstrom, Henrik Aamodt, Per Reidar Woldbaek, Odd Terje Brustugun, Aslaug Helland, Inger Oynebraten, Alexandre Corthay
Summary: The study found that human primary NSCLC tumors are dominated by Th2 and Treg cells, with fewer Th1 cells present. An increased Th1:Th2 ratio was associated with higher numbers of intratumoral CD8-T cells.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Radiology, Nuclear Medicine & Medical Imaging
Jason G. Parker, Mahsa Servati, Emily E. Diller, Sha Cao, Chang Ho, Robert Lober, Aaron Cohen-Gadol
Summary: This article proposes a new method for mapping cellular and molecular features in vivo to improve cancer treatment strategies in the brain. The method leverages the advantages of in vivo imaging, functional magnetic resonance signals, next-generation sequencing, and deep learning techniques. It also outlines design protocols to integrate bioinformation technologies, increased computational capability, and statistical classification techniques for rational treatment selection.
Article
Plant Sciences
Kashish Kamra, Joonhyung Jung, Joo-Hwan Kim
Summary: The plastid genome is an effective tool for studying plant phylogenetics. In this study, we conducted comparative genomics of the Iridaceae family, revealing its structural characteristics and evolutionary relationships. We also identified genomic events and gene deletions in some species. This study provides valuable insights for further research on the evolution and phylogenetic relationships of Iridaceae.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Genetics & Heredity
Juxuan Zhang, Jiaxing Deng, Xiao Feng, Yilong Tan, Xin Li, Yixin Liu, Mengyue Li, Haitao Qi, Lefan Tang, Qingwei Meng, Haidan Yan, Lishuang Qi
Summary: This study presents a transcriptional panel that accurately distinguishes the neuroendocrine (NE) and non-NE tumors in lung cancer, and determines the histological subtypes. The panel achieves high accuracy in both public validation datasets and clinical samples.
FRONTIERS IN GENETICS
(2022)
Article
Oncology
Michael P. Carducci, Baskaran Sundaram, Benjamin A. Greenberger, Maria Werner-Wasik, Gregory C. Kane
Summary: Approximately one third of patients receiving SBRT for lung tumors experience rib fractures, with 34% of them experiencing pain. Tumor location is the only independent risk factor, and CT scans show a unique discontinuity between the healing edges of post-SBRT rib fractures.
Review
Pathology
Lynnette Fernandez-Cuesta, Lise Mangiante, Nicolas Alcala, Matthieu Foll
Summary: The diagnosis and classification of malignant pleural mesothelioma (MPM) is challenging, requiring expert assessment and suitable biopsies. Recent advancements in molecular characterisation of MPM are discussed, highlighting the gaps in knowledge and the potential benefits for patient classification. Researchers delve into the molecular landscape of MPM and discuss the current state of understanding regarding intra-tumour heterogeneity.
Article
Mathematics, Interdisciplinary Applications
Maria Elena Acevedo-Mosqueda, Sandra Dinora Orantes-Jimenez, Marco Antonio Acevedo-Mosqueda, Ricardo Carreno Aguilera
Summary: This paper analyzes the ability of different machine learning algorithms to find patterns in gene expression levels for the accurate classification of five different types of tumors. The results demonstrate that Bayesian method, Decision Trees, and K-Nearest Neighbors perform well in terms of classifier performance.
FRACTALS-COMPLEX GEOMETRY PATTERNS AND SCALING IN NATURE AND SOCIETY
(2022)
Article
Multidisciplinary Sciences
Rui Yuan, Pek Jun Tiw, Lei Cai, Zhiyu Yang, Chang Liu, Teng Zhang, Chen Ge, Ru Huang, Yuchao Yang
Summary: The authors propose a hardware system that uses VO2 memristors to perform brain-like encoding and analysis of physiological signals, and is capable of identifying arrhythmia and epileptic seizures. The system demonstrates superior computing capabilities, achieving high accuracies in arrhythmia classification and epileptic seizure detection. This work highlights the potential of memristors in constructing efficient neuromorphic physiological signal processing systems and promoting next-generation human-machine interfaces.
NATURE COMMUNICATIONS
(2023)
Editorial Material
Multidisciplinary Sciences
Karen H. Miga
Summary: Since the publication of the human genome in 2001, advancements in sequencing technology have filled in many of the gaps in the original sequence, leading to a deeper knowledge of genome regulation, structure, and function.
Article
Public, Environmental & Occupational Health
Hilary A. Robbins, Karine Alcala, Elham Khodayari Moez, Florence Guida, Sera Thomas, Hana Zahed, Matthew T. Warkentin, Karl Smith-Byrne, Yonathan Brhane, David Muller, Xiaoshuang Feng, Demetrius Albanes, Melinda C. Aldrich, Alan A. Arslan, Julie Bassett, Christine D. Berg, Qiuyin Cai, Chu Chen, Michael P. A. Davies, Brenda Diergaarde, John K. Field, Neal D. Freedman, Wen-Yi Huang, Mikael Johansson, Michael Jones, Woon-Puay Koh, Stephen Lam, Qing Lan, Arnulf Langhammer, Linda M. Liao, Geoffrey Liu, Reza Malekzadeh, Roger L. Milne, Luis M. Montuenga, Thomas Rohan, Howard D. Sesso, Gianluca Severi, Mahdi Sheikh, Rashmi Sinha, Xiao-Ou Shu, Victoria L. Stevens, Martin C. Tammemaegi, Lesley F. Tinker, Kala Visvanathan, Ying Wang, Renwei Wang, Stephanie J. Weinstein, Emily White, David Wilson, Jian-Min Yuan, Xuehong Zhang, Wei Zheng, Christopher I. Amos, Paul Brennan, Mattias Johansson, Rayjean J. Hung
Summary: The INTEGRAL program aims to develop tools for optimizing LDCT lung cancer screening. It includes the Risk Biomarker and Nodule Malignancy projects, which investigate circulating protein markers for identifying individuals likely to benefit from screening and distinguishing benign versus malignant nodules. A total of 1161 and 1078 proteins were measured, and 21 proteins were selected for performance evaluation in the Risk Biomarker and Nodule Malignancy projects.
ANNALS OF EPIDEMIOLOGY
(2023)
Article
Oncology
Thomas Behrens, Calvin Ge, Roel Vermeulen, Benjamin Kendzia, Ann Olsson, Joachim Schuez, Hans Kromhout, Beate Pesch, Susan Peters, Luetzen Portengen, Per Gustavsson, Dario Mirabelli, Pascal Guenel, Daniele Luce, Dario Consonni, Neil E. Caporaso, Maria Teresa Landi, John K. Field, Stefan Karrasch, Heinz-Erich Wichmann, Jack Siemiatycki, Marie-Elise Parent, Lorenzo Richiardi, Lorenzo Simonato, Karl-Heinz Joeckel, Wolfgang Ahrens, Hermann Pohlabeln, Guillermo Fernandez-Tardon, David Zaridze, John R. McLaughlin, Paul A. Demers, Beata Swiatkowska, Jolanta Lissowska, Tamas Pandics, Eleonora Fabianova, Dana Mates, Vladimir Bencko, Lenka Foretova, Vladimir Janout, Paolo Boffetta, Bas Bueno-de-Mesquita, Francesco Forastiere, Kurt Straif, Thomas Bruening
Summary: Limited evidence exists regarding the exposure-effect relationship between lung-cancer risk and hexavalent chromium (Cr(VI)) or nickel. This study found that occupational exposure to Cr(VI) and nickel was associated with lung-cancer risks, particularly in men. In men, the highest quartile of cumulative exposure to CR(VI) and nickel were both significantly associated with increased odds ratios for lung cancer.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Article
Oncology
Volker Arndt, Daniela Doege, Stefan Froehling, Peter Albers, Hana Alguel, Ralf Bargou, Carsten Bokemeyer, Martin Bornhaeuser, Christian H. Brandts, Peter Brossart, Sara Yvonne Brucker, Tim H. Bruemmendorf, Hartmut Doehner, Norbert Gattermann, Michael Hallek, Volker Heinemann, Ulrich Keilholz, Thomas Kindler, Cornelia von Levetzow, Florian Lordick, Ulf Peter Neumann, Christoph Peters, Dirk Schadendorf, Stephan Stilgenbauer, Thomas Zander, Daniel Zips, Delia Braun, Thomas Seufferlein, Gerd Nettekoven, Michael Baumann
Summary: The capacities of German Comprehensive Cancer Centers (CCCs) in various aspects of oncology care were significantly affected during the first 2 years of the COVID-19 pandemic. Follow-up, psycho-oncologic care, and tumor surgery were particularly impacted, along with other areas of multidisciplinary oncological care. This study highlights the importance of developing strategies to prevent similar limitations in the future.
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY
(2023)
Letter
Genetics & Heredity
Ilyas Ahmad, Ayaz Khan, Hafiza Noor Ul Ayan, Birgit Budde, Janine Altmueller, Asad Aslam Korejo, Gudrun Nurnberg, Holger Thiele, Muhmmad Tariq, Peter Nuernberg, Jeanette Erdmann
JOURNAL OF HUMAN GENETICS
(2023)
Article
Hematology
Jorge Garcia Borrega, Boris Boell, Matthias Kochanek, Jan-Hendrik Naendrup, Florian Simon, Noelle Sieg, Michael Hallek, Peter Borchmann, Udo Holtick, Alexander Shimabukuro-Vornhagen, Dennis A. Eichenauer, Jan-Michel Heger
Summary: A retrospective analysis was conducted on patients admitted to the intensive care unit (ICU) during hospitalization for high-dose chemotherapy and autologous stem cell transplantation (ASCT). The study found that the overall outcome was favorable for these patients.
ANNALS OF HEMATOLOGY
(2023)
Article
Oncology
Nadine Kutsch, Emily Eva Holmes, Sandra Robrecht, Gudrun Schueler, Ursula Vehling-Kaiser, Thomas Decker, Sigrun Mueller-Hagen, Karin Heinisch, Sebastian Boettcher, Matthias Ritgen, Karl-Anton Kreuzer, Stephan Stilgenbauer, Anna Maria Fink, Kirsten Fischer, Barbara Eichhorst, Michael Hallek, Clemens-Martin Wendtner
LEUKEMIA & LYMPHOMA
(2023)
Article
Oncology
Jiajin Chen, Yunjie Song, Yi Li, Yongyue Wei, Sipeng Shen, Yang Zhao, Dongfang You, Li Su, Maria Moksnes Bjaanaes, Anna Karlsson, Maria Planck, Johan Staaf, Aslaug Helland, Manel Esteller, Hongbing Shen, David C. C. Christiani, Ruyang Zhang, Feng Chen
Summary: This study identified significant gene-gene interactions associated with non-small-cell lung cancer survival through a three-step analytic strategy. Two interactions were found at both the epigenetic and transcriptional levels, providing potential clues for precision treatment of NSCLC.
MOLECULAR ONCOLOGY
(2023)
Article
Oncology
Henrik Horndalsveen, Tine Norman Alver, Astrid Marie Dalsgaard, Lotte Victoria Rogg, Nina Helbekkmo, Bjorn Henning Gronberg, Tarje Onsoien Halvorsen, Christina Ramberg, Vilde Drageset Haakensen, Asa Kristina Ooejlert, Maria Moksnes Bjaanaes, Aslaug Helland
Summary: In this phase II trial, the combination of atezolizumab and stereotactic body radiotherapy was found to be safe and effective in treating advanced non-small-cell lung cancer patients. The study also highlighted the potential of circulating tumor DNA (ctDNA) as a biomarker for monitoring treatment response.
MOLECULAR ONCOLOGY
(2023)
Article
Oncology
Carolina Rosswog, Jana Fassunke, Angela Ernst, Birgid Schoemig-Markiefka, Sabine Merkelbach-Bruse, Christoph Bartenhagen, Maria Cartolano, Sandra Ackermann, Jessica Theissen, Mirjam Blattner-Johnson, Barbara Jones, Kathrin Schramm, Janine Altmueller, Peter Nuernberg, Monika Ortmann, Frank Berthold, Martin Peifer, Reinhard Buettner, Frank Westermann, Johannes H. Schulte, Thorsten Simon, Barbara Hero, Matthias Fischer
Summary: Genomic alterations of the ALK gene occur recurrently in neuroblastoma, with ALK mutations occurring in 10.5% of cases at diagnosis and increasing by 70% at relapse. However, the frequency of ALK amplifications does not change over the course of the disease. Regular monitoring of the genomic ALK status and evaluation of ALK-targeted treatment in intermediate-risk patients is recommended.
BRITISH JOURNAL OF CANCER
(2023)
Article
Biochemistry & Molecular Biology
Dan-Dan Wu, Andy T. Y. Lau, Yan-Ming Xu, Marjan Reinders-Luinge, Mihaly Koncz, Antal Kiss, Wim Timens, Marianne G. Rots, Machteld N. Hylkema
Summary: Ubiquitin carboxyl-terminal hydrolase L1 (UCHL1) is highly expressed in smokers and its molecular mechanism in airway epithelium and its role in extracellular matrix (ECM) remodeling are not well understood. Our study showed that cigarette smoke extract (CSE) stimulated UCHL1 expression in vitro and the methylation status of the UCHL1 gene was negatively associated with UCHL1 transcription at specific sites in airway epithelium. Inhibition of UCHL1 activity prevented the TGF-beta 1-induced upregulation of the ECM gene COL1A1, and downregulation of UCHL1 by epigenetic editing reduced mRNA expression of COL1A1 and fibronectin. These findings suggest that UCHL1 may serve as a therapeutic target in fibrosis-related disease.
Article
Genetics & Heredity
Franziska Schnabel, Elisabeth Schuler, Almundher Al-Maawali, Ankur Chaurasia, Steffen Syrbe, Adila Al-Kindi, Gandham SriLakshmi Bhavani, Anju Shukla, Janine Altmueller, Peter Nuernberg, Siddharth Banka, Katta M. Girisha, Yun Li, Bernd Wollnik, Goekhan Yigit
Summary: This study reports five patients from three families with a disorder characterized by congenital joint contractures affecting multiple body parts, including shoulder, elbow, hand, hip, knee, and foot, as well as scoliosis, reduced palmar and plantar skin folds, microcephaly, and facial dysmorphism. Exome sequencing identified homozygous truncating variants in the FILIP1 gene in all patients. FILIP1 is involved in the regulation of filamin homeostasis and is essential for cortical cell migration and muscle cell differentiation.
Article
Oncology
Birgitta I. Hiddinga, Dirk-Jan Slebos, T. David Koster, Lucie B. M. Hijmering-Kappelle, T. Jeroen N. Hiltermann, Hanneke Kievit, Anthonie J. van der Wekken, Gonda de Jonge, Rozemarijn Vliegenthart, Caroline Van De Wauwer, Wim Timens, Frederike Bensch
Summary: In this study, we evaluated the value of virtual bronchoscopy navigation in diagnosing solitary pulmonary nodules. The procedure had a good diagnostic yield and helped to prevent unnecessary invasive procedures and treatments without histological confirmation of cancer.
Article
Biochemistry & Molecular Biology
Lisa Sikkema, Ciro Ramirez-Suastegui, Daniel C. Strobl, Tessa E. Gillett, Luke Zappia, Elo Madissoon, Nikolay S. Markov, Laure-Emmanuelle Zaragosi, Yuge Ji, Meshal Ansari, Marie-Jeanne Arguel, Leonie Apperloo, Martin Banchero, Christophe Becavin, Marijn Berg, Evgeny Chichelnitskiy, Mei-i Chung, Antoine Collin, Aurore C. A. Gay, Janine Gote-Schniering, Baharak Hooshiar Kashani, Kemal Inecik, Manu Jain, Theodore S. Kapellos, Tessa M. Kole, Sylvie Leroy, Christoph H. Mayr, Amanda J. Oliver, Michael von Papen, Lance Peter, Chase J. Taylor, Thomas Walzthoeni, Chuan Xu, Linh T. Bui, Carlo De Donno, Leander Dony, Alen Faiz, Minzhe Guo, Austin J. Gutierrez, Lukas Heumos, Ni Huang, Ignacio L. Ibarra, Nathan D. Jackson, Preetish Kadur Lakshminarasimha Murthy, Mohammad Lotfollahi, Tracy Tabib, Carlos Talavera-Lopez, Kyle J. Travaglini, Anna Wilbrey-Clark, Kaylee B. Worlock, Masahiro Yoshida, Maarten van den Berge, Yohan Bosse, Tushar J. Desai, Oliver Eickelberg, Naftali Kaminski, Mark A. Krasnow, Robert Lafyatis, Marko Z. Nikolic, Joseph E. Powell, Jayaraj Rajagopal, Mauricio Rojas, Orit Rozenblatt-Rosen, Max A. Seibold, Dean Sheppard, Douglas P. Shepherd, Don D. Sin, Wim Timens, Alexander M. Tsankov, Jeffrey Whitsett, Yan Xu, Nicholas E. Banovich, Pascal Barbry, Thu Elizabeth Duong, Christine S. Falk, Kerstin B. Meyer, Jonathan A. Kropski, Dana Pe'er, Herbert B. Schiller, Purushothama Rao Tata, Joachim L. Schultze, Sara A. Teichmann, Alexander Misharin, Martijn C. Nawijn, Malte D. Luecken, Fabian J. Theis, Yuexin Chen, James S. Hagood, Ahmed Agami, Peter Horvath, Joakim Lundeberg, Charles-Hugo Marquette, Gloria Pryhuber, Chistos Samakovlis, Xin Sun, Lorraine B. Ware, Kun Zhang
Summary: Single-cell technologies are used to study human tissues, but individual studies have limitations in terms of sample size and cell type definitions. The integrated Human Lung Cell Atlas (HLCA) combines 49 datasets from 486 individuals to create a comprehensive atlas of the human respiratory system. The HLCA provides new annotations for different cell types and allows for the identification of gene modules associated with demographic variables and changes in gene expression.
Review
Oncology
Christophe Le Tourneau, Fabrice Andre, Aslaug Helland, Linda Mileshkin, Warnyta Minnaard, Anja Schiel, Kjetil Tasken, David M. Thomas, Maria Luisa Veronese, Gonzalo Duran-Pacheco, Lada Leyens, Kaspar Rufibach, Marlene Thomas, Alwin Kraemer
Summary: Personalised oncology is becoming an essential part of clinical care, guided by molecular tumour profiles and next-generation sequencing technology. Clinical trials have shifted towards biomarker-driven studies of molecularly guided therapies and cancer immunotherapies, requiring a multistakeholder perspective. Innovative technologies and dynamic design methodologies will be necessary for efficient translation of scientific discoveries into clinical utility in the future of cancer clinical trials.
EUROPEAN JOURNAL OF CANCER
(2023)
Editorial Material
Respiratory System
John K. Field
