Article
Biotechnology & Applied Microbiology
David W. McKellar, Madhav Mantri, Meleana M. Hinchman, John S. L. Parker, Praveen Sethupathy, Benjamin D. Cosgrove, Iwijn De Vlaminck
Summary: Spatial transcriptomics allows us to study the spatial context of gene expression. Current methods are limited to detecting a subset of RNA transcripts. By using enzymatic in situ polyadenylation of RNA, we are able to detect the full spectrum of RNAs, expanding the scope of research. Applying this approach, we studied skeletal muscle regeneration and viral-induced myocarditis, and made new discoveries.
NATURE BIOTECHNOLOGY
(2023)
Article
Oncology
Chun Yang, Si-Jia Chen, Bo-Wen Chen, Kai-Wen Zhang, Jing-Jie Zhang, Rong Xiao, Peng-Gao Li
Summary: Sporamin, a proteinase inhibitor from sweet potato, demonstrates potential anticancer effects against colorectal cancer by inhibiting cell migration and modulating gene expression related to metal ion homeostasis, enzyme activities, and DNA damage repair. Further studies are needed to verify the specific genes affected and elucidate the underlying mechanisms of action.
FRONTIERS IN ONCOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Hanan Bloomer, Richard H. Smith, Waleed Hakami, Andre Larochelle
Summary: Ex vivo gene correction of hematopoietic stem and progenitor cells (HSPCs) has shown promising results for treating inherited blood disorders. The novel NHEJ-based CRISPR-Cas9-mediated transgene knockin approach, known as HITI, has demonstrated improved site-specific integration frequencies in non-dividing cells, offering an effective alternative to HDR-based transgene integration in CD34+ HSPCs.
Article
Multidisciplinary Sciences
Peijie Zhou, Shuxiong Wang, Tiejun Li, Qing Nie
Summary: MuTrans is a method based on multiscale reduction technique that can identify the underlying stochastic dynamics governing cell-fate transitions, construct cell-fate dynamical manifold, distinguish stable and transition cells, and quantify transition probabilities between cell states. The method is consistent with Langevin equation and transition rate theory, and has been shown to robustly unravel complex cell fate dynamics induced by transition cells in various systems. It bridges data-driven and model-based approaches for single-cell resolution analysis of cell-fate transitions.
NATURE COMMUNICATIONS
(2021)
Article
Allergy
Lena Moebus, Elke Rodriguez, Inken Harder, Nicole Boraczynski, Silke Szymczak, Matthias Huebenthal, Dora Stoelzl, Sascha Gerdes, Andreas Kleinheinz, Susanne Abraham, Annice Heratizadeh, Christiane Handrick, Eva Haufe, Thomas Werfel, Jochen Schmitt, Stephan Weidinger
Summary: This study explored the blood transcriptomic features of moderate to severe atopic dermatitis (AD). The results showed that AD patients exhibited pronounced inflammatory expression signatures and could be stratified into eosinophilic and noneosinophilic endotypes. Additionally, treatment strategies for the eosinophil-high endotype may require more attention to the restoration of natural killer cell function.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Cindy Karouta, Robert Kucharski, Kristine Hardy, Kate Thomson, Ryszard Maleszka, Ian Morgan, Regan Ashby
Summary: Research on inhibiting myopia in animals has shown significant overlap in retinal molecular changes, with transcription factors playing a key role in growth regulation. These findings suggest that a defined set of transcriptome changes in the retina is crucial for regulating eye growth.
Article
Chemistry, Multidisciplinary
Ekaterini Koura, Adamantia Pistikoudi, Margaritis Tsifintaris, George Tsiolas, Evangelia Mouchtaropoulou, Christos Noutsos, Triantafyllos Karantakis, Athanasios Kouras, Athanasios Karanikolas, Anagnostis Argiriou, Irini Nianiou-Obeidat, Photini V. Mylona, Alexios N. Polidoros
Summary: This study explored the impact of seed maturity stages and phosphorus fertilization levels on gene expression in lentils and found that the seed maturity stage significantly influenced phenylpropanoid genes, while phosphorus fertilizer had a targeted effect on specific genes and gene clusters. These findings provide valuable information for enhancing lentil product quality through breeding programs.
APPLIED SCIENCES-BASEL
(2023)
Article
Biochemistry & Molecular Biology
Stephanie M. Zimmerman, Robin Fropf, Bridget R. Kulasekara, Maddy Griswold, Oliver Appelbe, Arya Bahrami, Rich Boykin, Derek L. Buhr, Kit Fuhrman, Margaret L. Hoang, Quoc Huynh, Lesley Isgur, Andrew Klock, Alecksandr Kutchma, Alexa E. Lasley, Yan Liang, Jill McKay-Fleisch, Jeffrey S. Nelson, Karen Nguyen, Erin Piazza, Aric Rininger, Daniel R. Zollinger, Michael Rhodes, Joseph M. Beechem
Summary: Emerging spatial profiling technology allows high-plex molecular profiling in biological tissues while preserving the spatial and morphological context of gene expression. By expanding the chemistry for the Digital Spatial Profiling platform, researchers have successfully quantified whole transcriptomes in human and mouse tissues, enabling applications in cancer research, molecular pathology, and developmental biology.
Review
Chemistry, Multidisciplinary
Andrei Anghel, Maria Sala-Cirtog, Catalin Marian, Corina Samoila, Ioan Ovidiu Sirbu
Summary: Soybean has been a part of the human diet for centuries and its dietary use has been proven to benefit human health. However, the impact of soy intake on global gene expression is still not fully understood. Comparing transcriptional changes upon soybean diet supplementation in fish and mammals identified common signaling pathways that may represent a conserved transcriptome response to a soy-enriched dietary challenge.
APPLIED SCIENCES-BASEL
(2021)
Article
Horticulture
Yanli Yao, Mingwei Li, Wenqiu Lin, Shenghui Liu, Qingsong Wu, Qiong Fu, Zhuying Zhu, Yuyao Gao, Xiumei Zhang
Summary: Watercore is a physiological disorder in pineapples that affects fruit quality and storage life. This study, using transcriptome analysis, revealed the molecular mechanism of watercore for the first time and identified key genes related to this disorder.
Article
Multidisciplinary Sciences
Mahashweta Basu, Kun Wang, Eytan Ruppin, Sridhar Hannenhalli
Summary: This study demonstrates that an individual's whole blood transcriptome can predict tissue-specific expression levels for around 60% of genes across various tissues, with particularly high accuracy in skeletal muscle. Predictions based on blood transcriptome are almost as effective as actual tissue expression in identifying disease states for six different complex disorders, surpassing the traditional blood transcriptome approach. The development of TEEBoT provides a valuable tool for further research in other medical conditions.
Article
Biochemical Research Methods
Romain Bulteau, Mirko Francesconi
Summary: RAPToR is a computational method based on transcriptomic data that precisely estimates the real age of a specimen. It can remove age as a confounding variable and recover the signal of interest in differential expression analysis.
Article
Biotechnology & Applied Microbiology
Hiroki Ura, Sumihito Togi, Yo Niida
Summary: This study compared the advantages and disadvantages of three RNA-Seq library preparation methods and found that TruSeq detected transcripts and splicing events better than the other methods, accurately measuring gene expression levels and splicing events. TeloPrime had higher coverage at the transcription start site, while SMARTer performed better than TeloPrime in terms of the number of detected transcripts and splicing events among the studied full-length double-stranded cDNA methods.
Article
Plant Sciences
Keyvan Esmaeilzadeh-Salestani, Masoud Tohidfar, Rahele Ghanbari Moheb Seraj, Banafsheh Khaleghdoust, Indrek Keres, Hashem Marawne, Evelin Loit
Summary: This study compares the effects of organic and mineral nitrogen fertilizers on gene activity in barley. The results show that mineral nitrogen fertilizer treatment leads to a higher number of differentially expressed genes compared to organic nitrogen fertilizer treatment. Pathways related to amino acid synthesis and ribosomal activities are upregulated in mineral fertilizer treatment, while pathways related to starch and sucrose metabolism and carotenoid biosynthesis are downregulated. Organic nitrogen fertilizer treatment enriches pathways related to phenylpropanoid biosynthesis and plant-pathogen interaction. These findings provide insights into the genetic regulation of barley growth in field conditions and can guide the development of sustainable cropping practices and low nitrogen input varieties.
Article
Genetics & Heredity
Philip Kam Weng Kwan, Gail B. Cross, Claire M. Naftalin, Bintou A. Ahidjo, Chee Keng Mok, Felic Fanusi, Intan Permata Sari, Siok Ching Chia, Shoban Krishna Kumar, Rawan Alagha, Sai Meng Tham, Sophia Archuleta, October M. Sessions, Martin L. Hibberd, Nicholas I. Paton
Summary: The study analyzed the whole-blood RNA expression profile of COVID-19 patients and found some unique features compared to other respiratory infections, which warrant further exploration. The disease score approach may have value, but it needs further validation in a population with a greater range of disease severity.
BMC MEDICAL GENOMICS
(2021)
Article
Gastroenterology & Hepatology
Michael B. Cook, Matthew J. Barnett, Cathryn H. Bock, Amanda J. Cross, Phyllis J. Goodman, Gary E. Goodman, Christopher A. Haiman, Kay-Tee Khaw, Marjorie L. McCullough, Christine C. Newton, Marie-Christine Boutron-Ruault, Eiliv Lund, Martin Rutegard, Mark D. Thornquist, Michael Spriggs, Carol Giffen, Neal D. Freedman, Troy Kemp, Candyce H. Kroenke, Loic Le Marchand, Jin Young Park, Michael Simon, Lynne R. Wilkens, Ligia Pinto, Allan Hildesheim, Peter T. Campbell
Article
Oncology
Leila Lujan-Barroso, Edoardo Botteri, Saverio Caini, Boerje Ljungberg, Nina Roswall, Anne Tjonneland, Bas Bueno-de-Mesquita, Inger T. Gram, Rosario Tumino, Lambertus A. Kiemeney, Fredrik Liedberg, Tanja Stocks, Marc J. Gunter, Neil Murphy, Iris Cervenka, Agnes Fournier, Marina Kvaskoff, Christel Haeggstroem, Kim Overvad, Eiliv Lund, Marit Waaseth, Renee Turzanski Fortner, Tilman Kuhn, Virginia Menendez, Maria-Jose Sanchez, Carmen Santiuste, Aurora Perez-Cornago, Raul Zamora-Ros, Amanda J. Cross, Antonia Trichopoulou, Anna Karakatsani, Eleni Peppa, Domenico Palli, Vittorio Krogh, Veronica Sciannameo, Amalia Mattiello, Salvatore Panico, Carla H. van Gils, N. Charlotte Onland-Moret, Aurelio Barricarte, Pilar Amiano, Kay-Tee Khaw, Heiner Boeing, Elisabete Weiderpass, Eric J. Duell
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2020)
Article
Oncology
Amedeo Gagliardi, Pierre-Antoine Dugue, Therese H. Nost, Melissa C. Southey, Daniel D. Buchanan, Daniel F. Schmidt, Enes Makalic, Allison M. Hodge, Dallas R. English, Nicole W. Doo, John L. Hopper, Gianluca Severi, Laura Baglietto, Alessio Naccarati, Sonia Tarallo, Luigia Pace, Vittorio Krogh, Domenico Palli, Salvatore Panico, Carlotta Sacerdote, Rosario Tumino, Eiliv Lund, Graham G. Giles, Barbara Pardini, Torkjel M. Sandanger, Roger L. Milne, Paolo Vineis, Silvia Polidoro, Giovanni Fiorito
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2020)
Article
Multidisciplinary Sciences
Karina Standahl Olsen, Marit Holden, Jean-Christophe Thalabard, Lill-Tove Rasmussen Busund, Eiliv Lund, Lars Holden
Summary: This explorative study aimed to assess time-dependent blood gene expression changes after breast cancer diagnosis. Results showed that there were close to 2,000 differentially expressed genes in the first year post-diagnosis, with a sharp decrease in the second year. A transient second increase was observed in women with metastatic disease who later died, potentially indicating the escape of metastatic cancer from the immune system.
Article
Nutrition & Dietetics
Silvia Pastorino, Tom Bishop, Stephen J. Sharp, Matthew Pearce, Tasnime Akbaraly, Natalia B. Barbieri, Maira Bes-Rastrollo, Joline W. J. Beulens, Zhengming Chen, Huaidong Du, Bruce B. Duncan, Atsushi Goto, Tommi Harkanen, Maryam Hashemian, Daan Kromhout, Ritva Jarvinen, Mika Kivimaki, Paul Knekt, Xu Lin, Eiliv Lund, Dianna J. Magliano, Reza Malekzadeh, Miguel Angel Martinez-Gonzalez, Grainne O'Donoghue, Donal O'Gorman, Hossein Poustchi, Charlotta Rylander, Norie Sawada, Jonathan E. Shaw, Maria Schmidt, Sabita S. Soedamah-Muthu, Liang Sun, Wanqing Wen, Alicja Wolk, Xiao-Ou Shu, Wei Zheng, Nicholas J. Wareham, Nita G. Forouhi
Summary: This study found a neutral association between total fish intake and type 2 diabetes in men, while a modest positive association was observed in women with heterogeneity across studies, which was influenced by geographical location and types of fish intake.
Article
Multidisciplinary Sciences
Therese H. Nost, Marit Holden, Tom Donnem, Hege Bovelstad, Charlotta Rylander, Eiliv Lund, Torkjel M. Sandanger
Summary: Recent studies have found functional genomic signals in blood years before cancer diagnosis. This study focused on gene expression in prospective blood samples from Norwegian Women and Cancer cohort, revealing subtle differences in metastatic case-control pairs 0-3 years before diagnosis. The genes and blood cell populations identified may indicate disruption of immunological processes in blood, suggesting potential circulating signals of disease-related processes in prospective blood samples.
SCIENTIFIC REPORTS
(2021)
Article
Public, Environmental & Occupational Health
Simon Lergenmuller, Reza Ghiasvand, Trude E. Robsahm, Adele C. Green, Eiliv Lund, Corina S. Rueegg, Marit B. Veierod
Summary: The study using data from the Norwegian Women and Cancer Study found no significant difference in risk of cutaneous squamous cell carcinoma between SPF >= 15 and SPF <15 sunscreens, suggesting their effects on long-term usage may be similar or diluted by incorrect application.
AMERICAN JOURNAL OF EPIDEMIOLOGY
(2022)
Letter
Dermatology
N. C. Stoer, E. Botteri, M. Busund, R. Ghiasvand, S. Vangen, E. Lund, E. Weiderpass, M. B. Veierod
BRITISH JOURNAL OF DERMATOLOGY
(2021)
Article
Public, Environmental & Occupational Health
Inger T. Gram, Arne Bastian Wiik, Eiliv Lund, Idlir Licaj, Tonje Braaten
Summary: The study found that women exposed to second-hand smoke from parents during childhood had an 11% higher risk of breast cancer compared to those who were not exposed, and this risk was not related to estrogen and progesterone receptor status. The proportion of breast cancer cases attributable to parental childhood second-hand smoke exposure was 10.3%.
INTERNATIONAL JOURNAL OF EPIDEMIOLOGY
(2021)
Article
Multidisciplinary Sciences
Mie Jareid, Igor Snapkov, Marit Holden, Lill-Tove Rasmussen Busund, Eiliv Lund, Therese Haugdahl Nost
Summary: Investigating gene expression in blood samples of epithelial ovarian cancer cases revealed no significant differences in all EOC cases, with the lowest p-values observed in gene expression of metastatic EOC. There was no common transcriptional profile indicated by the interval from blood sample collection to diagnosis. Despite limitations in sample size, findings suggested less variation in blood gene expression between women with similar tumor characteristics.
Article
Public, Environmental & Occupational Health
Dusan Petrovic, Barbara Bodinier, Sonia Dagnino, Matthew Whitaker, Maryam Karimi, Gianluca Campanella, Therese Haugdahl Nost, Silvia Polidoro, Domenico Palli, Vittorio Krogh, Rosario Tumino, Carlotta Sacerdote, Salvatore Panico, Eiliv Lund, Pierre-Antoine Dugue, Graham G. Giles, Gianluca Severi, Melissa Southey, Paolo Vineis, Silvia Stringhini, Murielle Bochud, Torkjel M. Sandanger, Roel C. H. Vermeulen, Florence Guida, Marc Chadeau-Hyam
Summary: This study investigated the CpG sites associated with lung cancer, both smoking-related and unrelated. The research found that these CpG sites can predict lung cancer more accurately and provide insights into the carcinogenesis of lung cancer and early identification of high-risk patients.
EUROPEAN JOURNAL OF EPIDEMIOLOGY
(2022)
Article
Public, Environmental & Occupational Health
Marit Waaseth, Martina Havelkova, Guro Forsdahl, Eiliv Lund, Tomas Log
Summary: This study aimed to validate self-reported current use of selective serotonin reuptake inhibitors (SSRI) in the Norwegian Women and Cancer study (NOWAC) and to identify factors associated with discordance between data sources. The study found high validity and consistency of self-reported SSRI use from the NOWAC questionnaires. Factors associated with discordance between information sources included poor health, comorbidity, marital status, employment status, and education level.
CLINICAL EPIDEMIOLOGY
(2022)
Article
Infectious Diseases
Erik Eik Anda, Tonje Braaten, Kristin Benjaminsen Borch, Therese Haugdahl Nost, Sairah L. F. Chen, Marko Lukic, Eiliv Lund, Frode Forland, David A. Leon, Brita Askeland Winje, Anne-Marte Bakken Kran, Mette Kalager, Fridtjof Lund Johansen, Torkjel M. Sandanger
Summary: This study from Norway provides insights into the seroprevalence of SARS-CoV-2 before the introduction of vaccines. The findings suggest low seroprevalence rates comparable to virologically detected cases, indicating effective preventive measures and compliance with physical distancing recommendations. Local efforts to contain outbreaks were also essential.
Article
Oncology
Merethe S. Hansen, Idlir Licaj, Tonje Braaten, Eiliv Lund, Inger Torhild Gram
Summary: The study found that active smoking significantly increased the risk of lung cancer in women, while passive smoking also had a slight effect on increasing the risk of lung cancer in non-smoking women. In Norway, more than 80% of lung cancer cases could have been prevented if women did not smoke.
BRITISH JOURNAL OF CANCER
(2021)
Article
Biology
Einar Holsbo, Vittorio Perduca, Lars Ailo Bongo, Eiliv Lund, Etienne Birmele
BMC RESEARCH NOTES
(2020)