Article
Multidisciplinary Sciences
Reza Mirzazadeh, Zaneta Andrusivova, Ludvig Larsson, Phillip T. Newton, Leire Alonso Galicia, Xesus M. Abalo, Mahtab Avijgan, Linda Kvastad, Alexandre Denadai-Souza, Nathalie Stakenborg, Alexandra B. Firsova, Alia Shamikh, Aleksandra Jurek, Niklas Schultz, Monica Nister, Christos Samakovlis, Guy Boeckxstaens, Joakim Lundeberg
Summary: Spatially resolved transcriptomics allows genome-wide mRNA expression profiling within tissue sections. The RNA quality is crucial for methods targeting mRNA polyA tails, and the high cost of current spatial transcriptomics assays requires careful sample screening. In this study, the authors introduce a workflow called RRST for mRNA recovery from fresh frozen specimens with moderate to low RNA quality, and demonstrate its robustness on different tissue types.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Stine Bottcher Jacobsen, Jacob Tfelt-Hansen, Morten Holdgaard Smerup, Jeppe Dyrberg Andersen, Niels Morling
Summary: The use of fresh tissue for molecular studies is preferred but often impossible. Frozen or formalin-fixed, paraffin-embedded (FFPE) tissues are widely used and valuable for retrospective studies. RNA extracted from FFPE tissues is highly degraded and yields different gene expression profiles compared to fresh and frozen tissues. However, protein-coding transcripts show high correlations among different storage conditions. Proper quality control and caution regarding technical variability are required when using frozen and FFPE tissues for gene expression analyses.
Article
Immunology
Hemant Suryawanshi, Klaas Max, Kimberly A. Bogardus, Anuoluwapo Sopeyin, Michael S. Chang, Pavel Morozov, Paula M. Castano, Thomas Tuschl, Zev Williams
Summary: This study analyzed gene expression in different trimesters of human placenta and identified temporal changes in gene expression patterns. The results showed that gene expression in the placenta varies throughout gestation but remains consistent spatially. The findings provide valuable insights into the pathology of pregnancy-related disorders.
JOURNAL OF REPRODUCTIVE IMMUNOLOGY
(2022)
Article
Clinical Neurology
Delphine Boche, Marcia N. Gordon
Summary: The review explores the diversity of microglial phenotypes in healthy brains, aging, and Alzheimer's disease, identifies knowledge gaps, and suggests areas for further research. Comparisons between human samples and mouse models are made to understand the molecular complexity of microglial response repertoire, which could lead to new therapeutic avenues for Alzheimer's disease.
ALZHEIMERS & DEMENTIA
(2022)
Article
Oncology
Trine B. Mattesen, Claus L. Andersen, Jesper B. Bramsen
Summary: Transcriptional analysis is crucial for cancer research, but high-quality RNA from FFPE tissue is often challenging to obtain. MethCORR method, based on DNA methylation data, successfully infers gene expression for various cancer types with high accuracy, providing a valuable resource for future transcriptional studies using archival FFPE material. The results demonstrate the robustness and clinical relevance of MethCORR for cancer research and patient stratification.
CLINICAL EPIGENETICS
(2021)
Article
Biotechnology & Applied Microbiology
Guy M. Harris, Shahroze Abbas, Michael F. Miles
Summary: The GCSscore algorithm utilizes GC-content of a given oligonucleotide probe to estimate non-specific binding for modern microarrays, providing differential expression analysis at gene-level and exon-level. The algorithm outperformed existing analysis approaches on newer microarrays, producing results with a higher number of DEGs and identifying cognate biological functions.
Article
Oncology
Alessandra Borgognone, Garazi Serna, Marc Noguera-Julian, Lidia Alonso, Mariona Parera, Francesc Catala-Moll, Lidia Sanchez, Roberta Fasani, Roger Paredes, Paolo Nuciforo
Summary: The comparison of fresh-frozen (FF) and FFPE colorectal cancer (CRC) tissues revealed differences in microbial diversity and composition, with FF samples enriched in representative CRC-associated bacteria and FFPE samples mainly enriched in typical contaminants. An internal quality index showed a correlation between the similarity within sample pairs and the dominance of contaminant taxa. These findings may provide useful indications for accurate and reproducible metagenomics analyses, especially in larger studies in human cancer genomics using FFPE specimens.
Article
Genetics & Heredity
Benjamin Chidester, Tianming Zhou, Shahul Alam, Jian Ma
Summary: Spatial transcriptomics is a method to reveal spatially resolved gene expression of diverse cells in complex tissues. SpiceMix, an interpretable method based on probabilistic, latent variable modeling, improves on the inference of cell types and their spatial patterns. By analyzing spatial transcriptome data of brain regions in human and mouse, SpiceMix enhances the inference of complex cell identities, reveals interpretable spatial metagenes, and uncovers differentiation trajectories. SpiceMix is a generalizable analysis framework for spatial transcriptome data to investigate cell-type composition and spatial organization of cells in complex tissues.
Article
Oncology
Apostolia M. Tsimberidou, Elena Fountzilas, Leonidas Bleris, Razelle Kurzrock
Summary: Transcriptomics is a valuable tool in understanding cancer mechanisms and identifying biomarkers. It enables the analysis of gene expression and identification of molecular alterations in tumor tissue, which can be used for clinical interventions. It also has applications in predicting and prognosticating biomarkers, improving risk stratification, and understanding the impact of genomic alterations. Additionally, transcriptomics can be used to identify markers predicting response to immunotherapy in clinical trials.
SEMINARS IN CANCER BIOLOGY
(2022)
Article
Biology
Luca Visentin, Giorgia Scarpellino, Giorgia Chinigo, Luca Munaron, Federico Alessandro Ruffinatti
Summary: BioTEA is a software tool for analyzing gene expression differences, which allows easy, quick, and reproducible analysis of gene expression data. It combines multiple functions, including gene filtering, batch effect handling, and sample pairing, to adapt to the structure of different datasets. Additionally, BioTEA has a detailed log file that provides accurate information about each step of the analysis.
Article
Cell Biology
Dominik Saul, Robyn Laura Kosinsky
Summary: The study analyzed the transcriptional patterns associated with aging in different types of cancer and found upregulation of aging-induced genes in malignant diseases, indicating their importance in cell development It was observed that all cancer entities analyzed in the study comprised cell populations expressing these aging-induced genes.
Review
Cell & Tissue Engineering
Hui-Qi Qu, Charlly Kao, Hakon Hakonarson
Summary: Single-cell RNA sequencing (scRNA-seq) is a revolutionary technology that has greatly contributed to our understanding of cellular heterogeneity and gene expression dynamics, particularly in stem cell research. Different types of scRNA-seq technologies have been developed and they offer distinct advantages in capturing cellular heterogeneity and characterizing rare cell populations within complex tissues.
Article
Neurosciences
Siqiao Wang, Weijin Qian, Shaofeng Chen, Shuyuan Xian, Minghao Jin, Yifan Liu, Hao Zhang, Hengwei Qin, Xinkun Zhang, Jiwen Zhu, Xi Yue, Chaofeng Shi, Penghui Yan, Runzhi Huang, Zongqiang Huang
Summary: This bibliometric study analyzed SCI-related studies from 2000 to 2022 and found that China was the most productive country, while the United States had the highest influence. Research hotspots mainly focused on molecular and pathological mechanisms of SCI, as well as novel therapies. Future studies should continue to explore more viable therapeutic methods for SCI.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Xinbin Tang, Jiayu Chen, Xinya Zhang, Xuzhu Liu, Zhaoxiang Xie, Kaipeng Wei, Jianlong Qiu, Weiyan Ma, Chen Lin, Rongqin Ke
Summary: Spatial transcriptomics allows the study of gene expression localization in tissues, revealing potential regulatory networks. Improved in situ sequencing (IISS) combines new probing and barcoding approaches with advanced image analysis pipelines for high-resolution targeted gene expression profiling. IISS can be used for single-cell level spatial gene expression analysis in both fresh frozen tissue and formalin-fixed paraffin-embedded tissue sections, enabling the construction of developmental trajectories and cell-cell communication networks.
JOURNAL OF GENETICS AND GENOMICS
(2023)
Article
Dentistry, Oral Surgery & Medicine
E. Horeth, J. Bard, M. Che, T. Wrynn, E. A. C. Song, B. Marzullo, M. S. Burke, S. Popat, T. Loree, J. Zemer, J. L. Tapia, J. Frustino, J. M. Kramer, S. Sinha, R. A. Romano
Summary: This study comprehensively characterizes the molecular features and expression profiles of human submandibular gland cells using single-cell and bulk RNA sequencing. It reveals a variety of cell types and provides insights into cell-cell communication and the dynamic process of differentiation.
JOURNAL OF DENTAL RESEARCH
(2023)
Article
Oncology
Amber N. Hurson, Mustapha Abubakar, Alina M. Hamilton, Kathleen Conway, Katherine A. Hoadley, Michael Love, Andrew F. Olshan, Charles M. Perou, Montserrat Garcia-Closas, Melissa A. Troester
Summary: This study identified breast cancer risk factors associated with RNA-based TP53 and ER, providing a new etiologic schema of interest in breast cancer prevention research.
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2022)
Article
Oncology
Achal Patel, Montserrat Garcia-Closas, Andrew F. Olshan, Charles M. Perou, Melissa A. Troester, Michael Love, Arjun Bhattacharya
Summary: This study identifies race-specific genetic associations with breast cancer risk of recurrence scores and suggests mediation of these associations by PAM50 subtype and expression, with implications for clinical interpretation of these scores.
Article
Environmental Sciences
Ashley M. Geczik, Roni T. Falk, Xia Xu, Beatrice Wiafe-Addai, Joel Yarney, Baffour Awuah, Richard Biritwum, Verna Vanderpuye, Florence Dedey, Ernest Adjei, Francis Aitpillah, Ernest Osei-Bonsu, Joseph Oppong, Nicholas Titiloye, Lawrence Edusei, Kofi Nyarko, Joe-Nat Clegg-Lamptey, Seth Wiafe, Daniel Ansong, Thomas U. Ahearn, Jonine Figueroa, Montserrat Garcia-Closas, Louise A. Brinton, Britton Trabert
Summary: This study provides evidence that the use of lye-based hair relaxer products may increase circulating levels of 16-pathway estrogens, particularly estriol and 16-epiestriol. Additionally, scalp burns among hair relaxer users were associated with elevated levels of unconjugated estrogens. However, no association was found between the use of skin lighteners and estrogen metabolism.
JOURNAL OF EXPOSURE SCIENCE AND ENVIRONMENTAL EPIDEMIOLOGY
(2023)
Correction
Environmental Sciences
Ashley M. Geczik, Roni T. Falk, Xia Xu, Beatrice Wiafe-Addai, Joel Yarney, Baffour Awuah, Richard Biritwum, Verna Vanderpuye, Florence Dedey, Ernest Adjei, Francis Aitpillah, Ernest Osei-Bonsu, Joseph Oppong, Nicholas Titiloye, Lawrence Edusei, Kofi Nyarko, Joe-Nat Clegg-Lamptey, Seth Wiafe, Daniel Ansong, Thomas U. Ahearn, Jonine Figueroa, Montserrat Garcia-Closas, Louise A. Brinton, Britton Trabert
JOURNAL OF EXPOSURE SCIENCE AND ENVIRONMENTAL EPIDEMIOLOGY
(2023)
Article
Oncology
Carey K. Anders, Mark G. Woodcock, Amanda E. D. Van Swearingen, Dominic T. Moore, Maria J. Sambade, Sonia Laurie, Alexander Robeson, Oleg Kolupaev, Luz A. Cuaboy, Amy L. Garrett, Karen McKinnon, Kristen Cowens, Dante Bortone, Benjamin C. Calhoun, Alec D. Wilkinson, Lisa Carey, Trevor Jolly, Hyman Muss, Katherine Reeder-Hayes, Rebecca Kaltman, Rachel Jankowitz, Vinay Gudena, Oludamilola Olajide, Charles Perou, E. Claire Dees, Benjamin G. Vincent, Jonathan S. Serody
Summary: This study evaluated the efficacy of using a low dose of cyclophosphamide (Cy) to deplete regulatory T cells (T-regs) before initiating pembrolizumab in patients with triple negative breast cancer (TNBC). The results showed that Cy did not significantly decrease T-regs before pembrolizumab and there was a rapid recovery in T-regs after the first cycle of therapy. Baseline samples with increased B cell gene expression were associated with clinical response and immune-related toxicity (IRT).
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2022)
Article
Oncology
Alina M. Hamilton, Amber N. Hurson, Linnea T. Olsson, Andrea Walens, Joseph Nsonwu-Farley, Erin L. Kirk, Yara Abdou, Stephanie M. Downs-Canner, Jonathan S. Serody, Charles M. Perou, Benjamin C. Calhoun, Melissa A. Troester, Katherine A. Hoadley
Summary: The immune microenvironment in breast cancer is closely related to race, age, tumor subtype, and grade. Black and young women have higher immune response, which may be associated with higher recurrence risk.
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2022)
Article
Neurosciences
Anna J. Stevenson, Daniel L. McCartney, Danni A. Gadd, Gemma Shireby, Robert F. Hillary, Declan King, Makis Tzioras, Nicola Wrobel, Sarah McCafferty, Lee Murphy, Barry W. McColl, Paul Redmond, Adele M. Taylor, Sarah E. Harris, Tom C. Russ, Andrew M. McIntosh, Jonathan Mill, Colin Smith, Ian J. Deary, Simon R. Cox, Riccardo E. Marioni, Tara L. Spires-Jones
Summary: The study found differences between blood-based inflammation and ageing-related DNA methylation patterns and brain-based patterns, depending on the evaluated regions. The highest epigenetic age acceleration was observed in the hippocampus, while inflammation-related DNA methylation signatures did not vary significantly across brain regions. Reactive microglial burdens were highest in the hippocampus, but the only association between blood- and brain-based methylation signatures and microglia was a significant positive association with acceleration of one epigenetic clock averaged over all five brain regions.
EUROPEAN JOURNAL OF NEUROSCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Rebecca E. Hughes, Richard J. R. Elliott, Xiaodun Li, Alison F. Munro, Ashraff Makda, Roderick N. Carter, Nicholas M. Morton, Kenji Fujihara, Nicholas J. Clemons, Rebecca Fitzgerald, J. Robert O'Neill, Ted Hupp, Neil O. Carragher
Summary: Esophageal adenocarcinoma is a globally concerning disease with increasing incidence and poor prognosis. Researchers have used a high-content Cell Painting assay to screen for small molecules that could be potential therapeutic targets for esophageal adenocarcinoma. They have identified and validated 51 selective small molecules, including elesclomol, disulfiram, and ammonium pyrrolidinedithiocarbamate, and uncovered a unified mechanism of action for these molecules.
ACS CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Neil A. Robertson, Eric Latorre-Crespo, Maria Terradas-Terradas, Jorge Lemos-Portela, Alison C. Purcell, Benjamin J. Livesey, Robert F. Hillary, Lee Murphy, Angie Fawkes, Louise MacGillivray, Mhairi Copland, Riccardo E. Marioni, Joseph A. Marsh, Sarah E. Harris, Simon R. Cox, Ian J. Deary, Linus J. Schumacher, Kristina Kirschner, Tamir Chandra
Summary: An analysis of blood samples reveals insights on the dynamics of clonal hematopoiesis and proposes a model for individualized clone monitoring. This model could help in understanding the relationship between clonal hematopoiesis and increased risk for malignancy, heart disease, and ischemic stroke.
Article
Biochemistry & Molecular Biology
Gisella Figlioli, Amandine Billaud, Thomas U. Ahearn, Natalia N. Antonenkova, Heiko Becher, Matthias W. Beckmann, Sabine Behrens, Javier Benitez, Marina Bermisheva, Marinus J. Blok, Natalia Bogdanova, Bernardo Bonanni, Barbara Burwinkel, Nicola J. Camp, Archie Campbell, Jose E. Castelao, Melissa H. Cessna, Stephen J. Chanock, Kamila Czene, Peter Devilee, Thilo Doerk, Christoph Engel, Mikael Eriksson, Peter A. Fasching, Jonine D. Figueroa, Marike Gabrielson, Manuela Gago-Dominguez, Montserrat Garcia-Closas, Anna Gonzalez-Neira, Felix Grassmann, Pascal Guenel, Melanie Gundert, Andreas Hadjisavvas, Eric Hahnen, Per Hall, Ute Hamann, Patricia A. Harrington, Wei He, Peter Hillemanns, Antoinette Hollestelle, Maartje J. Hooning, Reiner Hoppe, Anthony Howell, Keith Humphreys, Agnes Jager, Anna Jakubowska, Elza K. Khusnutdinova, Yon-Dschun Ko, Vessela N. Kristensen, Annika Lindblom, Jolanta Lissowska, Jan Lubinski, Arto Mannermaa, Siranoush Manoukian, Sara Margolin, Dimitrios Mavroudis, William G. Newman, Nadia Obi, Mihalis Panayiotidis, Muhammad U. Rashid, Valerie Rhenius, Matti A. Rookus, Emmanouil Saloustros, Elinor J. Sawyer, Rita K. Schmutzler, Mitul Shah, Reijo Sironen, Melissa C. Southey, Maija Suvanto, Rob A. E. M. Tollenaar, Ian Tomlinson, Therese Truong, Lizet E. van der Kolk, Elke M. van Veen, Barbara Wappenschmidt, Xiaohong R. Yang, Manjeet K. Bolla, Joe Dennis, Alison M. Dunning, Douglas F. Easton, Michael Lush, Kyriaki Michailidou, Paul D. P. Pharoah, Qin Wang, Muriel A. Adank, Marjanka K. Schmidt, Irene L. Andrulis, Jenny Chang-Claude, Heli Nevanlinna, Georgia Chenevix-Trench, D. Gareth Evans, Roger L. Milne, Paolo Radice, Paolo Peterlongo
Summary: Evidence from the BRIDGES study suggests that germline protein truncating variants (PTVs) in FANCM are associated with increased risk of ER-negative and triple-negative breast cancer (TNBC), particularly for those with a family history. This study further investigates the association between FANCM missense variants (MVs) and breast cancer risk using the BRIDGES study, analyzing a total of 689 MVs. The results indicate that FANCM MVs may be low/moderate risk factors for ER-negative and TNBC subtypes of breast cancer.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Immunology
Xue-Feng Li, Cigdem Selli, Han-Lin Zhou, Jian Cao, Shuiqing Wu, Ruo-Yu Ma, Ye Lu, Cheng-Bin Zhang, Bijie Xun, Alyson D. Lam, Xiao-Cong Pang, Anu Fernando, Zeda Zhang, Asier Unciti-Broceta, Neil O. Carragher, Prakash Ramachandran, Neil C. Henderson, Ling-Ling Sun, Hai-Yan Hu, Gui-Bo Li, Charles Sawyers, Bin-Zhi Qian
Summary: This study identified macrophages as the major component of the metastatic microenvironment in bone-metastatic prostate cancer. Macrophages were found to play a critical role in enzalutamide resistance through the induction of a wound-healing-like response and activation of the cytokine activin A- fibronectin-integrin alpha 5-tyrosine kinase Src signaling cascade. Depletion of macrophages or inhibition of Src significantly inhibited resistant growth, suggesting a potential therapeutic approach for treating metastatic prostate cancer.
JOURNAL OF EXPERIMENTAL MEDICINE
(2023)
Article
Multidisciplinary Sciences
Jonathan L. Gillan, Mithil Chokshi, Gareth R. Hardisty, Sara Clohisey Hendry, Daniel Prasca-Chamorro, Nicola J. Robinson, Benjamin Lasota, Richard Clark, Lee Murphy, Moira K. B. Whyte, J. Kenneth Baillie, Donald J. Davidson, Gang Bao, Robert D. Gray
Summary: An intense and nonresolving airway inflammatory response in cystic fibrosis (CF) leads to destructive lung disease. Dysregulation of macrophage immune function may play a key role in the progression of CF lung disease. Transcriptome sequencing revealed significantly distinct transcriptional programs in CF and non-CF macrophages, including a blunted type I interferon signaling response in CF macrophages. However, this immune defect can be reversed by treatment with CFTR modulators or gene editing.
Article
Oncology
Frederick M. Howard, James Dolezal, Sara Kochanny, Galina Khramtsova, Jasmine Vickery, Andrew Srisuwananukorn, Anna Woodard, Nan Chen, Rita Nanda, Charles M. Perou, Olufunmilayo I. Olopade, Dezheng Huo, Alexander T. Pearson
Summary: Gene expression-based recurrence assays are recommended for guiding chemotherapy in hormone receptor-positive, HER2-negative breast cancer, but their high cost and limited availability pose challenges. This study presents a deep learning model that utilizes digital histology and clinical risk factors to predict recurrence assay results and the risk of recurrence, surpassing the performance of established clinical nomograms. The model can identify patients with excellent prognoses who may not require further genomic testing.
Article
Medicine, General & Internal
Robert A. Hillary, Daniel D. McCartney, Hannah Smith, Elena Bernabeu, Danni Gadd, Aleksandra Chybowska, Yipeng M. Cheng, Lee Murphy, Nicola L. Wrobel, Archie M. Campbell, Rosie E. Walker, Caroline Hayward, Kathryn Evans, Andrew McIntosh, Riccardo Marioni
Summary: This study investigated the association between blood DNA methylation and the prevalence of 14 disease states and the incidence of 19 disease states in a population of over 18,000 Scottish individuals. The findings identified over 100 associations between blood methylation sites and common disease states, suggesting that blood DNA methylation could serve as a potential marker for various common diseases.