Article
Plant Sciences
Zhen Peng, Hongge Li, Gaofei Sun, Panhong Dai, Xiaoli Geng, Xiao Wang, Xiaomeng Zhang, Zhengzhen Wang, Yinhua Jia, Zhaoe Pan, Baojun Chen, Xiongming Du, Shoupu He
Summary: The paper introduces a cotton genomic variation database, CottonGVD, which provides cotton researchers with a comprehensive tool to exhibit genomic variations and GWAS results. Users can easily retrieve, browse, query, and visualize various cotton-related data using built-in tools and interactive maps provided in the database.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemical Research Methods
Genaro Camele, Sebastian Menazzi, Hernan Chanfreau, Agustin Marraco, Waldo Hasperue, Matias D. Butti, Martin C. Abba
Summary: Multiomix is an interactive cloud-based platform that helps biologists identify genetic and epigenetic events associated with the transcriptional modulation of cancer-related genes. Users can analyze data from public functional genomic databases or upload their own datasets. Multiomix provides a range of functions, pipelines, and a graphical user interface for retrieving, aggregating, analyzing, and visualizing different omics data sources.
Article
Oncology
Sam E. Wing, Hengrui Hu, Lisa Lopez, Ilana Solomon, Jenny Shen, Catherine Raquel, Melissa Sur, Joseph Chao, Mihaela Cristea, Marwan Fakih, Joanne Mortimer, Sumanta Pal, Karen Reckamp, Yuan Yuan, Stacy W. Gray
Summary: A study surveyed 85 cancer patients on their understanding of genetic test results, revealing that around 30% of patients did not recall having had testing, and 44% to 57% of patients did not accurately recall their specific gene variant results. The results indicate significant knowledge gaps in patients' recall of genomic testing, highlighting the critical need to improve patient education and return-of-results strategies.
Editorial Material
Medicine, Research & Experimental
Dawood Darbar
Summary: This study conducted the largest GWAS of European individuals with CHD to date, identifying common genetic variants associated with cardiac anomalies. Through single-cell analysis, the researchers revealed the roles of specific genes in heart development, advancing our understanding of the genetic basis of common forms of CHD.
JOURNAL OF CLINICAL INVESTIGATION
(2021)
Editorial Material
Multidisciplinary Sciences
Ludovic Orlando
Summary: An extensive genomic time series has been conducted on 356 humans from ice-age Europe, showing the impact of climate change on the migration patterns and cultural development of hunter-gatherer populations.
Editorial Material
Multidisciplinary Sciences
Aswin Sekar, Benjamin L. Ebert
Summary: Two studies on mutations in blood-forming cells shed light on the dynamics of blood production in humans and its correlation with aging.
Editorial Material
Microbiology
Mark R. Sullivan, Eric J. Rubin, Charles L. Dulberger
Summary: Mycobacterium abscessus (Mab) is highly tolerant to current antibiotic therapies, leading to a high failure rate of standard care. Phages may offer a promising alternative treatment with few side effects. Two studies shed light on the natural phage complement of Mab and the factors that may drive susceptibility to these phages, paving the way for more effective phage therapy development.
Article
Oncology
Xiaochen Zhang, Fang Liu, Hua Bao, Ao Wang, Ming Han, Xue Wu, Yanhong Gu, Leizhen Zheng
Summary: Gastric cancer, a common and deadly cancer type, has four subtypes with unique molecular alterations. Helicobacter pylori-positive gastric tumors tend to be genome stable and microsatellite stable, showing a distinct genomic landscape. Deep sequencing is promising for uncovering characteristics of microbial environment in tumors.
Article
Oncology
Han Luo, Xue Liao, Yun Qin, Qianqian Hou, Zhinan Xue, Yang Liu, Feiyang Shen, Yuelan Wang, Yong Jiang, Linlin Song, Haining Chen, Lingyun Zhang, Tao Wei, Lunzhi Dai, Li Yang, Wei Zhang, Zhihui Li, Heng Xu, Jingqiang Zhu, Yang Shu
Summary: The study revealed that mutations in CDK4 and TP53 genes during tumor evolution may contribute to lymph node and brain metastasis in papillary thyroid cancer (PTC).
FRONTIERS IN ONCOLOGY
(2021)
Article
Gastroenterology & Hepatology
Feng Wang, You-Sheng Huang, Hao-Xiang Wu, Zi-Xian Wang, Ying Jin, Yi-Chen Yao, Yan-Xing Chen, Qi Zhao, Shifu Chen, Ming-Ming He, Hui-Yan Luo, Miao-Zhen Qiu, De-Shen Wang, Feng-Hua Wang, Mingyan Xu, Yu-Hong Li, Rui-Hua Xu
Summary: The study investigated the genomic heterogeneity of circulating tumor DNA in patients with metastatic colorectal cancer during different treatments, revealing the impact of RAS/BRAF mutations on patients' treatment outcomes. The findings suggest that changes in plasma RAS/BRAF mutational status can significantly affect survival outcomes in these patients.
Editorial Material
Multidisciplinary Sciences
Eucharist Kun, Vagheesh M. Narasimhan
Summary: Scientists have mapped the regions of the human genome that rapidly evolved after the divergence of humans and chimpanzees. These regions contain unique genomic elements linked to neurodevelopment and disease.
Review
Biochemistry & Molecular Biology
Rahul Advani, Sara Luzzi, Emma Scott, Caroline Dalgliesh, Joachim Weischenfeldt, Jennifer Munkley, David J. Elliott
Summary: This article discusses the expression of splicing regulators ESRP1 and ESRP2 in aggressively proliferating primary prostate tumors as markers of disease progression. It suggests that ESRP1 and ESRP2 act as lineage survival oncogenes in prostate cancer and highlights the need to identify the gene expression targets controlled by these regulators to develop targeted therapies.
Article
Biochemistry & Molecular Biology
Eric Wootton, Claude Robert, Jolle Taillon, Steeve Cote, Aaron B. A. Shafer
Summary: In this study, the relationships between measures of inbreeding, genomic constraint, and mutational load were investigated in white-tailed deer, caribou, and mountain goat. The results showed that mountain goats had higher inbreeding coefficients and more evolutionarily constrained regions compared to caribou and white-tailed deer. Additionally, white-tailed deer had the highest mutational load, followed by caribou, while mountain goats had the lowest.
Article
Psychology, Clinical
Sabina Vatter, Timothy E. Schlub, Christine E. Napier, Megan C. Best, Nicci Bartley, Ilona Juraskova, Bettina Meiser, Mandy L. Ballinger, Barbara B. Biesecker, David Goldstein, David M. Thomas, Phyllis Butow
Summary: This study investigated the psychological state and related factors of advanced cancer patients after receiving comprehensive tumor genomic profiling (CGP) results. The study found that most patients did not experience significant distress after receiving the results, although hope decreased. General anxiety and CGP-specific anxiety also decreased. Psychological and demographic factors were associated with psychological status.
Article
Public, Environmental & Occupational Health
Amelia K. Smit, Nicci Bartley, Megan C. Best, Christine E. Napier, Phyllis Butow, Ainsley J. Newson, Kathy Tucker, Mandy L. Ballinger, David M. Thomas, Chris Jacobs, Bettina Meiser, David Goldstein, Jacqueline Savard, Ilona Juraskova
Summary: This study explored family communication about genomic sequencing, focusing on key themes such as family member interest, delayed discussion until results were received, shared capacity to understand and cope, and open communication within the family. Intentions to communicate after receiving results were influenced by disease severity, risk management options, degree of closeness in the family, sense of responsibility, and potential adverse impacts on the family.
PATIENT EDUCATION AND COUNSELING
(2021)
Article
Oncology
Holger Weishaupt, Matko Cancer, Gabriela Rosen, Karl O. Holmberg, Susana Haggqvist, Ignas Bunikis, Yiwen Jiang, Smitha Sreedharan, Ulf Gyllensten, Oren J. Becher, Lene Uhrbom, Adam Ameur, Fredrik J. Swartling
Summary: This study demonstrates a novel approach to tagging glioma genes using retroviral integration sites. By using a high-throughput pipeline coupled to a tumor model system, the researchers were able to detect retroviral integration sites in malignant stem cell lines from glioma biopsies. The results identified genes that have been dysregulated in glioma and also discovered novel potential cancer-causing genes.
Article
Oncology
Teijo Pellinen, Lassi Paavolainen, Alfonso Martin-Bernabe, Renata Papatella Araujo, Carina Strell, Artur Mezheyeuski, Max Backman, Linnea La Fleur, Oscar Bruck, Jonas Sjolund, Erik Holmberg, Katja Valimaki, Hans Brunnstrom, Johan Botling, Pablo Moreno-Ruiz, Olli Kallioniemi, Patrick Micke, Arne Ostman
Summary: This study used multiplex fluorescence immunohistochemistry to study the tumor microenvironment in non-small cell lung cancer (NSCLC) and identified multiple cancer-associated fibroblast (CAF) subsets. The results showed that CAFs play a significant role in NSCLC progression and may have potential as biomarkers or therapeutic targets.
JNCI-JOURNAL OF THE NATIONAL CANCER INSTITUTE
(2023)
Article
Oncology
Albrecht Stenzinger, Anders Edsjoe, Carolin Ploeger, Mikaela Friedman, Stefan Frohling, Valtteri Wirta, Thomas Seufferlein, Johan Botling, Justus Duyster, Michael Akhras, Robert Thimme, Thoas Fioretos, Michael Bitzer, Lucia Cavelier, Peter Schirmacher, Nisar Malek, Richard Rosenquist
Summary: In recent decades, advancements in technology and science have led to the integration of molecular sciences and clinical medicine, resulting in a better understanding of disease mechanisms and the development of novel therapies. Precision medicine, exemplified by precision oncology, holds great promise in various medical fields. Dedicated healthcare centers are required for the real-world implementation of precision medicine, gathering interdisciplinary expertise. Networks of such centers, like Genomic Medicine Sweden and the Centers for Personalized Medicine initiative in Germany, aim to provide a comprehensive framework for precision medicine. They seek to cover all aspects, from technology development to involvement of stakeholders, in order to ensure the sustainable and widespread implementation of precision medicine.
SEMINARS IN CANCER BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sara Goransson, Shan Chen, Helene Olofsson, Ola Larsson, Staffan Stromblad
Summary: A study found that breast cancer cells exhibit different phenotypes on matrices with different stiffness, and this stiffness-associated phenotype is related to the invasiveness of breast cancer, suggesting that matrix stiffness may be one of the mechanisms driving the transition from ductal carcinoma in situ (DCIS) to invasive breast cancer.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Josefin Johansson, Sarah Lideus, Carina Frykholm, Cecilia Gunnarsson, Filip Mihalic, Sanna Gudmundsson, Sara Ekvall, Anna-Maja Molin, Mai Pham, Mauno Vihinen, Kristina Lagerstedt-Robinson, Ann Nordgren, Per Jemth, Adam Ameur, Goeran Anneren, Maria Wilbe, Marie-Louise Bondeson
Summary: This study reveals the genetic and molecular factors underlying Gustavson syndrome, and identifies a novel in-frame deletion in the RBMX gene associated with this syndrome, leading to disrupted RNA polymerase II transcription and potentially reduced SH3 binding. These findings provide new insights into the pathogenesis of RBMX-related intellectual disabilities.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Letter
Biochemistry & Molecular Biology
Thierry Soussi
HUMAN MOLECULAR GENETICS
(2023)
Article
Cell Biology
Caroline Gelabert, Panagiotis Papoutsoglou, Irene Golan, Eric Ahlstrom, Adam Ameur, Carl-Henrik Heldin, Laia Caja, Aristidis Moustakas
Summary: This study demonstrates that LINC00707 interacts with Smad proteins, limiting the output of TGF beta signaling and suppressing cancer cell invasion.
CELL COMMUNICATION AND SIGNALING
(2023)
Article
Multidisciplinary Sciences
Kristine Bilgrav Saether, Daniel Nilsson, Hakan Thonberg, Emma Tham, Adam Ameur, Jesper Eisfeldt, Anna Lindstrand
Summary: The majority of rare diseases are genetic, and despite advances in genomics-based investigations, a large percentage of patients remain undiagnosed. A significant contributing factor to this is the limited understanding of transposable elements (TE), which make up a substantial portion of the human genome. This study aims to bridge this knowledge gap by characterizing TE insertions in different populations and highlights the potential clinical implications in rare disease diagnostics.
Article
Multidisciplinary Sciences
Josefin Johansson, Sarah Lideus, Ida Hoijer, Adam Ameur, Sanna Gudmundsson, Goeran Anneren, Marie-Louise Bondeson, Maria Wilbe
Summary: Researchers developed a novel strategy called XCI-ONT, which combines amplification-free Cas9 enrichment and Oxford nanopore technologies sequencing, to investigate and accurately quantify X-chromosome inactivation (XCI). The XCI-ONT strategy was shown to be more useful and reliable than the PCR-based golden standard technique, and it provides a valuable tool for studying X-linked traits in clinical and research settings.
SCIENTIFIC REPORTS
(2023)
Article
Genetics & Heredity
Daniel Schmitz, Zhiwei Li, Valeria Lo Faro, Mathias Rask-Andersen, Adam Ameur, Nima Rafati, Asa Johansson
Summary: This study characterized CNVs in a Swedish cohort using whole-genome sequencing and identified CNVs associated with plasma proteins. Validations were done using long-read sequencing. The findings provide insights into the structure and effects of common CNVs on the plasma proteome.
Article
Genetics & Heredity
Kimberly Sturk-Andreaggi, Martin Bodner, Joseph D. Ring, Adam Ameur, Ulf Gyllensten, Walther Parson, Charla Marshall, Marie Allen
Summary: The study analyzed the mitochondrial DNA (mtDNA) reads from the SweGen whole genome sequencing dataset to characterize mitogenome variation in Sweden. A total of 934 forensic-quality mitogenome haplotypes were identified, with almost 45% belonging to haplogroup H. The majority (99.1%) of the mitogenome haplotypes were assigned to European haplogroups, as expected. The study also observed signature haplogroups from northern Sweden and Finland, consistent with previous nuclear DNA analyses. The complete mitogenome analysis showed high haplotype diversity and a low random match probability.
Article
Multidisciplinary Sciences
Chiara Pederiva, Davide M. Trevisan, Dimitra Peirasmaki, Shan Chen, Sharon A. Savage, Ola Larsson, Jernej Ule, Laura Baranello, Federico Agostini, Marianne Farnebo
Summary: Posttranscriptional modifications of mRNA, including pseudouridylation, play a crucial role in gene expression regulation. In this study, dyskerin, a pseudouridine synthase, was found to bind to RNA polymerase II and be responsible for pseudouridylation of thousands of mRNAs. Dyskerin-mediated pseudouridylation was shown to interfere with translation and reduction of the modification led to enhanced protein synthesis. Furthermore, dyskeratosis congenita patients with mutations in the dyskerin-encoding gene showed severe reduction in mRNA pseudouridylation.
Article
Genetics & Heredity
Gregory Lazarian, Bernard Leroy, Floriane Theves, Myriam Hormi, Remi Letestu, Virginie Eclache, Giulia Tueur, Adam Ameur, Audrey Bidet, Pascale Cornillet-Lefebvre, Frederic Davi, Eric Delabesse, Marie-Helene Estienne, Pascaline Etancelin, Olivier Kosmider, Sophy Laibe, Marc Muller, Nathalie Nadal, Dina Naguib, Cedric Pastoret, Stephanie Poulain, Pierre Sujobert, Lauren Veronese, Samia Imache, Valerie Lefebvre, Florence Cymbalista, Fanny Baran-Marszak, Thierry Soussi
Summary: TP53 aberrations are a major predictive factor for resistance to chemoimmunotherapy in CLL. This study analyzed 1,056 TP53 variants from 683 patients in France and compared them to a dataset of 5,173 TP53 variants from published articles. The analysis identified CLL-specific hotspot mutations and a novel splice variant. The study also found frequent copy-neutral loss of heterozygosity in CLL and the presence of multiple TP53 variants in a high proportion of patients.
Meeting Abstract
Biochemistry & Molecular Biology
Josefin Johansson, Sarah Lideus, Filip Mihalic, Mauno Vihinen, Carina Frykholm, Sanna Gudmundsson, Adam Ameur, Per Jemth, Marie-Louise Bondeson, Maria Wilbe
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Meeting Abstract
Biochemistry & Molecular Biology
Jonas Mattisson, Moeen Riaz, Galina Polekhina, Andrew Bakshi, Jonatan Halvardson, Marcus Danielsson, Adam Ameur, John McNeil, Lars Forsberg, Paul Lacaze
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)