Review
Cell Biology
Mauro Scaravilli, Sonja Koivukoski, Leena Latonen
Summary: Androgens and their receptor play crucial roles in various diseases, particularly in prostate cancer. Genetic fusions regulated by androgens are more common in prostate cancer compared to other tumors, raising questions that require further investigation.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Voelundur Hafstao, Jari Hakkinen, Helena Persson
Summary: This article presents a method for validating fusion transcripts detected by RNA sequencing in matched whole-genome sequencing data. The pipeline uses discordant read pairs and soft-clipped read alignments to identify supported fusion events and determine genomic breakpoints. The method is faster and more sensitive than commonly used structural variant detection software BreakDancer and Manta.
BMC BIOINFORMATICS
(2023)
Article
Oncology
Yaroslav Ilnytskyy, Lars Petersen, John b. McIntyre, Mie Konno, Adrijana D'Silva, Michelle Dean, Anifat Elegbede, Andrey Golubov, Olga Kovalchuk, Igor Kovalchuk, Gwyn Bebb
Summary: This study investigated the transcript fusions in early-stage non-small cell lung cancer (NSCLC) and identified several recurrent fusions that were significantly associated with clinicopathological variables. Some of these fusions were related to well-known oncogenes. The findings of this study provide valuable information for researchers to identify, select, and validate potential candidates for targeted clinical interventions.
CANCER GENOMICS & PROTEOMICS
(2023)
Article
Plant Sciences
Hyun-Seung Park, Jae-Hyeon Jeon, Woohyeon Cho, Yeonjeong Lee, Jee Young Park, Jiseok Kim, Young Sang Park, Hyun Jo Koo, Jung Hwa Kang, Taek Joo Lee, Sang Hoon Kim, Jin-Baek Kim, Hae-Yun Kwon, Suk-Hwan Kim, Nam-Chon Paek, Geupil Jang, Jeong-Yong Suh, Tae-Jin Yang
Summary: By studying the complete plastid genomes in chimeric plants, we identified 14 different point mutations in eight functional plastid genes related to plastid-encoded RNA polymerase or photosystems, which caused albinism in the chimeric plants. We found that in some plants, the plastomes were identical between green and albino tissues, while in others there were mutations between the two tissues.
HORTICULTURE RESEARCH
(2023)
Review
Oncology
Kumiko Umemoto, Yu Sunakawa
Summary: Promising targets and novel therapeutic drugs have been identified in KRAS wild-type PC, including NRG1 fusion and other potentially actionable alterations. Targeted therapies for NRG1 fusion-positive tumors and aberrations like BRAF, NTRK, and ALK fusion in KRAS wildtype PC have shown activity in clinical trials.
CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY
(2021)
Article
Virology
Bingyu Yan, Srishti Chakravorty, Carmen Mirabelli, Luopin Wang, Jorge L. Trujillo-Ochoa, Daniel Chauss, Dhaneshwar Kumar, Michail S. Lionakis, Matthew R. Olson, Christiane E. Wobus, Behdad Afzali, Majid Kazemian
Summary: The pathogenic mechanisms behind severe SARS-CoV-2 infection are still not fully understood, with recent studies suggesting potential viral integration into the human genome through host-virus chimeric RNA. However, investigation into the biological authenticity of these events raises doubts about their validity.
JOURNAL OF VIROLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Michael Hagemann-Jensen, Christoph Ziegenhain, Rickard Sandberg
Summary: Smart-seq3xpress is a simplified and miniaturized version of the Smart-seq3 protocol, which allows high-throughput single-cell RNA sequencing from full transcripts while reducing reagent usage. Analysis of peripheral blood mononuclear cells using Smart-seq3xpress revealed a comprehensive atlas of common and rare cell types. Compared with droplet-based methods, Smart-seq3xpress also provided additional coverage of cell-type-associated isoform variation.
NATURE BIOTECHNOLOGY
(2022)
Article
Genetics & Heredity
Chen Chen, Samuel Haddox, Yue Tang, Fujun Qin, Hui Li
Summary: This study identified chimeric RNAs in different non-neoplastic cell lines, investigated their expression and distribution patterns, and validated 17 chimeric RNAs across different classifications. The research also demonstrated the ubiquitous expression of these validated chimeric RNAs in both cancer and non-cancer cells, including blood samples from healthy donors.
Article
Biochemical Research Methods
Kun Sun, Huating Wang, Hao Sun
Summary: Recent research focuses on novel transcripts and coding potential in plants, presenting a classifier NAMS optimized for plants and demonstrating its high accuracy and performance improvements on a comprehensive dataset from various plant species. The webserver also offers functional annotations to provide informative clues on transcript functions.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Amin Talebi, Parisa Rokni, Mohammad Amin Kerachian
Summary: This study provides insights into the underlying mechanisms of CRC-LM and offers potential new options for personalized medicine in terms of diagnosis, prognosis, and therapeutic molecular selection.
MOLECULAR AND CELLULAR PROBES
(2022)
Article
Biochemistry & Molecular Biology
Andreea Newtson, Henry Reyes, Eric J. Devor, Michael J. Goodheart, Jesus Gonzalez Bosquet
Summary: The study revealed a higher number of fusion transcripts in high grade serous ovarian cancer compared to normal fallopian tubes, with certain fusion transcripts significantly associated with overall survival. Validation was conducted using various analytical platforms and algorithms to identify fusion transcripts.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Genetics & Heredity
Zhenling Deng, Huige Yan, Zhan Shi, Xinyu Tian, Zhuan Cui, Yingchun Sun, Song Wang, Danxia Zheng, Xiaoyan Qiu, Yue Wang
Summary: This study confirmed that podocytes can produce Igs in normal conditions and increase diversity in pathological situations. The Ig repertoire in podocytes exhibited classic rearrangements with nucleotide additions and somatic hypermutations. Podocytes from patients expressed more classes of Ig, V(H)DJ(H) patterns, and somatic hypermutations compared to those from healthy controls.
Article
Biochemistry & Molecular Biology
Fan Gao, Fang Wang, Huifen Cao, Yue Chen, Yong Diao, Philipp Kapranov
Summary: The human genome contains various noncoding transcripts that have been traditionally categorized into long or small based on their lengths. However, the functions and biological significance of most of these transcripts are still unknown. In this study, a high-throughput assay was developed to test the functionality of small noncoding RNAs (sncRNAs) by overexpressing them in human cells. Surprisingly, a significant fraction of unannotated sncRNAs were found to have biological relevance, challenging the assumption that they are merely degradation products. These findings suggest the potential existence of multiple functional sncRNAs in the small noncoding transcriptome.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Celine Everaert, Jasper Verwilt, Kimberly Verniers, Niels Vandamme, Alvaro Marcos Rubio, Jo Vandesompele, Pieter Mestdagh
Summary: RNA sequencing is widely used for transcriptome analysis, but quantification of low-abundant transcripts remains challenging. Researchers have developed a strategy using high-affinity RNA-binding oligonucleotides to reduce the abundance of specific RNA transcripts in sequencing libraries. This method is efficient, reproducible, and can be easily integrated into existing RNA sequencing protocols, improving transcriptome coverage and complexity.
BIOLOGICAL PROCEDURES ONLINE
(2023)
Article
Biotechnology & Applied Microbiology
Federico Agostini, Julian Zagalak, Jan Attig, Jernej Ule, Nicholas M. Luscombe
Summary: The study investigates the transcriptional activity of unannotated regions in the human genome, revealing that most transcripts originate from fuzzy transcription of known genes and a small portion from putative long non-coding RNA loci. The transcriptional activity and sensitivity of intergenic RNAs were validated using various methods, providing insights into their processing and degradation pathways.
Article
Biochemistry & Molecular Biology
Karen Hoffmann, Hilmar Berger, Hagen Kulbe, Sukanija Thillainadarasan, Hans-Joachim Mollenkopf, Tomasz Zemojtel, Eliane Taube, Silvia Darb-Esfahani, Mandy Mangler, Jalid Sehouli, Radoslav Chekerov, Elena Braicu, Thomas F. Meyer, Mirjana Kessler
Article
Biochemistry & Molecular Biology
Paulina J. Dziubanska-Kusibab, Hilmar Berger, Federica Battistini, Britta A. M. Bouwman, Amina Iftekhar, Riku Katainen, Tatiana Cajuso, Nicola Crosetto, Modesto Orozco, Lauri A. Aaltonen, Thomas F. Meyer
Article
Cell Biology
Audrey Xavier, Munir A. Al-Zeer, Thomas F. Meyer, Oliver Daumke
Article
Microbiology
Iratxe Estibariz, Florent Ailloud, Sabrina Woltemate, Boyke Bunk, Cathrin Sproeer, Joerg Overmann, Toni Aebischer, Thomas F. Meyer, Christine Josenhans, Sebastian Suerbaum
Article
Cell Biology
Cindrilla Chumduri, Rajendra Kumar Gurumurthy, Hilmar Berger, Oliver Dietrich, Naveen Kumar, Stefanie Koster, Volker Brinkmann, Kirstin Hoffmann, Marina Drabkina, Panagiota Arampatzi, Dajung Son, Uwe Klemm, Hans-Joachim Mollenkopf, Hermann Herbst, Mandy Mangler, Jorg Vogel, Antoine-Emmanuel Saliba, Thomas F. Meyer
Summary: The transition zones of squamous and columnar epithelia are prone to cancer, often associated with metaplasia. Through mouse models and single-cell RNA sequencing, it was discovered that the cervical epithelial cells in the endo- and ectocervix have distinct origins from stem cells regulated by opposing Wnt signals from the stroma. Additionally, a mouse model of cervical metaplasia showed that the stroma in the endocervix undergoes remodeling and increases expression of the Wnt inhibitor DKK2, promoting the outgrowth of ectocervical stem cells.
NATURE CELL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Amina Iftekhar, Hilmar Berger, Nassim Bouznad, Julian Heuberger, Francesco Boccellato, Ulrich Dobrindt, Heiko Hermeking, Michael Sigal, Thomas F. Meyer
Summary: Genotoxic colibactin-producing pks+ Escherichia coli infection induces characteristics of colorectal cancer cells in organoids, including enhanced proliferation, Wnt independence, and impaired differentiation. Mutations in genes related to the p53 pathway contribute to Wnt-independence in these organoids, suggesting a functional interplay between p53 and Wnt pathways in promoting transformation. The basis of transformation in these organoids is proposed to be larger chromosomal alterations and aneuploidy, consistent with the early appearance of chromosomal instability in colorectal cancer.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Emanuel Wyler, Kirstin Moesbauer, Vedran Franke, Asija Diag, Lina Theresa Gottula, Roberto Arsie, Filippos Klironomos, David Koppstein, Katja Hoenzke, Salah Ayoub, Christopher Buccitelli, Karen Hoffmann, Anja Richter, Ivano Legnini, Andranik Ivanov, Tommaso Mari, Simone Del Giudice, Jan Papies, Samantha Praktiknjo, Thomas F. Meyer, Marcel Alexander Mueller, Daniela Niemeyer, Andreas Hocke, Matthias Selbach, Altuna Akalin, Nikolaus Rajewsky, Christian Drosten, Markus Landthaler
Summary: Detailed analysis of SARS-CoV-2 infection in comparison with SARS-CoV reveals a stronger induction of innate immune response, including the upregulation of miRNA-155. Infected cells show broad upregulation of genes, while interferon beta/lambda genes and pro-inflammatory cytokines like IL-6 are expressed in only a small subset of cells. Time analysis suggests that interferon regulatory factors are activated before nuclear factor kappa B in response to infection, with heat shock protein 90 (HSP90) identified as a relevant protein for viral replication and inflammatory cytokine expression.
Article
Gastroenterology & Hepatology
Sarah Woelffling, Alice Anna Daddi, Aki Imai-Matsushima, Kristin Fritsche, Christian Goosmann, Jan Traulsen, Richard Lisle, Monika Schmid, Maria del Mar Reines-Benassar, Lennart Pfannkuch, Volker Brinkmann, Jan Bornschein, Peter Malfertheiner, Jurgen Ordemann, Alexander Link, Thomas F. Meyer, Francesco Boccellato
Summary: The study identified signals inducing differentiation of surface mucus-, zymogen-, and gastric acid-producing cells using gastric glands as a model. Epidermal growth factor was shown to be the major fate determinant distinguishing different cell types in human gastric glands. This finding provides insights into the differentiation and patterning of human tissue and the signaling microenvironment in the gastric glands.
Article
Biochemical Research Methods
Marion Rother, Christiane Dimmler, Friderike Weege, Hans-Joachim Mollenkopf, Thomas F. Meyer, Michael Naumann
Summary: Emerging mosquito-borne RNA viruses, such as the Zika virus, have caused significant health complications globally. The lack of antiviral therapy and vaccination has led to a focus on investigating ZIKV-host interactions to understand molecular infection mechanisms. A method for analyzing ZIKV host dependency factors has been established, with potential to identify essential factors for placental infection as targets for antiviral treatment.
JOURNAL OF VIROLOGICAL METHODS
(2021)
Article
Genetics & Heredity
Semen A. Leyn, Jaime E. Zlamal, Oleg V. Kurnasov, Xiaoqing Li, Marinela Elane, Lourdes Myjak, Mikolaj Godzik, Alban de Crecy, Fernando Garcia-Alcalde, Martin Ebeling, Andrei L. Osterman
Summary: Understanding the dynamics and mechanisms of acquired drug resistance is crucial for optimizing current therapies and developing novel ones. Through experimental evolution and genomic sequencing, it was found that E. coli develops robust resistance to triclosan mainly through missense mutations in the fabI gene, with other mutations occurring at earlier stages.
MICROBIAL GENOMICS
(2021)
Article
Biochemistry & Molecular Biology
Gunter Maubach, Michelle C. C. Lim, Olga Sokolova, Steffen Backert, Thomas F. Meyer, Michael Naumann
Summary: The study identifies a dual function of TIFA in activating both classical and alternative NF-kappa B signaling pathways in H. pylori-infected gastric epithelial cells, with TRAF6 and TRAF2 acting as the binding partners of TIFA to facilitate the process.
Article
Microbiology
Jaime E. Zlamal, Semen A. Leyn, Mallika Iyer, Marinela L. Elane, Nicholas A. Wong, James W. Wamsley, Maarten Vercruysse, Fernando Garcia-Alcalde, Andrei L. Osterman
Summary: Resistance to the broad-spectrum antibiotic ciprofloxacin is detected at high rates in various bacterial pathogens, with early resistance primarily caused by single mutations in DNA gyrase target genes. Further genetic alterations influence drug efflux mechanisms and secondary target genes, leading to increased resistance levels. The study highlights shared and unique evolutionary aspects across different species, providing insights for the development of novel antibiotics with reduced resistance tendencies.
Article
Multidisciplinary Sciences
Nils C. Gassen, Jan Papies, Thomas Bajaj, Jackson Emanuel, Frederik Dethloff, Robert Lorenz Chua, Jakob Trimpert, Nicolas Heinemann, Christine Niemeyer, Friderike Weege, Katja Hoenzke, Tom Aschman, Daniel E. Heinz, Katja Weckmann, Tim Ebert, Andreas Zellner, Martina Lennarz, Emanuel Wyler, Simon Schroeder, Anja Richter, Daniela Niemeyer, Karen Hoffmann, Thomas F. Meyer, Frank L. Heppner, Victor M. Corman, Markus Landthaler, Andreas C. Hocke, Markus Morkel, Nikolaus Osterrieder, Christian Conrad, Roland Eils, Helena Radbruch, Patrick Giavalisco, Christian Drosten, Marcel A. Mueller
Summary: Viruses such as SARS-CoV-2 can manipulate cellular metabolism and suppress autophagy, leading to dysregulated immune responses. Studying SARS-CoV-2-infected cells revealed potential host pathways that can be targeted with specific compounds to inhibit virus propagation. This research highlights the importance of understanding host-virus interactions in developing treatment strategies against COVID-19.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Rajendra Kumar Gurumurthy, Stefanie Koster, Naveen Kumar, Thomas F. Meyer, Cindrilla Chumduri
Summary: The cervix is a crucial part of the female reproductive system, playing important roles in fertility, pregnancy maintenance, and infection prevention. Current in vitro models for studying cervix biology are limited in reflecting the physiological and functional properties of the two types of cervical epithelium. This study presents a protocol for establishing adult epithelial stem cell-derived endocervical and ectocervical organoids, which recapitulate the native tissue architecture and can be used to study cervix biology, infections, and cancer evolution.
Review
Oncology
Dongying Wang, Jiaxing He, Junxue Dong, Thomas F. Meyer, Tianmin Xu
AMERICAN JOURNAL OF CANCER RESEARCH
(2020)