Article
Immunology
Ibrahim A. Akkouh, Timothy Hughes, Vidar M. Steen, Joel C. Glover, Ole A. Andreassen, Srdjan Djurovic, Attila Szabo
Summary: Despite the high heritability of schizophrenia, the detailed pathophysiology and etiology are still unknown. Recent findings suggest that abnormal inflammatory regulation and miRNAs are involved. Comparative analysis of miRNome in SCZ astrocytes revealed four differentially expressed miRNAs with lower baseline expression compared to healthy controls. Peripheral blood analysis also showed significantly lower expression of specific target genes in SCZ patients, further enhancing the understanding of SCZ pathobiology.
BRAIN BEHAVIOR AND IMMUNITY
(2021)
Article
Agricultural Engineering
Li Xu, Jiajia Li, Victor M. Gonzalez Ramos, Christina Lyra, Ad Wiebenga, Igor V. Grigoriev, Ronald P. de Vries, Miia R. Makela, Mao Peng
Summary: This study presents a comparative analysis of sugar transporters (STs) in four filamentous fungi, revealing their diversity at the genomic/transcriptomic level and showing complex regulation patterns. The findings provide valuable insights into the function of STs and their potential applications in metabolic engineering.
BIORESOURCE TECHNOLOGY
(2024)
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.
Article
Biotechnology & Applied Microbiology
Tithi S. Trivedi, Naman Mangukia, Mansi Bhavsar, Archana U. Mankad, Rakesh M. Rawal, Saumya K. Patel
Summary: This study reports the mechanistic actions and influences of miRNAs from Picrorhiza kurroa on human target genes using a cross-kingdom computational approach. 14 human target genes associated with cystic fibrosis were predicted. This research provides important findings for future exploration of using plant miRNAs as therapeutic targets for various diseases including cystic fibrosis through cross-kingdom regulation.
HUMAN GENE THERAPY
(2023)
Article
Biochemistry & Molecular Biology
Melanie D. Smith, Katherine Pillman, Tanja Jankovic-Karasoulos, Dale McAninch, Qianhui Wan, K. Justinian Bogias, Dylan McCullough, Tina Bianco-Miotto, James Breen, Claire T. Roberts
Summary: This study investigated the role of miRNAs in early gestation human placenta using 96 placentas from presumed normal pregnancies and matched profiles from maternal plasma. The results showed a clear gestational age gradient in miRNA expression and differential expression of miRNAs between 6-10 weeks and 11-23 weeks gestation. The data presented may serve as a clinically important reference set for studying early placenta development and potentially developing minimally invasive methods for monitoring placental health.
Article
Plant Sciences
Zhao Liu, Tao Xiong, Yingwei Zhao, Bingfa Qiu, Hao Chen, Xiangyang Kang, Jun Yang
Summary: In this study, GLK transcription factors were identified and characterized in Eucalyptus grandis. The analysis of gene structure, motif composition, chromosome distribution, phylogenetic relationship, and cis-regulatory elements provided insights into the evolutionary conservation and potential functions of GLK genes in chloroplast development and chlorophyll synthesis. Transcriptome analysis and co-expression network analysis revealed the differential expression of GLK genes and their potential positive regulatory relationship with chlorophyll synthesis. Furthermore, miRNAs were predicted to play a role in the regulation of GLK gene expression. This research contributes valuable information to the understanding of GLK genes in Eucalyptus.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Gang Chen, Hong-Mei Qian, Jing Chen, Jie Wang, Ji-Tian Guan, Zai-Long Chi
Summary: The study systematically screened key non-coding RNAs in retinal neurogenesis through whole-transcriptome sequencing. The validated non-coding RNAs and their circular RNA/long non-coding RNA-microRNA-messenger RNA network involve neurotransmitter transport and multicellular organism growth during retinal development.
Article
Biochemistry & Molecular Biology
Xiao Ping Xu, Qing Ying Cao, Qing Xu Guan, Mohammad Aqa Mohammadi, Rou Di Cai, Xiao Hui Chen, Zi Hao Zhang, Yu Kun Chen, Xu Xuhan, Yu Ling Lin, Zhong Xiong Lai
Summary: Dynamic alterations in cell wall biosynthesis contribute to plant somatic embryogenesis. This study identified 36 candidate miRNAs associated with cell wall biosynthesis and validated the specific targeting of four cell wall-related genes by miRNAs. Furthermore, it was found that dlo-miR397a and dlo-miR408-3p played differential roles in early somatic embryogenesis in longan.
Article
Veterinary Sciences
Lihong Gu, Qicheng Jiang, Youyi Chen, Xinli Zheng, Hailong Zhou, Tieshan Xu
Summary: This study found that miRNAs, in conjunction with m6A modification, played a key role in the embryonic breast muscle development of Wenchang chickens. The results of this paper offer a theoretical basis for the study of m6A function in muscle development and fat deposition of Wenchang chickens.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Rongxin Zhang, Yajun Liu, Xingxing Zhang, Ke Xiao, Yue Hou, Hongde Liu, Xiao Sun
Summary: The study profiles and depicts RNA G-quadruplexes in the human transcriptome using DMS-seq and bioinformatics pipeline, revealing their significant association with immune pathways and COVID-19-related gene sets. The bioinformatics analysis also suggests potential regulatory functions of G-quadruplexes on miRNA targeting at the whole transcriptome level. Moreover, G-quadruplexes are found to be depleted in putative, but not real, PAS-strong poly(A) sites, weakening their likelihood of being actual cleaved sites.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Pouria Samadi, Meysam Soleimani, Fatemeh Nouri, Fatemeh Rahbarizadeh, Rezvan Najafi, Akram Jalali
Summary: This study using a systems biology approach investigated potential molecular biomarkers and therapeutic targets related to the progression of colorectal cancer (CRC) from early stages to metastasis. The results identified several potential therapeutic targets and biomarkers, with lncRNA LINC00974 found to be an important and novel biomarker.
Review
Virology
Janine Zeng, Di Cao, Shaomin Yang, Dabbu Kumar Jaijyan, Xiaolian Liu, Songbin Wu, Ruth Cruz-Cosme, Qiyi Tang, Hua Zhu
Summary: Human cytomegalovirus (HCMV) is a widespread pathogen with a large genome that encodes various types of RNAs. These RNAs play important roles in viral processes, immune modulation, and host cell effects. This review provides an overview of HCMV and current research on its transcriptome during lytic and latent infection.
Article
Biochemistry & Molecular Biology
Xiaoxiao Yang, Yang Tong, Gerui Liu, Jiapei Yuan, Yang Yang
Summary: Alternative polyadenylation (APA) is recognized as a crucial step in post-transcriptional regulation of eukaryotic genes, with tissue- and cell-type-specific occurrences. However, there is currently no database incorporating cell-type level information on APA. Single-cell RNA-seq technology enables analysis of APA at the cell-type level, and the scAPAatlas provides a comprehensive resource for exploring APA across different cell types and interpreting potential biological functions.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Victor Camberos, Jonathan Baio, Ana Mandujano, Aida F. Martinez, Leonard Bailey, Nahidh Hasaniya, Mary Kearns-Jonker
Summary: The study investigated the transcriptome of cardiovascular progenitors cultured in space for 30 days, revealing that they acquire a gene expression profile representative of an early-stage, dedifferentiated, stem-like state regardless of age. Spaceflight induced signaling pathways that support cell proliferation and survival, along with transcripts related to cell cycle re-entry, cardiovascular development, and oxidative stress. These findings provide new insight into the multifaceted influence of reduced gravitational environments.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Microbiology
Xiaohui Ju, Fang Li, Jingrui Li, Chunyan Wu, Guangtao Xiang, Xiaomin Zhao, Yuchen Nan, Dongming Zhao, Qiang Ding
Summary: The study suggests that ASFV infection causes a strong suppression of host immune responses, leading to dysregulation of host chemokine axis and metabolic pathways in porcine alveolar macrophages.
VETERINARY MICROBIOLOGY
(2021)
Letter
Hematology
Piers Blombery, Georgina L. Ryland, Lucy C. Fox, Zornitza Stark, Meg Wall, Anna Jarmolowicz, Ain Roesley, Ella R. Thompson, Sean M. Grimmond, Shyam Panicker, Fiona Kwok
BRITISH JOURNAL OF HAEMATOLOGY
(2022)
Article
Genetics & Heredity
Jenette Creaney, Ann-Marie Patch, Venkateswar Addala, Sophie A. Sneddon, Katia Nones, Ian M. Dick, Y. C. Gary Lee, Felicity Newell, Ebony J. Rouse, Marjan M. Naeini, Olga Kondrashova, Vanessa Lakis, Apostolos Nakas, David Waller, Annabel Sharkey, Pamela Mukhopadhyay, Stephen H. Kazakoff, Lambros T. Koufariotis, Aimee L. Davidson, Priya Ramarao-Milne, Oliver Holmes, Qinying Xu, Conrad Leonard, Scott Wood, Sean M. Grimmond, Raphael Bueno, Dean A. Fennell, John Pearson, Bruce W. Robinson, Nicola Waddell
Summary: This study analyzed the genomic and immune features of malignant pleural mesothelioma (MPM) samples and identified driver genes, mutational signatures, and the tumor immune environment associated with MPM. The findings suggest that accounting for genomic and immune microenvironment status may influence future therapeutic planning.
Letter
Pathology
Stefanie Aranza, Christina Roydhouse, Catherine Mitchell, Joseph H. A. Vissers, Wing-Yee Lo, Sean M. Grimmond, Jane Kho
Letter
Pathology
C. Mitchell, V. Malalasekera, A. J. Gill, J. H. A. Vissers, S. J. Luen, S. M. Grimmond, J. Lewin
Letter
Hematology
Georgina L. Ryland, Masayuki Umeda, Linda Holmfeldt, Soren Lehmann, Morten Krogh Herlin, Jing Ma, Mahsa Khanlari, Jeffrey E. Rubnitz, Rhonda E. Ries, Hansen J. Kosasih, Paul G. Ekert, Hwee Ngee Goh, Ing S. Tiong, Sean M. Grimmond, Claudia Haferlach, Ryan B. Day, Timothy J. Ley, Soheil Meshinchi, Xiaotu Ma, Piers Blombery, Jeffery M. Klco
Article
Multidisciplinary Sciences
Magnus Zethoven, Luciano Martelotto, Andrew Pattison, Blake Bowen, Shiva Balachander, Aidan Flynn, Fernando J. Rossello, Annette Hogg, Julie A. Miller, Zdenek Frysak, Sean Grimmond, Lauren Fishbein, Arthur S. Tischler, Anthony J. Gill, Rodney J. Hicks, Patricia L. M. Dahia, Roderick Clifton-Bligh, Karel Pacak, Richard W. Tothill
Summary: This study characterizes the molecular subtypes and gene expression patterns associated with metastasis in pheochromocytomas and paragangliomas using single-nuclei and bulk-tissue RNA-seq techniques.
NATURE COMMUNICATIONS
(2022)
Correction
Multidisciplinary Sciences
Ludmil B. Alexandrov, Jaegil Kim, Nicholas J. Haradhvala, Mi Ni Huang, Alvin Wei Tian Ng, Yang Wu, Arnoud Boot, Kyle R. Covington, Dmitry A. Gordenin, Erik N. Bergstrom, S. M. Ashiqul Islam, Nuria Lopez-Bigas, Leszek J. Klimczak, John R. McPherson, Sandro Morganella, Radhakrishnan Sabarinathan, David A. Wheeler, Ville Mustonen, Gad Getz, Steven G. Rozen, Michael R. Stratton
Correction
Multidisciplinary Sciences
Yilong Li, Nicola D. Roberts, Jeremiah A. Wala, Ofer Shapira, Steven E. Schumacher, Kiran Kumar, Ekta Khurana, Sebastian Waszak, Jan O. Korbel, James E. Haber, Marcin Imielinski, Joachim Weischenfeldt, Rameen Beroukhim, Peter J. Campbell
Correction
Multidisciplinary Sciences
Moritz Gerstung, Clemency Jolly, Ignaty Leshchiner, Stefan C. Dentro, Santiago Gonzalez, Daniel Rosebrock, Thomas J. Mitchell, Yulia Rubanova, Pavana Anur, Kaixian Yu, Maxime Tarabichi, Amit Deshwar, Jeff Wintersinger, Kortine Kleinheinz, Ignacio Vazquez-Garcia, Kerstin Haase, Lara Jerman, Subhajit Sengupta, Geoff Macintyre, Salem Malikic, Nilgun Donmez, Dimitri G. Livitz, Marek Cmero, Jonas Demeulemeester, Steven Schumacher, Yu Fan, Xiaotong Yao, Juhee Lee, Matthias Schlesner, Paul C. Boutros, David D. Bowtell, Hongtu Zhu, Gad Getz, Marcin Imielinski, Rameen Beroukhim, S. Cenk Sahinalp, Yuan Ji, Martin Peifer, Florian Markowetz, Ville Mustonen, Ke Yuan, Wenyi Wang, Quaid D. Morris, Paul T. Spellman, David C. Wedge, Peter Van Loo
Correction
Multidisciplinary Sciences
Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah A. Wala, Ofer Shapira, Grace Tiao, Henrik Hornshoj, Julian M. Hess, Randi Istrup Juul, Ziao Lin, Lars Feuerbach, Radhakrishnan Sabarinathan, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andres Lanzos, Carl Herrmann, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin, Pratiti Bandopadhayay, Johanna Bertl, Keith A. Boroevich, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, David Craft, Priyanka Dhingra, Klev Diamanti, Nuno A. Fonseca, Abel Gonzalez-Perez, Qianyun Guo, Mark P. Hamilton, Nicholas J. Haradhvala, Chen Hong, Keren Isaev, Todd A. Johnson, Malene Juul, Andre Kahles, Abdullah Kahraman, Youngwook Kim, Jan Komorowski, Kiran Kumar, Sushant Kumar, Donghoon Lee, Kjong-Van Lehmann, Yilong Li, Eric Minwei Liu, Lucas Lochovsky, Keunchil Park, Oriol Pich, Nicola D. Roberts, Gordon Saksena, Steven E. Schumacher, Nikos Sidiropoulos, Lina Sieverling, Nasa Sinnott-Armstrong, Chip Stewart, David Tamborero, Jose M. C. Tubio, Husen M. Umer, Liis Uuskuela-Reimand, Claes Wadelius, Lina Wadi, Xiaotong Yao, Cheng-Zhong Zhang, Jing Zhang, James E. Haber, Asger Hobolth, Marcin Imielinski, Manolis Kellis, Michael S. Lawrence, Christian von Mering, Hidewaki Nakagawa, Benjamin J. Raphael, Mark A. Rubin, Chris Sander, Lincoln D. Stein, Joshua M. Stuart, Tatsuhiko Tsunoda, David A. Wheeler, Rory Johnson, Jueri Reimand, Mark Gerstein, Ekta Khurana, Peter J. Campbell, Nuria Lopez-Bigas, Joachim Weischenfeldt, Rameen Beroukhim, Inigo Martincorena, Jakob Skou Pedersen, Gad Getz
Article
Genetics & Heredity
Zornitza Stark, Tiffany Boughtwood, Matilda Haas, Jeffrey Braithwaite, Clara L. Gaff, Ilias Goranitis, Amanda B. Spurdle, David P. Hansen, Oliver Hofmann, Nigel Laing, Sylvia Metcalfe, Ainsley J. Newson, Hamish S. Scott, Natalie Thorne, Robyn L. Ward, Marcel E. Dinger, Stephanie Best, Janet C. Long, Sean M. Grimmond, John Pearson, Nicola Waddell, Christopher P. Barnett, Matthew Cook, Michael Field, David Fielding, Stephen B. Fox, Jozef Gecz, Adam Jaffe, Richard J. Leventer, Paul J. Lockhart, Sebastian Lunke, Andrew J. Mallett, Julie McGaughran, Linda Mileshkin, Katia Nones, Tony Roscioli, Ingrid E. Scheffer, Christopher Semsarian, Cas Simons, David M. Thomas, David R. Thorburn, Richard Tothill, Deborah White, Sally Dunwoodie, Peter T. Simpson, Peta Phillips, Marie-Jo Brion, Keri Finlay, Michael CJ. Quinn, Tessa Mattiske, Emma Tudini, Kirsten Boggs, Sean Murray, Kathy Wells, John Cannings, Andrew H. Sinclair, John Christodoulou, Kathryn N. North
Summary: Australian Genomics is a national collaborative partnership that aims to integrate genomics into healthcare through a whole-of-system approach. It has evaluated genomic testing outcomes in over 5,200 individuals across rare disease and cancer studies and provided evidence-based changes in policy and practice, resulting in government funding and access to genomic tests. It has also developed national skills, infrastructure, policy, and data resources to support data sharing and improve clinical genomic delivery.
AMERICAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Ronnie Ren Jie Low, Ka Yee Fung, Hugh Gao, Adele Preaudet, Laura F. Dagley, Jumana Yousef, Belinda Lee, Samantha J. Emery-Corbin, Rune H. Larsen, Nadia J. Kershaw, Antony W. Burgess, Peter Gibbs, Frederic Hollande, Michael D. W. Griffin, Sean M. Grimmond, Tracy L. Putoczki
Summary: Epithelial-mesenchymal transition (EMT) is a continuum associated with cancer progression, invasive capabilities, and metastasis. Through a sporadic model of pancreatic cancer, a murine organoid biobank was generated to study the different EMT states. It was found that organoid morphology predicts the EMT state, and that TGF beta 1 induces changes in the S100 family, complete EMT, and high-grade tumors. S100A4 may serve as a biomarker for predicting EMT state, disease progression, and outcome in pancreatic cancer patients.
CELL DEATH AND DIFFERENTIATION
(2023)
Article
Oncology
Genevieve Dall, Cassandra J. J. Vandenberg, Ksenija Nesic, Gayanie Ratnayake, Wenying Zhu, Joseph H. A. Vissers, Justin Bedo, Jocelyn Penington, Matthew J. J. Wakefield, Damien Kee, Amandine Carmagnac, Ratana Lim, Kristy Shield-Artin, Briony Milesi, Amanda Lobley, Elizabeth L. L. Kyran, Emily O'Grady, Joshua Tram, Warren Zhou, Devindee Nugawela, Kym Pham Stewart, Reece Caldwell, Lia Papadopoulos, Ashley P. P. Ng, Alexander Dobrovic, Stephen B. B. Fox, Orla McNally, Jeremy D. D. Power, Tarek Meniawy, Teng Han Tan, Ian M. M. Collins, Oliver Klein, Stephen Barnett, Inger Olesen, Anne Hamilton, Oliver Hofmann, Sean Grimmond, Anthony T. T. Papenfuss, Clare L. L. Scott, Holly E. E. Barker
Summary: This study identified mutations in DNA repair genes in a subset of uterine leiomyosarcoma patients and found that these patients may benefit from PARP inhibitor therapy. Patient-derived xenograft models confirmed the efficacy of this treatment approach.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2023)
Article
Oncology
Jessica L. Chitty, Michelle Yam, Lara Perryman, Amelia L. Parker, Joanna N. Skhinas, Yordanos F. I. Setargew, Ellie T. Y. Mok, Emmi Tran, Rhiannon D. Grant, Sharissa L. Latham, Brooke A. Pereira, Shona C. Ritchie, Kendelle J. Murphy, Michael Trpceski, Alison D. Findlay, Pauline Melenec, Elysse C. Filipe, Audrey Nadalini, Sipiththa Velayuthar, Gretel Major, Kaitlin Wyllie, Michael Papanicolaou, Shivanjali Ratnaseelan, Phoebe A. Phillips, George Sharbeen, Janet Youkhana, Alice Russo, Antonia Blackwell, Jordan F. Hastings, Morghan C. Lucas, Cecilia R. Chambers, Daniel A. Reed, Janett Stoehr, Claire Vennin, Ruth Pidsley, Anaiis Zaratzian, Andrew M. Da Silva, Michael Tayao, Brett Charlton, David Herrmann, Max Nobis, Susan J. Clark, Andrew V. Biankin, Amber L. Johns, David R. Croucher, Adnan Nagrial, Anthony J. Gill, Sean M. Grimmond, Marina Pajic, Paul Timpson, Wolfgang Jarolimek, Thomas R. Cox
Summary: By inhibiting the activity of pan-lysyl oxidase, PXS-5505 can reduce fibrosis and stiffness in pancreatic tumors, decrease cancer cell invasion and metastasis, and enhance the efficacy of chemotherapy.
Review
Oncology
Kevin Tran, Owen W. J. Prall, Catherine Mitchell, Angela Chou, Anthony J. Gill, Sean M. Grimmond, Grace Kong, Gareth Kiernan, Cristina Torche, Lara Lipton, Benjamin Thomson, H. S. Ko
Summary: Pancreatic acinar cell carcinoma (ACC) is a rare pancreatic neoplasm that is often difficult to diagnose due to lack of awareness and knowledge about its clinical, radiological, and pathological characteristics. Accurate diagnosis is crucial as it can be easily mistaken for pancreatic ductal adenocarcinoma (PDAC) or pancreatic neuroendocrine tumor (PNET). This case study highlights the importance of integrating clinical, imaging, molecular histopathological, and genomic analysis for the diagnosis and treatment of complex pancreatic ACC.
CURRENT PROBLEMS IN CANCER: CASE REPORTS
(2023)