Review
Medicine, Research & Experimental
Szonja Anna Kovacs, Balazs Gyorffy
Summary: The availability of immune-checkpoint inhibitors (ICI) has changed the paradigm in oncology. Transcriptomic datasets can help identify biomarkers for predicting immune response and improving clinical treatment outcomes. This review summarizes available transcriptomic data, discusses limitations, and provides an overview of animal studies.
JOURNAL OF TRANSLATIONAL MEDICINE
(2022)
Article
Multidisciplinary Sciences
Lin Jiang, Yueheng Peng, Runyang He, Qingqing Yang, Chanlin Yi, Yuqin Li, Bin Zhu, Yajing Si, Tao Zhang, Bharat B. Biswal, Dezhong Yao, Lan Xiong, Fali Li, Peng Xu
Summary: Human cognition is supported by intrinsic structure and functional neural co-activation in spatially distributed brain regions. This study proposes a multimodal covariance network (MCN) construction approach to capture interregional covarying of the structural skeleton and transient functional activities for a single individual. The findings reveal the correlation between structural-functional differences and brain-wide gene expression patterns, providing insights into cognitive processes and psychiatric disorders.
Article
Biochemical Research Methods
Rebeca Queiroz Figueiredo, Sara Diaz del Ser, Tamara Raschka, Martin Hofmann-Apitius, Alpha Tom Kodamullil, Sarah Mubeen, Daniel Domingo-Fernandez
Summary: Distinct gene expression patterns within various contexts were explored in this study to reveal specific functional roles and biological processes. By utilizing co-expression networks, unique and common patterns were identified, and pathway-level analysis further investigated the relationship between gene expression and specific contexts. The data and tools from this study are important for a deeper understanding of the relationship between gene expression and biological processes.
BMC BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Yiru Sheng, R. Ayesha Ali, Andreas Heyland
Summary: CoRMAP is a meta-analysis tool that retrieves comparative gene expression data from any RNA-Seq dataset using de novo assembly, standardized gene expression tools, and implementing OrthoMCL. It ensures accurate comparison of gene expression levels between experiments and species by using orthogroup assignments.
BMC BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Lulu Yan, Xiaoqiang Sun
Summary: This research comprehensively evaluates 14 deconvolution methods and proposes a new ensemble learning-based method, EnDecon, for more accurate deconvolution. The results show that cell2location, RCTD, and spatialDWLS are more accurate than other methods. Additionally, the study finds differences in the robustness of different methods to sequencing depth, spot size, and normalization choices, and most methods perform best when using the normalization method described in their original papers. This study provides valuable information and guidelines for the practical application of ST deconvolution tools and the development of new and more effective methods.
Editorial Material
Multidisciplinary Sciences
Lyla Atta, Jean Fan
Summary: New computational analysis methods are needed for spatially resolved transcriptomic data, with opportunities for standardized benchmarking metrics and data-sharing infrastructure to drive innovation.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Benjamin L. Walker, Qing Nie
Summary: NeST is a method that extracts spatial gene expression structure through coexpression hotspots, which can identify structure on any spatial scale and any subset of genes, and are highly explainable. Furthermore, NeST performs spatial analysis of cell-cell interactions via ligand-receptor, identifying active areas without restriction of cell type or other groupings.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Yun Long, Qianqian Qin, Jiajun Zhang, Zhan Zhu, Yin Liu, Longjiang Gu, Haiyang Jiang, Weina Si
Summary: Heat stress leads to cellular homeostasis imbalance, growth impairment and yield loss in crop production. Transcriptome analysis of two maize inbreds revealed that CIMBL55 had higher thermotolerance and different metabolic pathways were altered in response to heat stress. Co-expression analysis identified hub genes related to heat stress response and recovery in CIMBL55, which are promising for breeding.
Article
Biochemical Research Methods
Susanna Holmstrom, Sampsa Hautaniemi, Antti Hakkinen
Summary: In this study, a method called POIBM was proposed for batch correction in RNA sequencing. The method learns virtual reference samples directly from the data to correct batch effects without requiring prior phenotypic information. The results showed that POIBM outperforms or matches the performance of previous methods in various cancer datasets, effectively discovers true replicates, and improves cancer subtyping.
Article
Neurosciences
Ahmad Seif Kanaan, Dongmei Yu, Riccardo Metere, Andreas Schaefer, Torsten Schlumm, Berkin Bilgic, Alfred Anwandera, Carol A. Mathews, Jeremiah M. Scharf, Kirsten Mueller-Vahl, Harald E. Moeller
Summary: Quantitative susceptibility mapping (QSM) was performed on 28 patients with Gilles de la Tourette syndrome (GTS) and 26 matched controls, revealing significant reductions in brain iron content in GTS patients. Tic severity was negatively associated with striatal susceptibility. Correlations between susceptibility reductions and gene-expression patterns suggest disruptions in iron regulatory mechanisms are involved in GTS pathophysiology.
NEUROBIOLOGY OF DISEASE
(2023)
Article
Food Science & Technology
Eleni-Anna Kokkoni, Nikolaos Andritsos, Christina Sakarikou, Sofia Michailidou, Anagnostis Argiriou, Efstathios Giaouris
Summary: The study focused on the transcriptomic effects of sublethal antimicrobial exposure on two L. monocytogenes strains. Overall, most of the studied genes either remained stable or were significantly downregulated following antimicrobial exposure. Thymol was particularly effective in downregulating gene expression, while also causing upregulation of important invasion genes in ser. 4b strain.
Article
Biochemistry & Molecular Biology
Alice Nevone, Francesca Lattarulo, Monica Russo, Giada Panno, Paolo Milani, Marco Basset, Maria Antonietta Avanzini, Giampaolo Merlini, Giovanni Palladini, Mario Nuvolone
Summary: In the next-generation sequencing era, RT-qPCR remains widely used for quantifying nucleic acids due to its popularity, versatility, and cost-effectiveness. However, accurate measurement of transcriptional levels requires appropriate reference genes for normalization. Here, we present a strategy that utilizes publicly available transcriptomic datasets to select suitable reference genes for specific clinical or experimental settings and includes a pipeline for RT-qPCR assay design and validation. We demonstrated the efficacy of this strategy by identifying and validating reference genes for transcriptional studies of bone-marrow plasma cells in AL amyloidosis patients. This strategy can be applied to other settings with publicly available transcriptomic datasets.
Review
Plant Sciences
Arijit Mukherjee
Summary: This article discusses the interactions between crops and plant growth-promoting bacteria (PGPB) and the lack of knowledge regarding the mechanisms involved. However, recent transcriptomic studies have made important progress in understanding the regulation of host plant gene expression during these interactions.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemical Research Methods
Hung Mai, Jingxuan Bao, Paul M. Thompson, Dokyoon Kim, Li Shen
Summary: In this study, S-PrediXcan analysis was performed on GWAS summary data from two large imaging genetics initiatives to identify tissue-specific transcriptomic effects on brain volume. The analysis identified 10 genes highly associated with both total brain volume and intracranial volume. These genes were also found to be correlated with cognitive and behavioral traits, providing important insights into the genetic mechanisms of the human brain.
BMC BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Karolina Hanna Prazanowska, Su Bin Lim
Summary: As the importance of single-cell RNA sequencing (scRNA-seq) in studying cellular heterogeneity grows, the number of available scRNA-seq datasets has also increased rapidly. However, reusing such data is often difficult due to small cohort size, limited cell types, and insufficient information on cell type classification. Here, we present a large integrated scRNA-seq dataset containing 224,611 cells from human primary non-small cell lung cancer (NSCLC) tumors. We preprocess and integrate seven independent scRNA-seq datasets using an anchor-based approach, with validation using two additional datasets. This integrated data serves as a valuable resource for studying NSCLC transcriptome at the single cell level.
Article
Biochemistry & Molecular Biology
Haloom Rafehi, Cherie Green, Kiymet Bozaoglu, Greta Gillies, Martin B. Delatycki, Paul J. Lockhart, Ingrid E. Scheffer, Melanie Bahlo
Summary: This study identified a family with myotonic dystrophy type 2 caused by an expansion of a specific STR, which could be detected through screening of WGS datasets. The findings have implications for diagnosis and genetic counseling.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Antony Kaspi, Michael S. Hildebrand, Victoria E. Jackson, Ruth Braden, Olivia van Reyk, Tegan Howell, Simone Debono, Mariana Lauretta, Lottie Morison, Matthew J. Coleman, Richard Webster, David Coman, Himanshu Goel, Mathew Wallis, Gabriel Dabscheck, Lilian Downie, Emma K. Baker, Bronwyn Parry-Fielder, Kirrie Ballard, Eva Harrold, Shaun Ziegenfusz, Mark F. Bennett, Erandee Robertson, Longfei Wang, Amber Boys, Simon E. Fisher, David J. Amor, Ingrid E. Scheffer, Melanie Bahlo, Angela T. Morgan
Summary: This study identified new candidate genes associated with childhood apraxia of speech (CAS) through genome sequencing and bioinformatic analysis. The findings highlight the roles of chromatin organization and gene regulation in CAS, and confirm co-expression of CAS-related genes during brain development.
MOLECULAR PSYCHIATRY
(2023)
Article
Genetics & Heredity
Haloom Rafehi, Justin Read, David J. Szmulewicz, Kayli C. Davies, Penny Snell, Liam G. Fearnley, Liam Scott, Mirja Thomsen, Greta Gillies, Kate Pope, Mark F. Bennett, Jacob E. Munro, Kathie J. Ngo, Luke Chen, Mathew J. Wallis, Ernest G. Butler, Kishore R. Kumar, Kathy H. C. Wu, Susan E. Tomlinson, Stephen Tisch, Abhishek Malhotra, Matthew Lee-Archer, Egor Dolzhenko, Michael A. Eberle, Leslie J. Roberts, Brent L. Fogel, Norbert Bruggemann, Katja Lohmann, Martin B. Delatycki, Melanie Bahlo, Paul J. Lockhart
Summary: This study identified an intronic (GAA) repeat expansion in FGF14 and demonstrated that (GAA)>335 is a disease-causing variant while (GAA)>250 is likely pathogenic. Affected individuals presented with adult-onset cerebellar ataxia with variable features.
AMERICAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Biochemistry & Molecular Biology
David I. Francis, Zornitza Stark, Ingrid E. Scheffer, Tiong Yang Tan, Krithika Murali, Lyndon Gallacher, David J. Amor, Himanshu Goel, Lilian Downie, Chloe A. Stutterd, Emma I. Krzesinski, Anand Vasudevan, Ralph Oertel, Vida Petrovic, Amber Boys, Vivian Wei, Trent Burgess, Karen Dun, Karen L. Oliver, Anne Baxter, Anna Hackett, Samantha Ayres, Sebastian Lunke, Paul Kalitsis, Meaghan Wall
Summary: This study aimed to compare the diagnostic yield of saliva and blood for pathogenic copy number variants (CNVs). The results showed that saliva microarray testing had increased diagnostic utility over blood testing in individuals with syndromic intellectual disability (ID). Mosaic pathogenic CNVs or aneuploidy were detected in saliva but not in blood.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Correction
Biochemistry & Molecular Biology
Antony Kaspi, Michael S. Hildebrand, Victoria E. Jackson, Ruth Braden, Olivia van Reyk, Tegan Howell, Simone Debono, Mariana Lauretta, Lottie Morison, Matthew J. Coleman, Richard Webster, David Coman, Himanshu Goel, Mathew Wallis, Gabriel Dabscheck, Lilian Downie, Emma K. Baker, Bronwyn Parry-Fielder, Kirrie Ballard, Eva Harrold, Shaun Ziegenfusz, Mark F. Bennett, Erandee Robertson, Longfei Wang, Amber Boys, Simon E. Fisher, David J. Amor, Ingrid E. Scheffer, Melanie Bahlo, Angela T. Morgan
MOLECULAR PSYCHIATRY
(2023)
Article
Genetics & Heredity
Dongmao Wang, Paul Trevillian, Stephen May, Peter Diakumis, Yanyan Wang, Deb Colville, Melanie Bahlo, Una Greferath, Erica Fletcher, Barbara Young, Heather G. Mack, Judy Savige
Summary: Scalp-Ear-Nipple syndrome, caused by pathogenic KCTD1 variants, is characterized by scalp defect, prominent ears, and rudimentary breasts. This study found further clinical associations in the eye and kidney.
OPHTHALMIC GENETICS
(2023)
Article
Clinical Neurology
Cinzia Costa, Karen L. Oliver, Carmen Calvello, Jillian M. Cameron, Valentina Imperatore, Laura Tonelli, Davide Colavito, Silvana Franceschetti, Laura Canafoglia, Samuel F. Berkovic, Paolo Prontera
Summary: Progressive myoclonus epilepsies (PMEs) are a diverse group of neurodegenerative disorders that typically occur in late childhood. Through genome-wide molecular studies, pathogenic variants in the IRF2BPL gene were identified in patients with PME, suggesting its involvement in the disease. These findings expand the phenotypic spectrum of IRF2BPL-related disorders and highlight the importance of considering this gene in the diagnosis of patients with PME.
Article
Clinical Neurology
Jillian M. Cameron, John A. Damiano, Bronwyn Grinton, Patrick W. Carney, Penny McKelvie, Peter Silbert, Nicholas Lawn, Ingrid E. Scheffer, Karen L. Oliver, Michael S. Hildebrand, Samuel F. Berkovic
Summary: This study analyzed the phenotypic features of a group of patients with protracted CLN3 disease in order to improve recognition of the disorder. The results showed that visual impairment was the initial symptom, with onset at 5-9 years, similar to classic CLN3 disease. The disease is often accompanied by progressive generalized and focal seizures.
Article
Clinical Neurology
Karen L. Oliver, Marina Trivisano, Simone A. Mandelstam, Angela De Dominicis, David I. Francis, Timothy E. Green, Alison M. Muir, Apoorva Chowdhary, Christoph Hertzberg, Klaus Goldhahn, Julia Metreau, Christine Prager, Jason Pinner, Michael Cardamone, Kenneth A. Myers, Richard J. Leventer, Gaetan Lesca, Melanie Bahlo, Michael S. Hildebrand, Heather C. Mefford, Angela M. Kaindl, Nicola Specchio, Ingrid E. Scheffer
Summary: This study analyzed the epileptology and imaging features of WWOX-DEE, and investigated genotype-phenotype correlations, particularly with regard to survival. The results showed that biallelic WWOX pathogenic variants cause an early infantile developmental and epileptic encephalopathy syndrome, with focal seizures and epileptic spasms being the most common seizure types. Patients with two null WWOX pathogenic variants have higher mortality risk.
Letter
Medicine, General & Internal
Melanie Bahlo
MEDICAL JOURNAL OF AUSTRALIA
(2023)
Correction
Multidisciplinary Sciences
Katie L. Ayers, Stefanie Eggers, Ben N. Rollo, Katherine R. Smith, Nadia M. Davidson, Nicole A. Siddall, Liang Zhao, Josephine Bowles, Karin Weiss, Ginevra Zanni, Lydie Burglen, Shay Ben-Shachar, Jenny Rosensaft, Annick Raas-Rothschild, Anne Jorgensen, Ralf B. Schittenhelm, Cheng Huang, Gorjana Robevska, Jocelyn van den Bergen, Franca Casagranda, Justyna Cyza, Svenja Pachernegg, David K. Wright, Melanie Bahlo, Alicia Oshlack, Terrence J. O'Brien, Patrick Kwan, Peter Koopman, Gary R. Hime, Nadine Girard, Chen Hoffmann, Yuval Shilon, Amnon Zung, Enrico Bertini, Mathieu Milh, Bochra Ben Rhouma, Neila Belguith, Anu Bashamboo, Kenneth McElreavey, Ehud Banne, Naomi Weintrob, Bruria BenZeev, Andrew H. Sinclair
NATURE COMMUNICATIONS
(2023)
Article
Endocrinology & Metabolism
Courtney R. Green, Roberto Bonelli, Brendan R. E. Ansell, Simone Tzaridis, Michal K. Handzlik, Grace H. McGregor, Barbara Hart, Jennifer Trombley, Mary M. Reilly, Paul S. Bernstein, Catherine Egan, Marcus Fruttiger, Martina Wallace, Melanie Bahlo, Martin Friedlander, Christian M. Metallo, Marin L. Gantner
Summary: Metabolomic analysis of MacTel, HSAN1, and dual diagnosed patients revealed metabolic distinctions in amino acid and sphingolipid metabolism. MacTel patients exhibited alterations in amino acids resembling diabetes, as well as changes in sphingolipid levels. HSAN1 patients showed abnormal sphingolipid metabolism compared to controls. These findings have implications for further research and therapeutic approaches for these neurodegenerative diseases.
MOLECULAR METABOLISM
(2023)
Article
Endocrinology & Metabolism
Roberto Bonelli, Sasha M. Woods, Sarah Lockwood, Paul N. Bishop, Kamron N. Khan, Melanie Bahlo, Brendan R. E. Ansell, Marcus Fruttiger
Summary: The primate retina has specialized regional functions, with the macula being specialized for high acuity vision. Different regions in the retina have different susceptibility to diseases, with the macula being primarily affected.
Article
Medicine, Research & Experimental
Kevin T. Eade, Brendan Robert E. Ansell, Sarah Giles, Regis Fallon, Sarah Harkins-Perry, Takayuki Nagasaki, Simone Tzaridis, Martina Wallace, Elizabeth A. Mills, Samaneh Farashi, Alec Johnson, Lydia Sauer, Barbara Hart, M. Elena Diaz-Rubio, Melanie Bahlo, Christian Metallo, Rando Allikmets, Marin L. Gantner, Paul S. Bernstein, Martin Friedlander
Summary: Patient-derived iPSCs are a powerful tool for studying disease mechanisms, with MacTel iRPE cells showing reduced serine levels and dysregulation of central carbon metabolism. Mitochondrial dysfunction in these cells may represent an alternative disease mechanism beyond the known serine/sphingolipid pathway.
JOURNAL OF CLINICAL INVESTIGATION
(2023)