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Article ; Online: Disparities in spatially variable gene calling highlight the need for benchmarking spatial transcriptomics methods.

Charitakis, Natalie / Salim, Agus / Piers, Adam T / Watt, Kevin I / Porrello, Enzo R / Elliott, David A / Ramialison, Mirana

Genome biology

2023 Volume 24, Issue 1, Page(s) 209

Abstract: Identifying spatially variable genes (SVGs) is a key step in the analysis of spatially resolved transcriptomics data. SVGs provide biological insights by defining transcriptomic differences within tissues, which was previously unachievable using RNA- ... ...

Abstract	Identifying spatially variable genes (SVGs) is a key step in the analysis of spatially resolved transcriptomics data. SVGs provide biological insights by defining transcriptomic differences within tissues, which was previously unachievable using RNA-sequencing technologies. However, the increasing number of published tools designed to define SVG sets currently lack benchmarking methods to accurately assess performance. This study compares results of 6 purpose-built packages for SVG identification across 9 public and 5 simulated datasets and highlights discrepancies between results. Additional tools for generation of simulated data and development of benchmarking methods are required to improve methods for identifying SVGs.
MeSH term(s)	Transcriptome ; Benchmarking ; Gene Expression Profiling
Language	English
Publishing date	2023-09-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-023-03045-1
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Book ; Online: Comparative Analysis of Packages and Algorithms for the Analysis of Spatially Resolved Transcriptomics Data

Charitakis, Natalie / Ramialison, Mirana / Nim, Hieu T.

2021

Abstract: The technology to generate Spatially Resolved Transcriptomics (SRT) data is rapidly being improved and applied to investigate a variety of biological tissues. The ability to interrogate how spatially localised gene expression can lend new insight to ... ...

Abstract	The technology to generate Spatially Resolved Transcriptomics (SRT) data is rapidly being improved and applied to investigate a variety of biological tissues. The ability to interrogate how spatially localised gene expression can lend new insight to different tissue development is critical, but the appropriate tools to analyse this data are still emerging. This chapter reviews available packages and pipelines for the analysis of different SRT datasets with a focus on identifying spatially variable genes (SVGs) alongside other aims, while discussing the importance of and challenges in establishing a standardised 'ground truth' in the biological data for benchmarking. Comment: 32 pages, Figures 3
Keywords	Quantitative Biology - Quantitative Methods ; Quantitative Biology - Genomics
Publishing date	2021-08-03
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: MonaGO: a novel gene ontology enrichment analysis visualisation system.

Xin, Ziyin / Cai, Yujun / Dang, Louis T / Burke, Hannah M S / Revote, Jerico / Charitakis, Natalie / Bienroth, Denis / Nim, Hieu T / Li, Yuan-Fang / Ramialison, Mirana

BMC bioinformatics

2022 Volume 23, Issue 1, Page(s) 69

Abstract: Background: Gene ontology (GO) enrichment analysis is frequently undertaken during exploration of various -omics data sets. Despite the wide array of tools available to biologists to perform this analysis, meaningful visualisation of the overrepresented ...

Abstract	Background: Gene ontology (GO) enrichment analysis is frequently undertaken during exploration of various -omics data sets. Despite the wide array of tools available to biologists to perform this analysis, meaningful visualisation of the overrepresented GO in a manner which is easy to interpret is still lacking. Results: Monash Gene Ontology (MonaGO) is a novel web-based visualisation system that provides an intuitive, interactive and responsive interface for performing GO enrichment analysis and visualising the results. MonaGO supports gene lists as well as GO terms as inputs. Visualisation results can be exported as high-resolution images or restored in new sessions, allowing reproducibility of the analysis. An extensive comparison between MonaGO and 11 state-of-the-art GO enrichment visualisation tools based on 9 features revealed that MonaGO is a unique platform that simultaneously allows interactive visualisation within one single output page, directly accessible through a web browser with customisable display options. Conclusion: MonaGO combines dynamic clustering and interactive visualisation as well as customisation options to assist biologists in obtaining meaningful representation of overrepresented GO terms, producing simplified outputs in an unbiased manner. MonaGO will facilitate the interpretation of GO analysis and will assist the biologists into the representation of the results.
MeSH term(s)	Cluster Analysis ; Gene Ontology ; Probability ; Reproducibility of Results ; Software
Language	English
Publishing date	2022-02-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-022-04594-1
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: A cis-regulatory-directed pipeline for the identification of genes involved in cardiac development and disease

Nim, Hieu T. / Dang, Louis / Thiyagarajah, Harshini / Bakopoulos, Daniel / See, Michael / Charitakis, Natalie / Sibbritt, Tennille / Eichenlaub, Michael P. / Archer, Stuart K. / Fossat, Nicolas / Burke, Richard E. / Tam, Patrick P. L. / Warr, Coral G. / Johnson, Travis K. / Ramialison, Mirana

Genome biology. 2021 Dec., v. 22, no. 1

2021

Abstract: BACKGROUND: Congenital heart diseases are the major cause of death in newborns, but the genetic etiology of this developmental disorder is not fully known. The conventional approach to identify the disease-causing genes focuses on screening genes that ... ...

Abstract	BACKGROUND: Congenital heart diseases are the major cause of death in newborns, but the genetic etiology of this developmental disorder is not fully known. The conventional approach to identify the disease-causing genes focuses on screening genes that display heart-specific expression during development. However, this approach would have discounted genes that are expressed widely in other tissues but may play critical roles in heart development. RESULTS: We report an efficient pipeline of genome-wide gene discovery based on the identification of a cardiac-specific cis-regulatory element signature that points to candidate genes involved in heart development and congenital heart disease. With this pipeline, we retrieve 76% of the known cardiac developmental genes and predict 35 novel genes that previously had no known connectivity to heart development. Functional validation of these novel cardiac genes by RNAi-mediated knockdown of the conserved orthologs in Drosophila cardiac tissue reveals that disrupting the activity of 71% of these genes leads to adult mortality. Among these genes, RpL14, RpS24, and Rpn8 are associated with heart phenotypes. CONCLUSIONS: Our pipeline has enabled the discovery of novel genes with roles in heart development. This workflow, which relies on screening for non-coding cis-regulatory signatures, is amenable for identifying developmental and disease genes for an organ without constraining to genes that are expressed exclusively in the organ of interest.
Keywords	Drosophila ; adults ; death ; etiology ; genes ; heart ; heart diseases ; mortality
Language	English
Dates of publication	2021-12
Size	p. 335.
Publishing place	BioMed Central
Document type	Article
ZDB-ID	2040529-7
ISSN	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-021-02539-0
Database	NAL-Catalogue (AGRICOLA)

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Article: NUMT Confounding Biases Mitochondrial Heteroplasmy Calls in Favor of the Reference Allele.

Maude, Hannah / Davidson, Mira / Charitakis, Natalie / Diaz, Leo / Bowers, William H T / Gradovich, Eva / Andrew, Toby / Huntley, Derek

Frontiers in cell and developmental biology

2019 Volume 7, Page(s) 201

Abstract: Homology between mitochondrial DNA (mtDNA) and nuclear DNA of mitochondrial origin (nuMTs) causes confounding when aligning short sequence reads to the reference human genome, as the true sequence origin cannot be determined. Using a ... ...

Abstract	Homology between mitochondrial DNA (mtDNA) and nuclear DNA of mitochondrial origin (nuMTs) causes confounding when aligning short sequence reads to the reference human genome, as the true sequence origin cannot be determined. Using a systematic
Language	English
Publishing date	2019-09-25
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2737824-X
ISSN	2296-634X
ISSN	2296-634X
DOI	10.3389/fcell.2019.00201
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Article ; Online: A cis-regulatory-directed pipeline for the identification of genes involved in cardiac development and disease.

Nim, Hieu T / Dang, Louis / Thiyagarajah, Harshini / Bakopoulos, Daniel / See, Michael / Charitakis, Natalie / Sibbritt, Tennille / Eichenlaub, Michael P / Archer, Stuart K / Fossat, Nicolas / Burke, Richard E / Tam, Patrick P L / Warr, Coral G / Johnson, Travis K / Ramialison, Mirana

Genome biology

2021 Volume 22, Issue 1, Page(s) 335

Abstract: Background: Congenital heart diseases are the major cause of death in newborns, but the genetic etiology of this developmental disorder is not fully known. The conventional approach to identify the disease-causing genes focuses on screening genes that ... ...

Abstract	Background: Congenital heart diseases are the major cause of death in newborns, but the genetic etiology of this developmental disorder is not fully known. The conventional approach to identify the disease-causing genes focuses on screening genes that display heart-specific expression during development. However, this approach would have discounted genes that are expressed widely in other tissues but may play critical roles in heart development. Results: We report an efficient pipeline of genome-wide gene discovery based on the identification of a cardiac-specific cis-regulatory element signature that points to candidate genes involved in heart development and congenital heart disease. With this pipeline, we retrieve 76% of the known cardiac developmental genes and predict 35 novel genes that previously had no known connectivity to heart development. Functional validation of these novel cardiac genes by RNAi-mediated knockdown of the conserved orthologs in Drosophila cardiac tissue reveals that disrupting the activity of 71% of these genes leads to adult mortality. Among these genes, RpL14, RpS24, and Rpn8 are associated with heart phenotypes. Conclusions: Our pipeline has enabled the discovery of novel genes with roles in heart development. This workflow, which relies on screening for non-coding cis-regulatory signatures, is amenable for identifying developmental and disease genes for an organ without constraining to genes that are expressed exclusively in the organ of interest.
MeSH term(s)	Animals ; Computational Biology ; Drosophila/genetics ; Drosophila/physiology ; Gene Expression Regulation, Developmental ; Genetic Testing ; Genome ; Genomics ; Heart/growth & development ; Heart Defects, Congenital/genetics ; RNA Interference ; Regulatory Elements, Transcriptional ; Ribosomal Proteins/genetics
Chemical Substances	Ribosomal Proteins ; ribosomal protein L14
Language	English
Publishing date	2021-12-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-021-02539-0
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Parallel use of human stem cell lung and heart models provide insights for SARS-CoV-2 treatment.

Rudraraju, Rajeev / Gartner, Matthew J / Neil, Jessica A / Stout, Elizabeth S / Chen, Joseph / Needham, Elise J / See, Michael / Mackenzie-Kludas, Charley / Yang Lee, Leo Yi / Wang, Mingyang / Pointer, Hayley / Karavendzas, Kathy / Abu-Bonsrah, Dad / Drew, Damien / Yang Sun, Yu Bo / Tan, Jia Ping / Sun, Guizhi / Salavaty, Adrian / Charitakis, Natalie /

Nim, Hieu T / Currie, Peter D / Tham, Wai-Hong / Porrello, Enzo / Polo, Jose M / Humphrey, Sean J / Ramialison, Mirana / Elliott, David A / Subbarao, Kanta

Stem cell reports

2023 Volume 18, Issue 6, Page(s) 1308–1324

Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) primarily infects the respiratory tract, but pulmonary and cardiac complications occur in severe coronavirus disease 2019 (COVID-19). To elucidate molecular mechanisms in the lung and heart, we ...

Abstract	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) primarily infects the respiratory tract, but pulmonary and cardiac complications occur in severe coronavirus disease 2019 (COVID-19). To elucidate molecular mechanisms in the lung and heart, we conducted paired experiments in human stem cell-derived lung alveolar type II (AT2) epithelial cell and cardiac cultures infected with SARS-CoV-2. With CRISPR-Cas9-mediated knockout of ACE2, we demonstrated that angiotensin-converting enzyme 2 (ACE2) was essential for SARS-CoV-2 infection of both cell types but that further processing in lung cells required TMPRSS2, while cardiac cells required the endosomal pathway. Host responses were significantly different; transcriptome profiling and phosphoproteomics responses depended strongly on the cell type. We identified several antiviral compounds with distinct antiviral and toxicity profiles in lung AT2 and cardiac cells, highlighting the importance of using several relevant cell types for evaluation of antiviral drugs. Our data provide new insights into rational drug combinations for effective treatment of a virus that affects multiple organ systems.
MeSH term(s)	Humans ; SARS-CoV-2 ; Angiotensin-Converting Enzyme 2 ; COVID-19 ; Stem Cells ; Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; Lung
Chemical Substances	Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; Antiviral Agents
Language	English
Publishing date	2023-06-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2720528-9
ISSN	2213-6711 ; 2213-6711
ISSN (online)	2213-6711
ISSN	2213-6711
DOI	10.1016/j.stemcr.2023.05.007
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Parallel use of pluripotent human stem cell lung and heart models provide new insights for treatment of SARS-CoV-2.

Rudraraju, Rajeev / Gartner, Matthew J / Neil, Jessica A / Stout, Elizabeth S / Chen, Joseph / Needham, Elise J / See, Michael / Mackenzie-Kludas, Charley / Yang Lee, Leo Yi / Wang, Mingyang / Pointer, Hayley / Karavendzas, Kathy / Abu-Bonsrah, Dad / Drew, Damien / Sun, Yu Bo Yang / Tan, Jia Ping / Sun, Guizhi / Salavaty, Abbas / Charitakis, Natalie /

Nim, Hieu T / Currie, Peter D / Tham, Wai-Hong / Porrello, Enzo / Polo, Jose / Humphrey, Sean J / Ramialison, Mirana / Elliott, David A / Subbarao, Kanta

bioRxiv : the preprint server for biology

2022

Abstract: SARS-CoV-2 primarily infects the respiratory tract, but pulmonary and cardiac complications occur in severe COVID-19. To elucidate molecular mechanisms in the lung and heart, we conducted paired experiments in human stem cell-derived lung alveolar type ... ...

Abstract	SARS-CoV-2 primarily infects the respiratory tract, but pulmonary and cardiac complications occur in severe COVID-19. To elucidate molecular mechanisms in the lung and heart, we conducted paired experiments in human stem cell-derived lung alveolar type II (AT2) epithelial cell and cardiac cultures infected with SARS-CoV-2. With CRISPR- Cas9 mediated knock-out of ACE2, we demonstrated that angiotensin converting enzyme 2 (ACE2) was essential for SARS-CoV-2 infection of both cell types but further processing in lung cells required TMPRSS2 while cardiac cells required the endosomal pathway. Host responses were significantly different; transcriptome profiling and phosphoproteomics responses depended strongly on the cell type. We identified several antiviral compounds with distinct antiviral and toxicity profiles in lung AT2 and cardiac cells, highlighting the importance of using several relevant cell types for evaluation of antiviral drugs. Our data provide new insights into rational drug combinations for effective treatment of a virus that affects multiple organ systems. One-sentence summary: Rational treatment strategies for SARS-CoV-2 derived from human PSC models.
Language	English
Publishing date	2022-09-21
Publishing country	United States
Document type	Preprint
DOI	10.1101/2022.09.20.508614
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Article ; Online: 3D-cardiomics: A spatial transcriptional atlas of the mammalian heart.

Mohenska, Monika / Tan, Nathalia M / Tokolyi, Alex / Furtado, Milena B / Costa, Mauro W / Perry, Andrew J / Hatwell-Humble, Jessica / van Duijvenboden, Karel / Nim, Hieu T / Ji, Yuan M M / Charitakis, Natalie / Bienroth, Denis / Bolk, Francesca / Vivien, Celine / Knaupp, Anja S / Powell, David R / Elliott, David A / Porrello, Enzo R / Nilsson, Susan K /

Del Monte-Nieto, Gonzalo / Rosenthal, Nadia A / Rossello, Fernando J / Polo, Jose M / Ramialison, Mirana

Journal of molecular and cellular cardiology

2021 Volume 163, Page(s) 20–32

Abstract: Understanding the spatial gene expression and regulation in the heart is key to uncovering its developmental and physiological processes, during homeostasis and disease. Numerous techniques exist to gain gene expression and regulation information in ... ...

Abstract	Understanding the spatial gene expression and regulation in the heart is key to uncovering its developmental and physiological processes, during homeostasis and disease. Numerous techniques exist to gain gene expression and regulation information in organs such as the heart, but few utilize intuitive true-to-life three-dimensional representations to analyze and visualise results. Here we combined transcriptomics with 3D-modelling to interrogate spatial gene expression in the mammalian heart. For this, we microdissected and sequenced transcriptome-wide 18 anatomical sections of the adult mouse heart. Our study has unveiled known and novel genes that display complex spatial expression in the heart sub-compartments. We have also created 3D-cardiomics, an interface for spatial transcriptome analysis and visualization that allows the easy exploration of these data in a 3D model of the heart. 3D-cardiomics is accessible from http://3d-cardiomics.erc.monash.edu/.
MeSH term(s)	Animals ; Gene Expression Profiling/methods ; Heart ; Mammals ; Mice ; Transcriptome
Language	English
Publishing date	2021-10-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80157-4
ISSN	1095-8584 ; 0022-2828
ISSN (online)	1095-8584
ISSN	0022-2828
DOI	10.1016/j.yjmcc.2021.09.011
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Article ; Online: Parallel use of pluripotent human stem cell lung and heart models provide new insights for treatment of SARS-CoV-2

Rudraraju, Rajeev / Gartner, Matthew J / Neil, Jessica A / Stout, Elizabeth S / Chen, Joseph / Needham, Elise J / See, Michael / Mackenzie-Kludas, Charley / Yang, Leo Yi / Wang, Mingyang / Pointer, Hayley / Karavendzas, Kathy / Abu-Bonsrah, Dad / Drew, Damien / Sun, Yu Bo Yang / Tan, Jia Ping / Sun, Guizhi / Salavaty, Abbas / Charitakis, Natalie /

Nim, Hieu T / Currie, Peter D / Tham, Wai-Hong / Porrello, Enzo / Polo, Jose / Humphrey, Sean J / Ramialison, Mirana / Elliott, David A / Subbarao, Kanta

bioRxiv

Abstract	SARS-CoV-2 primarily infects the respiratory tract, but pulmonary and cardiac complications occur in severe COVID-19. To elucidate molecular mechanisms in the lung and heart, we conducted paired experiments in human stem cell-derived lung alveolar type II (AT2) epithelial cell and cardiac cultures infected with SARS-CoV-2. With CRISPR-Cas9 mediated knock-out of ACE2, we demonstrated that angiotensin converting enzyme 2 (ACE2) was essential for SARS-CoV-2 infection of both cell types but further processing in lung cells required TMPRSS2 while cardiac cells required the endosomal pathway. Host responses were significantly different; transcriptome profiling and phosphoproteomics responses depended strongly on the cell type. We identified several antiviral compounds with distinct antiviral and toxicity profiles in lung AT2 and cardiac cells, highlighting the importance of using several relevant cell types for evaluation of antiviral drugs. Our data provide new insights into rational drug combinations for effective treatment of a virus that affects multiple organ systems.
Keywords	covid19
Language	English
Publishing date	2022-09-21
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2022.09.20.508614
Database	COVID19

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