A Transcriptome-Wide Isoform Landscape of Melanocytic Nevi and Primary Melanomas Identifies Gene Isoforms Associated with Malignancy

Hakobyan, Siras; Loeffler‐Wirth, Henry; Arakelyan, Arsen; Binder, Hans; Kunz, Manfred

doi:10.3390/ijms22137165

Cited by 8 publications

(6 citation statements)

References 63 publications

(96 reference statements)

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“…As the collagen-like domain is the site for ligand binding, this may indicate that cancer derived ligands work via MSR1 to help drive the formation of the metastatic form of the disease. On the other hand, the most upregulated isoform in benign nevi was a non-coding transcript with loss of an open reading frame ( 188 ). Further suggesting a role for MSR1 in benign to malignant transformation of tumours.…”

Section: Msr1-positive Tumour Associated Macrophages In Cancermentioning

confidence: 99%

The role of macrophage scavenger receptor 1 (MSR1) in inflammatory disorders and cancer

Gudgeon

Marín-Rubio²,

Trost³

2022

Front. Immunol.

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Macrophage scavenger receptor 1 (MSR1), also named CD204, holds key inflammatory roles in multiple pathophysiologic processes. Present primarily on the surface of various types of macrophage, this receptor variably affects processes such as atherosclerosis, innate and adaptive immunity, lung and liver disease, and more recently, cancer. As highlighted throughout this review, the role of MSR1 is often dichotomous, being either host protective or detrimental to the pathogenesis of disease. We will discuss the role of MSR1 in health and disease with a focus on the molecular mechanisms influencing MSR1 expression, how altered expression affects disease process and macrophage function, the limited cell signalling pathways discovered thus far, the emerging role of MSR1 in tumour associated macrophages as well as the therapeutic potential of targeting MSR1.

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Section: Msr1-positive Tumour Associated Macrophages In Cancermentioning

confidence: 99%

The role of macrophage scavenger receptor 1 (MSR1) in inflammatory disorders and cancer

Gudgeon

Marín-Rubio²,

Trost³

2022

Front. Immunol.

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“…The pathways which were significantly deregulated only on coding gene expression level had isoform content change in their genes. Particularly, in the cAMP signaling pathway 9 genes (GRIA1, FXYD1, AKT3, NFATC1, NPY1R, PPP1CB, CAMK4, CFTR, PIK3CA) had switched isoforms (e.g., coding isoforms were replaced with noncoding isoforms while the gene expression remained unchanged in groups) which were detected with IsoformSwitchAnalyzeR R package in our previous study ( Hakobyan et al, 2021 ). Another two pathways (AMPK and JAK-STAT signaling) which were also significantly deregulated on coding gene expression analysis also contained isoform switches in 7 genes (TBC1D1, AKT3, RAB2A, CAB39L, PPP2R5E, CFTR, PIK3CA; AKT3, SOCS6, CCND3, IL3RA, IL3RA, PIK3CA, GHR).…”

Section: Resultsmentioning

confidence: 95%

PSF toolkit: an R package for pathway curation and topology-aware analysis

Hakobyan,

Stepanyan,

Nersisyan

et al. 2023

Front. Genet.

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Most high throughput genomic data analysis pipelines currently rely on over-representation or gene set enrichment analysis (ORA/GSEA) approaches for functional analysis. In contrast, topology-based pathway analysis methods, which offer a more biologically informed perspective by incorporating interaction and topology information, have remained underutilized and inaccessible due to various limiting factors. These methods heavily rely on the quality of pathway topologies and often utilize predefined topologies from databases without assessing their correctness. To address these issues and make topology-aware pathway analysis more accessible and flexible, we introduce the PSF (Pathway Signal Flow) toolkit R package. Our toolkit integrates pathway curation and topology-based analysis, providing interactive and command-line tools that facilitate pathway importation, correction, and modification from diverse sources. This enables users to perform topology-based pathway signal flow analysis in both interactive and command-line modes. To showcase the toolkit’s usability, we curated 36 KEGG signaling pathways and conducted several use-case studies, comparing our method with ORA and the topology-based signaling pathway impact analysis (SPIA) method. The results demonstrate that the algorithm can effectively identify ORA enriched pathways while providing more detailed branch-level information. Moreover, in contrast to the SPIA method, it offers the advantage of being cut-off free and less susceptible to the variability caused by selection thresholds. By combining pathway curation and topology-based analysis, the PSF toolkit enhances the quality, flexibility, and accessibility of topology-aware pathway analysis. Researchers can now easily import pathways from various sources, correct and modify them as needed, and perform detailed topology-based pathway signal flow analysis. In summary, our PSF toolkit offers an integrated solution that addresses the limitations of current topology-based pathway analysis methods. By providing interactive and command-line tools for pathway curation and topology-based analysis, we empower researchers to conduct comprehensive pathway analyses across a wide range of applications.

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“…Therefore, we contemplated that the absence of ycf3 gene introns in H. bogdanii is unusual. Previous research has suggested that a species that a lack of gene introns in a species may indicate that it has taken on additional functions in diverse areas such as protease, RNA polymerase, and ribosomal pathways ( Hakobyan et al., 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Complete chloroplast genomes of three wild perennial Hordeum species from Central Asia: genome structure, mutation hotspot, phylogenetic relationships, and comparative analysis

Yuan¹,

Nie²,

Jia³

et al. 2023

Front. Plant Sci.

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Hordeum L. is widely distributed in mountain or plateau of subtropical and warm temperate regions around the world. Three wild perennial Hordeum species, including H. bogdanii, H. brevisubulatum, and H. violaceum, have been used as forage and for grassland ecological restoration in high-altitude areas in recent years. To date, the degree of interspecies sequence variation in the three Hordeum species within existing gene pools is still not well-defined. Herein, we sequenced and assembled chloroplast (cp) genomes of the three species. The results revealed that the cp genome of H. bogdanii showed certain sequence variations compared with the cp genomes of the other two species (H. brevisubulatum and H. violaceum), and the latter two were characterized by a higher relative affinity. Parity rule 2 plot (PR2) analysis illuminated that most genes of all ten Hordeum species were concentrated in nucleotide T and G. Numerous single nucleotide polymorphism (SNP) and insertion/deletion (In/Del) events were detected in the three Hordeum species. A series of hotspots regions (tRNA-GGU ~ tRNA-GCA, tRNA-UGU ~ ndhJ, psbE ~ rps18, ndhF ~ tRNA-UAG, etc.) were identified by mVISTA procedures, and the five highly polymorphic genes (tRNA-UGC, tRNA-UAA, tRNA-UUU, tRNA-UAC, and ndhA) were proved by the nucleotide diversity (Pi). Although the distribution and existence of cp simple sequence repeats (cpSSRs) were predicted in the three Hordeum cp genomes, no rearrangement was found between them. A similar phenomenon has been found in the cp genome of the other seven Hordeum species, which has been published so far. In addition, evolutionary relationships were reappraised based on the currently reported cp genome of Hordeum L. This study offers a framework for gaining a better understanding of the evolutionary history of Hordeum species through the re-examination of their cp genomes, and by identifying highly polymorphic genes and hotspot regions that could provide important insights into the genetic diversity and differentiation of these species.

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A Transcriptome-Wide Isoform Landscape of Melanocytic Nevi and Primary Melanomas Identifies Gene Isoforms Associated with Malignancy

Cited by 8 publications

References 63 publications

The role of macrophage scavenger receptor 1 (MSR1) in inflammatory disorders and cancer

The role of macrophage scavenger receptor 1 (MSR1) in inflammatory disorders and cancer

PSF toolkit: an R package for pathway curation and topology-aware analysis

Complete chloroplast genomes of three wild perennial Hordeum species from Central Asia: genome structure, mutation hotspot, phylogenetic relationships, and comparative analysis

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