Roles of Human Endogenous Retroviruses and Endogenous Virus-Like Elements in Cancer Development and Innate Immunity

Katoh, Hirokazu; Honda, Tomoyuki

doi:10.3390/biom13121706

Cited by 6 publications

(2 citation statements)

References 155 publications

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“…3 ab). Significantly, we observed certain TEs with expression patterns linked to crucial glioma gene markers like EGFR [29,30] and TE markers including HUERS-P1-int [31], HERVK-int [32], along with immune cell gene markers such as CD74 [33,34] and TE marker LTR2B [35,36] (Fig. 3 b).…”

Section: Mates Quantifies Disease-related Te Expression In a Full-lengthmentioning

confidence: 99%

MATES: A Deep Learning-Based Model for Locus-specific Quantification of Transposable Elements in Single Cell

Wang,

Zheng,

Zhang

et al. 2024

Preprint

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Transposable elements (TEs) are crucial for genetic diversity and gene regulation. Current single-cell quantification methods often align multi-mapping reads to either `best-mapped' or `random-mapped' locations and categorize them at sub-family levels, overlooking the biological necessity for accurate, locus-specific TE quantification. Moreover, these existing methods are primarily designed for and focused on transcriptomics data, which restricts their adaptability to single-cell data of other modalities. To address these challenges, here we introduce MATES, a novel deep-learning approach that accurately allocates multi-mapping reads to specific loci of TEs, utilizing context from adjacent read alignments flanking the TE locus. When applied to diverse single-cell omics datasets, MATES shows improved performance over existing methods, enhancing the accuracy of TE quantification and aiding in the identification of marker TEs for identified cell populations. This development enables exploring single-cell heterogeneity and gene regulation through the lens of TEs, offering a transformative tool for the single-cell genomics community.

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Section: Mates Quantifies Disease-related Te Expression In a Full-lengthmentioning

confidence: 99%

MATES: A Deep Learning-Based Model for Locus-specific Quantification of Transposable Elements in Single Cell

Wang,

Zheng,

Zhang

et al. 2024

Preprint

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“…Human endogenous retroviruses (hERVs) are usually not able to replicate but there has been evidence that expression can occur tissue-specifically as well as in malignant cells, as reviewed in [275]. Retroviral elements include HERVs, LINEs, or SINEs [276,277].…”

Section: Human Endogenous Retrovirusesmentioning

confidence: 99%

Tumor Antigens beyond the Human Exome

Emilius,

Bremm,

Binder

et al. 2024

IJMS

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With the advent of immunotherapeutics, a new era in the combat against cancer has begun. Particularly promising are neo-epitope-targeted therapies as the expression of neo-antigens is tumor-specific. In turn, this allows the selective targeting and killing of cancer cells whilst healthy cells remain largely unaffected. So far, many advances have been made in the development of treatment options which are tailored to the individual neo-epitope repertoire. The next big step is the achievement of efficacious “off-the-shelf” immunotherapies. For this, shared neo-epitopes propose an optimal target. Given the tremendous potential, a thorough understanding of the underlying mechanisms which lead to the formation of neo-antigens is of fundamental importance. Here, we review the various processes which result in the formation of neo-epitopes. Broadly, the origin of neo-epitopes can be categorized into three groups: canonical, noncanonical, and viral neo-epitopes. For the canonical neo-antigens that arise in direct consequence of somatic mutations, we summarize past and recent findings. Beyond that, our main focus is put on the discussion of noncanonical and viral neo-epitopes as we believe that targeting those provides an encouraging perspective to shape the future of cancer immunotherapeutics.

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From the genome's perspective: Bearing somatic retrotransposition to leverage the regulatory potential of L1 RNAs

Mangoni,

Mazzetti,

Ansaloni

et al. 2024

BioEssays

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Transposable elements (TEs) are mobile genomic elements constituting a big fraction of eukaryotic genomes. They ignite an evolutionary arms race with host genomes, which in turn evolve strategies to restrict their activity. Despite being tightly repressed, TEs display precisely regulated expression patterns during specific stages of mammalian development, suggesting potential benefits for the host. Among TEs, the long interspersed nuclear element (LINE‐1 or L1) has been found to be active in neurons. This activity prompted extensive research into its possible role in cognition. So far, no specific cause‐effect relationship between L1 retrotransposition and brain functions has been conclusively identified. Nevertheless, accumulating evidence suggests that interactions between L1 RNAs and RNA/DNA binding proteins encode specific messages that cells utilize to activate or repress entire transcriptional programs. We summarize recent findings highlighting the activity of L1 RNAs at the non‐coding level during early embryonic and brain development. We propose a hypothesis suggesting a mutualistic relationship between L1 mRNAs and the host cell. In this scenario, cells tolerate a certain rate of retrotransposition to leverage the regulatory effects of L1s as non‐coding RNAs on potentiating their mitotic potential. In turn, L1s benefit from the cell's proliferative state to increase their chance to mobilize.

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Roles of Human Endogenous Retroviruses and Endogenous Virus-Like Elements in Cancer Development and Innate Immunity

Cited by 6 publications

References 155 publications

MATES: A Deep Learning-Based Model for Locus-specific Quantification of Transposable Elements in Single Cell

MATES: A Deep Learning-Based Model for Locus-specific Quantification of Transposable Elements in Single Cell

Tumor Antigens beyond the Human Exome

From the genome's perspective: Bearing somatic retrotransposition to leverage the regulatory potential of L1 RNAs

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