An isoform-resolution transcriptomic atlas of colorectal cancer from long-read single-cell sequencing

Li, Zhongxiao; Zhang, Bin; Chan, Jia Jia; Tabatabaeian, Hossein; Tong, Qing; Chew, Xiao Hong; Fan, Xiaonan; Driguez, Patrick; Chan, Charlene; Cheong, F.H.K.; Wang, Shi; Siew, Bei En; Tan, Ian Jse-Wei; Lee, Kai Yin; Lieske, Bettina; Cheong, Wai-Kit; Kappei, Dennis; Tan, Ker‐Kan; Gao, Xin; Tay, Yvonne

doi:10.1101/2023.04.21.536771

Cited by 3 publications

(1 citation statement)

References 79 publications

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“…An important advantage of TGS is the capacity to generate full-length mRNA transcripts, thereby providing complete information about alternative splicing events, isoforms, alternative polyadenylation, and gene fusions [34][35][36]. Despite the very high accuracy of PacBio mRNA sequencing (long-read isoform sequencing, or Iso-seq), on par with NGS, one limitation has been the lower number of reads per sequencing cell compared to NGS and ONT platforms.…”

Section: Advantages Of Tgsmentioning

confidence: 99%

The Application of Long-Read Sequencing to Cancer

Ermini,

Driguez

2024

Cancers

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Cancer is a multifaceted disease arising from numerous genomic aberrations that have been identified as a result of advancements in sequencing technologies. While next-generation sequencing (NGS), which uses short reads, has transformed cancer research and diagnostics, it is limited by read length. Third-generation sequencing (TGS), led by the Pacific Biosciences and Oxford Nanopore Technologies platforms, employs long-read sequences, which have marked a paradigm shift in cancer research. Cancer genomes often harbour complex events, and TGS, with its ability to span large genomic regions, has facilitated their characterisation, providing a better understanding of how complex rearrangements affect cancer initiation and progression. TGS has also characterised the entire transcriptome of various cancers, revealing cancer-associated isoforms that could serve as biomarkers or therapeutic targets. Furthermore, TGS has advanced cancer research by improving genome assemblies, detecting complex variants, and providing a more complete picture of transcriptomes and epigenomes. This review focuses on TGS and its growing role in cancer research. We investigate its advantages and limitations, providing a rigorous scientific analysis of its use in detecting previously hidden aberrations missed by NGS. This promising technology holds immense potential for both research and clinical applications, with far-reaching implications for cancer diagnosis and treatment.

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Section: Advantages Of Tgsmentioning

confidence: 99%

The Application of Long-Read Sequencing to Cancer

Ermini,

Driguez

2024

Cancers

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RoCK and ROI: Single-cell transcriptomics with multiplexed enrichment of selected transcripts and region-specific sequencing

Moro,

Mallona,

Maillard

et al. 2024

Preprint

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Various tools have been developed to reliably identify, trace and analyze single cells in complex tissues. In recent years, these technologies have been combined with transcriptomic profiling approaches to explore molecular mechanisms that drive development, health, and disease. However, current methods still fall short of profiling single cell transcriptomes comprehensively, with one major challenge being high non-detection rates of specific transcripts and transcript regions. Such information is often crucial to understanding the biology of cells or tissues and includes lowly expressed transcripts, sequence variations and exon junctions. Here, we developed a scRNAseq workflow, RoCK and ROI (Robust Capture of Key transcripts and Regions Of Interest), that tackles these limitations. RoCKseq uses targeted capture to enrich for key transcripts, thereby supporting the detection and identification of cell types and complex phenotypes in scRNAseq experiments. ROIseq directs a subset of reads to a specific region of interest via selective priming to ensure detection. Importantly, RoCK and ROI guarantees efficient retrieval of specific sequence information without compromising overall single cell transcriptome information and our workflow is supported by a novel bioinformatics pipeline to analyze the multimodal information. RoCK and ROI represents a significant enhancement over non-targeted single cell sequencing, particularly when cell categorization depends on transcripts that are missed in standard scRNAseq experiments. In addition, it also allows exploration of biological questions that require assessment of specific sequence elements along the targets to be addressed.

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Gene Regulation via RNA Isoform Variations

Zhang,

2024

Genetics

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The completion of the draft and complete human genome has revealed that there are only around 20,000 genes encoding proteins. Nonetheless, these genes can generate eight times more RNA transcript isoforms, while this number is still growing with the accumulation of high-throughput RNA sequencing (RNA-seq) data. In general, over 90% of genes generate various RNA isoforms emerging from variations at the 5′ and 3′ ends, as well as different exon combinations, known as alternative transcription start site (TSS), alternative polyadenylation (APA), and alternative splicing (AS). In this chapter, our focus will be on introducing the significance of these three types of isoform variations in gene regulation and their underlying molecular mechanisms. Additionally, we will highlight the historical, current, and prospective technological advancements in elucidating isoform regulations, from both the computational side such as deep-learning-based artificial intelligence, and the experimental aspect such as the long-read third-generation sequencing (TGS).

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An isoform-resolution transcriptomic atlas of colorectal cancer from long-read single-cell sequencing

Cited by 3 publications

References 79 publications

The Application of Long-Read Sequencing to Cancer

The Application of Long-Read Sequencing to Cancer

RoCK and ROI: Single-cell transcriptomics with multiplexed enrichment of selected transcripts and region-specific sequencing

Gene Regulation via RNA Isoform Variations

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