Multifunctional barcoding with ClonMapper enables high-resolution study of clonal dynamics during tumor evolution and treatment

Gutierrez, Catherine; Al’Khafaji, Aziz; Brenner, Eric; Johnson, Kaitlyn E.; Gohil, Satyen; Lin, Ziao; Knisbacher, Binyamin A.; Durrett, Richard; Li, Shuqiang; Parvin, Salma; Biran, Anat; Zhang, Wandi; Rassenti, Laura Z.; Kipps, Thomas J.; Livak, Kenneth J.; Neuberg, Donna; Letaï, Anthony; Getz, Gad; Wu, Catherine J.; Brock, Amy

doi:10.1038/s43018-021-00222-8

Cited by 66 publications

(79 citation statements)

References 88 publications

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“…The deconvolution of CLL subclonal dynamics through an integration of multimodal single-cell biological data necessitates the deployment of robust methodologies to track individual subclones over time, a process known as lineage tracing. The use of synthetic sequencing barcodes enables prospective lineage tracing within in vitro and in vivo CLL models ( 50 ), and is being increasingly explored across cancer systems. With the currently available tools, however, such a strategy is largely unfeasible to use in primary biospecimens from CLL patients given the well-known obstacles to efficiently introduce such barcodes into primary B cells.…”

Section: Harnessing Technological Advances To Interrogate Cll Clonal Evolutionmentioning

confidence: 99%

“…With the currently available tools, however, such a strategy is largely unfeasible to use in primary biospecimens from CLL patients given the well-known obstacles to efficiently introduce such barcodes into primary B cells. Instead, retrospective approaches for lineage tracing that exploit heritable native barcodes such as SNVs/CNAs, mitochondrial DNA (mtDNA) heteroplasmy or epimutations have been used to identify and mark each individual subclone ( 50 – 57 ). These approaches will each be elaborated in more detail.…”

Section: Harnessing Technological Advances To Interrogate Cll Clonal Evolutionmentioning

confidence: 99%

“…Finally, recent innovations in synthetic barcode technology for single-cell sequencing promise to revolutionize the use of in vitro and in vivo models to interrogate CLL clonal evolution. An example of this is ClonMapper that enforces expression of unique single-guide RNA (sgRNA) barcodes within single cells ( 50 ). These barcodes can be captured subsequently during scRNA-seq, thereby coupling clonal identity with single-cell transcriptomics, and allowing for the isolation of subclones of interest for further integrative multiomics study.…”

Section: Harnessing Technological Advances To Interrogate Cll Clonal Evolutionmentioning

confidence: 99%

“…These barcodes can be captured subsequently during scRNA-seq, thereby coupling clonal identity with single-cell transcriptomics, and allowing for the isolation of subclones of interest for further integrative multiomics study. To illustrate the applicability of this technology for modelling clonal evolution in high-risk CLL, Gutierrez and colleagues implemented this platform to monitor subclonal diversification in a CLL cell line in response to treatment, uncovering a host of genomic and transcriptomic cell state changes, and unique subclonal dynamics ( 50 ). Although this study was carried out in vitro , one can envisage the use of similar barcode technology within various murine models of CLL, including Eµ-TCL1, CLL patient-derived xenografts and newer CRISPR/Cas9-engineered transgenic models ( 58 – 61 ), opening up unprecedented opportunities for the prospective investigation of clonal evolution under experimental CLL therapies or therapeutic combinations.…”

Section: Harnessing Technological Advances To Interrogate Cll Clonal Evolutionmentioning

confidence: 99%

“…In some cases, certain subclones can acquire exponential growth which could be a harbinger for subsequent disease acceleration. Moreover, as recently suggested by in vitro models, the persistence of clonal equilibrium may also be predicated upon dynamic intracellular interactions between subclonal CLL populations, the disruption of which may perturb this delicate balance resulting in specific subclonal outgrowth ( 50 ).…”

Section: The Molecular Basis Of Cll Intratumoral Heterogeneity and Evolutionmentioning

confidence: 99%

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Clonal Evolution of High-Risk Chronic Lymphocytic Leukemia: A Contemporary Perspective

Kwok

2021

Front. Oncol.

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Clonal evolution represents the natural process through which cancer cells continuously search for phenotypic advantages that enable them to develop and expand within microenvironmental constraints. In chronic lymphocytic leukemia (CLL), clonal evolution underpins leukemic progression and therapeutic resistance, with differences in clonal evolutionary dynamics accounting for its characteristically diverse clinical course. The past few years have witnessed profound changes in our understanding of CLL clonal evolution, facilitated by a maturing definition of high-risk CLL and an increasing sophistication of next-generation sequencing technology. In this review, we offer a modern perspective on clonal evolution of high-risk CLL, highlighting recent discoveries, paradigm shifts and unresolved questions. We appraise recent advances in our understanding of the molecular basis of CLL clonal evolution, focusing on the genetic and non-genetic sources of intratumoral heterogeneity, as well as tumor-immune dynamics. We review the technological innovations, particularly in single-cell technology, which have fostered these advances and represent essential tools for future discoveries. In addition, we discuss clonal evolution within several contexts of particular relevance to contemporary clinical practice, including the settings of therapeutic resistance to CLL targeted therapy and immunotherapy, as well as Richter transformation of CLL to high-grade lymphoma.

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Section: Harnessing Technological Advances To Interrogate Cll Clonal Evolutionmentioning

confidence: 99%

Section: Harnessing Technological Advances To Interrogate Cll Clonal Evolutionmentioning

confidence: 99%

Section: Harnessing Technological Advances To Interrogate Cll Clonal Evolutionmentioning

confidence: 99%

Section: Harnessing Technological Advances To Interrogate Cll Clonal Evolutionmentioning

confidence: 99%

Section: The Molecular Basis Of Cll Intratumoral Heterogeneity and Evolutionmentioning

confidence: 99%

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Clonal Evolution of High-Risk Chronic Lymphocytic Leukemia: A Contemporary Perspective

Kwok

2021

Front. Oncol.

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Cancer's second genome: Microbial cancer diagnostics and redefining clonal evolution as a multispecies process

et al. 2022

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The presence and role of microbes in human cancers has come full circle in the last century. Tumors are no longer considered aseptic, but implications for cancer biology and oncology remain underappreciated. Opportunities to identify and build translational diagnostics, prognostics, and therapeutics that exploit cancer's second genome—the metagenome—are manifold, but require careful consideration of microbial experimental idiosyncrasies that are distinct from host‐centric methods. Furthermore, the discoveries of intracellular and intra‐metastatic cancer bacteria necessitate fundamental changes in describing clonal evolution and selection, reflecting bidirectional interactions with non‐human residents. Reconsidering cancer clonality as a multispecies process similarly holds key implications for understanding metastasis and prognosing therapeutic resistance while providing rational guidance for the next generation of bacterial cancer therapies. Guided by these new findings and challenges, this Review describes opportunities to exploit cancer's metagenome in oncology and proposes an evolutionary framework as a first step towards modeling multispecies cancer clonality. Also see the video abstract here: https://youtu.be/-WDtIRJYZSs

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Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes

2023

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Random DNA barcodes are a versatile tool for tracking cell lineages, with applications ranging from development to cancer to evolution. Here, we review and critically evaluate barcode designs as well as methods of barcode sequencing and initial processing of barcode data. We first demonstrate how various barcode design decisions affect data quality and propose a new design that balances all considerations that we are currently aware of. We then discuss various options for the preparation of barcode sequencing libraries, including inline indices and Unique Molecular Identifiers (UMIs). Finally, we test the performance of several established and new bioinformatic pipelines for the extraction of barcodes from raw sequencing reads and for error correction. We find that both alignment and regular expression-based approaches work well for barcode extraction, and that error-correction pipelines designed specifically for barcode data are superior to generic ones. Overall, this review will help researchers to approach their barcoding experiments in a deliberate and systematic way.

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Multifunctional barcoding with ClonMapper enables high-resolution study of clonal dynamics during tumor evolution and treatment

Cited by 66 publications

References 88 publications

Clonal Evolution of High-Risk Chronic Lymphocytic Leukemia: A Contemporary Perspective

Clonal Evolution of High-Risk Chronic Lymphocytic Leukemia: A Contemporary Perspective

Cancer's second genome: Microbial cancer diagnostics and redefining clonal evolution as a multispecies process

Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes

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