Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing

Casasent, Anna; Schalck, Aislyn; Gao, Ruli; Sei, Emi; Long, Annalyssa N; Pangburn, William; Casasent, Tod D.; Meric‐Bernstam, Funda; Edgerton, Mary E.; Navin, Nicholas E.

doi:10.1016/j.cell.2017.12.007

Cited by 348 publications

(352 citation statements)

References 62 publications

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“…Our data showed that the lymph node metastasis likely was derived from a minor subclone of the InvF. Our data also suggest that the sequenced DCIS cells arose from a subclone and were not a precursor or a separate entity, an observation in line with another recent study (29). Further, single cancer cells located in areas of morphologically normal lymph nodes distant from the lymph node metastasis had gained additional mutations compared with single cells in the solid lymph node metastasis, indicating a case of a linear model of metastasis.…”

Section: Discussionsupporting

confidence: 79%

Coexisting genomic aberrations associated with lymph node metastasis in breast cancer

Bao¹,

Qian²,

Lyng³

et al. 2018

Journal of Clinical Investigation

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Section: Discussionsupporting

confidence: 79%

Coexisting genomic aberrations associated with lymph node metastasis in breast cancer

Bao¹,

Qian²,

Lyng³

et al. 2018

Journal of Clinical Investigation

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“…For the detection of CNVs in fetal cells, it is desirable to have the highest resolution possible, so that also (de novo) microdeletions/duplications are detected, such as the 2 to 3 Mb 22q11.2 deletion causing DiGeorge syndrome, the 1.5‐Mb deletion causing Williams syndrome or the 1.5‐Mb CMT1A duplication. Reliable CNV detection at 220 kb resolution has been described in single tumor cells by Casasent, Schalck , and Gao and a new WGA method reported by Chen et al, reported the detection of micro CNVs as small as 100 kb. From a clinical perspective, we believe that CNV detection at 0.5 Mb is a reasonable short‐term goal for cell‐based NIPT.…”

Section: Discussionmentioning

confidence: 99%

Reliable detection of subchromosomal deletions and duplications using cell‐based noninvasive prenatal testing

et al. 2018

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Objective To gather additional data on the ability to detect subchromosomal abnormalities of various sizes in single fetal cells isolated from maternal blood, using low‐coverage shotgun next‐generation sequencing for cell‐based noninvasive prenatal testing (NIPT). Method Fetal trophoblasts were recovered from approximately 30 mL of maternal blood using maternal white blood cell depletion, density‐based cell separation, immunofluorescence staining, and high‐resolution scanning. These trophoblastic cells were picked as single cells and underwent whole genome amplification for subsequent genome‐wide copy number analysis and genotyping to confirm the fetal origin of the cells. Results Applying our fetal cell isolation method to a series of 125 maternal blood samples, we detected on average 4.17 putative fetal cells/sample. The series included 15 cases with clinically diagnosed fetal aneuploidies and five cases with subchromosomal abnormalities. This method was capable of detecting findings that were 1 to 2 Mb in size, and all were concordant with the microarray or karyotype data obtained on a fetal sample. A minority of fetal cells showed evidence of genome degradation likely related to apoptosis. Conclusion We demonstrate that this cell‐based NIPT method has the capacity to reliably diagnose fetal chromosomal abnormalities down to 1 to 2 Mb in size.

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“…Because G&T-seq allowed us to extract and analyze DNA and RNA from the same tissue samples, we sought to validate the clonal assignment of our cell clusters and confirm the relationships among the CNV, SNV, and RNA clones identified. To visualize these relationships, we employed tanglegrams generated using the R package software Dendextend (Galili, 2015), whereby two phylogenetic trees are drawn opposite of each other, and auxiliary lines are used to connect corresponding cell clusters (Scornavacca et al, 2011, Casasent et al, 2018. Tanglegrams comparing the relationship between the CNV and SNV clones demonstrated that, with the exception of a single cell cluster, cell clusters designated as a CNV A, CNV B, or CNV C clone mapped to a corresponding SNV A, SNV B or SNV C clone (Fig.3B).…”

Section: G and T Sequencing Enables Direct Comparison Between Dna And Rmentioning

confidence: 99%

Genome profiles of lymphovascular breast cancer cells reveal multiple clonally differentiated outcomes with multi-regional LCM and G&T-seq

Zhu

Wang

Lin

et al. 2019

Preprint

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The authors declare that there is no conflict of interest regarding the publication of this article.Character count: 52,408 (60,000 characters MAX including spaces and main figure legends but excluding STAR Methods text, supplemental item legends, and References section): Summary (Currently 120 words): 120 words MAXWe comprehensively analyzed the genomic and transcriptional profiles of 97 laser capture microdissection (LCM) isolated cell clusters from a single patient with triple negative breast cancer (TNBC). By performing simultaneous genome and transcriptome amplification and sequencing (G&T-seq) on these clusters, we identified four RNA cancer cell clones that were directly linked to DNA clone counterparts. We also detected the presence of a lymphovascular invasive (LVI) clone characterized by chromosome instability (CIN), and a specific genomic and transcriptional pattern shared with several primary cancer cell clusters. Furthermore, combination phylogeny analysis pointed to three evolutionarily distinct metastatic pathways in this patient, and hub gene evaluation found the down regulation of ribosomal protein mRNA to be a potential prognostic marker for breast cancer.Keywords: Triple negative breast cancer (TNBC), lymphovascular invasion (LVI), metastasis, lymphatics, laser capture microdissection (LCM), G&T-seq (genome and transcriptome sequencing) Significance (Currently 120 words): 120 words MAXThe lymphatic system is a unidirectional vascular network responsible for trafficking immune cells and lymphatic fluid. However, many cancer cell types use this system as a primary means of metastatic spread to regional lymph nodes. We describe the use of laser capture microdissection in the isolation of lymphovascular invasive (LVI) cancer cell clusters from within lymphatic vessels of a single breast cancer patient. Genomic and transcriptional profiling of LVI associated cancer cells, and cancer cell clusters derived from the primary tumor and lymph nodes of this patient, was performed using G&T-seq. Our findings improve our understanding of LVI metastatic mechanisms, and reveal that poor breast cancer survival outcomes may be related to the extensive down-regulation of transcripts encoding ribosomal proteins. Highlights:1. LVI clone shares a specific genome and transcriptome pattern with a small proportion of primary cancer cell clusters.2. G&T sequencing revealed RNA cancer cell clones to be highly correlative to DNA clones.3. Three evolutionarily and transcriptionally distinct pathways of tumor clone development and metastasis were found in one TNBC patient using combination phylogeny analysis. 4.Extensive ribosomal protein down-regulation may be a potential marker of poor prognosis in breast cancer patients.

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Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing

Cited by 348 publications

References 62 publications

Coexisting genomic aberrations associated with lymph node metastasis in breast cancer

Coexisting genomic aberrations associated with lymph node metastasis in breast cancer

Reliable detection of subchromosomal deletions and duplications using cell‐based noninvasive prenatal testing

Genome profiles of lymphovascular breast cancer cells reveal multiple clonally differentiated outcomes with multi-regional LCM and G&T-seq

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