Molecular Characterization of Circulating Tumor DNA in Pediatric Rhabdomyosarcoma: A Feasibility Study

Olivia Ruhen; Nathalie S M Lak; Janine Stutterheim; Sara G Danielli; Mathieu Chicard; Yasmine Iddir; Alexandra Saint-Charles; Virginia Di Paolo; Lucia Tombolan; Susanne A Gatz; Ewa Aladowicz; Paula Proszek; Sabri Jamal; Reda Stankunaite; Deborah Hughes; Paul Carter; Elisa Izquierdo; Ajla Wasti; Julia C Chisholm; Sally L George; Erika Pace; Louis Chesler; Isabelle Aerts; Gaelle Pierron; Sakina Zaidi; Olivier Delattre; Didier Surdez; Anna Kelsey; Michael Hubank; Paolo Bonvini; Gianni Bisogno; Angela Di Giannatale; Gudrun Schleiermacher; Beat W Schäfer; Godelieve A M Tytgat; Janet Shipley

doi:10.1200/PO.21.00534

Molecular Characterization of Circulating Tumor DNA in Pediatric Rhabdomyosarcoma: A Feasibility Study

Olivia Ruhen
, Nathalie S M Lak
, Janine Stutterheim
, Sara G Danielli
, Mathieu Chicard
, Yasmine Iddir
, Alexandra Saint-Charles
, Virginia Di Paolo
, Lucia Tombolan
, Susanne A Gatz
, Ewa Aladowicz
, Paula Proszek
, Sabri Jamal
, Reda Stankunaite
, Deborah Hughes
, Paul Carter
, Elisa Izquierdo
, Ajla Wasti
, Julia C Chisholm
, Sally L George

Erika Pace, Louis Chesler, Isabelle Aerts, Gaelle Pierron, Sakina Zaidi, Olivier Delattre, Didier Surdez, Anna Kelsey, Michael Hubank, Paolo Bonvini, Gianni Bisogno, Angela Di Giannatale, Gudrun Schleiermacher, Beat W Schäfer, Godelieve A M Tytgat, Janet Shipley^*

^*Corresponding author for this work

Cancer and Genomic Sciences

Research output: Contribution to journal › Article › peer-review

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Abstract

PURPOSE: Rhabdomyosarcomas (RMS) are rare neoplasms affecting children and young adults. Efforts to improve patient survival have been undermined by a lack of suitable disease markers. Plasma circulating tumor DNA (ctDNA) has shown promise as a potential minimally invasive biomarker and monitoring tool in other cancers; however, it remains underexplored in RMS. We aimed to determine the feasibility of identifying and quantifying ctDNA in plasma as a marker of disease burden and/or treatment response using blood samples from RMS mouse models and patients.

METHODS: We established mouse models of RMS and applied quantitative polymerase chain reaction (PCR) and droplet digital PCR (ddPCR) to detect ctDNA within the mouse plasma. Potential driver mutations, copy-number alterations, and DNA breakpoints associated with PAX3/7-FOXO1 gene fusions were identified in the RMS samples collected at diagnosis. Patient-matched plasma samples collected from 28 patients with RMS before, during, and after treatment were analyzed for the presence of ctDNA via ddPCR, panel sequencing, and/or whole-exome sequencing.

RESULTS: Human tumor-derived DNA was detectable in plasma samples from mouse models of RMS and correlated with tumor burden. In patients, ctDNA was detected in 14/18 pretreatment plasma samples with ddPCR and 7/7 cases assessed by sequencing. Levels of ctDNA at diagnosis were significantly higher in patients with unfavorable tumor sites, positive nodal status, and metastasis. In patients with serial plasma samples (n = 18), fluctuations in ctDNA levels corresponded to treatment response.

CONCLUSION: Comprehensive ctDNA analysis combining high sensitivity and throughput can identify key molecular drivers in RMS models and patients, suggesting potential as a minimally invasive biomarker. Preclinical assessment of treatments using mouse models and further patient testing through prospective clinical trials are now warranted.

Original language	English
Article number	e2100534
Number of pages	12
Journal	JCO Precision Oncology
Volume	6
DOIs	https://doi.org/10.1200/PO.21.00534
Publication status	Published - 20 Oct 2022

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

Humans
Child
Mice
Animals
Circulating Tumor DNA/genetics
Feasibility Studies
Prospective Studies
Biomarkers, Tumor/genetics
Mutation
Neoplasms
Rhabdomyosarcoma, Embryonal

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Ruhen, O., Lak, N. S. M., Stutterheim, J., Danielli, S. G., Chicard, M., Iddir, Y., Saint-Charles, A., Di Paolo, V., Tombolan, L., Gatz, S. A., Aladowicz, E., Proszek, P., Jamal, S., Stankunaite, R., Hughes, D., Carter, P., Izquierdo, E., Wasti, A., Chisholm, J. C., ... Shipley, J. (2022). Molecular Characterization of Circulating Tumor DNA in Pediatric Rhabdomyosarcoma: A Feasibility Study. JCO Precision Oncology, 6, Article e2100534. https://doi.org/10.1200/PO.21.00534

@article{d9791fdcb6c446fc94f14940578eaf7f,

title = "Molecular Characterization of Circulating Tumor DNA in Pediatric Rhabdomyosarcoma: A Feasibility Study",

abstract = "PURPOSE: Rhabdomyosarcomas (RMS) are rare neoplasms affecting children and young adults. Efforts to improve patient survival have been undermined by a lack of suitable disease markers. Plasma circulating tumor DNA (ctDNA) has shown promise as a potential minimally invasive biomarker and monitoring tool in other cancers; however, it remains underexplored in RMS. We aimed to determine the feasibility of identifying and quantifying ctDNA in plasma as a marker of disease burden and/or treatment response using blood samples from RMS mouse models and patients.METHODS: We established mouse models of RMS and applied quantitative polymerase chain reaction (PCR) and droplet digital PCR (ddPCR) to detect ctDNA within the mouse plasma. Potential driver mutations, copy-number alterations, and DNA breakpoints associated with PAX3/7-FOXO1 gene fusions were identified in the RMS samples collected at diagnosis. Patient-matched plasma samples collected from 28 patients with RMS before, during, and after treatment were analyzed for the presence of ctDNA via ddPCR, panel sequencing, and/or whole-exome sequencing.RESULTS: Human tumor-derived DNA was detectable in plasma samples from mouse models of RMS and correlated with tumor burden. In patients, ctDNA was detected in 14/18 pretreatment plasma samples with ddPCR and 7/7 cases assessed by sequencing. Levels of ctDNA at diagnosis were significantly higher in patients with unfavorable tumor sites, positive nodal status, and metastasis. In patients with serial plasma samples (n = 18), fluctuations in ctDNA levels corresponded to treatment response.CONCLUSION: Comprehensive ctDNA analysis combining high sensitivity and throughput can identify key molecular drivers in RMS models and patients, suggesting potential as a minimally invasive biomarker. Preclinical assessment of treatments using mouse models and further patient testing through prospective clinical trials are now warranted.",

keywords = "Humans, Child, Mice, Animals, Circulating Tumor DNA/genetics, Feasibility Studies, Prospective Studies, Biomarkers, Tumor/genetics, Mutation, Neoplasms, Rhabdomyosarcoma, Embryonal",

author = "Olivia Ruhen and Lak, \{Nathalie S M\} and Janine Stutterheim and Danielli, \{Sara G\} and Mathieu Chicard and Yasmine Iddir and Alexandra Saint-Charles and \{Di Paolo\}, Virginia and Lucia Tombolan and Gatz, \{Susanne A\} and Ewa Aladowicz and Paula Proszek and Sabri Jamal and Reda Stankunaite and Deborah Hughes and Paul Carter and Elisa Izquierdo and Ajla Wasti and Chisholm, \{Julia C\} and George, \{Sally L\} and Erika Pace and Louis Chesler and Isabelle Aerts and Gaelle Pierron and Sakina Zaidi and Olivier Delattre and Didier Surdez and Anna Kelsey and Michael Hubank and Paolo Bonvini and Gianni Bisogno and \{Di Giannatale\}, Angela and Gudrun Schleiermacher and Sch{\"a}fer, \{Beat W\} and Tytgat, \{Godelieve A M\} and Janet Shipley",

year = "2022",

month = oct,

day = "20",

doi = "10.1200/PO.21.00534",

language = "English",

volume = "6",

journal = "JCO Precision Oncology",

issn = "2473-4284",

publisher = "American Society of Clinical Oncology",

}

Ruhen, O, Lak, NSM, Stutterheim, J, Danielli, SG, Chicard, M, Iddir, Y, Saint-Charles, A, Di Paolo, V, Tombolan, L, Gatz, SA, Aladowicz, E, Proszek, P, Jamal, S, Stankunaite, R, Hughes, D, Carter, P, Izquierdo, E, Wasti, A, Chisholm, JC, George, SL, Pace, E, Chesler, L, Aerts, I, Pierron, G, Zaidi, S, Delattre, O, Surdez, D, Kelsey, A, Hubank, M, Bonvini, P, Bisogno, G, Di Giannatale, A, Schleiermacher, G, Schäfer, BW, Tytgat, GAM & Shipley, J 2022, 'Molecular Characterization of Circulating Tumor DNA in Pediatric Rhabdomyosarcoma: A Feasibility Study', JCO Precision Oncology, vol. 6, e2100534. https://doi.org/10.1200/PO.21.00534

TY - JOUR

T1 - Molecular Characterization of Circulating Tumor DNA in Pediatric Rhabdomyosarcoma

T2 - A Feasibility Study

AU - Ruhen, Olivia

AU - Lak, Nathalie S M

AU - Stutterheim, Janine

AU - Danielli, Sara G

AU - Chicard, Mathieu

AU - Iddir, Yasmine

AU - Saint-Charles, Alexandra

AU - Di Paolo, Virginia

AU - Tombolan, Lucia

AU - Gatz, Susanne A

AU - Aladowicz, Ewa

AU - Proszek, Paula

AU - Jamal, Sabri

AU - Stankunaite, Reda

AU - Hughes, Deborah

AU - Carter, Paul

AU - Izquierdo, Elisa

AU - Wasti, Ajla

AU - Chisholm, Julia C

AU - George, Sally L

AU - Pace, Erika

AU - Chesler, Louis

AU - Aerts, Isabelle

AU - Pierron, Gaelle

AU - Zaidi, Sakina

AU - Delattre, Olivier

AU - Surdez, Didier

AU - Kelsey, Anna

AU - Hubank, Michael

AU - Bonvini, Paolo

AU - Bisogno, Gianni

AU - Di Giannatale, Angela

AU - Schleiermacher, Gudrun

AU - Schäfer, Beat W

AU - Tytgat, Godelieve A M

AU - Shipley, Janet

PY - 2022/10/20

Y1 - 2022/10/20

N2 - PURPOSE: Rhabdomyosarcomas (RMS) are rare neoplasms affecting children and young adults. Efforts to improve patient survival have been undermined by a lack of suitable disease markers. Plasma circulating tumor DNA (ctDNA) has shown promise as a potential minimally invasive biomarker and monitoring tool in other cancers; however, it remains underexplored in RMS. We aimed to determine the feasibility of identifying and quantifying ctDNA in plasma as a marker of disease burden and/or treatment response using blood samples from RMS mouse models and patients.METHODS: We established mouse models of RMS and applied quantitative polymerase chain reaction (PCR) and droplet digital PCR (ddPCR) to detect ctDNA within the mouse plasma. Potential driver mutations, copy-number alterations, and DNA breakpoints associated with PAX3/7-FOXO1 gene fusions were identified in the RMS samples collected at diagnosis. Patient-matched plasma samples collected from 28 patients with RMS before, during, and after treatment were analyzed for the presence of ctDNA via ddPCR, panel sequencing, and/or whole-exome sequencing.RESULTS: Human tumor-derived DNA was detectable in plasma samples from mouse models of RMS and correlated with tumor burden. In patients, ctDNA was detected in 14/18 pretreatment plasma samples with ddPCR and 7/7 cases assessed by sequencing. Levels of ctDNA at diagnosis were significantly higher in patients with unfavorable tumor sites, positive nodal status, and metastasis. In patients with serial plasma samples (n = 18), fluctuations in ctDNA levels corresponded to treatment response.CONCLUSION: Comprehensive ctDNA analysis combining high sensitivity and throughput can identify key molecular drivers in RMS models and patients, suggesting potential as a minimally invasive biomarker. Preclinical assessment of treatments using mouse models and further patient testing through prospective clinical trials are now warranted.

AB - PURPOSE: Rhabdomyosarcomas (RMS) are rare neoplasms affecting children and young adults. Efforts to improve patient survival have been undermined by a lack of suitable disease markers. Plasma circulating tumor DNA (ctDNA) has shown promise as a potential minimally invasive biomarker and monitoring tool in other cancers; however, it remains underexplored in RMS. We aimed to determine the feasibility of identifying and quantifying ctDNA in plasma as a marker of disease burden and/or treatment response using blood samples from RMS mouse models and patients.METHODS: We established mouse models of RMS and applied quantitative polymerase chain reaction (PCR) and droplet digital PCR (ddPCR) to detect ctDNA within the mouse plasma. Potential driver mutations, copy-number alterations, and DNA breakpoints associated with PAX3/7-FOXO1 gene fusions were identified in the RMS samples collected at diagnosis. Patient-matched plasma samples collected from 28 patients with RMS before, during, and after treatment were analyzed for the presence of ctDNA via ddPCR, panel sequencing, and/or whole-exome sequencing.RESULTS: Human tumor-derived DNA was detectable in plasma samples from mouse models of RMS and correlated with tumor burden. In patients, ctDNA was detected in 14/18 pretreatment plasma samples with ddPCR and 7/7 cases assessed by sequencing. Levels of ctDNA at diagnosis were significantly higher in patients with unfavorable tumor sites, positive nodal status, and metastasis. In patients with serial plasma samples (n = 18), fluctuations in ctDNA levels corresponded to treatment response.CONCLUSION: Comprehensive ctDNA analysis combining high sensitivity and throughput can identify key molecular drivers in RMS models and patients, suggesting potential as a minimally invasive biomarker. Preclinical assessment of treatments using mouse models and further patient testing through prospective clinical trials are now warranted.

KW - Humans

KW - Child

KW - Mice

KW - Animals

KW - Circulating Tumor DNA/genetics

KW - Feasibility Studies

KW - Prospective Studies

KW - Biomarkers, Tumor/genetics

KW - Mutation

KW - Neoplasms

KW - Rhabdomyosarcoma, Embryonal

U2 - 10.1200/PO.21.00534

DO - 10.1200/PO.21.00534

M3 - Article

C2 - 36265118

SN - 2473-4284

VL - 6

JO - JCO Precision Oncology

JF - JCO Precision Oncology

M1 - e2100534

ER -

Molecular Characterization of Circulating Tumor DNA in Pediatric Rhabdomyosarcoma: A Feasibility Study

Abstract

UN SDGs

Keywords

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