The Rokita Lab

Publications

Below, you’ll find a selection of our recent publications that highlight our contributions to pediatric oncology research and precision medicine. These papers showcase our commitment to advancing knowledge, developing innovative tools, and collaborating with the broader scientific community. Dive in to explore the insights we’ve gained and the impact we’re making!

Link to PubMed

Publications by Year

2024

A proteogenomic surfaceome study identifies DLK1 as an immunotherapeutic target in neuroblastoma.
A proteogenomic surfaceome study identifies DLK1 as an immunotherapeutic target in neuroblastoma.
Amber K Hamilton, Alexander B Radaoui, Matthew Tsang, Daniel Martinez, Karina L Conkrite, …, Patrick H van Berkel, Malcolm A Smith, Benjamin A Garcia, John M Maris, Sharon J Diskin
Cancer cell  ·  23 Oct 2024  ·  pubmed:39454577
The Open Pediatric Cancer Project.
The Open Pediatric Cancer Project.
Zhuangzhuang Geng, Eric Wafula, Ryan J Corbett, Yuanchao Zhang, Run Jin, …, Ammar S Naqvi, Noel Coleman, Weiping Ma, Deanne Taylor, Jo Lynne Rokita
bioRxiv : the preprint server for biology  ·  11 Jul 2024  ·  pubmed:39026781
The Open Pediatric Cancer Project
Manuscript Source
Manubot
open-science collaboration pediatric-cancer genomics
AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification.
AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification.
Jung Kim, Ammar S Naqvi, Ryan J Corbett, Rebecca S Kaufman, Zalman Vaksman, …, Phillip B Storm, Adam C Resnick, Douglas R Stewart, Jo Lynne Rokita, Sharon J Diskin
Bioinformatics (Oxford, England)  ·  29 Feb 2024  ·  pubmed:38426335
AutoGVP
open-science germline cancer
BARD1 germline variants induce haploinsufficiency and DNA repair defects in neuroblastoma.
BARD1 germline variants induce haploinsufficiency and DNA repair defects in neuroblastoma.
Michael P Randall, Laura E Egolf, Zalman Vaksman, Minu Samanta, Matthew Tsang, …, Mehdi Layeghifard, Adam Shlien, John M Maris, Sharon J Diskin, Kristopher R Bosse
Journal of the National Cancer Institute  ·  10 Jan 2024  ·  pubmed:37688570
A proteogenomic surfaceome study identifies DLK1 as an immunotherapeutic target in neuroblastoma.
A proteogenomic surfaceome study identifies DLK1 as an immunotherapeutic target in neuroblastoma.
Amber K Weiner, Alexander B Radaoui, Matthew Tsang, Daniel Martinez, Simone Sidoli, …, Patrick H van Berkel, Malcolm A Smith, Benjamin A Garcia, John M Maris, Sharon J Diskin
bioRxiv : the preprint server for biology  ·  07 Jan 2024  ·  pubmed:38106022

2023

AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification.
AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification.
Jung Kim, Ammar S Naqvi, Ryan J Corbett, Rebecca S Kaufman, Zalman Vaksman, …, Phillip B Storm, Adam C Resnick, Douglas R Stewart, Jo Lynne Rokita, Sharon J Diskin
bioRxiv : the preprint server for biology  ·  01 Dec 2023  ·  pubmed:38076939
Everolimus for Children With Recurrent or Progressive Low-Grade Glioma: Results From the Phase II PNOC001 Trial.
Everolimus for Children With Recurrent or Progressive Low-Grade Glioma: Results From the Phase II PNOC001 Trial.
Daphne A Haas-Kogan, Mariam S Aboian, Jane E Minturn, Sarah E S Leary, Mohamed S Abdelbaki, …, Joanna J Phillips, Michael Prados, Annette M Molinaro, Sebastian M Waszak, Sabine Mueller
Journal of clinical oncology : official journal of the American Society of Clinical Oncology  ·  17 Nov 2023  ·  pubmed:37978951
Alternative lengthening of telomeres (ALT) in pediatric high-grade gliomas can occur without ATRX mutation and is enriched in patients with pathogenic germline mismatch repair (MMR) variants.
Alternative lengthening of telomeres (ALT) in pediatric high-grade gliomas can occur without ATRX mutation and is enriched in patients with pathogenic germline mismatch repair (MMR) variants.
Jennifer L Stundon, Heba Ijaz, Krutika S Gaonkar, Rebecca S Kaufman, Run Jin, …, Suzanne P MacFarland, Douglas R Stewart, Sharon J Diskin, Jo Lynne Rokita, Kristina A Cole
Neuro-oncology  ·  06 Jul 2023  ·  pubmed:36541551
OpenPBTA: The Open Pediatric Brain Tumor Atlas.
OpenPBTA: The Open Pediatric Brain Tumor Atlas.
Joshua A Shapiro, Krutika S Gaonkar, Stephanie J Spielman, Candace L Savonen, Chante J Bethell, …, Miguel A Brown, Adam C Resnick, Casey S Greene, Jo Lynne Rokita, Jaclyn N Taroni
Cell genomics  ·  31 May 2023  ·  pubmed:37492101
Macrophages in SHH subgroup medulloblastoma display dynamic heterogeneity that varies with treatment modality.
Macrophages in SHH subgroup medulloblastoma display dynamic heterogeneity that varies with treatment modality.
Mai T Dang, Michael V Gonzalez, Krutika S Gaonkar, Komal S Rathi, Patricia Young, …, Candace Savonen, Fernanda Mafra, Hakon Hakonarson, Tom Curran, Malay Haldar
Cell reports  ·  25 May 2023  ·  pubmed:37235472
Identification of candidate genes for nicotine withdrawal in C57BL/6J × DBA/2J recombinant inbred mice.
Identification of candidate genes for nicotine withdrawal in C57BL/6J × DBA/2J recombinant inbred mice.
Maren L Smith, Kristin M Mignogna, Jo L Rokita, Lorna MacLeod, M Imad Damaj, Michael F Miles
Genes, brain, and behavior  ·  13 Feb 2023  ·  pubmed:36781202
BARD1 germline variants induce haploinsufficiency and DNA repair defects in neuroblastoma
BARD1 germline variants induce haploinsufficiency and DNA repair defects in neuroblastoma
Michael P Randall, Laura E Egolf, Zalman Vaksman, Minu Samanta, Matthew Tsang, …, Mehdi Layeghifard, Adam Shlien, John M Maris, Sharon J Diskin, Kristopher R Bosse
bioRxiv : the preprint server for biology  ·  03 Feb 2023  ·  pubmed:36778420
Enhancing childhood cancer targetability.
Enhancing childhood cancer targetability.
Ammar S Naqvi, Jo Lynne Rokita
Nature cancer  ·  01 Feb 2023  ·  pubmed:36585448

2022

The children's brain tumor network (CBTN) - Accelerating research in pediatric central nervous system tumors through collaboration and open science.
The children's brain tumor network (CBTN) - Accelerating research in pediatric central nervous system tumors through collaboration and open science.
Jena V Lilly, Jo Lynne Rokita, Jennifer L Mason, Tatiana Patton, Stephanie Stefankiewiz, …, Phillip B Storm, Rishi R Lulla, Michael Prados, Adam C Resnick, Angela J Waanders
Neoplasia (New York, N.Y.)  ·  03 Nov 2022  ·  pubmed:36335802
Upfront Biology-Guided Therapy in Diffuse Intrinsic Pontine Glioma: Therapeutic, Molecular, and Biomarker Outcomes from PNOC003.
Upfront Biology-Guided Therapy in Diffuse Intrinsic Pontine Glioma: Therapeutic, Molecular, and Biomarker Outcomes from PNOC003.
Cassie Kline, Payal Jain, Lindsay Kilburn, Erin R Bonner, Nalin Gupta, …, Michael Prados, Adam Resnick, Sebastian M Waszak, Javad Nazarian, Sabine Mueller
Clinical cancer research : an official journal of the American Association for Cancer Research  ·  15 Sep 2022  ·  pubmed:35852795
Development of GPC2-directed chimeric antigen receptors using mRNA for pediatric brain tumors.
Development of GPC2-directed chimeric antigen receptors using mRNA for pediatric brain tumors.
Jessica B Foster, Crystal Griffin, Jo Lynne Rokita, Allison Stern, Cameron Brimley, …, Phillip B Storm, David M Barrett, Adam C Resnick, John M Maris, Kristopher R Bosse
Journal for immunotherapy of cancer  ·  01 Sep 2022  ·  pubmed:36167467
Characterization of aberrant splicing in pediatric central nervous system tumors reveals
Characterization of aberrant splicing in pediatric central nervous system tumors reveals
Ammar S Naqvi, Ryan J Corbett, Priyanka Seghal, Karina L Conkrite, Komal S Rathi, …, Peter J Madsen, Sharon J Diskin, Andrei Thomas-Tikhonenko, Adam C Resnick, Jo Lynne Rokita
bioRxiv : the preprint server for biology  ·  22 Aug 2022  ·  pubmed:39149264
Characterization of aberrant splicing in pediatric central nervous system tumors reveals CLK1 as a candidate oncogenic dependency
pediatric-cancer splicing

2021

Macrophages in SHH subgroup medulloblastoma display dynamic heterogeneity that varies with treatment modality.
Macrophages in SHH subgroup medulloblastoma display dynamic heterogeneity that varies with treatment modality.
Mai T Dang, Michael V Gonzalez, Krutika S Gaonkar, Komal S Rathi, Patricia Young, …, Candace Savonen, Fernanda Mafra, Hakon Hakonarson, Tom Curran, Malay Haldar
Cell reports  ·  30 Mar 2021  ·  pubmed:33789113
GAS7 Deficiency Promotes Metastasis in MYCN-Driven Neuroblastoma.
GAS7 Deficiency Promotes Metastasis in MYCN-Driven Neuroblastoma.
Zhiwei Dong, Kok Siong Yeo, Gonzalo Lopez, Cheng Zhang, Erin N Dankert Eggum, …, Jan M van Deursen, Hu Li, Jennifer J Westendorf, John M Maris, Shizhen Zhu
Cancer research  ·  18 Feb 2021  ·  pubmed:33602789

2020

annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions.
annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions.
Krutika S Gaonkar, Federico Marini, Komal S Rathi, Payal Jain, Yuankun Zhu, …, Pichai Raman, Adam C Resnick, Konstantin Strauch, Jaclyn N Taroni, Jo Lynne Rokita
BMC bioinformatics  ·  14 Dec 2020  ·  pubmed:33317447
Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer.
Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer.
Francesca Petralia, Nicole Tignor, Boris Reva, Mateusz Koptyra, Shrabanti Chowdhury, …, Amanda G Paulovich, Adam C Resnick, Phillip B Storm, Brian R Rood, Pei Wang
Cell  ·  25 Nov 2020  ·  pubmed:33242424
A transcriptome-based classifier to determine molecular subtypes in medulloblastoma.
A transcriptome-based classifier to determine molecular subtypes in medulloblastoma.
Komal S Rathi, Sherjeel Arif, Mateusz Koptyra, Ammar S Naqvi, Deanne M Taylor, Phillip B Storm, Adam C Resnick, Jo Lynne Rokita, Pichai Raman
PLoS computational biology  ·  29 Oct 2020  ·  pubmed:33119584
LIN28B promotes neuroblastoma metastasis and regulates PDZ binding kinase.
LIN28B promotes neuroblastoma metastasis and regulates PDZ binding kinase.
Dongdong Chen, Julie Cox, Jayabhargav Annam, Melanie Weingart, Grace Essien, …, Daisy Li, Cara Shields, Oskar Laur, John M Maris, Robert W Schnepp
Neoplasia (New York, N.Y.)  ·  24 Apr 2020  ·  pubmed:32339949
Limited antitumor activity of combined BET and MEK inhibition in neuroblastoma.
Limited antitumor activity of combined BET and MEK inhibition in neuroblastoma.
Jason R Healy, Lori S Hart, Alexander L Shazad, Maria E Gagliardi, Matthew Tsang, …, Olena Barbash, Vandana Batra, Minu Samanta, John M Maris, Robert W Schnepp
Pediatric blood & cancer  ·  19 Apr 2020  ·  pubmed:32307821
Epigenomic profiling of neuroblastoma cell lines.
Epigenomic profiling of neuroblastoma cell lines.
Kristen Upton, Apexa Modi, Khushbu Patel, Nathan M Kendsersky, Karina L Conkrite, …, Gregory I Sacks, Paolo Fortina, Sharon J Diskin, John M Maris, Jo Lynne Rokita
Scientific data  ·  14 Apr 2020  ·  pubmed:32286315
Telomere Maintenance Mechanisms Define Clinical Outcome in High-Risk Neuroblastoma.
Telomere Maintenance Mechanisms Define Clinical Outcome in High-Risk Neuroblastoma.
Balakrishna Koneru, Gonzalo Lopez, Ahsan Farooqi, Karina L Conkrite, Thinh H Nguyen, …, Shengping Yang, David A Wheeler, John M Maris, Sharon J Diskin, C Patrick Reynolds
Cancer research  ·  14 Apr 2020  ·  pubmed:32291317
CAMKV Is a Candidate Immunotherapeutic Target in
CAMKV Is a Candidate Immunotherapeutic Target in
Robyn T Sussman, Jo Lynne Rokita, Kevin Huang, Pichai Raman, Komal S Rathi, …, Maria Lane, Lori S Hart, Tricia Bhatti, Bruce Pawel, John M Maris
Frontiers in oncology  ·  06 Mar 2020  ·  pubmed:32211329
Pediatric high-grade glioma resources from the Children's Brain Tumor Tissue Consortium.
Pediatric high-grade glioma resources from the Children's Brain Tumor Tissue Consortium.
Heba Ijaz, Mateusz Koptyra, Krutika S Gaonkar, Jo Lynne Rokita, Valerie P Baubet, …, Maria Rita Santi, Phillip B Storm, Adam Resnick, Angela J Waanders, Kristina A Cole
Neuro-oncology  ·  11 Jan 2020  ·  pubmed:31613963

2019

ASCL1 is a MYCN- and LMO1-dependent member of the adrenergic neuroblastoma core regulatory circuitry.
ASCL1 is a MYCN- and LMO1-dependent member of the adrenergic neuroblastoma core regulatory circuitry.
Lu Wang, Tze King Tan, Adam D Durbin, Mark W Zimmerman, Brian J Abraham, …, Jo Lynne Rokita, John M Maris, Richard A Young, A Thomas Look, Takaomi Sanda
Nature communications  ·  09 Dec 2019  ·  pubmed:31819055
Combined innate and adaptive immunotherapy overcomes resistance of immunologically cold syngeneic murine neuroblastoma to checkpoint inhibition.
Combined innate and adaptive immunotherapy overcomes resistance of immunologically cold syngeneic murine neuroblastoma to checkpoint inhibition.
Julie Voeller, Amy K Erbe, Jacob Slowinski, Kayla Rasmussen, Peter M Carlson, …, John Maris, Jacquelyn A Hank, Zachary S Morris, Alexander L Rakhmilevich, Paul M Sondel
Journal for immunotherapy of cancer  ·  06 Dec 2019  ·  pubmed:31810498
Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design.
Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design.
Jo Lynne Rokita, Komal S Rathi, Maria F Cardenas, Kristen A Upton, Joy Jayaseelan, …, Malcolm A Smith, Richard B Lock, Pichai Raman, David A Wheeler, John M Maris
Cell reports  ·  05 Nov 2019  ·  pubmed:31693904
YAP1 Mediates Resistance to MEK1/2 Inhibition in Neuroblastomas with Hyperactivated RAS Signaling.
YAP1 Mediates Resistance to MEK1/2 Inhibition in Neuroblastomas with Hyperactivated RAS Signaling.
Grace E Coggins, Alvin Farrel, Komal S Rathi, Colin M Hayes, Laura Scolaro, Jo Lynne Rokita, John M Maris
Cancer research  ·  31 Oct 2019  ·  pubmed:31672841
Germline 16p11.2 Microdeletion Predisposes to Neuroblastoma.
Germline 16p11.2 Microdeletion Predisposes to Neuroblastoma.
Laura E Egolf, Zalman Vaksman, Gonzalo Lopez, Jo Lynne Rokita, Apexa Modi, Patricia V Basta, Hakon Hakonarson, Andrew F Olshan, Sharon J Diskin
American journal of human genetics  ·  29 Aug 2019  ·  pubmed:31474320
The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution.
The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution.
Deanne M Taylor, Bruce J Aronow, Kai Tan, Kathrin Bernt, Nathan Salomonis, …, Yi Xing, Sek Won Kong, Carsten G Bönnemann, Kenneth D Mandl, Peter S White
Developmental cell  ·  28 Mar 2019  ·  pubmed:30930166

2018

Cross-Cohort Analysis Identifies a TEAD4-MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma.
Cross-Cohort Analysis Identifies a TEAD4-MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma.
Presha Rajbhandari, Gonzalo Lopez, Claudia Capdevila, Beatrice Salvatori, Jiyang Yu, …, Antonio Iavarone, Anna Lasorella, Jose M Silva, John M Maris, Andrea Califano
Cancer discovery  ·  06 Mar 2018  ·  pubmed:29510988

2017

Corrigendum: Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines.
Corrigendum: Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines.
Jo Lynne Harenza, Maura A Diamond, Rebecca N Adams, Michael M Song, Heather L Davidson, Lori S Hart, Maiah H Dent, Paolo Fortina, C Patrick Reynolds, John M Maris
Scientific data  ·  05 Dec 2017  ·  pubmed:29206221
Identification of GPC2 as an Oncoprotein and Candidate Immunotherapeutic Target in High-Risk Neuroblastoma.
Identification of GPC2 as an Oncoprotein and Candidate Immunotherapeutic Target in High-Risk Neuroblastoma.
Kristopher R Bosse, Pichai Raman, Zhongyu Zhu, Maria Lane, Daniel Martinez, …, Marco A Marra, Michael D Taylor, Dimiter S Dimitrov, Crystal L Mackall, John M Maris
Cancer cell  ·  11 Sep 2017  ·  pubmed:28898695
Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines.
Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines.
Jo Lynne Harenza, Maura A Diamond, Rebecca N Adams, Michael M Song, Heather L Davidson, Lori S Hart, Maiah H Dent, Paolo Fortina, C Patrick Reynolds, John M Maris
Scientific data  ·  28 Mar 2017  ·  pubmed:28350380

2016

International Comparison of Enumeration-Based Quantification of DNA Copy-Concentration Using Flow Cytometric Counting and Digital Polymerase Chain Reaction.
International Comparison of Enumeration-Based Quantification of DNA Copy-Concentration Using Flow Cytometric Counting and Digital Polymerase Chain Reaction.
Hee-Bong Yoo, Sang-Ryoul Park, Lianhua Dong, Jing Wang, Zhiwei Sui, …, Jim F Huggett, Helen Parkes, Margaret C Kline, Jo Lynne Harenza, Peter M Vallone
Analytical chemistry  ·  30 Nov 2016  ·  pubmed:28193036

2011

Genetic analysis of the neurosteroid deoxycorticosterone and its relation to alcohol phenotypes: identification of QTLs and downstream gene regulation.
Genetic analysis of the neurosteroid deoxycorticosterone and its relation to alcohol phenotypes: identification of QTLs and downstream gene regulation.
Patrizia Porcu, Todd K O’Buckley, Soomin C Song, Jo Lynne Harenza, Lu Lu, Xusheng Wang, Robert W Williams, Michael F Miles, A Leslie Morrow
PloS one  ·  08 Apr 2011  ·  pubmed:21494628