May 20, 2019 | Jola Glotzer
Nano-hmC-Seal helps identify neuroblastoma biomarkers
Four UChicago scientists with multiple ties to the CBC contribute to a recent study: Bob Grossman, Lucy Godley, Barbara Stranger and Chuan He
Congratulations to the UChicago team for their recent publication in the American Society of Clinical Oncology’s JCO Precision Oncology journal, “5-Hydroxymethylcytosine Profiles Are Prognostic of Outcome in Neuroblastoma and Reveal Transcriptional Networks That Correlate With Tumor Phenotype.” Among the senior authors are four CBC affiliates and awardees, Bob Grossman, Barbara Stranger, Chuan He and Lucy Godley, who also is the CBC Scientific Director for UChicago. Listed below the article is more information about the authors’ ties to the CBC.
Using Nano-hmC-Seal (a novel technique developed in the lab of Chuan He), the authors evaluate 5-hydroxymethylcytosine (5-hmC) genomic imprint in neuroblastoma tissue samples. The findings allow the team to categorize neuroblastoma into two “types:” those that are more and those that are less likely to respond to currently available treatments. It is a positive step towards using personalized medicine in the treatment of this deadly cancer that primarily affects children and has a survival rate of only 50%. Establishment of the promising biomarkers will undoubtedly encourage further work on the development of new neuroblastoma therapeutics.
New research helps identify high-risk pediatric cancer
UChicago Medicine, At the forefront | by Kat Carlton, | May 16, 2019
Researchers at the University of Chicago Medicine have discovered a new way to identify potentially high-risk pediatric neuroblastoma tumors, according to research published today in the American Society of Clinical Oncology’s JCO Precision Oncology journal.
Neuroblastoma is one of the most common cancers in childhood, typically occurring in the abdomen or chest of patients. It accounts for 6 percent of all pediatric cancers, with about 800 new cases diagnosed each year, according to the American Cancer Society. Currently, only 50 percent of those who are diagnosed with high-risk cases will survive in the long term.
“Neuroblastoma is an especially challenging disease to develop precision treatment strategies, because unlike in cancers that commonly affect adults, neuroblastoma tumors have few DNA mutations that would help us predict who will to respond to certain therapies,” said Mark Applebaum, MD, an assistant professor of pediatrics at UChicago Medicine and first author of the new study.
Tissue samples from consenting patients were used with a relatively new technology developed at the University of Chicago by chemistry professor Chuan He. Called Nano-hmC-Seal, this low-cost, genome-wide technology requires minimal amounts of tissue input to analyze the DNA profiles.
The profiles of a DNA modification called 5-hydroxymethylcytosine (5-hmC), which has the power to switch genes on and off, have been found in recent years to be strong biomarkers, or indicators, for how adult cancers will act. Researchers in the study identified 577 genes with differential 5-hmC. Using this information, they were able to identify two clusters of patients, or “favorable” and “unfavorable” clusters.
“We determined that 5-hmC profiles may be optimal DNA-based biomarkers for this disease,” said Applebaum. “A deeper dive into the process of how these 5-hmC profiles reflect aggressive tumor biology can help us better understand the characteristics of our patients’ tumors in order to tailor their therapy more precisely.”
Applebaum said he and his team hope their research will lead to therapies that are better targeted to the different mechanisms that cause neuroblastoma tumors to become so deadly. They are also using the Nano-hmC-Seal technology in blood samples to get better at earlier identification of patients who are responding to standard therapy and those who may benefit from alternate approaches.
In addition to Mark A. Applebaum, MD, authors of the paper include: Erin K. Barr, MD; Jason Karpus, PhD; Ji Nie, PhD; Zhou Zhang, MS, PhD; Amy E. Armstrong, MD; Sakshi Uppal, PhD; Madina Sukhanova, PhD; Wei Zhang, PhD; Alexandre Chlenski, PhD; Helen R. Salwen; Emma Wilkinson; Marija Dobratic MS; Robert Grossman, PhD; Lucy A. Godley, MD, PhD; Barbara E. Stranger, PhD; Chuan He, PhD; and Susan L. Cohn, MD.
Citation:
Applebaum MA, Barr EK, Karpus J, Nie J, Zhang Z, Armstrong AE, Uppal S, Sukhanova M, Zhang W, Chlenski A, Salwen HR, Wilkinson E, Dobratic M, Grossman R, Godley LA, Stranger BE, He C, Cohn SL. 5-Hydroxymethylcytosine Profiles Are Prognostic of Outcome in Neuroblastoma and Reveal Transcriptional Networks That Correlate With Tumor Phenotype. JCO Precision Oncology – published online May 16, 2019. (ascopubs.org)
Source:
Adapted (with modifications) from UChicago Medicine, At the forefront by Kat Carlton, published on May 16, 2019.
Featured CBC Community member(s):
Robert Grossman, UChicago
- CBC Lever Award (2008):
▸ Chicago Center for Systems Biology (CCSB)
PIs: Kevin White (UChicago), Robert Grossman (UChicago; at UIC then), Richard Morimoto (NU) and Luis Amaral (NU) - Spark Council (2008-2010):
Robert Grossman (UChicago; at UIC then) — Council Member - Catalyst Review Board (CRB) (2006-2008):
▸ Current CRB Members
Robert Grossman (UChicago; at UIC then) — Board Member - CBC Proteomics & Infrastructure Award (2006):
CBC Proteomic Repository: Development and Research
PI: Robert Grossman (UChicago; at UIC then) - 1st Annual CBC Symposium (2002):
▸ The New Biology: Technological Innovations Applied to Health and Disease
Robert Grossman (UChicago; at UIC then) — Symposium Speaker
Lucy Godley, UChicago
- CBC Scientific Director, UChicago (2016-present):
▸ The CBC welcomes new Scientific Director for The University of Chicago, Lucy Godley - CBC Accelerator Network (CBCAN) (October 26, 2017):
▸ Overview of the CBC’s new Entrepreneurial Fellows (EF) Award program. Moving forward with the Accelerator Award program.
Lucy Godley (UChicago) — Breakout Session Moderator - CBC Accelerator Network (CBCAN) (July 20, 2018):
▸ Overview of CBCAN and the CBC Accelerator Award program
Lucy Godley (UChicago) — CBCAN Speaker and Panel Moderator - 15th Annual CBC Symposium (2017):
▸ Small Molecule Discovery
Lucy Godley (UChicago) — Symposium Organizer - CBC Lever Award (2015):
▸ Chicago Center for Physical Science-Oncology Innovation and Translation
PIs: Vadim Backman (NU), Lucy Godley (UChicago) and Jack Kaplan (UIC) - CBC Exploratory Workshop (2012):
▸ Control of cellular differentiation and gene expression by 5- hydroxymethlcytosine (5-hmc)
Lucy Godley (UChicago) — Workshop Organizer - CBC Catalyst Review Board (2011):
Lucy Godley (UChicago) — Board Member
Barbara Stranger, UChicago
- 14th CBC Annual Symposium
▸ Genetics of Neurological and Psychiatric Disorders
Barbara Stranger (UChicago) – Symposium Speaker
Chuan He, UChicago
- CBC Accelerator Award (2018):
▸ A Highly Sensitive and Robust Test for Early Colorectal Cancer Diagnosis
PI: Chuan He (UChicago) - CBC Accelerator Network (CBCAN) (February 12, 2018):
▸ CBC Accelerator Network Forum
Chuan He (UChicago) — Accelerator Award program LOI presenter and award finalist - CBC Accelerator Network (CBCAN) (April 7, 2017):
▸ CBC Accelerator Network Forum
Chuan He (UChicago) — CBCAN Speaker - CBC Catalyst Award (2016):
▸ Deciphering RNA Methylation in Regulating Neuronal Functions in Health and Disease
PIs: Chuan He (UChicago) and Yongchao Ma (NU) - CBC Postdoctoral Research Award (2016):
▸ Novel Sequencing Method to Profile 5mC and 5hmC in Single Cell at Base Resolution
PIs: Lulu Hu (postdoc) and Chuan He (UChicago) - CBC Postdoctoral Research Award (2015):
▸ Novel Sequencing Method to Profile N6-Methyldeoxyadenosine in Single-base resolution
PIs: Guan-Zheng Luo (postdoc) and Chuan He (UChicago) - CBC Postdoctoral Research Award (2014):
▸ Screening of Small Molecule Inhibitors for Nuclear RNA M6a Methyltransferase Complex
PIs: Jianzhao Liu (postdoc) and Chuan He (UChicago) - CBC Postdoctoral Research Award (2014):
▸ Pseudouridine Sequencing – A Roadmap to the New Biology of Mrna Pseudouridine Modification
PIs: Dan Dominissini (postdoc) and Chuan He (UChicago) - CBC Scholars “Loop Connections” Seminar (2013):
▸ Reversible RNA and DNA Methylation in Biological Regulation
Chuan He (UChicago) — Seminar Speaker - 10th Annual CBC Symposium (2012):
▸ Epigenomics
Chuan He (UChicago) — Symposium Speaker - CBC Catalyst Award (2011):
▸ Capturing Kinetically Labile Multiprotein Assemblies on DNA by Chemical Crosslinking
PIs: Jung-Hyun Min (UIC) and Chuan He (UChicago) - CBC Catalyst Award (2009):
▸ Virulence and latency regulation in M. tuberculosis
PIs: Chuan He (UChicago) and Scott Franzblau (UIC)