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Monday, February 28, is Rare Disease Day – a time to pause and help raise awareness about the 300 million people worldwide living with a rare disease, their families, and caregivers.

At Arima Genomics, we are passionate about helping scientists and clinicians better understand human health and disease through the power of 3D genomics. Recently, our Hi-C technology has been used to help better understand the mechanisms of several rare diseases, including glioma, Ewing Sarcoma, and beta thalassemia.

So today, we would like to highlight and celebrate the work of some of these intrepid scientists and clinicians striving to improve the lives of those affected by rare diseases.



Using 3D Genomics to Understand Rare Disease Mechanisms and Identify Novel Therapeutic Targets


Ependymoma is a rare tumor type, occurring more often in children than adults. Ependymoma is a form of glioma that arises in ependymal cells in the brain or spinal cord. The causes of ependymoma vary by disease sub-type and include both gene fusion events and epigenetic regulatory mechanisms.

An international team of scientists, led by Lukas Chavez, PhD, of UC, San Diego, used genome-wide Hi-C to help identify novel intra- and inter-chromosomal structural variants and several genes, including RCOR2, ITGA6, LAMC1, and ARL4C. They concluded that these tumor-dependency genes and pathways play a central role in the oncogenic mechanisms of ependymoma and offer potential novel therapeutic targets. Learn more about this research:

Hear from Lukas Chaves in his talk entitled Unraveling Complex Structural Variants and ecDNA in Childhood Brain Tumors.


High-grade Gliomas

Pediatric high-grade gliomas, including glioblastoma multiforme (GBM) and diffuse intrinsic pontine glioma (DIPG), cause brain tumors with low survival rates ­– the median survival range being from only 8-11 months for DIPG.

Scientists from Northwestern University explored the effects of mutations in histone protein H3K27M on chromatin structure and transcriptional regulation. Their results identified tumor-specific enhancers and regulatory networks for known oncogenes, as well as structural variations that lead to potential enhancer hijacking and gene coamplification events. Ultimately, they demonstrated that 3D genome alterations might play a critical role in the epigenetic landscape and contribute to tumorigenesis in pediatric high-grade gliomas. Read more about this research


Ewing Sarcoma

Ewing sarcoma is a highly aggressive pediatric cancer, causing bone tumors in children and adolescents. Genetically, Ewing sarcomas are characterized by chromosomal translocations between one gene and a transcription factor, resulting in dysregulation of thousands of downstream targets and oncogenesis.

Research led by Stephen Lessnick and Emily Theisen at Nationwide Children’s Hospital used Arima Hi-C to precisely define the global changes in chromatin structure associated with Ewing sarcoma and further link these structural changes to alterations in gene expression. Specifically, they demonstrated the critical role of EWS/FLI in mediating genome-wide changes in chromatin configuration and that fusion transcription factors serve as master regulators through 3D reprogramming of chromatin. Learn more about this research.



Mutations in the adult beta-globin gene can lead to various hemoglobinopathies, including sickle cell disease and beta thalassemia, which cause abnormal clotting, decreased red blood cell production, and anemia. However, studies have shown that the activation of gamma-globin — a subunit of fetal hemoglobin — can alleviate the symptoms of these diseases.

Xiaotian Zhang of the University of Michigan and colleagues used CRISPR-Cas9 to delete a portion of the 3′ end of the β-globin locus that includes a CTCF binding site and used Arima Hi-C technology to understand how this altered the 3D chromatin organization. They found that editing the gene-altered chromosomal loops in the beta-globin locus induced gamma-globin gene activation, suggesting genetic editing of this binding site can have therapeutic implications for treating hemoglobinopathies. Learn more about this research:

Hear from Xiaotian Zhang in his presentation entitled Paving the Way for 3D Genome Engineering and Therapy in Hemoglobinopathies.



How to Support the Rare Disease Community

There are many ways to support those living with rare diseases, their caregivers, and research into the causes and potential treatments.

  • Participate in Rare Disease Day activities every February 28 and show your support on your favorite social channels using #RareDiseaseDay and @rarediseaseday
  • Share your story about rare diseases and their impact on peoples’ lives to help raise awareness
  • Support the rare disease research being undertaken at universities and children’s hospitals worldwide


If you are interested in using Arima technology to study a rare disease, please connect with us.