Shimamura Laboratory | Our Research

The broad interest of the Shimamura lab is the genetic and molecular mechanisms regulating hematopoiesis and clonal evolution to MDS and leukemia. The Shimamura lab studies inherited bone marrow failure syndromes and myelodysplastic syndromes, which are characterized by impaired blood cell production and leukemia predisposition. The lab studies primary patient samples and has developed cellular models of marrow failure and MDS. Genetic and genomic studies of marrow failure and MDS are ongoing.
 
Our work has identified novel genes causing bone marrow failure, MDS, and cancer predisposition. It is increasingly recognized that germline genetic factors contribute to bone marrow failure, MDS, and leukemia in a significant subset of pediatric and young adult patients. Genetic studies of familial marrow failure and familial MDS/leukemias are ongoing. We have established a repository of clinically annotated blood and marrow samples for these studies. The molecular functions of novel genes in hematopoiesis and leukemogenesis are under investigation.
 
We are particularly interested in ribosomal disorders causing marrow failure and leukemia. How disorders of the ribosome, an essential cellular organelle, result in such tissue-specific phenotypes remains a fascinating and critical question. Shwachman Diamond syndrome (SDS) is an autosomal recessive disorder characterized by bone marrow failure and leukemia predisposition. Mutations in the SBDS gene are found in around 90% of cases of SDS but a subset of patients remain genetically undefined. We are conducting translational studies to understand how SBDS mutations result in hematopoietic failure and promote clonal evolution to MDS and AML. To understand the clinical complications and molecular pathogenesis of SDS, an SDS Registry was organized together with collaborators at Cincinnati Children’s Hospital for the collection of clinical data and annotated biological samples for clinical and laboratory investigation (www.sdsregistry.org). The goal of these studies is to improve diagnosis, inform medical management, and develop more effective treatments with less toxicity.

Current Lab Projects

1. Genetic and molecular pathogenesis of bone marrow failure, MDS, and leukemia predisposition

    These projects involve whole exome and whole genome sequencing to identify causative genes for bone marrow failure, MDS, and leukemia predisposition. Gene variants are queried using genetic, molecular, biochemical, cell biology, genomic, and transcriptomic approaches to understand the molecular functions of novel genes in hematopoiesis and clonal evolution. We are conducting pre-clinical studies of potential new therapies in collaboration with other investigators such as Dr. Dan Bauer and Dr. Christian Brendel (Gene Therapy Program), Dr. Timothy Yu (Genetics and Genomics), and Dr. Christopher Bahl (Institute for Protein Innovation).
2. Leukemia interception in cancer predisposition
   In collaboration with Dr. Coleman Lindsley at the Dana Farber Cancer Instititue, we are characterizing the somatic genomic landscape of SDS to elucidate the biology driving clonal evolution and to inform risk stratification. We identified adaptive pathways that rescue the underlying germline genetic ribosomal stress, and maladaptive pathways that improve cellular fitness by inactivating anti-oncogenic checkpoint controls.
3. Inflammation in bone marrow failure
   Inflammation has been implicated in bone marrow failure and MDS. We have identified the TGFbeta pathway as a potential therapeutic target to treat bone marrow failure in SDS and are pursuing mechanistic studies.
4. High-throughput screening using small molecule compounds and functional genomics to identify novel therapeutic targets for bone marrow failure and MDS.
    We are conducting high-thoughput screening to identify promising small molecules or target genes to treat bone marrow failure and MDS/leukemia.

Laboratory techniques used by the lab

• Protein biochemistry
• Molecular biology
• Genomic sequencing and analysis
• RNA-Seq transcriptome analysis
• Single cell genomic and transcriptome analysis
• Immunofluorescence microscopy
• Flow cytometry
• Hematopoiesis assays using primary human CD34+ cells or human induced pluripotent stem cells
• Lentiviral transduction to introduce cDNAs or knockdown gene expression
• High throughput screens using small molecule compounds or functional genomics
• Establishment of primary patient-derived cell cultures

Clinical research

Dr. Shimamura leads several translational research studies in bone marrow failure and genetic predispositon to MDS. She directs the North American Shwachman Diamond Syndrome Registry (SDSR) together with Dr. Kasiani Myers at Cincinnati Children’s Hospital. The SDSR (www.sdsregistry.org) collects clinical data and biological samples to investigate the clinical complications and molecular and genetic causes of SDS with the goal of improving diagnosis, medical management, and treatment. Dr. Shimamura also leads to Coordinating Center of the North American Pediatric Aplastic Anemia Consortium (NAPAAC) which is comprised of over 40 pediatric hematology centers across the country working together to improve the diagnosis, treatment, and outcomes of pediatric aplastic anemia.

We are currently conducting a clinical trial of Fanconi anemia in collaboration with Dr. Markus Grompe at OHSU and Dr. Alan D'Andrea at DFCI.