American Society of Hematology highlights St. Jude research in sickle cell, leukemia

Leukemia

Sickle Cell Disease

Hemophilia

Genetics

When: Sunday, Dec. 2, 2-4 p.m. PST
Location: San Diego Convention Center, Hall AB
Title: Multiplex CRISPR/Cas9-Based Genome Editing of Mouse Hematopoietic Stem Cells Recapitulates Acute Erythroid Leukemia and Identifies Therapeutic Targets
Abstract: 5

Genome editing helps mimic genomic complexity of high-risk leukemia and reveals drug sensitivities

St. Jude researchers have lifted the veil on the biology of acute erythroid leukemia (AEL) to reveal the genomic basis and therapeutic vulnerabilities of the subtypes of this high-risk leukemia.

The research is one of six studies selected from thousands of submissions for presentation at the plenary scientific session of the American Society of Hematology’s annual meeting. The findings will be presented by Ilaria Iacobucci, PhD, a scientist in the laboratory of Charles Mullighan, MBBS, MD, a member of the St. Jude Department of Pathology.

“This project marks a paradigm shift in our understanding and possibly treatment of acute erythroid leukemia,” Mullighan said. AEL is a rare subtype of acute myeloid leukemia (AML) that affects children and adults. AEL has a poor prognosis. Until this study, the genetic basis was poorly understood.

Researchers previously used integrated genomic analysis to compare 159 patients with AEL to 1,509 patients with AML or related red-blood disorders. Five age-related subtypes of AEL were identified, each with distinct genomic features and survival rates.

Using CRISPR/Cas9 genome editing, researchers developed mouse models of the AEL subtypes. This was done by simultaneously inactivating different combinations of nine genes in mouse blood stem and progenitor cells. The genes were frequently mutated in the AEL subtypes. The method helped to capture the genomic complexity of AEL and identify the mutations driving the leukemia. For example, inactivating the genes Tp53, Bcor and Dnmt3a or Tp53, Bcor, Rb1 and Nfix promoted development of AEL. Inactivating a different constellation of genes—Tp53, Bcor, Tet2—promoted development of B-ALL.

The mouse models were then used to screen the subtypes for sensitivity to almost 200 chemotherapy agents and other compounds, including precision medicines that target specific pathways.

“We found that leukemic cells driven by different mutations have different sensitivities and vulnerabilities to drugs,” Iacobucci said. For example, AEL subtypes with NUP98-fusions were highly sensitive to various classes of BET inhibitors and resistant to common chemotherapeutic drugs. Tp53 wild-type tumors without gene fusions were highly sensitive to a variety of standard chemotherapy agents. In contrast, leukemia subtypes with Tp53 mutations were resistant to certain chemotherapy drugs, but sensitive to compounds called PARP inhibitors.

Mullighan said: “These results make a strong case for using genomics to classify patients and then use the information to help guide therapies, since leukemic cells with different genotypes do not respond to treatment the same way.”

When: Sunday, Dec. 2, Noon, PST
Location: San Diego Convention Center, Room 25B
Title: Leukemia Risk Gene ARID5B is a Crucial Regulator of B-Cell Development 
Abstract: 385

Leukemia risk gene revealed as an important regulator of B-cell development

Certain genetic variation in the gene ARID5B is linked to as much as a two-fold increased risk of childhood acute lymphoblastic leukemia (ALL), but until now the biology behind this association and the function of the ARID5B protein have been poorly understood.

Charnise Goodings-Harris, PhD, a St. Jude postdoctoral fellow in the St. Jude laboratory of Jun J. Yang, PhD, will present evidence that ARID5B is an important regulator of B-cell development. “These results fill a knowledge gap regarding the roles this protein plays during blood cell development,” Yang said. “which can then help us understand how variations in the gene influence risk of pediatric ALL.”

For this study, researchers developed a mouse that overexpressed Arid5b and tracked how that affected development of B cells and other blood components. B-ALL is the most common childhood cancer.

Previous work by Yang and others identified inherited variations in ARID5B that were associated with elevated susceptibility to ALL in childhood and to a poor prognosis. Compared to children of European ancestry, the high-risk variations were found more frequently in children of Hispanic ethnicity, who are at an increased risk of the disease.

When: Sunday, Dec. 2, 4:45 p.m. PST
Location: San Diego Convention Center, Room 25B
Title: 410 The DNA Methylation Maintenance Protein UHRF1 Regulates Fetal Globin Expression Independent of HBG Promoter DNA Methylation
Abstract: 410

Researchers home in on the mechanism to turn back the clock on hemoglobin production

St. Jude researchers will offer new details of the mechanism by which red blood cells switch from producing fetal hemoglobin to adult hemoglobin. That change leaves individuals with the inherited blood disorders sickle cell disease and beta-thalassemia at risk for debilitating, sometimes life-threatening complications. Increasing fetal hemoglobin levels is proven to ease symptoms in affected individuals.

For this study, researchers identified the protein UHRF1 in a gene editing-based screen to find proteins that facilitate the fetal-to-adult hemoglobin switch.

“UHRF1 is the guardian of methylation throughout the genome,” said senior author Mitchell Weiss, MD, PhD, chair of the St. Jude Department of Hematology. Methylation, the process for adding or removing methyl groups from DNA, regulates gene expression.

“In this study, we detail efforts to pinpoint where methylation is most important for turning off fetal hemoglobin with the goal of reactivating it in individuals with sickle cell disease or beta-thalassemia to alleviate their symptoms. This study contributes to that effort,” Weiss said.

Ruopeng Feng, PhD, a postdoctoral fellow in the Weiss laboratory, will present the results.

When: Sunday, Dec. 2, 5 p.m. PST
Location: San Diego Convention Center, Room 25B
Title: Activation of ULK1 Kinase Mediates Clearance of Free Alpha-Globin in Human Beta-Thalassemic Erythroblasts
Abstract: 411

Immunosuppression agent may offer new treatment of beta thalassemia

An immunosuppressive drug best known for protecting organ transplants from rejection may also help to ease symptoms of β thalassemia, a common inherited blood disorder.

The drug is rapamycin. St. Jude researchers found that rapamycin reduced the effects of β-thalassemia in mice and in cultured red blood cells of β-thalassemia patients. Rapamycin combats b-thalassemia by activating an enzyme (Ulk1) that reduces the toxic build-up of hemoglobin components.

Hemoglobin is the protein in red blood cells that carries oxygen. Normal hemoglobin has four protein chains—two alpha-globin and two β-globin. β-thalassemia patients have too little β-globin, which leads to a toxic build-up of a-globin in red blood cells and the developing cells that give rise to them. Patients develop anemia and other, sometimes life-threatening, symptoms associated with the disorder.

“Rapamycin treatment significantly reduced and in some cases fully corrected the accumulation of a-globin in the developing blood cells of patients with β-thalassemia,” said Mitchell Weiss, MD, PhD, chair of the St. Jude Department of Hematology.

St. Jude researchers hope the findings will lead to a clinical trial of the drug in β-thalassemia patients.

Christophe Lechauve, PhD, a staff scientist in the Weiss laboratory, will present the research.

When: Sunday, Dec. 2, 5:30 p.m. PST
Location: San Diego Convention Center, Room 6B
Title: Adeno-Associated Mediated Gene Transfer for Hemophilia B: 8 Year Follow up and Impact of Removing "Empty Viral Particles" on Safety and Efficacy of Gene Transfer
Abstract: 491

Gene therapy provides long-term relief for men with severe hemophilia

Eight years after the first men with severe hemophilia B received gene therapy developed in Memphis and London, researchers will report the therapy is still working. The therapy was pioneered by researchers at St. Jude Children’s Research Hospital, University College London and the Royal Free Hospital.

“This is the first report that gene therapy provides a safe, reliable supply of the blood clotting factor for such an extended period after a single infusion,” said co-author Ulrike Reiss, M.D., of the St. Jude Department of Hematology. “The findings address lingering concerns that factor IX levels might decline with time.”

Not only were the initial increased levels in clotting factor IX maintained in the 10 men enrolled in the study, but their bleeding episodes decreased 82 percent. Their use of clotting factor concentrate to prevent or treat spontaneous bleeds dropped 66 percent.

A mutation in the factor IX gene leaves individuals with hemophilia B, who are mostly men, with sometimes dramatically reduced or absent levels of the clotting factor. That leaves patients at risk for painful episodes of spontaneous bleeding that can result in crippling joint damage early in life as well as potentially fatal bleeds in the brain.

For this study researchers modified the adeno-associated virus (AAV8) to serve as the delivery device (vector) to carry the genetic material for making factor IX into liver cells, where it is normally produced.

Researchers also reported that a new vector preparation method failed to prevent an asymptomatic increase in liver enzymes that some patients experienced. Enzyme levels returned to the normal range following steroid treatment. Investigators had tried removing empty viral particles before the gene therapy was infused into patients in case they were triggering an immune response. This finding suggests other factors are involved.

While this study is closed to new patients, St. Jude, University College London and the Royal Free Hospital have opened another gene therapy trial for patients with severe hemophilia B. This clinical trial involves a new vector that researchers believe is even more effective.

When: Monday, Dec. 3, 7 a.m. PST
Location: San Diego Convention Center, Room 25B
Title: Characterization of Novel Subtypes in B Progenitor Acute Lymphoblastic Leukemia
Abstract: 565

RNA sequencing helps uncover mutations that launch most common childhood cancer

Researchers led by St. Jude Children’s Research Hospital have identified eight new subtypes of the most common form of acute lymphoblastic leukemia (ALL), which is also the most common childhood cancer. The finding means that more than 90 percent of B-ALL cases can now be classified by subtype.

“Prior to this study, 30 percent of B-ALL cases could not be classified into subtypes,” said corresponding author Charles Mullighan, MBBS, MD, of the St. Jude Department of Pathology. “These patients lacked precision medicine approaches to treatment and commonly relapsed.”

The research, which identified 23 B-ALL subtypes, involved integrated genomic analysis, including RNA sequencing, of almost 2,000 children and adults with B-ALL. The research highlighted RNA sequencing as a tool to recognize chromosomal rearrangements, gene-expression profiles, novel point mutations and other alterations that are difficult to detect using whole genome or whole exome sequencing.

The newly identified subtypes are strongly associated with prognosis in children and adults. The list includes two that involve the PAX5 gene, notably PAX5 P80R, the first point mutation identified that initiates leukemia. Researchers reported that the mutation blocked B cell differentiation and maturation, and in a mouse model created by CRISPR/Cas9 genome editing, resulted in the development of leukemia in mice. The PAX5 subtypes accounted for almost 10 percent of previously uncategorized B-ALL cases.

The study provides a new framework for classifying ALL in children and adults and shows the utility of RNA-sequencing to provide much of the information required for accurate diagnosis of B-ALL. Zhaohui Gu, PhD, a postdoctoral fellow in Mullighan’s laboratory, will present the results Monday. Patient-derived samples of many B-ALL subtypes are available to researchers worldwide through a St. Jude resource called PROPEL (Public Resource of Patient-derived and Expanded Leukemias). The PROPEL data portal provides access to more than 200 human leukemia samples. The cancers were grown in mice and are known as patient-derived xenografts.

When: Monday, Dec. 3, 7 a.m. PST
Location: Marriott Marquis San Diego Marina, Pacific Ballroom 24
Title: FBXO11 Activates Erythroid Gene Transcription by Degrading Heterochromatin-Associated Protein BAHD1
Abstract: 529

Tumor suppressor protein also plays key role in red blood cell development

St. Jude researchers have identified an intriguing new role for the tumor suppressor protein FBXO11 and a new mechanism important for red blood cell maturation.

FBXO11 is a type of enzyme called ubiquitin ligase, which tags unneeded or unwanted proteins for degradation. Previous studies showed that loss-of-function mutations in the FBOX11 gene arrest the development of normal lymphoid cells and promote their transformation to cancer. In this study, researchers found that FBXO11 is essential for the development of human and mouse red blood cells.

“Evidence suggests that FBXO11 acts early in red blood cell development to degrade a repressor protein called BAHD1, thereby activating the expression of hundreds of genes essential for maturation of red blood cells,” said Mitchell Weiss, MD, PhD, chair of the St. Jude Department of Hematology. “The finding may help explain how FBXO11 works in other tissues and prevents cancer.”

Peng Xu, PhD, a postdoctoral fellow in Weiss’ laboratory, will present the research.

When: Monday, Dec. 3, 7:45 a.m. PST 
Location: San Diego Convention Center, Room 10
Title: Expression of TCF3-ZNF384 in Human Hematopoietic Cells Induces Lineage Disruption in Vitro and Acute Leukemia In Vivo
Abstract: 550

Gene rearrangement drives high-risk leukemia

Charles Mullighan, MBBS, MD, of the St. Jude Department of Pathology, and his colleagues recently identified a subtype of acute leukemia defined by rearrangements involving the transcription factor gene ZNF384. These tumor cells typically have features of both B lymphocytes and myeloid cells, and may be diagnosed as B-ALL or mixed phenotype acute leukemia (MPAL).

Researchers had shown that the ZNF384 fusion proteins cause leukemia when expressed in mouse bone marrow, and that the fusions are first acquired in primitive human blood stem cells.

This study examined the effects of expressing the fusion in human blood stem cells. Using stem cells isolated from umbilical cord blood, the researchers showed that the TCF3-ZNF384 fusion, but not normal ZNF384, skewed blood cell development to resemble that of human leukemic cells. In addition, the stem cells resulted in development of B/myeloid leukemia in mice.

“This is the first human model of mixed phenotype leukemia, and provides the foundation to probe the mechanism, including associated epigenetic changes, induced by the fusion gene,” Mullighan said. Patient-derived samples of the subtype are available to researchers through the PROPEL data portal.

Kirsten Dickerson, a graduate student in the Mullighan laboratory, will present the research.

When: Monday, Dec. 3, 3:15 p.m. PST
Location: San Diego Convention Center, Room 29C
Title: Data Access and Interactive Visualization of Whole Genome Sequence of Sickle Cell Patients within the St. Jude Cloud
Abstract: 723

Online resource offers rich source of genomic and clinical data on sickle cell disease

St. Jude researchers have developed a data portal to fuel collaboration and advance understanding of the genomic landscape of sickle cell disease, particularly genetic factors that contribute to disease severity and complications. Lance Palmer, PhD, of the St. Jude Department of Computational Biology, will outline the initiative.

The Sickle Cell Disease Portal includes whole-genome sequencing data and select clinical information from more than 800 individuals with the chronic inherited blood disorder. It is one of the first such sickle cell disease data sets available to researchers worldwide. The resource is expected to grow as whole-genome sequencing data from more individuals with sickle cell disease are added as well as visualization tools for scientists.

Each year about 300,000 infants are born worldwide with sickle cell disease. It is caused by inherited mutations in the HBB gene that results in stiff, brittle red blood cells with a characteristic sickle shape. Affected individuals are at risk for premature death and a variety of complications, including episodes of acute pain, stroke and progressive organ damage.

“Not every patient gets every complication,” said Mitchell Weiss, MD, PhD, chair of the St. Jude Department of Hematology. “Genetics plays a role in who develops which complications, but many of those genetic modifiers are unknown or poorly understood.

“The Sickle Cell Disease Portal is designed to complement existing resources and help address the knowledge gaps by fueling the collaboration that is essential to change the outcomes for patients,” he said.

The portal includes whole-genome sequencing data of 503 St. Jude patients, primarily individuals enrolled in the Sickle Cell Clinical Research and Intervention Program (SCCRIP). This long-term St. Jude study follows individuals with sickle cell disease throughout their lives. The goal is to better understand how the disease progresses and assess efficacy of treatments.

The site also includes whole-genome sequencing data from 304 sickle cell patients treated at Baylor College of Medicine in Houston.

Overall, more than 98 percent of the Sickle Cell Disease Portal data come from African-American participants. Along with whole-genome sequencing, the site includes such clinical information as hemoglobin and fetal hemoglobin levels as well as some known genetic modifiers of the disease. Identifying patient information has been removed.

The information is available through St. Jude Cloud, a data-sharing resource developed to make it easier for scientists worldwide to access raw sequencing data along with analytic and visualization tools for pediatric cancer and sickle cell disease.

Data-access requests will be handled by a data-access committee. Along with whole-genome sequencing data, access may include coded clinical and demographic information.

When: Monday, Dec. 3, 2:45 p.m., PST
Location: Marriott Marquis San Diego Marina, Pacific Ballroom 24
Title: Leukemia Predisposition Syndromes
Session: Spotlight Sessions

During this session, Kim E. Nichols, MD, Director of the Cancer Predisposition Division at St. Jude Children’s Research Hospital, will discuss the approaches being used for germline genetic testing and how these approaches are improving the understanding of inherited predisposition to cancer. This session addresses the latest advances as they relate to the evaluation and management of individuals at increased genetic risk for cancer.

These sessions provide an opportunity for a small number of attendees to meet with a scientific expert in a setting that fosters interaction. Each year, ASH invites experts from around the world to facilitate informal discussions, allowing participants to present their questions and gain new perspectives. A boxed lunch is provided.