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Discovery adds to evidence that some children are predisposed to develop leukemia

St. Jude Children's Research Hospital scientists have discovered a fourth gene that can predispose carriers to the most common childhood cancer, expanding the list of genes to include in cancer screening

Memphis, Tennessee, April 19, 2018

Authors of the study Charles Mullighan MBBS, M.D.,  Michelle Churchman Ph.D., Max Qian Ph.D., Jun Yang, Ph.D.

Authors of the study Charles Mullighan MBBS, M.D.,  Michelle Churchman Ph.D., Max Qian Ph.D., Jun Yang, Ph.D.

St. Jude Children's Research Hospital researchers have made a discovery that expands the list of genes to include when screening individuals for possible increased susceptibility to childhood leukemia. The finding is reported online today in the journal Cancer Cell.

The gene is IKZF1, which encodes the transcription factor IKAROS that regulates gene expression. IKZF1 is the fourth gene identified that—like the genes TP53, ETV6 and PAX5—can predispose carriers to develop B-cell acute lymphoblastic leukemia (ALL). Variants in IKZF1 can also influence how some patients respond to treatment.

Researchers found a rare IKZF1 germline variant in three generations of a German family affected by pediatric ALL. St. Jude researchers then analyzed data from almost 5,000 young ALL patients and found that 0.9 percent of patients with B-cell ALL, the most common pediatric ALL, also carried germline variations in IKZF1. Germline variants are usually inherited, carried in DNA found in most cells.

"This finding adds to the growing body of evidence that, while germline variations still account for a small percentage of pediatric ALL cases overall, more children than previously recognized inherit a predisposition to develop ALL," said Charles Mullighan, MBBS, M.D., a member of the St. Jude Department of Pathology.

Jun J. Yang, Ph.D., an associate member of the St. Jude Department of Pharmaceutical Sciences and Department of Oncology, added: "The results also show that germline variants influence the response of leukemia cells to specific chemotherapeutic agents.” Mullighan and Yang are the study’s corresponding authors.

"This will expand the number of genes to consider when screening for predisposition to leukemia, particularly B-ALL. And while not everyone carrying a germline IKZF1 variant will develop leukemia, these results will help us educate families about the potential risk of leukemia," said co-author Kim Nichols, M.D., director of the St. Jude Cancer Predisposition Division. As a group, Mullighan, Yang and Nichols have led research that identified the four known pediatric ALL predisposition genes.

IKZF1 frequently mutated in leukemic cells

The discovery comes a decade after Mullighan and his colleagues reported that IKZF1 was frequently mutated in leukemic cells and a harbinger of poor treatment outcomes.

The search for germline IKZF1 variants associated with ALL susceptibility began in Singapore. Nichols and Yang were there to talk about germline genetics of ALL and inherited (familial) cancer. During that visit, co-author Rupert Handgretinger, M.D., of Children’s University Hospital, Tuebingen, Germany, mentioned three generations of a German family with a germline variation in IKZF1 and a family history of B-ALL.

Two of the five family members with the variant had developed pediatric ALL and died. The remaining three are apparently healthy despite having reduced numbers of B cells.

Targeted sequencing of IKZF1 in 4,963 children with ALL identified 43 patients with 27 IKZF1 variants, almost exclusively patients with B-ALL. "The pattern of IKZF1 variants was surprising because many of the variants were in regions of the gene that are rarely mutated in leukemic cells; these regions of the gene have not been well characterized," Yang said.

IKZF1 variants affect IKAROS function

Extensive laboratory testing found at least 22 of the 28 variants affected protein functions. For example, IKZF1 variants resulted in IKAROS migrating outside the nucleus, which is where the protein normally functions. In other cases, variants were associated with increased cell adhesion.

"Based on existing models, we would have predicted only 60 percent of the newly identified IKZF1 variants would be deleterious," said Michelle Churchman, Ph.D., of St. Jude Pathology. Churchman, Maoxiang Qian, Ph.D., of St. Jude Pharmaceutical Sciences, and Geertruy te Kronnie, of the University of Padova, Italy, are the first authors.

IKZF1 variants require a second "hit" to cause cancer

"In IKZF1 and the other ALL predisposition genes, cells may require an additional cooperating mutation to develop into leukemia," Mullighan said. "While familial ALL is rare, these cases can point to genes and novel biology to examine in a larger patient population.

"This study demonstrates the power of sequencing large groups of seemingly sporadic cases that reveal the genetic underpinnings of the disease," he said.

The study's other authors include Wenjian Yang, Paige Tedrick, Rebekah Baskin, Katherine Verbist, Jennifer Peters, Ian Moore, Zhaohui Gu, Chunxu Qu, Hiroki Yoshihara, Shaina Porter, Shondra Pruett-Miller, Gang Wu, William Evans, Mary Relling and Ching-Hon Pui, all of St. Jude; Hui Zhang of St. Jude and Guangzhou Women and Children’s Medical Center, China; and researchers at 12 institutions in the U.S., China and Germany.

The patients in this analysis were enrolled in clinical research conducted by St. Jude and the Children’s Oncology Group, a cooperative clinical research network.

The study was funded in part by the St. Baldrick’s Foundation, grants (GM115279, CA021765, CA176063, CA19769501A1, CA98543, CA114766, CA98413, CA180886, CA180899) from the National Institutes of Health; and ALSAC, the fundraising and awareness organization of St. Jude.

St. Jude Children's Research Hospital

St. Jude Children's Research Hospital is leading the way the world understands, treats and cures childhood cancer and other life-threatening diseases. It is the only National Cancer Institute-designated Comprehensive Cancer Center devoted solely to children. Treatments developed at St. Jude have helped push the overall childhood cancer survival rate from 20% to 80% since the hospital opened more than 50 years ago. St. Jude shares the discoveries it makes, and every child saved at St. Jude means doctors and scientists worldwide can use that knowledge to save thousands more children. To learn more, visit or follow St. Jude on social media at @stjuderesearch.