Researchers at Children’s Hospital of Philadelphia (CHOP) have elucidated the significant role that alternative splicing – a process whereby a single gene produces multiple proteins by rearranging its messenger RNA segments in different combinations – plays in resistance to chemotherapy in relapsed or refractory B-cell acute lymphoblastic leukemia (B-ALL). The study was published today in the journal Cancer Research.
Leukemia is the most common cancer in children, adolescents, and young adults, making up nearly a third of all pediatric cancers, and B-ALL is the most common form of leukemia among children. The chance of long-term survival after a relapse is approximately 50%, with poorer outcomes for subsequent relapses, leading to high rates of pediatric cancer-related deaths. Although most B-ALL cases are diagnosed in children, most deaths occur in adults due to relapsed or refractory disease.
Until now, the molecular mechanisms responsible for treatment failures in relapsed or refractory B-ALL were thought to involve gene mutations; yet in many cases no relevant mutations could be found. In this study, researchers helped explain that paradox by analyzing RNA sequencing datasets to identify an alternative mechanism of gene dysregulation, such as alternative spicing. They discovered pervasive alternative splicing patterns linked to relapse that could have contributed to resistance to anti-leukemia therapeutics, including glucocorticoids, anti-folates, and thiopurines.
“These findings provide critical insights into the mechanisms of chemoresistance in children with B-ALL who relapse despite aggressive treatment,” said Andrei Thomas-Tikhonenko, PhD, the study’s senior author and Chief of the Division of Cancer Pathobiology and Director of the Experimental Pathology Branch at CHOP. “Our research suggests that alternative splicing acts as a parallel mechanism to genetic alterations, driving resistance in cases where no mutations in known chemoresistance genes are evident. This knowledge is particularly important for identifying patients who might experience treatment failures. Our study also sheds light on the important role of RNA-based diagnostic in the management of childhood leukemia."
Researchers discovered a new version of the NT5C2 gene, which includes an additional segment called exon 6a, makes the protein more active, and causes resistance to certain chemotherapy drugs. The authors observed alternative splicing-driven chemotherapy resistance in leukemia cells, both in vitro and in vivo, similar to resistance found in cells with a known gain-of-function NT5C2 mutation. However, this gene change also made the cells more sensitive to a different drug called mizoribine, which affects the production of RNA and DNA. This finding suggests that drugs widely prescribed to suppress the immune system could serve an alternate therapeutic option for treating leukemias that resist standard chemotherapy.
The study, led by Manuel Torres Diz, PhD, further highlighted that alternative splicing events may impact other chemoresistance-related genes, such a CREBBP and FPGS, resulting in loss-of-function isoforms. For example, CREBBP exon 25/26 skipping led to a deficiency in histone acetyltransferase activity – a process involved in several key pathways in cancerous and non-cancerous cells alike – while FPGS splicing changes were linked to resistance to methotrexate, a common chemotherapy drug.
The study was supported by grants from the NIH | National Cancer Institute, Pennsylvania Department of Health, CURE Non-Formula Collaborative Research on Childhood and Adolescent Blood Cancers, United States Department of Defense, St. Baldrick's Foundation, EPICC Team and St. Baldrick’s-Stand Up to Cancer Dream Team Translational Cancer Research Grant, The V Foundation for Cancer Research, The Emerson Collective, Alex’s Lemonade Stand Foundation and the Leukemia & Lymphoma Society. The authors also received support from the SPROUT Program at CHOP, Accelerating Cancer Therapeutics (ACT) Program at Columbia University, and The Ellen Weisberg Fund: Advancing Breakthroughs in Pediatric Cancer.
Torres-Diz et al. “An Alternatively Spliced Gain-of-Function NT5C2 Isoform Contributes to Chemoresistance in Acute Lymphoblastic Leukemia.” Cancer Research. Online October 15, 2024. DOI: 10.1158/0008-5472.CAN-23-3804.
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Researchers at Children’s Hospital of Philadelphia (CHOP) have elucidated the significant role that alternative splicing – a process whereby a single gene produces multiple proteins by rearranging its messenger RNA segments in different combinations – plays in resistance to chemotherapy in relapsed or refractory B-cell acute lymphoblastic leukemia (B-ALL). The study was published today in the journal Cancer Research.
Leukemia is the most common cancer in children, adolescents, and young adults, making up nearly a third of all pediatric cancers, and B-ALL is the most common form of leukemia among children. The chance of long-term survival after a relapse is approximately 50%, with poorer outcomes for subsequent relapses, leading to high rates of pediatric cancer-related deaths. Although most B-ALL cases are diagnosed in children, most deaths occur in adults due to relapsed or refractory disease.
Until now, the molecular mechanisms responsible for treatment failures in relapsed or refractory B-ALL were thought to involve gene mutations; yet in many cases no relevant mutations could be found. In this study, researchers helped explain that paradox by analyzing RNA sequencing datasets to identify an alternative mechanism of gene dysregulation, such as alternative spicing. They discovered pervasive alternative splicing patterns linked to relapse that could have contributed to resistance to anti-leukemia therapeutics, including glucocorticoids, anti-folates, and thiopurines.
“These findings provide critical insights into the mechanisms of chemoresistance in children with B-ALL who relapse despite aggressive treatment,” said Andrei Thomas-Tikhonenko, PhD, the study’s senior author and Chief of the Division of Cancer Pathobiology and Director of the Experimental Pathology Branch at CHOP. “Our research suggests that alternative splicing acts as a parallel mechanism to genetic alterations, driving resistance in cases where no mutations in known chemoresistance genes are evident. This knowledge is particularly important for identifying patients who might experience treatment failures. Our study also sheds light on the important role of RNA-based diagnostic in the management of childhood leukemia."
Researchers discovered a new version of the NT5C2 gene, which includes an additional segment called exon 6a, makes the protein more active, and causes resistance to certain chemotherapy drugs. The authors observed alternative splicing-driven chemotherapy resistance in leukemia cells, both in vitro and in vivo, similar to resistance found in cells with a known gain-of-function NT5C2 mutation. However, this gene change also made the cells more sensitive to a different drug called mizoribine, which affects the production of RNA and DNA. This finding suggests that drugs widely prescribed to suppress the immune system could serve an alternate therapeutic option for treating leukemias that resist standard chemotherapy.
The study, led by Manuel Torres Diz, PhD, further highlighted that alternative splicing events may impact other chemoresistance-related genes, such a CREBBP and FPGS, resulting in loss-of-function isoforms. For example, CREBBP exon 25/26 skipping led to a deficiency in histone acetyltransferase activity – a process involved in several key pathways in cancerous and non-cancerous cells alike – while FPGS splicing changes were linked to resistance to methotrexate, a common chemotherapy drug.
The study was supported by grants from the NIH | National Cancer Institute, Pennsylvania Department of Health, CURE Non-Formula Collaborative Research on Childhood and Adolescent Blood Cancers, United States Department of Defense, St. Baldrick's Foundation, EPICC Team and St. Baldrick’s-Stand Up to Cancer Dream Team Translational Cancer Research Grant, The V Foundation for Cancer Research, The Emerson Collective, Alex’s Lemonade Stand Foundation and the Leukemia & Lymphoma Society. The authors also received support from the SPROUT Program at CHOP, Accelerating Cancer Therapeutics (ACT) Program at Columbia University, and The Ellen Weisberg Fund: Advancing Breakthroughs in Pediatric Cancer.
Torres-Diz et al. “An Alternatively Spliced Gain-of-Function NT5C2 Isoform Contributes to Chemoresistance in Acute Lymphoblastic Leukemia.” Cancer Research. Online October 15, 2024. DOI: 10.1158/0008-5472.CAN-23-3804.
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