Children with pathogenic TP53 variants face increased risk of hard-to-treat ALL

Pathogenic loss-of-function germline variants in the TP53 gene predispose children to acute lymphoblastic leukemia (ALL), and, later, to solid tumors that may be related to cancer therapy, according to results from a genetic sequencing study.

Researchers at St. Jude Children’s Hospital in Memphis have identified 49 unique variants of the gene among 3,801 children with newly diagnosed B-cell ALL; 22 variants were deemed pathogenic. Children with these variants were at a “dramatically higher risk” of secondary cancers, which occurred in 25% within 5 years of ALL treatment, compared with 0.7% among children without the pathogenic genetic signal, according to Maoxiang Qian, PhD, and colleagues. The report was published in the Journal of Clinical Oncology.

The increased risk of secondary cancers is probably related to a common characteristic of the pathogenic variants: the ablation of the p53-mediated DNA damage response. This increases the risk of the genotoxic therapy given during ALL treatment, according to the researchers.

“In fact, of the five patients with TP53 pathogenic variants who also had second cancers, two received irradiation therapy, including total body irradiation, and both subsequently developed solid tumors,” the researchers wrote. “The exact lifelong risk of second cancer in these patients is difficult to ascertain as many patients might have succumbed to relapsed ALL before they had the chance to develop second cancers.”

The research team conducted targeted sequencing of TP53 coding regions in 3,801 children who were enrolled in two trials sponsored by the Children’s Oncology Group (AALL0232 and P9900). They compared the results to TP53 mutations seen in almost 61,000 children enrolled in the Exome Aggregation Consortium (ExAC) cohort.

The researchers identified nine exonic nonsilent TP53 variants in the ALL cohort, all of which had an allele frequency of less than 0.5%. Of the variants, 22 were deemed pathogenic: Twelve showed a complete loss of transcriptional activity, three showed a partial loss of p53 function, and seven showed loss of the critical core DNA-binding domain in p53. The rest of the variants were deemed of unknown significance (VUS).

Pathogenic variants occurred in 26 children in the ALL cohort – significantly more often than in the control cohort (0.7% vs. 0.1%; odds ratio, 5.2). The VUS risk was not significantly elevated compared to controls, however.

Children with the pathogenic variants were significantly older at ALL diagnosis (15.5 vs. 6.6 years) and had significantly lower leukocyte count. Of the 26 with a pathogenic variant, 17 (65.4%) showed hypodiploidy in ALL blasts.

Pathogenic variants negatively affected ALL treatment outcomes, quadrupling the risk of lower event-free survival and lower overall survival (hazard ratio, 4.2 and 3.9, respectively) in both ALL cohorts.

Of the children with pathogenic variants, 14 experienced a pathological clinical event, including five ALL relapses and five second cancers, each accounting for 36% of all events.

“This pattern of events was dramatically different from that in patients with wild-type TP53 or VUS, for whom ALL relapse accounted for 75% of all events, with only 4% as second cancers,” the researchers wrote. “In fact, within hypodiploid ALL patients who experienced an event, the frequency of second cancer was significantly higher in those with TP53 pathogenic variants than in those without [50% vs. 5%], which additionally suggests that germline TP53 variation, instead of hypodiploid ALL, was the underlying cause of second cancers in these patients.”

The study was supported by grants from the National Institutes of Health and the American Lebanese Syrian Associated Charities. Dr. Qian reported having no financial disclosures. Other researchers reported funding from various pharmaceutical companies.

[email protected]

SOURCE: Qian et al. JCO 2018 Jan 4. doi: 10.1200/JCO.2017.75.5215

Pathogenic loss-of-function germline variants in the TP53 gene predispose children to acute lymphoblastic leukemia (ALL), and, later, to solid tumors that may be related to cancer therapy, according to results from a genetic sequencing study.

Researchers at St. Jude Children’s Hospital in Memphis have identified 49 unique variants of the gene among 3,801 children with newly diagnosed B-cell ALL; 22 variants were deemed pathogenic. Children with these variants were at a “dramatically higher risk” of secondary cancers, which occurred in 25% within 5 years of ALL treatment, compared with 0.7% among children without the pathogenic genetic signal, according to Maoxiang Qian, PhD, and colleagues. The report was published in the Journal of Clinical Oncology.

The increased risk of secondary cancers is probably related to a common characteristic of the pathogenic variants: the ablation of the p53-mediated DNA damage response. This increases the risk of the genotoxic therapy given during ALL treatment, according to the researchers.

“In fact, of the five patients with TP53 pathogenic variants who also had second cancers, two received irradiation therapy, including total body irradiation, and both subsequently developed solid tumors,” the researchers wrote. “The exact lifelong risk of second cancer in these patients is difficult to ascertain as many patients might have succumbed to relapsed ALL before they had the chance to develop second cancers.”

The research team conducted targeted sequencing of TP53 coding regions in 3,801 children who were enrolled in two trials sponsored by the Children’s Oncology Group (AALL0232 and P9900). They compared the results to TP53 mutations seen in almost 61,000 children enrolled in the Exome Aggregation Consortium (ExAC) cohort.

The researchers identified nine exonic nonsilent TP53 variants in the ALL cohort, all of which had an allele frequency of less than 0.5%. Of the variants, 22 were deemed pathogenic: Twelve showed a complete loss of transcriptional activity, three showed a partial loss of p53 function, and seven showed loss of the critical core DNA-binding domain in p53. The rest of the variants were deemed of unknown significance (VUS).

Pathogenic variants occurred in 26 children in the ALL cohort – significantly more often than in the control cohort (0.7% vs. 0.1%; odds ratio, 5.2). The VUS risk was not significantly elevated compared to controls, however.

Children with the pathogenic variants were significantly older at ALL diagnosis (15.5 vs. 6.6 years) and had significantly lower leukocyte count. Of the 26 with a pathogenic variant, 17 (65.4%) showed hypodiploidy in ALL blasts.

Pathogenic variants negatively affected ALL treatment outcomes, quadrupling the risk of lower event-free survival and lower overall survival (hazard ratio, 4.2 and 3.9, respectively) in both ALL cohorts.

Of the children with pathogenic variants, 14 experienced a pathological clinical event, including five ALL relapses and five second cancers, each accounting for 36% of all events.

“This pattern of events was dramatically different from that in patients with wild-type TP53 or VUS, for whom ALL relapse accounted for 75% of all events, with only 4% as second cancers,” the researchers wrote. “In fact, within hypodiploid ALL patients who experienced an event, the frequency of second cancer was significantly higher in those with TP53 pathogenic variants than in those without [50% vs. 5%], which additionally suggests that germline TP53 variation, instead of hypodiploid ALL, was the underlying cause of second cancers in these patients.”

The study was supported by grants from the National Institutes of Health and the American Lebanese Syrian Associated Charities. Dr. Qian reported having no financial disclosures. Other researchers reported funding from various pharmaceutical companies.

[email protected]

SOURCE: Qian et al. JCO 2018 Jan 4. doi: 10.1200/JCO.2017.75.5215

Pathogenic loss-of-function germline variants in the TP53 gene predispose children to acute lymphoblastic leukemia (ALL), and, later, to solid tumors that may be related to cancer therapy, according to results from a genetic sequencing study.

Researchers at St. Jude Children’s Hospital in Memphis have identified 49 unique variants of the gene among 3,801 children with newly diagnosed B-cell ALL; 22 variants were deemed pathogenic. Children with these variants were at a “dramatically higher risk” of secondary cancers, which occurred in 25% within 5 years of ALL treatment, compared with 0.7% among children without the pathogenic genetic signal, according to Maoxiang Qian, PhD, and colleagues. The report was published in the Journal of Clinical Oncology.

The increased risk of secondary cancers is probably related to a common characteristic of the pathogenic variants: the ablation of the p53-mediated DNA damage response. This increases the risk of the genotoxic therapy given during ALL treatment, according to the researchers.

“In fact, of the five patients with TP53 pathogenic variants who also had second cancers, two received irradiation therapy, including total body irradiation, and both subsequently developed solid tumors,” the researchers wrote. “The exact lifelong risk of second cancer in these patients is difficult to ascertain as many patients might have succumbed to relapsed ALL before they had the chance to develop second cancers.”

The research team conducted targeted sequencing of TP53 coding regions in 3,801 children who were enrolled in two trials sponsored by the Children’s Oncology Group (AALL0232 and P9900). They compared the results to TP53 mutations seen in almost 61,000 children enrolled in the Exome Aggregation Consortium (ExAC) cohort.

The researchers identified nine exonic nonsilent TP53 variants in the ALL cohort, all of which had an allele frequency of less than 0.5%. Of the variants, 22 were deemed pathogenic: Twelve showed a complete loss of transcriptional activity, three showed a partial loss of p53 function, and seven showed loss of the critical core DNA-binding domain in p53. The rest of the variants were deemed of unknown significance (VUS).

Pathogenic variants occurred in 26 children in the ALL cohort – significantly more often than in the control cohort (0.7% vs. 0.1%; odds ratio, 5.2). The VUS risk was not significantly elevated compared to controls, however.

Children with the pathogenic variants were significantly older at ALL diagnosis (15.5 vs. 6.6 years) and had significantly lower leukocyte count. Of the 26 with a pathogenic variant, 17 (65.4%) showed hypodiploidy in ALL blasts.

Pathogenic variants negatively affected ALL treatment outcomes, quadrupling the risk of lower event-free survival and lower overall survival (hazard ratio, 4.2 and 3.9, respectively) in both ALL cohorts.

Of the children with pathogenic variants, 14 experienced a pathological clinical event, including five ALL relapses and five second cancers, each accounting for 36% of all events.

“This pattern of events was dramatically different from that in patients with wild-type TP53 or VUS, for whom ALL relapse accounted for 75% of all events, with only 4% as second cancers,” the researchers wrote. “In fact, within hypodiploid ALL patients who experienced an event, the frequency of second cancer was significantly higher in those with TP53 pathogenic variants than in those without [50% vs. 5%], which additionally suggests that germline TP53 variation, instead of hypodiploid ALL, was the underlying cause of second cancers in these patients.”

The study was supported by grants from the National Institutes of Health and the American Lebanese Syrian Associated Charities. Dr. Qian reported having no financial disclosures. Other researchers reported funding from various pharmaceutical companies.

[email protected]

SOURCE: Qian et al. JCO 2018 Jan 4. doi: 10.1200/JCO.2017.75.5215