Somatic and germline cohesins alterations in pediatric acute lymphoblastic leukemia

Leukemia's molecular mechanisms are not fully understood. Cohesin complex mutations may affect chromosomal stability and contribute to pathogenesis. Cohesin genes have canonical DNA binding and non-canonical gene expression roles. Somatic mutations are known in Myeloproliferative disorders and pediatric Acute Lymphoblastic Leukemia (ALL), while germline ones cause Cohesinopathies, like Cornelia de Lange Syndrome (CdLS). Our report of the first CdLS patient with ALL suggested cohesins germline mutations involvement in ALL pathogenesis, indeed we demonstrated that STAG1 germline mutations could predispose to pediatric hematological malignancies. Therefore, both germline and somatic alterations of cohesin genes are possibly linked to ALL. By a DNA-targeted NGS screening of 120 consecutive pediatric ALL diagnoses (enrolled in AIEOP-BFM protocol in Italian Centers), we found 11 germline cohesin mutations (6/11 missense, 4/11 3’/5’ UTR, 1/11 splice-acceptor). Through CRISPR/Cas9 we generated in vitro models of two STAG1 mutations in a healthy Lymphoblastoid Cell Line, RNAseq preliminary analyses on these cell lines revealed 619 differentially expressed genes (DEGs), many involved in intracellular signaling. Moreover, we developed a computational analysis pipeline to detect fusion transcripts from RNAseq of 371 consecutive diagnoses and 65 relapses of pediatric ALL (309/371 B-ALL, 58/371 T-ALL). Our findings firstly propose cohesins as candidates in fusion genes in pediatric ALL: we identified 3 B-ALL cases carrying fusion transcripts of STAG1, STAG2 and RAD21, two of them relapsed after complete remission. Gene signature and DEGs analyses on these cases produced heterogeneous results likely due to different partner genes. Collectively, these observations depict a role for germline and somatic cohesins events in pediatric ALL, potentially defining a new subclass of leukemia. Leukemia's molecular mechanisms are not fully understood. Cohesin complex mutations may affect chromosomal stability and contribute to pathogenesis. Cohesin genes have canonical DNA binding and non-canonical gene expression roles. Somatic mutations are known in Myeloproliferative disorders and pediatric Acute Lymphoblastic Leukemia (ALL), while germline ones cause Cohesinopathies, like Cornelia de Lange Syndrome (CdLS). Our report of the first CdLS patient with ALL suggested cohesins germline mutations involvement in ALL pathogenesis, indeed we demonstrated that STAG1 germline mutations could predispose to pediatric hematological malignancies. Therefore, both germline and somatic alterations of cohesin genes are possibly linked to ALL. By a DNA-targeted NGS screening of 120 consecutive pediatric ALL diagnoses (enrolled in AIEOP-BFM protocol in Italian Centers), we found 11 germline cohesin mutations (6/11 missense, 4/11 3’/5’ UTR, 1/11 splice-acceptor). Through CRISPR/Cas9 we generated in vitro models of two STAG1 mutations in a healthy Lymphoblastoid Cell Line, RNAseq preliminary analyses on these cell lines revealed 619 differentially expressed genes (DEGs), many involved in intracellular signaling. Moreover, we developed a computational analysis pipeline to detect fusion transcripts from RNAseq of 371 consecutive diagnoses and 65 relapses of pediatric ALL (309/371 B-ALL, 58/371 T-ALL). Our findings firstly propose cohesins as candidates in fusion genes in pediatric ALL: we identified 3 B-ALL cases carrying fusion transcripts of STAG1, STAG2 and RAD21, two of them relapsed after complete remission. Gene signature and DEGs analyses on these cases produced heterogeneous results likely due to different partner genes. Collectively, these observations depict a role for germline and somatic cohesins events in pediatric ALL, potentially defining a new subclass of leukemia.