A novel germline variant in <scp> <i>PIK3R1</i> </scp> results in <scp>SHORT</scp> syndrome associated with <scp> <i>TAL</i> </scp> <i>/</i> <scp> <i>LMO</i> </scp> T‐cell acute lymphoblastic leukemia
Authors: Antonio Marzollo, Giacomo Maestrini, Roberta La Starza, Loredana Elia, Francesco Malfona, Tiziana Pierini, Caterina Tretti Parenzan, Alessandro Coppe, Stefania Bortoluzzi, Alessandra Biffi, Cristina Mecucci, Silvia Bresolin, Anna Maria Testi
Journal: American Journal of Hematology (2020)

Acute lymphoblastic leukemia is the most frequent neoplasm in children and T-cell ALL (T-ALL), accounting for 12-15% of cases. TAL/LMO is the most represented genetic subgroup, characterizing 40-50% of pediatric T-ALL.1, 2 Somatically acquired abnormalities affecting the PI3K/AKT/mTOR pathway, mainly PTEN deletions/mutations, and AKT or PIK3R1 mutations are enriched in the TAL/LMO subgroup and have been related to a dismal outcome.3 Herein, we report results of our molecular and cytogenetic studies in a pediatric patient with a novel germline variant in PIK3R1 causing SHORT syndrome who developed a TAL/LMO T-ALL. The legal guardians of the patient provided written informed consent for the publication of the present report. Our patient was born from healthy, non-consanguineous parents of Italian origin at 32 weeks of gestation. Birth weight was 1900 g (<3° centile), length was 41.5 cm (<3° centile) and head circumference 33 cm (<3° centile). From the age of 2 years, the patient had a delay in reaching motor milestones. Growth hormone (GH) was administered for 2 years for short stature, without benefit. He had no history of severe or recurrent infections and immunoglobulin levels were within normal range. At the age of 13 years, the patient presented with vomiting, diarrhea, and abdominal pain. On physical examination, short stature (140 cm, <3° centile), obesity (43 kg, BMI 22 kg/m2, 75° centile), hyperextensibility of joints, lipodystrophy around the elbows, and typical facial gestalt including triangular-shaped face, prominent forehead, deep-set eyes, small chin, thin lip, and downturned mouth were noted. Thoracic CT-scan detected a large mediastinal mass (100 × 90 mm). Full blood count revealed marked leukocytosis (WBC 89.91 × 109/L). On peripheral blood and bone marrow (BM) examination, blasts had a lymphoid-like L1 morphology and were negative for myeloperoxidase. Flow-cytometry (FCM) analysis was consistent with a diagnosis of pre-T-ALL (CD99+/CD7+/cCD3+/CD2+/CD5+/TdT+/CD8±/CD4±,sCD3-/CD1a-/CD34-/CD117-/TCRαβ-/TCRγδ-/CD10-/HLA-DR-/CD13-/CD33-/CD56-/MPO-/cCD79a-). The cerebrospinal fluid cell count was <5/μL, but blasts were present (ie, stratification as CNS2). Conventional cytogenetics showed a normal 46,XY male karyotype. Integrated molecular-cytogenetic studies detected the SIL-TAL1 fusion, classifying the leukemia in the TAL/LMO subgroup. Additional events were the biallelic deletion of CDKN2AB/9p21 and the monoallelic deletion of PTEN/10q23 (Appendix S1 and Table S1). The patient was treated according to AIEOP-BFM ALL-2009 protocol and was stratified as non-high risk. CNS remission was obtained after the first intrathecal chemotherapy. However, during re-induction (phase IIA), an isolated CNS relapse occurred and he required intensive systemic and intrathecal chemotherapy to reach the second CNS and BM remission (negative RQ-PCR for the SIL-TAL transcript). The patient underwent hematopoietic stem cell transplantation from a matched unrelated donor and is currently alive in complete remission at 13 months after ALL diagnosis. The DNA extracted from peripheral blood at remission was analyzed by custom gene panel sequencing to explore the genetic causes of the clinical phenotype and to investigate the possibility of a germline genetic predisposition to the development of leukemia. We identified the NM_181523.3:c.1457C>T, p.(Ala486Val) variant in the PIK3R1 gene (Figure 1A and Supplemental Methods). This variant falls in the iSH2 domain of PIK3R1 (Figure 1B) and is not reported in GnomAD. Polyphen2, SIFT, CADD-Phred, and MutationTaster software indicate with high confidence a deleterious effect of the variant on the protein, and comparative tools—such as PhyloP, GERP, and PhastCons—indicate that the genomic position is highly conserved. The germline origin of the variant was confirmed by Sanger sequencing in a non-hematopoietic tissue (oral swab, Supplemental Figure 1A). Segregation analysis showed that the variant occurred de novo in our patient (Figure 1C). PIK3R1 encodes for the regulatory subunit of the phosphoinositide-3-kinase (PI3K) complex and is involved in the PIK3/AKT/mTOR pathway controlling growth and cell proliferation. Germline variants in PIK3R1 have been associated with SHORT syndrome, which is a disorder characterized by Short stature, Hyperextensibility of joints or hernias, Ocular depression, Rieger anomaly, and delays of Tooth eruption.4 Other manifestations include insulin resistance and characteristic facies. Our patient has phenotypic signs and symptoms of SHORT syndrome, supporting the genotype-phenotype correlation. Moreover, even if blood glucose values were normal at diagnosis, he developed severe hyperglycemia during induction, being poorly responsive to insulin and requiring asparaginase discontinuation. The novel variant found in our patient lies in the iSH2 domain, whereas almost all variants previously associated with SHORT syndrome were detected in cSH2 domain.4 Interestingly, variants in the iSH2 domain of PIK3R1 are somatically acquired in several solid tumors and lymphoid malignancies.5 Most importantly, variants in iSH2 domain of PIK3R1 are found in 6.4% of childhood T-ALL and are associated with TAL1 rearrangements, as was observed in our patient.2 The pivotal leukemogenic role of the PI3K/AKT/mTOR pathway in our patient is strengthened by the acquisition of a PTEN deletion. Thus, we hypothesize that the germline PIK3R1 variant represented an early leukemia-predisposing event and that the acquisition of additional abnormalities contributed to the development of full-blown leukemia. Indeed, most leukemia-predisposing syndromes are associated with germline variants in genes encoding hematopoietic transcription factors implicated in leukemogenesis and harboring somatic variants in sporadic leukemia (eg, IKZF1, ETV6, PAX5).6 Also, germline variants in other genes encoding for members or modulators of the PI3K/AKT/mTOR pathway have been associated with an inherited cancer-predisposing syndrome, namely PTEN hamartoma tumor syndrome. In conclusion, our clinical observation suggests that SHORT syndrome due to variants in the iSH2 domain of PIK3R1 might be a novel leukemia predisposing syndrome. The authors would like to acknowledge support from Fondazione Città della Speranza ONLUS (http://cittadellasperanza.org/) to AM, Associazione di Promozione Sociale “Genitori in fuga” (https://www.genitoriinfuga.org/) to AM and SBr, Associazione sportiva dilettantistica “NCO Crew” to AM and SBr, PRIN 2017 (code 2017PPS2X4) to SBo, CM and RLS, Associazione Sergio Luciani Association, Fabriano to CM, Comitato per la vita “Daniele Chianelli,” Perugia to RLS, Fondazione Cassa di Risparmio Perugia (Grant number 2018.0418.021) to RLS, Fondazione Cariparo (Grant 17/07_1FCR) to SBr, and AIRC (IG 2017 #20052) to SBo. Our most heart-felt thanks go to our patient and his family. The authors would like also to thank Prof. Anna Savoia (IRCSS “Burlo Garofalo,” Trieste) for her help in establishing the collaboration and discussing the case, and Dr. Cristina Tea Natalucci, Dr. Maddalena Martella, and Dr. Martina Pigazzi for their support in genetic testing. The authors have no conflict of interest to disclose. AM, GM, RLS, SBr, and AMT drafted the paper; GM, LE, FM, and AMT provided clinical care to the patient; RLS, TP, and CM performed and interpreted the integrated molecular-cytogenetic on T-ALL blasts; AM, CT, AC, AB, and SBr designed, performed, and interpreted the germline genetic studies; SBr, AC, and SB performed NGS pipeline; all authors approved the final version. Appendix S1: Supporting Information. Table S1 List of filtered variants identified in the proband by Next Generation Sequencing and subsequently evaluated by manual curation. Applied filters are: SNFeff: “MODERATE” or “HIGH”; gnomAD_genome_ALL frequency < 0.001. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.