Congenital Sideroblastic Anemia: Phenotypes, Genotypes, and Literature Review, Lecture notes of Medicine

Download Congenital Sideroblastic Anemia: Phenotypes, Genotypes, and Literature Review and more Lecture notes Medicine in PDF only on Docsity! P os te d on A u th or ea 4 F eb 20 21 — T h e co p y ri gh t h ol d er is th e au th or /f u n d er . A ll ri g h ts re se rv ed . N o re u se w it h ou t p er m is si on . — h tt p s: // d oi .o rg /1 0. 22 54 1/ au .1 61 24 40 27 .7 27 66 59 4/ v 1 — T h is a p re p ri n t an d h a s n o t b ee n p ee r re v ie w ed . D a ta m ay b e p re li m in a ry . SLC25A38 Congenital Sideroblastic Anemia: Phenotypes and genotypes of 31 individuals from 24 families, including 11 novel mutations, and a review of the literature Matthew Heeney1, Simon Berhe2, Dean Campagna2, Joseph Oved3, Peter Kurre3, Peter Shaw4, Juliana Teo4, Mayada Abu Shanap5, Hoda Hassab6, Bertil Glader7, Sanjay Shah8, Ayami Yoshimi9, Afshin Ameri10, Joseph Antin11, Jeanne Boudreaux12, Michael Briones12, Kathryn Dickerson13, Conrad Fernandez14, Roula Farah15, Henrik Hasle16, Sioban Keel17, Timothy Olson3, Jacquelyn Powers18, Melissa Rose19, Akiko Schimamura1, Sylvia Bottomley20, and Mark Fleming21 1Dana-Farber/Boston Children’s Cancer and Blood Disorders Center 2Boston Children’s Hospital Department of Pathology 3The Children’s Hospital of Philadelphia 4Children’s Hospital at Westmead 5King Hussein Medical Center 6Alexandria University 7Lucile Packard Children’s Hospital at Stanford Pediatrics 8Phoenix Children’s Hospital Center for Cancer and Blood Disorders 9University of Freiburg 10Augusta University 11Dana-Farber Cancer Institute 12Children’s Healthcare of Atlanta Inc 13The University of Texas Southwestern Medical Center 14Dalhousie University 15Lebanese American University 16Aarhus University Hospital 17Seattle Cancer Care Alliance 18Texas Children’s Hospital 19Nationwide Children’s Hospital 20The University of Oklahoma College of Medicine 21Boston Children’s Hospital February 4, 2021 Abstract The congenital sideroblastic anemias (CSAs) are a heterogeneous group of inherited disorders of erythropoiesis characterized by pathologic deposits of iron in the mitochondria of developing erythroblasts. Mutations in the mitochondrial glycine carrier SLC25A38 cause the most common recessive form of CSA. Nonetheless, the disease is still rare, there being fewer than 70 reported families. Here we describe the clinical phenotype and genotypes of 31 individuals from 24 families, including 11 novel 1 P os te d on A u th or ea 4 F eb 20 21 — T h e co p y ri gh t h ol d er is th e au th or /f u n d er . A ll ri g h ts re se rv ed . N o re u se w it h ou t p er m is si on . — h tt p s: // d oi .o rg /1 0. 22 54 1/ au .1 61 24 40 27 .7 27 66 59 4/ v 1 — T h is a p re p ri n t an d h a s n o t b ee n p ee r re v ie w ed . D a ta m ay b e p re li m in a ry . mutations. We also review the spectrum of reported mutations and genotypes associated with the disease, describe the unique localization of missense mutations in transmembrane domains and account for the reoccurrence of several alleles in different populations. MUTATION UPDATE SLC25A38 SLC25A38 Congenital Sideroblastic Anemia : Phenotypes and genotypes of 31 individuals from 24 families, including 11 novel mutations, and a review of the literature Matthew M. Heeney1*, Simon Berhe2*, Dean R. Campagna2*, Joseph H. Oved3, Peter Kurre4, Peter J. Shaw5, Juliana Teo6, Mayada Abu Shanap7, Hoda M. Hassab8, Bertil E. Glader9, Sanjay Shah10, Ayami Yoshimi11, Afshin Ameri12, Joseph H. Antin13, Jeanne Boudreaux14, Michael Briones14, Kathryn E. Dickerson15, Conrad V. Fernandez16, Roula Farah17, Henrik Hasle18, Sioban B. Keel19, Timothy S. Olson20, Jacquelyn M. Powers21, Melissa J. Rose22, Akiko Shimamura1, Sylvia S. Bottomley23, Mark D. Fleming2 1Division of Hematology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center and Depart- ment of Pediatrics, Harvard Medical School, Boston, MA, USA 2Department of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA 3Cellular Therapy and Transplant Section, Division of Oncology and Comprehensive Bone Marrow Failure Center, Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA 4Pediatric Comprehensive Bone Marrow Failure Center, Children’s Hospital of Philadelphia, Philadelphia, PA, USA 5BMT Services, Children’s Hospital at Westmead; Faculty of Medicine and Health, University of Sydney, Sydney, AU 6Department of Haematology, Children’s Hospital at Westmead, Sydney, AU 7King Hussein Medical Center, Amman, Jordan 8Department of Paediatrics, Faculty of Medicine, Alexandria University, Alexandria, Egypt 9Division of Hematology-Oncology, Lucille Packard Children’s Hospital, Stanford, CA, USA 10Center for Cancer and Blood Disorders, Phoenix Children’s Hospital, Phoenix, AZ, USA 11Department of Paediatrics and Adolescent Medicine, Division of Paediatric Haematology and Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany 12Division of Pediatric Hematology/Oncology, Department of Pediatrics, Augusta University, Augusta, GA, USA 13Hematopoietic Stem Cell Transplantation Program, Dana-Farber Cancer Institute, and Harvard Medical School, Boston, MA, USA 14Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta and Emory University, Atlanta, GA, USA 15Department of Pediatrics, University of Texas Southwestern, Dallas, TX, USA 16Division of Hematology-Oncology, IWH Center, Dalhousie University, Halifax, NS, Canada 17Department of Pediatrics, Lebanese American University Medical Center, Beirut, Lebanon 18Department of Pediatrics, Aarhus University Hospital, Aarhus University, Aarhus, Denmark 19Division of Hematology, Department of Medicine, University of Washington and Seattle Cancer Care Alliance, Seattle, WA, USA 2 P os te d on A u th or ea 4 F eb 20 21 — T h e co p y ri gh t h ol d er is th e au th or /f u n d er . A ll ri g h ts re se rv ed . N o re u se w it h ou t p er m is si on . — h tt p s: // d oi .o rg /1 0. 22 54 1/ au .1 61 24 40 27 .7 27 66 59 4/ v 1 — T h is a p re p ri n t an d h a s n o t b ee n p ee r re v ie w ed . D a ta m ay b e p re li m in a ry . erythroblasts. In several cases, RS were absent or only rare. In most, but not all, cases, there was an erythroid hyperplasia in the bone marrow; in some there was an erythroid hypoplasia. Conspicuous dyserythropoiesis and variable fibrosis were present in a minority of samples. Anemic siblings were sometimes diagnosed with CSA by genetic testing alone, as was the case with patient 20.2, whose older sibling (20.1), has previously been reported (Kim et al., 2018). Three patients from two families (patients 2.1, 2.2, and 18.1) were initially regarded as having an atypical form of Diamond-Blackfan anemia (DBA). In family 2, the eventual identification of rare siderocytes in the peripheral blood suggested CSA, which was confirmed by candidate gene sequencing. Because of the unusual, apparently syndromic features in patient 14.1, this patient’s diagnosis was established by whole exome sequencing. In patient 18.1, SLC25A38 mutations were identified by whole exome sequencing years after successful hematopoietic stem cell transplantation for “DBA.” Most patients did not have abnormalities in other organ systems that were not attributable to chronic anemia or iron overload (e.g. growth failure, endocrine abnormalities, liver disease, cardiomyopathy), but several potentially syndromic features were observed in a number of patients (Table 1): unilateral corneal clouding (13.1), a “box-shaped” hyperostotic skull (14.1, 24.1), macrocephaly (8.2, 17.1), syndromic facies (28.1), meningomyelocoele/club foot (17.1), genital abnormalities (18.1, 22.3, 22.4), behavioral issues (18.1 and 22.1), aortic root/coronary abnormalities (20.2, 22.2, 22.3). Therapy All of the patients have required transfusions, most chronically and beginning in the neonatal period or infancy (Table 3). Of the 28 patients in whom data are available, 2 patients received their first transfusions in utero (13.1 and 22.4), 12 in the neonatal period, 11 in infancy, and 3 between age 4- and 8-years. All but one was maintained on regular transfusions with a transfusion interval of between 2 and 8 weeks. In 20 of 20 patients for whom oral pyridoxine was prescribed, there was no improvement in the hemoglobin (HGB). All patients surviving early childhood have developed secondary iron overload and have required chelation. A variety of agents including deferoxamine, deferisirox, deferiprone alone or in combination have been employed. One patient (2.1), poorly compliant with chelation, died at age 18 from cardiomyopathy. Another (17.1), age 3, died of line-associated sepsis. Three patients who were status-post splenectomy experienced thrombocytosis and/or thrombotic events. The median age of patients alive at the time of last follow-up is 11 years (range 1-39 years). Nine patients have undergone allogeneic hematopoietic stem cell transplantation (Table 4) with a median follow up of 7 years (range 1 mos. to 17 yrs.). All transplanted patients are alive; 8 of 9 had full engraftment and became transfusion independent. One patient (14.1) had secondary graft failure at 18-months post- transplant with auto recovery; she is transfusion dependent and being prepared for second transplant. Four patients received myeloablative conditioning, and 4 other received reduced intensity conditioning. Donors were matched unrelated donor (n=4), matched related donors (one matched family donor and three were matched sibling donors), and one patient had one antigen mismatch sibling donor. Methotrexate and a calcineurin inhibitors were the most common graft versus host disease prophylaxis. Acute and chronic graft versus host disease were seen in 1 and 3 patients, respectively. One patient developed chronic post-transplant autoimmune hemolytic anemia requiring transfusion. Mutation Analysis The 24 families carry 27 distinct SLC25A38 mutations (Table 2). Sixteen (16) of these muta- tions have been described by us and others previously. Eleven (11) mutations are novel, includ- ing one MS allele (c.388G>A; p.Gly130Arg), 5 frameshift (FS) alleles (c.207 214del, p.Met70Cysfs*80; c.362del, p.Pro121Glnfs*26; c.475del, p.Glu159Argfs*7; c.669 682del, p.Cys223Trpfs*67; and c.809dup, p.Phe271Leufs*24), and 5 variants predicted to interrupt splicing (c.70-2A>C, c.276+1G>A, c.277-2A>C, c.457-1G>T, and c.792+5G>C). In contrast to many of the previously reported pathogenic alleles, which are generally more common (see below), only one of these variants occurs in a sequence with a predisposition to mutation: the c.207 214del involves a deletion of a 7 base-pair direct repeat. Furthermore, only two of the novel mutations, c.457-1G>T (rs1448237170, MAF 4.00x10-6) and c.669 682del (rs781372292, MAF 1.77x10-5), are recorded in references databases such as gnomAD (gnomad.broadinstitute.org). 5 P os te d on A u th or ea 4 F eb 20 21 — T h e co p y ri gh t h ol d er is th e au th or /f u n d er . A ll ri g h ts re se rv ed . N o re u se w it h ou t p er m is si on . — h tt p s: // d oi .o rg /1 0. 22 54 1/ au .1 61 24 40 27 .7 27 66 59 4/ v 1 — T h is a p re p ri n t an d h a s n o t b ee n p ee r re v ie w ed . D a ta m ay b e p re li m in a ry . As expected in a rare recessive disease, 19 of the 24 families (79%) are homozygous for the pathogenic mutation. In the patients with homozygous mutations, 10 are known to be consanguineous and 5 are from geographically or ethnically restricted populations that may be genetically less diverse. In this cohort, we detected no difference in age of onset of anemia, age at initial transfusion, pre-transfusion HGB, or transfusion interval among patients with two null alleles, two splicing alleles, or at least one MS mutation (data not shown). The SLC25A38 mutation spectrum Currently, there are 16 publications, including the current one, describing, a total of 92 SLC25A38 CSA families from diverse geographic and ethnic backgrounds (Table 5). As is true of our sample, approximately three-quarters (77%) of the reported probands carry homozygous mutant alleles (Figure 1A). In one case, ho- mozygosity is the result of constitutional uniparental isodisomy (Andolfo et al., 2020). MS (36%), frameshift (27%) and stop-gained (27%) alleles each constitute one-quarter to one-third of alleles detected in probands (Figure 1B). Variants predicted to affect splicing (9%) or cause a stop-loss (EXT, 1%) are comparatively rare. Two MS variants, c.560G>C; p.Arg187Pro and c.625G>C; p.Asp209His, are also predicted to affect splicing, the former likely activating a cryptic splice acceptor site within exon 5 and the latter altering the conserved G at the last base pair of exon 5. Patients homozygous for MS mutations are most common, constituting approximately one-third (31%) of all reported probands (Figure 1C). Whereas 42% of patients bear at least one MS allele and may retain some transport function, 46% have two stop-gained or frameshift (or a combination of both) presumptive null alleles, and another 12% have two splicing alleles or a splicing allele in trans of a frameshift or stop-loss allele, also likely to retain little transport activity (Figure 1D). Of the 47 reported disease-associated mutations, 12 occur at sequences prone to recurrence, including 9 at CpG dinucleotides and 3 at a direct or simple repeat. Of the 21 apparently recurrent mutations, 9 are at a CpG or repeat (Figure 2). Pathogenic MS mutations are distributed nearly exclusively in the transmembrane (TM) domains. Of the 21 pathogenic MS mutations, 19 are located in amino acids within a TM domain (Table 5 and Figure 2). One of the remaining two, c.625G>C; p.Asp209His, is also predicted to affect splicing. The remaining variant, c.469G>C; p.Gly157Arg, in addition to be located between TM3 and TM4, is conserved neither in SLC25 family members, nor in SLC25A38 orthologues. There is no difference in the relative conservation of amino acids in TM and non-TM regions of SLC25A38 orthologues (Mann-Whitney P=0.385) whereas there is an unexpected predominance of disease-causing mutations present in TMs (χ2 P<0.001). Of the TM residues with pathogenic mutations, there is a trend toward being relatively conserved compared to other TM amino acids (Mann-Whitney P=0.085) DISCUSSION This is the largest series of patients with SLC25A38 associated CSA yet reported, describing 31 individuals from 24 different families and 11 novel mutations, expanding the total number of reported families and pathogenic alleles to 92 and 47, respectively. Despite the diversity of mutations, there are several unexpected aspects of the SLC25A38 anemia revealed by these studies worth noting. First is the very limited evidence that there is a genotype-phenotype correla- tion. Essentially all patients present at birth or infancy with a severe hypochromic, microcytic anemia that eventually requires chronic transfusion. This is in stark contrast with the most common form of hypochromic microcytic, non-syndromic CSA, XLSA, which is the major differential diagnosis. Male patients with XLSA may present at birth to older adulthood. The most severe XLSA cases tend to present at an earlier age, but it is unusual for a patient to have transfusion dependent anemia as is typical of SLC25A38 disease. Indeed, the anemia in XLSA is frequently incidental and may be discovered only by screening or as a result of investiga- tion of unexplained iron overload. There are, however, several exceptional cases of patients with SLC25A38 disease coming to medical attention in their teens or twenties. Three of these patients had homozygous mutations at codon 134 [p.Arg134His or p.Arg134Cys] (Fouquet et al., 2019; Hanina, Bain, Clark, & Layton, 6 P os te d on A u th or ea 4 F eb 20 21 — T h e co p y ri gh t h ol d er is th e au th or /f u n d er . A ll ri g h ts re se rv ed . N o re u se w it h ou t p er m is si on . — h tt p s: // d oi .o rg /1 0. 22 54 1/ au .1 61 24 40 27 .7 27 66 59 4/ v 1 — T h is a p re p ri n t an d h a s n o t b ee n p ee r re v ie w ed . D a ta m ay b e p re li m in a ry . 2018; Le Rouzic et al., 2017). However, two other patients homozygous for the p.Arg134Cys allele presented at age 2 months and 2 years (W. An et al., 2015; W. B. An et al., 2019; Kannengiesser et al., 2011). In our own cohort, a patient with a homozygous variant at the only incompletely conserved +5 position of a splice donor site (c.792+5G>C) presented in his mid-teens. It is certainly possible that other genotype-phenotype correlations are masked by the clinical imperative to initiate transfusions in a patient with a HGB less than ˜9 g/dL. Indeed, in the publications in which an initial diagnostic HGB is reported, only one individual, a neonate, had a hemoglobin >9 g/dL (Guernsey et al., 2009; Hanina et al., 2018; Kannengiesser et al., 2011; Liu et al., 2013; Wong et al., 2015). Although clinical practice to transfuse these patients may disguise the subtle differences between SLC25A38 genotypes, it is abundantly evident that an SLC25A38 null genotype does not preclude some mitochondrial glycine being available for heme synthesis. This may be due to other, less specific transporters, possibly including the highly homologous protein SLC25A39, or pathways that produce glycine from other amino acids, such as serine (Amelio, Cutruzzola, Antonov, Agostini, & Melino, 2014; Kory et al., 2018). Leveraging these pathways may provide an avenue for therapy. However, based on limited data, it is unlikely that glycine supplementation alone will suffice (Fernandez-Murray et al., 2016; LeBlanc et al., 2016). The SLC25A38 anemia is regarded as non-syndromic. Nevertheless, twelve of the 31 patients described here had developmental or intellectual disabilities. Similar abnormalities, including psychomotor delay, hypotonia, facial dysmorphism (Fouquet et al., 2019), Hypospadias (W. An et al., 2015), congenital myelomeningocele, patent ductus arteriosus and ventricular septal defects (Wong et al., 2015) have been reported in several other patients, but no abnormality is unusually prevalent across multiple families to suggest a specific syndromic association. Three patients who underwent splenectomy developed thrombocytosis and/or recurrent thrombosis, further supporting the notion that splenectomy may be contraindicated in SLC25A38 CSA as has generally been advocated in other patients with microcytic CSAs (Bottomley & Fleming, 2014; Fouquet et al., 2019). The 47 described SLC25A38 pathogenic mutations occur at 40 different codons. However, nearly one-third (27 of 92) families carry at least one copy of either the c.324 325del or the c.349C>T allele. The latter has been identified in families of Acadian (Guernsey et al., 2009), African American (current report), South Asian (Ravindra et al., 2020), Greek (Guernsey et al., 2009), and Northern European (this report) origin, suggesting that it has reoccurred on multiple occasions. In fact, in one case (21.1), the patient is homozygous for the c.349C>T allele, associated null allele, but one copy also carries a MS variant in a non-conserved residue in cis (c.[161G>A;349C>T]; p.[Arg54His;Arg117X]). Reanalysis of other SLC25A38 anemia patients previously reported by us (Guernsey et al., 2009) identified one other patient having this compound mutant chromosome (data not shown). Both of these variants occur at hypermutable cytosine-guanosine (CpG) dinucleotides. This would support the notion that the p.Arg117X allele has occurred on multiple occasions and that homozygosity for a disease-associated variant in SLC25A38 should not necessarily be taken as evidence of identity by descent. Because of the severity and great similarity of the disorder to transfusion-dependent β-thalassemia (tha- lassemia major), all of the patients in our cohort were at one time managed with transfusion and iron chelation in a manner similar to thalassemia. This is similarly true of nearly all of the patients described in the literature. Just as we identified no consistent, distinctive syndromic aspects of the disease outside the anemia, we did not observe any complications or undue toxicity as a result of transfusion or iron overload. The oldest patient in this cohort was 39 years of age, and we are aware of at least two patients in their early fifties (Guernsey et al., 2009), suggesting that modern transfusion and chelation regimens support long-term survival. Nonetheless, 9 of our patients underwent allogenic HSCT at varying times during their disease course. Ten other patients (Guernsey et al., 2009; Kannengiesser et al., 2011; Uminski et al., 2020) as well as the sibling of one patient included in this series (Kim et al., 2018) are reported to have been transplanted. Comprehensive details are unavailable for most of these patients, but when stated, similar to those described here, HSCT 7 P os te d on A u th or ea 4 F eb 20 21 — T h e co p y ri gh t h ol d er is th e au th or /f u n d er . A ll ri g h ts re se rv ed . N o re u se w it h ou t p er m is si on . — h tt p s: // d oi .o rg /1 0. 22 54 1/ au .1 61 24 40 27 .7 27 66 59 4/ v 1 — T h is a p re p ri n t an d h a s n o t b ee n p ee r re v ie w ed . D a ta m ay b e p re li m in a ry . Ravindra, N., Athiyarath, R., S, E., S, S., Kulkarni, U., N, A. F., . . . Edison, E. S. (2020). Novel frameshift variant (c.409dupG) in SLC25A38 is a common cause of congenital sideroblastic anaemia in the Indian subcontinent. J Clin Pathol . doi:10.1136/jclinpath-2020-206647 Ruprecht, J. J., & Kunji, E. R. S. (2020). The SLC25 Mitochondrial Carrier Family: Structure and Mecha- nism.Trends Biochem Sci, 45 (3), 244-258. doi:10.1016/j.tibs.2019.11.001 Shefer Averbuch, N., Steinberg-Shemer, O., Dgany, O., Krasnov, T., Noy-Lotan, S., Yacobovich, J., . . . Tamary, H. (2018). Targeted next generation sequencing for the diagnosis of patients with rare congenital anemias. Eur J Haematol, 101 (3), 297-304. doi:10.1111/ejh.13097 Ulirsch, J. C., Verboon, J. M., Kazerounian, S., Guo, M. H., Yuan, D., Ludwig, L. S., . . . Gazda, H. T. (2019). The Genetic Landscape of Diamond-Blackfan Anemia. Am J Hum Genet, 104 (2), 356. doi:10.1016/j.ajhg.2018.12.011 Uminski, K., Houston, D. S., Hartley, J. N., Liu, J., Cuvelier, G. D. E., & Israels, S. J. (2020). Clinical characterization and hematopoietic stem cell transplant outcomes for congenital sideroblastic anemia caused by a novel pathogenic variant in SLC25A38. Pediatr Blood Cancer , e28623. doi:10.1002/pbc.28623 Wong, W. S., Wong, H. F., Cheng, C. K., Chang, K. O., Chan, N. P., Ng, M. H., & Wong, K. F. (2015). Congenital sideroblastic anaemia with a novel frameshift mutation in SLC25A38. J Clin Pathol, 68 (3), 249-251. doi:10.1136/jclinpath-2014-202211 Hosted file SLC25A38 Mutation Update Figure Legends Final.pdf available at https://authorea.com/ users/393689/articles/507269-slc25a38-congenital-sideroblastic-anemia-phenotypes-and- genotypes-of-31-individuals-from-24-families-including-11-novel-mutations-and-a-review- of-the-literature 10 P os te d on A u th or ea 4 F eb 20 21 — T h e co p y ri gh t h ol d er is th e au th or /f u n d er . A ll ri g h ts re se rv ed . N o re u se w it h ou t p er m is si on . — h tt p s: // d oi .o rg /1 0. 22 54 1/ au .1 61 24 40 27 .7 27 66 59 4/ v 1 — T h is a p re p ri n t an d h a s n o t b ee n p ee r re v ie w ed . D a ta m ay b e p re li m in a ry . Hosted file SLC25A38 Mutation Update Tables Plain Text Final.pdf available at https://authorea.com/ users/393689/articles/507269-slc25a38-congenital-sideroblastic-anemia-phenotypes-and- genotypes-of-31-individuals-from-24-families-including-11-novel-mutations-and-a-review- of-the-literature 11