Unknown Genetic Basis Research Articles

ODP401 A new FGFR1 mutation causing Idiopathic Hypogonadotropic Hypogonadism and Polydactyly

Abstract Introduction Congenital idiopathic hypogonadotropic hypogonadism (IHH) is a heterogeneous condition with unknown genetic basis in approximately 30% of patients. We describe a case with normosmic IHH and an unreported FGFR1 mutation. Case Report A 23-year-old hispanic man, with a history of polydactyly presented to our clinic for evaluation of delayed puberty. He had no facial hair and minimal pubic and axillary hair. He reported fatigue, low libido and scant ejaculation. He denied anosmia, eating disorders, learning disability, urological malformations, obesity, galactorrhea, testicular trauma, mumps, or use of androgenic steroids. Family history was significant for polydactyly in his mother. Physical exam findings showed normal vitals, height 185 cm, BMI 24 kg/m2, eunuchoid body habitus, bilateral gynecomastia, no facial hair, scant axillary and pubic hair, prepubertal 2 ml testicles within the scrotum and a micro-penis. Serum total testosterone was 7 ng/dl (250-1100 ng/dl), free testosterone 0.9 pg/ml (9.3-26.5 pg/ml), FSH 2.2 mIU/ml (1.6-8. 0 mIU/ml), LH 0.8 mIU/ml (1.5-9.3 mIU/ml), Prolactin 4.1 ng/ml (4-15.2 ng/ml), TSH 1.68 mIU/ml (0.4-5.5 mIU/ml), free t4 1.2 ng/dl (0.8-1.7 ng/dl), growth hormone 0.3 ng/ml (0. 0-10 ng/ml), IGF-1 175 ng/ml (155-432 ng/ml), ACTH 14.6 pg/ml (7.2-63 pg/ml), cortisol (not am) 3. 0 ug/dl (6.2-19.4 ug/dl). Pituitary MRI revealed no focal sellar/suprasellar lesions with normal enhancement of the pituitary gland . DXA scan showed a low bone density for his age with Z-scores below -2. 0 in all regions. Chromosome analysis revealed a normal male 46, XY karyotype. Genetic testing of both patient and mother, using Invitae test kit, revealed an heterozygous mutation in FGFR1 gene, exon 9, variant c.1231C>A (p. Gln411Lys), not described in medical literature. A diagnosis of normosmic idiopathic hypogonadotropic hypogonadism (nIHH) was made. Testosterone cypionate IM 100 mg once weekly was initiated and after 6 months he experienced improvement in energy, libido, muscle mass, facial and body hair, and virilization of his voice. Conclusions The heterogeneity in phenotypic presentation of IHH makes its diagnosis a challenge. Furthermore, the genetic basis for these multiple phenotypes are still not fully described. We report a new FGFR1 mutation causing hypogonadism. Reference: Ferreira Gontijo, L., Latronico, A. Approach to the Patient With Hypogonadotropic Hypogonadism. JES, Vol. 98, Issue 5, 1 May 2013, P. 1781–1788. Presentation: No date and time listed

International Society of Blood Transfusion Working Party on Red Cell Immunogenetics and Blood Group Terminology Report of Basel and three virtual business meetings: Update on blood group systems.

Under the ISBT, the Working Party (WP) for Red Cell Immunogenetics and Blood Group Terminology is charged with ratifying blood group systems, antigens and alleles. This report presents the outcomes from four WP business meetings, one located in Basel in 2019 and three held as virtual meetings during the COVID-19 pandemic in 2020 and 2021. As in previous meetings, matters pertaining to blood group antigen nomenclature were discussed. New blood group systems and antigens were approved and named according to the serologic, genetic, biochemical and cell biological evidence presented. Seven new blood group systems, KANNO (defined numerically as ISBT 037), SID (038), CTL2 (039), PEL (040), MAM (041), EMM (042) and ABCC1 (043) were ratified. Two (039 and 043) were de novo discoveries, and the remainder comprised reported antigens where the causal genes were previously unknown. A further 15 blood group antigens were added to the existing blood group systems: MNS (002), RH (004), LU (005), DI (010), SC (013), GE (020), KN (022), JMH (026) and RHAG (030). The ISBT now recognizes 378 antigens, of which 345 are clustered within 43 blood group systems while 33 still have an unknown genetic basis. The ongoing discovery of new blood group systems and antigens underscores the diverse and complex biology of the red cell membrane. The WP continues to update the blood group antigen tables and the allele nomenclature tables. These can be found on the ISBT website (http://www.isbtweb.org/working-parties/red-cell-immunogenetics-and-blood-group-terminology/).

A KIT Variant Associated with Increased White Spotting Epistatic to MC1R Genotype in Horses (Equus caballus).

Simple SummaryAlthough over 40 genetic variants are known to influence white spotting and markings on the horse, many still have unknown genetic causes. Furthermore, some seem to be influenced by pigmentation (base coat color) genes. We investigated two horses demonstrating a heritable white spotting pattern of no known genetic cause. Through sequencing of the coding region of candidate genes, we identified a mutation in the KIT proto-oncogene, receptor tyrosine kinase (KIT) gene changing the coded amino acid, predicted to be deleterious to protein function. We further evaluated this variant in a population of 147 horses, characterized using photographs scored by three independent observers using a standardized Average Grade of White score. The KIT mutation is significantly associated with a quantitative increase in white pattern (p = 3.3 × 10−12) and demonstrates an influence of the MC1R Extension locus. We also report a complete link between the previously reported KIT W19 allele and this mutation. We propose to name this mutation W34, following established nomenclature. Given the quantitative effect on white markings and MC1R influence, genetic testing for this allele can be of value for horse owners that desire to select for white patterns.Over 40 identified genetic variants contribute to white spotting in the horse. White markings and spotting are under selection for their impact on the economic value of an equine, yet many phenotypes have an unknown genetic basis. Previous studies also demonstrate an interaction between MC1R and ASIP pigmentation loci and white spotting associated with KIT and MITF. We investigated two stallions presenting with a white spotting phenotype of unknown cause. Exon sequencing of the KIT and MITF candidate genes identified a missense variant in KIT (rs1140732842, NC_009146.3:g.79566881T>C, p.T391A) predicted by SIFT and PROVEAN as not tolerated/deleterious. Three independent observers generated an Average Grade of White (AGW) phenotype score for 147 individuals based on photographs. The KIT variant demonstrates a significant QTL association to AGW (p = 3.3 × 10−12). Association with the MC1R Extension locus demonstrated that, although not in LD, MC1R e/e (chestnut) individuals had higher AGW scores than MC1R E/- individuals (p = 3.09 × 10−17). We also report complete linkage of the previously reported KIT W19 allele to this missense variant. We propose to term this variant W34, following the standardized nomenclature for white spotting variants within the equine KIT gene, and report its epistatic interaction with MC1R.

Biallelic Variants in Lanosterol Synthase (LSS) Cause Palmoplantar Keratoderma-Congenital Alopecia Syndrome Type 2

Palmoplantar keratoderma-congenital alopecia syndrome type 2 is an autosomal recessive disorder with an unknown genetic basis. In this study, we identified biallelic variants in the LSS gene in two unrelated palmoplantar keratoderma-congenital alopecia syndrome type 2 cases (c.3G>A, p.Met1? and c.1025T>G, p.Ile342Ser in patient 1; c.1522G>T, p.Gly508Trp and c.428+42T>A in patient 2) presenting with additional clinical features, including early-onset cataracts, pseudoainhum, and agenesis of the corpus callosum. LSS encodes lanosterol synthase (LSS), which functions in the cholesterol biosynthesis pathway by converting (S)-2,3-oxidosqualene to lanosterol. The c.3G>A variant resulted in an alternative translation initiation at residue Met81, producing an N-terminal truncated protein (LSS-ΔN80), as shown by immunoblotting. The c.428+42T>A variant introduced a potential splicing site, leading to a premature stop codon. Exvivo studies revealed downregulation of LSS in both patients. Remarkably decreased lanosterol levels were found invitro in three LSS variants, LSS-ΔN80, p.Ile342Ser, and p.Gly508Trp, suggesting a loss of enzymatic activity. Transmission electron microscopy and immunofluorescence showed abnormal cornified envelope formation in the stratum corneum of the patients. Taken together, our findings indicate LSS as a causative gene for palmoplantar keratoderma-congenital alopecia syndrome type 2, which emphasizes the importance of the cholesterol synthesis pathway in human skin cornification.

A novel truncating variant in the FGD1 gene associated with Aarskog–Scott syndrome in a family previously diagnosed with Tel Hashomer camptodactyly

Tel Hashomer camptodactyly syndrome is a long-known entity characterized by camptodactyly with muscular hypoplasia, skeletal dysplasia, and abnormal palmar creases. Currently, the genetic basis for this disorder is unknown, thus there is a possibility that this clinical presentation may be contained within another genetic diagnosis. Here, we present a multiplex family with a previous clinical diagnosis of Tel Hashomer camptodactyly syndrome. Whole exome sequencing and pedigree-based analysis revealed a novel hemizygous truncating variant c.269_270dup (p.Phe91Alafs*34) in the FGD1 gene (NM_004463.3) in all three symptomatic patients, congruous with a diagnosis of Aarskog-Scott syndrome. Our report adds to the limited data on Aarskog-Scott syndrome, and emphasizes the importance of unbiased comprehensive molecular testing toward establishing a diagnosis for genetic syndromes with unknown genetic basis.

Expanding the genetic landscape of oral-facial-digital syndrome with two novel genes.

Oral‐facial‐digital syndromes (OFDS) are a heterogeneous and rare group of Mendelian disorders characterized by developmental abnormalities of the oral cavity, face, and digits caused by dysfunction of the primary cilium, a mechanosensory organelle that exists atop most cell types that facilitates organ patterning and growth. OFDS is inherited both in an X‐linked dominant, X‐linked recessive, and autosomal recessive manner. Importantly, though many of the causal genes for OFDS have been identified, up to 40% of OFD syndromes are of unknown genetic basis. Here we describe three children with classical presentations of OFDS including lingual hamartomas, polydactyly, and characteristic facial features found by exome sequencing to harbor variants in causal genes not previously associated with OFDS. We describe a female with hypothalamic hamartoma, urogenital sinus, polysyndactyly, and multiple lingual hamartomas consistent with OFDVI with biallelic pathogenic variants in CEP164, a gene associated with ciliopathy‐spectrum disease, but never before with OFDS. We additionally describe two unrelated probands with postaxial polydactyly, multiple lingual hamartomas, and dysmorphic features both found to be homozygous for an identical TOPORS missense variant, c.29 C>A; (p.Pro10Gln). Heterozygous TOPORS pathogenic gene variants are associated with autosomal dominant retinitis pigmentosa, but never before with syndromic ciliopathy. Of note, both probands are of Dominican ancestry, suggesting a possible founder allele.

Fibular Aplasia, Tibial Campomelia, Oligo-Syndactyly Syndrome and Probable Femur Fibula Ulna Syndrome- Case Reports

One in two thousand neonates suffer from congenital limb deficiencies. Fibular hemimelia, a birth defect, has an estimated incidence of 5.7 to 20 cases per 1 million births. Fibular Aplasia, Tibial Campomelia and Oligo-Syndactyly (FATCO) syndrome is one such which is a triad of fibular hemimelia (aplasia/hypoplasia of fibula), tibial campomelia (bending of tibial bone) and oligo syndactyly. It is a syndrome of unknown genetic basis and inheritance. Very few cases on this condition have been reported so far. This article reports two cases on this condition, wherein the babies had considerable variability of limb malformations. The first is a newborn with FATCO, and the second is a two-month-old male infant with FATCO associated with right focal femoral deficiency. In view of paucity of the cases, there is a need to report every case which may help in creating awareness and a standardised management approach.

Lack of the multidrug transporter MRP4/ABCC4 defines the PEL-negative blood group and impairs platelet aggregation

AbstractThe rare PEL-negative phenotype is one of the last blood groups with an unknown genetic basis. By combining whole-exome sequencing and comparative global proteomic investigations, we found a large deletion in the ABCC4/MRP4 gene encoding an ATP-binding cassette (ABC) transporter in PEL-negative individuals. The loss of PEL expression on ABCC4-CRISPR-Cas9 K562 cells and its overexpression in ABCC4-transfected cells provided evidence that ABCC4 is the gene underlying the PEL blood group antigen. Although ABCC4 is an important cyclic nucleotide exporter, red blood cells from ABCC4null/PEL-negative individuals exhibited a normal guanosine 3′,5′-cyclic monophosphate level, suggesting a compensatory mechanism by other erythroid ABC transporters. Interestingly, PEL-negative individuals showed an impaired platelet aggregation, confirming a role for ABCC4 in platelet function. Finally, we showed that loss-of-function mutations in the ABCC4 gene, associated with leukemia outcome, altered the expression of the PEL antigen. In addition to ABCC4 genotyping, PEL phenotyping could open a new way toward drug dose adjustment for leukemia treatment.

The Multidrug Transporter MRP4/ABCC4 Involved in the Leukemia Clinical Course Specifies the Novel PEL Human Blood Group System

Introduction Most blood antigen-carrying proteins have important functions not only in red blood cells (RBCs) but also in other tissues. Hence, because of their polymorphisms and the existence of natural null phenotypes, blood groups also represent powerful tools to investigate human diseases. The PEL-negative rare blood type is one of the last with an unknown genetic basis. Family studies showed that the PEL-negative phenotype was inherited as an autosomal recessive trait, but the PEL locus remained undetermined since the first description of the corresponding antibody in French-Canadian individuals in 1996. Results Combining whole-exome sequencing and comparative global proteomic approaches using genomic DNA and red cell membrane proteins from four unrelated French-Canadian PEL-negative individuals and from controls, we identified i) the Multidrug Resistance-Associated Protein 4 (MRP4), also known as ABCC4, as the only missing protein in all PEL-negative RBCs and ii) a large deletion removing the last 10 exons of the ABCC4 gene. Western blot analyses confirmed that ABCC4 was present in the membrane of PEL-positive control RBCs but totally absent in the PEL-negative RBCs (Fig 1A). Western blot and flow cytometry analyses of transfected HEK293 cells revealed that over-expression of ABCC4 results in a significant increase in PEL antigen cell-surface expression (Fig 1B). Conversely, similar analyses of ABCC4-knockout K562 cells generated by the CRISPR-Cas9 strategy showed that the complete loss of ABCC4 abolished the expression of the PEL antigen (Fig 1C). PEL-negative individuals are therefore the first ever reported population lacking the complete expression of the ABCC4 protein. Surprisingly, despite the expected biological importance of ABCC4 as a cyclic nucleotide transporter, no apparent mutual symptoms or diseases were identified after investigation of the clinical history of the 12 PEL-negative members within the 4 families analyzed in this study. However, platelet investigation from one PEL-negative individual supported the role of this protein in the modulation of platelet aggregation, as previously observed in ABCC4-knockout mice studies To better understand the function of ABCC4 in mature RBCs, we measured the intracellular cGMP level in RBCs from 5 PEL-negative individuals and 5 controls. We showed that the cGMP level was not significantly impaired in the absence of ABCC4 suggesting that another cGMP transporter could compensate for the absence of ABCC4 on the RBC membrane. Interestingly, proteomic and flow cytometry analyses indicated that among the five other ABC transporters (ABCC1, ABCA7, ABCB6, ABCC5 and ABCG2) expressed on RBCs, only ABCG2 was increased in PEL-negative/ABCC4null RBCs compared to controls (1.3-fold; p=0.0007). This suggested that the absence of ABCC4 in PEL-negative individuals could be compensated by the over-expression of ABCG2. Our data, together with previous studies indicating that both ABCC4 and ABCG2 export cGMP, strongly suggest that the over-expression of ABCG2 in PEL-negative RBCs represents a compensatory mechanism for the lack of ABCC4, which could explain the absence of hematological abnormalities in PEL-negative individuals. Discussion Using genetic, molecular and cellular approaches, we demonstrated that ABCC4 is the gene underlying the novel PEL blood group system and that homozygosity for a large deletion in this gene is responsible for the rare PEL-negative phenotype. ABCC4 represents the third ABC transporter carrying a blood group system after ABCG2 (JR) and ABCB6 (LAN). The expression level of ABCC4 is strongly involved in drug resistance and toxicity, and in the clinical course of leukemia. As ABCC4 carries the PEL antigen, PEL phenotyping could be useful in the adjustment of an optimal drug dose and prevention of chemotherapy side effects in leukemia. Our findings are of immediate and important relevance in transfusion medicine and in a personalized medicine approach for chemotherapy treatment follow-up in leukemia. Furthermore, the exceptional natural "knockouts" of ABC transporters are highly valuable in understanding their function, not only in erythroid cells, but also in other cells or tissues. Disclosures Hermine: Novartis: Research Funding; Celgene: Research Funding; AB Science: Consultancy, Equity Ownership, Honoraria, Research Funding.

Advances in molecular diagnosis and therapeutics in nephrotic syndrome and focal and segmental glomerulosclerosis.

The widespread adoption of next-generation sequencing by research and clinical laboratories has begun to uncover the previously unknown genetic basis of many diseases. In nephrology, one of the best examples of this is seen in focal and segmental glomerulosclerosis (FSGS) and nephrotic syndrome. We review advances made in 2017 as a result of human and molecular genetic studies as it relates to FSGS and nephrotic syndrome. There are more than 50 monogenic genes described in steroid-resistant nephrotic syndrome and FSGS, with seven reported in 2017. In individuals presenting with FSGS or nephrotic syndrome before or at the age of 18 years, the commonest genes in which a mutation is found continues to be limited to only a few including NPHS1 and NPHS2 based on multiple studies. For FSGS or nephrotic syndrome that presents after 18 years, mutations in COl4A3/4/5, traditionally associated with Alport syndrome, are increasingly being reported. Despite the extensive genetic heterogeneity in FSGS, there is evidence that some of these genes converge onto common pathways. There are also reports of in-vivo models exploring apolipoprotein 1 biology, variants in which account for part of the increased risk of nondiabetic kidney disease in African-Americans. Finally, genetic testing has several clinical uses including clarification of diagnosis and treatment; identification of suitable young biologic relatives for kidney donation; and preimplantation genetic diagnosis. CRISPR gene editing is currently an experimental tool only, but the recent reports of excising mutations in embryos could be a therapeutic option for individuals with any monogenic disorder in the future. Sequencing efforts are bringing novel variants into investigation and directing the efforts to understand how these lead to disease phenotypes. Expanding our understanding of the genetic basis of health and disease processes is the necessary first step to elaborate the repertoire of therapeutic agents available for patients with FSGS and nephrotic syndrome.

The role of ClpX in erythropoietic protoporphyria

Hemoglobin is an essential biological component of human physiology and its production in red blood cells relies upon proper biosynthesis of heme and globin protein. Disruption in the synthesis of these precursors accounts for a number of human blood disorders found in patients. Mutations in genes encoding heme biosynthesis enzymes are associated with a broad class of metabolic disorders called porphyrias. In particular, one subtype – erythropoietic protoporphyria – is caused by the accumulation of protoporphyrin IX. Erythropoietic protoporphyria patients suffer from photosensitivity and a higher risk of liver failure, which is the principle cause of morbidity and mortality. Approximately 90% of these patients carry loss-of-function mutations in the enzyme ferrochelatase (FECH), while 5% of cases are associated with activating mutations in the C-terminus of ALAS2. Recent work has begun to uncover novel mechanisms of heme regulation that may account for the remaining 5% of cases with previously unknown genetic basis. One erythropoietic protoporphyria family has been identified with inherited mutations in the AAA+ protease ClpXP that regulates ALAS activity. In this review article, recent findings on the role of ClpXP as both an activating unfoldase and degrading protease and its impact on heme synthesis will be discussed. This review will also highlight the role of ClpX dysfunction in erythropoietic protoporphyria.

Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort.

BackgroundGene discovery has provided remarkable biological insights into amyotrophic lateral sclerosis (ALS). One challenge for clinical application of genetic testing is critical evaluation of the significance of reported variants.MethodsWe use whole exome sequencing (WES) to develop a clinically relevant approach to identify a subset of ALS patients harboring likely pathogenic mutations. In parallel, we assess if DNA methylation can be used to screen for pathogenicity of novel variants since a methylation signature has been shown to associate with the pathogenic C9orf72 expansion, but has not been explored for other ALS mutations. Australian patients identified with ALS‐relevant variants were cross‐checked with population databases and case reports to critically assess whether they were “likely causal,” “uncertain significance,” or “unlikely causal.”ResultsPublished ALS variants were identified in >10% of patients; however, in only 3% of patients (4/120) could these be confidently considered pathogenic (in SOD1 and TARDBP). We found no evidence for a differential DNA methylation signature in these mutation carriers.ConclusionsThe use of WES in a typical ALS clinic demonstrates a critical approach to variant assessment with the capability to combine cohorts to enhance the largely unknown genetic basis of ALS.

Redox Stress Defines the Small Artery Vasculopathy of Hypertension: How Do We Bridge the Bench-to-Bedside Gap?

Although convincing experimental evidence demonstrates the importance of vascular reactive oxygen and nitrogen species (RONS), oxidative stress, and perturbed redox signaling as causative processes in the vasculopathy of hypertension, this has not translated to the clinic. We discuss this bench-to-bedside disparity and the urgency to progress vascular redox pathobiology from experimental models to patients by studying disease-relevant human tissues. It is only through such approaches that the unambiguous role of vascular redox stress will be defined so that mechanism-based therapies in a personalized and precise manner can be developed to prevent, slow, or reverse progression of small-vessel disorders and consequent hypertension. Considering the high prevalence of hypertension worldwide, the excess heart disease and stroke that it predisposes to, and the fact that it is the strongest modifiable risk factor for cardiovascular disease, it is not surprising that the American Heart Association funded a Strategically Focused Research Network on hypertension and that the Lancet commissioned a call-to-action and a life-course strategy to address the global burden of raised blood pressure (BP).1 Despite significant advances in understanding the pathophysiology of hypertension and the availability of numerous effective drugs, suboptimal BP control remains the primary predisposing factor for cardiovascular morbidity and mortality. This Hypertension Paradox of more uncontrolled hypertension despite improved therapies, defined by Chobanian,2 is multifactorial and may relate largely to the still unknown genetic basis and elusive causal molecular mechanisms of hypertension. Genetics plays some role in human primary hypertension as evidenced in twin studies and monogenetic forms of hypertension where the kidney is a key target. Genome-wide association studies have been disappointing and have failed to identify specific genes that underpin hypertension. Few loci have been validated or translated into therapeutic targets, with multiple genes and their variants collectively accounting for <2.5% of BP variation. In one of …

A Female Newborn Infant with FATCO Syndrome Variant (Fibular Hypoplasia, Tibial Campomelia, Oligosyndactyly) - A Case Report.

Congenital limb deficiencies are common birth defects occurring in 1 in 2000 neonates, characterized by the aplasia or hypoplasia of bones of the limbs. Fibular hemimelia is a rare congenital deficiency or absence of the fibula. The disease spectrum ranges from mild fibular hypoplasia to fibular aplasia. Fibular aplasia, tibial campomelia, and oligosyndactyly (FATCO syndrome) are purely descriptive terms for a syndrome of unknown genetic basis and inheritance.We report on a newborn female with malformations consisting of fibular hypoplasia, tibial campomelia, and oligosyndactyly, a second FATCO variant case. We also review previously reported cases. Given the paucity of reports on this rare syndrome and the lack of a standardized treatment approach, it is important that each case of FATCO syndrome is reported.

A novel HCFC1 variant in male siblings with intellectual disability and microcephaly in the absence of cobalamin disorder

Approximately 10-15% of intellectual disability (ID) cases are caused by genetic aberrations affecting chromosome X, a condition termed X-linked ID (XLID). Examination by whole-exome sequencing of two male siblings with microcephaly and suspected XLID with an unknown genetic basis revealed that they were both hemizygous for a predicted pathogenic variant (p.Ala897Val) causing a non-synonymous substitution of an evolutionary conserved amino acid within the host cell factor C1 (HCFC1) gene. Subsequent analysis determined that this was a rare variant not identified in 100 control individuals or in online databases of control individuals. Recent studies have reported mutations affecting HCFC1 in patients with ID and dysmorphic features that are associated with defective cobalamin metabolism. Biochemical investigations did not find evidence of an association between the variant identified in the present study and cobalamin metabolic disorder. This study offers further support for mutations of HCFC1 being implicated in XLID and microcephaly, but that these are not necessarily associated with cobalamin disorder.

Frequent Activating Somatic Alterations in T-Cell Receptor / NF-κb Signaling in Adult T-Cell Leukemia/Lymphoma

Adult T-cell leukemia/lymphoma (ATL) is a peripheral T-cell neoplasm of largely unknown genetic basis, which is associated with human T-cell leukemia virus type-1 (HTLV-1) infection. To delineate a genetic landscape of somatic alterations in ATL, we have performed an integrated genetic study, in which whole-genome/exome (WGS/WES) and transcriptome sequencing (RNA-seq) was performed for a cohort of 83 paired ATL samples, followed by extensive validation using targeted sequencing of detected mutations in 370 follow-up samples.A striking feature of driver lesions in ATL was their strong enrichment in the components of T-cell receptor (TCR) / NF-κB pathway. Accounting for more than 90% of ATL cases, these lesions were characterized by the predominance of activating alterations, including hotspot missense mutations in PLCG1 (36%), PRKCB (33%), CARD11 (24%), VAV1 (18%), IRF4 (14%) and FYN (4%). Among these, most frequently mutated was PLCG1, which encodes phospholipase C γ1 (PLCγ1), a key regulator of the proximal TCR signaling. Besides the S345F and S520F mutations recently reported in cutaneous T-cell lymphoma, we identified an additional hotspot mutations (R48W, E1163K, and D1165H).The second most frequently mutated gene was PRKCB, encoding a member of the protein kinase C (PKC) family of proteins (PKCβ), a pivotal signaling molecule downstream of PLCγ. The frequent mutations of PKCβ were unexpected, because it is PKCθ that has been implicated in TCR signaling, whereas PKCβ has been more focused in the context of B-cell receptor signaling. Approximately 93% of the PRKCB mutations were confined to the catalytic domain with a prominent hotspot at D427, suggesting gain-of-function nature of these mutations. Consistent with this, when transduced with the D427N PKCβ mutant, HEK293T and/or Jurkat cells showed increased membrane translocation after PMA/Ionomycin-stimulation, enhanced IKK phosphorylation and p65 nuclear translocation, and augmented NF-κB transcription, compared to wild-type PKCβ-transduced cells. Thus, these PRKCB mutations are the first activating mutations of this family identified in human cancers.Downstream to PKC lies CARD11, a scaffolding protein required for antigen receptor-induced NF-κB activation. Although previously reported in B-cell lymphomas, CARD11 mutations were more common in ATL (24%). In B-cell lymphomas, mutations are largely limited to the coiled-coil (CC) domain, whereas in ATL, they were clustered not only within the CC domain, but also within the PKC-responsive inhibitory domain, showing a prominent mutational hotspot at E626. The inhibitory domain has been implicated in autoinhibition, whose deletion leads to constitutive activation of CARD11. Intriguingly, WGS identified small intragenic deletions confined to this domain (exons 14-17) in 4 cases (8%) without canonical mutations, and RNA-seq confirmed the skipping of the corresponding exons in these cases. Remarkably, CARD11 mutation significantly co-occurred with PRKCBmutations, suggesting potential functional synergism between these lesions. Actually, overexpression of wild-type CARD11 induced NF-κB activation, which was further augmented by E626K mutation. Similarly, when both CARD11 (E626K) and PRKCB (D427N) mutants were co-expressed, more enhanced NF-κB activation was observed.RNA-seq and follow-up RT-PCR screening also identified novel gene fusions in TCR / NF-κB pathway: five CTLA4-CD28 and three ICOS-CD28 fusions were observed in seven (7%) of the 105 cases examined, of whom one patient carried both chimeric fusions. WGS revealed tandem duplications of 2q33.2 segments containing CD28, CTLA4, and ICOS, compatible with the corresponding fusion transcripts. B7/CD28 co-signaling molecules, including CD28, CTLA4, and ICOS co-receptors, play pivotal roles in positive and negative regulations of TCR signaling. All the predicted chimeric proteins had the cytoplasmic part of CD28, and are expected to be expressed under the control of the regulatory element of CTLA4 or ICOS, likely leading to prolonged expression of CD28 co-stimulator.Our findings suggest that deregulated TCR / NF-κB pathway caused by genetic alterations is a hallmark of ATL pathogenesis. The predominance of gain-of-function mutations in this pathway offers good opportunities for exploiting these mutations for the targets of novel drugs to better manage patients. DisclosuresTobinai:Gilead Sciences: Research Funding. Miyazaki:Sumitomo Dainippon: Honoraria; Celgene Japan: Honoraria; Chugai: Honoraria, Research Funding; Shin-bio: Honoraria; Kyowa-Kirin: Honoraria, Research Funding. Watanabe:Daiichi Sankyo Co., Ltd.: Research Funding.

Integrated molecular analysis of adult T cell leukemia/lymphoma.

Adult T cell leukemia/lymphoma (ATL) is a peripheral T cell neoplasm of largely unknown genetic basis, associated with human T cell leukemia virus type-1 (HTLV-1) infection. Here we describe an integrated molecular study in which we performed whole-genome, exome, transcriptome and targeted resequencing, as well as array-based copy number and methylation analyses, in a total of 426 ATL cases. The identified alterations overlap significantly with the HTLV-1 Tax interactome and are highly enriched for T cell receptor-NF-κB signaling, T cell trafficking and other T cell-related pathways as well as immunosurveillance. Other notable features include a predominance of activating mutations (in PLCG1, PRKCB, CARD11, VAV1, IRF4, FYN, CCR4 and CCR7) and gene fusions (CTLA4-CD28 and ICOS-CD28). We also discovered frequent intragenic deletions involving IKZF2, CARD11 and TP73 and mutations in GATA3, HNRNPA2B1, GPR183, CSNK2A1, CSNK2B and CSNK1A1. Our findings not only provide unique insights into key molecules in T cell signaling but will also guide the development of new diagnostics and therapeutics in this intractable tumor.

QTL mapping of fungicide sensitivity reveals novel genes and pleiotropy with melanization in the pathogen Zymoseptoria tritici

A major problem associated with the intensification of agriculture is the emergence of fungicide resistance. Azoles are ergosterol biosynthesis inhibitors that have been widely used in agriculture and medicine since the 1970s, leading to emergence of increasingly resistant fungal populations. The known genetic mechanisms underlying lower azole sensitivity include mutations affecting the CYP51 gene that encodes the target protein, but in many cases azole resistance is a more complex trait with an unknown genetic basis. We used quantitative trait locus (QTL) mapping to identify genes affecting azole sensitivity in two crosses of Zymoseptoria tritici, the most damaging wheat pathogen in Europe. Restriction site associated DNA sequencing (RADseq) was used to genotype 263 (cross 1) and 261 (cross 2) progeny at ∼8500 single nucleotide polymorphisms (SNP) and construct two dense linkage maps. Azole sensitivity was assessed using high-throughput digital image analysis of colonies growing on Petri dishes with or without the fungicide propiconazole. We identified three QTLs for azole sensitivity, including two that contained novel fungicide sensitivity genes. One of these two QTLs contained only 16 candidate genes, among which four most likely candidates were identified. The third QTL contained ERG6, encoding another protein involved in ergosterol biosynthesis. Known genes in QTLs affecting colony growth included CYP51 and PKS1, a gene affecting melanization in Z. tritici. PKS1 showed compelling evidence for pleiotropy, with a rare segregating allele that increased melanization while decreasing growth rate and propiconazole sensitivity. This study resolved the genetic architecture of an important agricultural trait and led to identification of novel genes that are likely to affect azole sensitivity in Z. tritici. It also provided insight into fitness costs associated with lowered azole sensitivity and suggests a novel fungicide mixture strategy.

Human phenotype ontology annotation and cluster analysis to unravel genetic defects in 707 cases with unexplained bleeding and platelet disorders.

BackgroundHeritable bleeding and platelet disorders (BPD) are heterogeneous and frequently have an unknown genetic basis. The BRIDGE-BPD study aims to discover new causal genes for BPD by high throughput sequencing using cluster analyses based on improved and standardised deep, multi-system phenotyping of cases.MethodsWe report a new approach in which the clinical and laboratory characteristics of BPD cases are annotated with adapted Human Phenotype Ontology (HPO) terms. Cluster analyses are then used to characterise groups of cases with similar HPO terms and variants in the same genes.ResultsWe show that 60% of index cases with heritable BPD enrolled at 10 European or US centres were annotated with HPO terms indicating abnormalities in organ systems other than blood or blood-forming tissues, particularly the nervous system. Cases within pedigrees clustered closely together on the bases of their HPO-coded phenotypes, as did cases sharing several clinically suspected syndromic disorders. Cases subsequently found to harbour variants in ACTN1 also clustered closely, even though diagnosis of this recently described disorder was not possible using only the clinical and laboratory data available to the enrolling clinician.ConclusionsThese findings validate our novel HPO-based phenotype clustering methodology for known BPD, thus providing a new discovery tool for BPD of unknown genetic basis. This approach will also be relevant for other rare diseases with significant genetic heterogeneity.Electronic supplementary materialThe online version of this article (doi:10.1186/s13073-015-0151-5) contains supplementary material, which is available to authorized users.

Whole exome sequencing identifies RAI1 mutation in a morbidly obese child diagnosed with ROHHAD syndrome.

The current obesity epidemic is attributed to complex interactions between genetic and environmental factors. However, a limited number of cases, especially those with early-onset severe obesity, are linked to single gene defects. Rapid-onset obesity with hypothalamic dysfunction, hypoventilation and autonomic dysregulation (ROHHAD) is one of the syndromes that presents with abrupt-onset extreme weight gain with an unknown genetic basis. To identify the underlying genetic etiology in a child with morbid early-onset obesity, hypoventilation, and autonomic and behavioral disturbances who was clinically diagnosed with ROHHAD syndrome. Design/Setting/Intervention: The index patient was evaluated at an academic medical center. Whole-exome sequencing was performed on the proband and his parents. Genetic variants were validated by Sanger sequencing. We identified a novel de novo nonsense mutation, c.3265 C>T (p.R1089X), in the retinoic acid-induced 1 (RAI1) gene in the proband. Mutations in the RAI1 gene are known to cause Smith-Magenis syndrome (SMS). On further evaluation, his clinical features were not typical of either SMS or ROHHAD syndrome. This study identifies a de novo RAI1 mutation in a child with morbid obesity and a clinical diagnosis of ROHHAD syndrome. Although extreme early-onset obesity, autonomic disturbances, and hypoventilation are present in ROHHAD, several of the clinical findings are consistent with SMS. This case highlights the challenges in the diagnosis of ROHHAD syndrome and its potential overlap with SMS. We also propose RAI1 as a candidate gene for children with morbid obesity.