Stop-gain Mutation Research Articles

A novel stop-gain mutation in DPYS gene causing Dihidropyrimidinase deficiency, a case report

BackgroundDihidropyrimidinase (DHP) deficiency is an inherited inborn error of pyrimidine metabolism with a variable clinical presentation and even asymptomatic subjects. Dihydropyrimidinase is encoded by the DPYS gene, thus pathogenic mutations in this gene can cause DHP deficiency. To date, several variations in the DPYS gene have been reported but only 23 of them have been confirmed to be pathogenic. Therefore, the biochemical, clinical and genetic aspects of this disease are still unclear.Case presentationHere, we report a 22-year-old woman with DHP deficiency. To identify the genetic cause of DHP deficiency in this patient, Whole Exome Sequencing (WES) was performed, which revealed a novel homozygote stop gain mutation (NM_001385: Exon 9, c.1501 A > T, p.K501X) in the DPYS gene. Sanger sequencing was carried out on proband and other family members in order to confirm the identified mutation. According to the homozygote genotype of the patient and heterozygote genotype of her parents, the autosomal recessive pattern of inheritance was confirmed. In addition, bioinformatics analysis of the identified variant using Mutation Taster and T-Coffee Multiple Sequence Alignment showed the pathogenicity of mutation. Moreover, mRNA expression level of DPYS gene in the proband’s liver biopsy showed about 6-fold reduction compared to control, which strongly suggested the pathogenicity of the identified mutation.ConclusionsThis study identified a novel pathogenic stop gain mutation in DPYS gene in a DHP deficient patient. Our findings can improve the knowledge about the genetic basis of the disease and also provide information for accurate genetic counseling for the families at risk of these types of disorders.

Novel Genetic Variations in Acute Myeloid Leukemia in Pakistani Population.

Acute myeloid leukemia (AML) is a hematological malignancy characterized by clonal expansion of blast cells that exhibit great genetic heterogeneity. In this study, we describe the mutational landscape and its clinico-pathological significance in 26 myeloid neoplasm patients from a South Asian population (Pakistan) by using ultra-deep targeted next-generation DNA sequencing of 54 genes (∼5000×) and its subsequent bioinformatics analysis. The data analysis indicated novel non-silent somatic mutational events previously not reported in AML, including nine non-synonymous and one stop-gain mutations. Notably, two recurrent somatic non-synonymous mutations, i.e., STAG2 (causing p.L526F) and BCORL1 (p.A400V), were observed in three unrelated cases each. The BCOR was found to have three independent non-synonymous somatic mutations in three cases. Further, the SRSF2 with a protein truncating somatic mutation (p.Q88X) was observed for the first time in AML in this study. The prioritization of germline mutations with ClinVar, SIFT, Polyphen2, and Combined Annotation Dependent Depletion (CADD) highlighted 18 predicted deleterious/pathogenic mutations, including two recurrent deleterious mutations, i.e., a novel heterozygous non-synonymous SNV in GATA2 (p.T358P) and a frameshift insertion in NPM1 (p.L258fs), found in two unrelated cases each. The WT1 was observed with three independent potential detrimental germline mutations in three different cases. Collectively, non-silent somatic and/or germline mutations were observed in 23 (88.46%) of the cases (0.92 mutation per case). Furthermore, the pharmGKB database exploration showed a missense SNV rs1042522 in TP53, exhibiting decreased response to anti-cancer drugs, in 19 (73%) of the cases. This genomic profiling of AML provides deep insight into the disease pathophysiology. Identification of pharmacogenomics markers will help to adopt personalized approach for the management of AML patients in Pakistan.

A Stop-Gain Mutation within MLPH Is Responsible for the Lilac Dilution Observed in Jacob Sheep.

A coat color dilution, called lilac, was observed within the Jacob sheep breed. This dilution results in sheep appearing gray, where black would normally occur. Pedigree analysis suggested an autosomal recessive inheritance. Whole-genome sequencing of a dilute case, a known carrier, and sixteen non-dilute sheep was used to identify the molecular variant responsible for the coat color change. Through investigation of the genes MLPH, MYO5A, and RAB27A, we discovered a nonsynonymous mutation within MLPH, which appeared to match the reported autosomal recessive nature of the lilac dilution. This mutation (NC_019458.2:g.3451931C>A) results in a premature stop codon being introduced early in the protein (NP_001139743.1:p.Glu14*), likely losing its function. Validation testing of additional lilac Jacob sheep and known carriers, unrelated to the original case, showed a complete concordance between the mutation and the dilution. This stop-gain mutation is likely the causative mutation for dilution within Jacob sheep.

Novel mutations of SYK gene in solid tumors.

e13519 Background: Spleen tyrosine kinase ( SYK) is a non-receptor tyrosine kinase (NRTK) in cytoplasmic and plays a crucial role in multiple signaling pathways. The deletion of SYK gene expression will lead to the formation and metastasis of multiple solid tumors. Previous studies focus on the methylation of the SYK gene promoter and the protein isomers, including SYK (L) and SYK (S) which are differed by 23 amino acids in functional domains. Nevertheless, the knowledge of mutations in SYK remains poorly understood. Herein, next generation sequencing were performed to explore SYK mutations for further clinical research. Methods: We retrospectively analyzed the somatic mutations from a comprehensive genomic profiling in tumor tissue or blood ctDNA of 4,093 patients with pan-cancer, of which 2,213 patients using 528 genes panel and 1,880 patients using 539 genes panel, both of the panels contained all exon regions of SYK gene. SYK mutations analyzed by TCGA database was used as validation to our results. Results: In 4093 patients with pan-carcinoma, 36 patients were found mutations in SYK gene and the mutation frequency was 0.880%, of which 4 intron mutations and 32 cases of exon mutations were found in patients, respectively. A number of 9 mutations might affect protein function, which were stop-gained mutations and frameshift mutations and their proportion was 0.220%. The mutation frequency of SYK was consistent with TCGA. Among 9 mutations, 3 mutations were also found in TCGA, which were R574*, M34fs, E376*, respectively. And the rest 6 mutations were newly found, which were V395fs, N615fs, Y74*, G185*, Y74fs, Q145*, respectively. Colorectal cancer was the most common cancer type harboring SYK mutations, and TP53 was the most frequently co-mutated gene of SYK which was counted 5 both in our detected results and in TCGA database. Conclusions: Firstly report of 6 novel stop-gained and frame-shift mutations in SYK gene expanded the understanding of SYK in solid tumors. As a retrospective study in pan-cancer with a relatively small population and the mechanism is unclear, the conclusions of this study needed to be verified with a larger sample.

MON-509 RET Mutations in the MEN1 Syndrome: Is It an Innocent Bystander?

IntroductionMENIN and RET mutations in MEN1 families, are rare, and, when they co-exist either mutation may predominate the clinical picture.We report a family, with both mutations, and, suspect that the RET mutation may not be an innocent bystander.Clinical CasesGM (36M): 2009: Presented with skin lesions and a lactotroph adenoma causing chiasmal compression. Treatment: Hypophysectomy and Cabergoline. This resulted in restoration of sexual function and fertility.2013: Developed hyperparathyroidism [Calcium 10.6mg% (8.5-10.5); PTH 610pg/ml (10-65); MIBG Scan: parathyroid adenomas]. Treatment: Subtotal parathyroidectomy with allotransplant.2015: Developed Zollinger-Ellison Syndrome [multiple gastric ulcers; S Gastrin: 516pg/ml; (0-180)]. Treatment: Pantoprazole.MRI Abdomen: Calcific atrophic pancreas and bilateral non-functioning adrenal adenomas.HM (32M): 2008: Skin lesions and Lactotroph adenoma. Treatment with Cabergoline resulted in restoration of sexual function and a reduction in breast and tumour size.2013: Hyperparathyroidism [Calcium 10.9mg%; PTH: 166pg/ml; Calcium excretion: 1160mg/24hrs (100-250); BMD: Osteopenia. MIBG 123 Scan: Avid uptake in Right Inferior parathyroid gland]. He underwent a subtotal parathyroidectomy with allotransplant.2015: Recurrent Hyperparathyroidism (Calcium 10.7mg%; PTH: 116pg/ml; MIBG 123 scan: Hyperfunction of the transplanted gland). Stable on treatment with Cinacalcet.Their mother, AM (42F): 1980: Detected to have a lactotroph adenoma when investigated for primary infertility and galactorrhoea. She was treated with Bromocriptine and delivered the boys in 1980 and 1984 respectively. She had recurrent renal calculi and hydronephrosis (? hyperparathyroidism). She succumbed to renal failure following surgery for a benign pancreatic cystadenoma in 1990.DiscussionWhole exome sequencing of GM and HM showed pathogenic mutations of both, MENIN and RET gene. The precise mutation was a stop gain mutation at exon 3 MENIN.C511T:p.Q171X . They (GM/HM) also harboured a mutation in the RET gene at exon 14 c. G2492T: p.G831V; g. chr10. This may be the first family in which the rare combination of these two mutations has been reported.The genomics and the clinical presentation suggest that the MENIN mutation predominates in the family, but the presence of bilateral adrenal adenomas in GM are significant on account of RET mutation. The latter may be a harbinger of serious disease in the future. The situation is further compounded by the recurrence of hyperparathyroidism in the allograft of HM. This may be caused due to chance or an unknown genetic/ epigenetic phenomenon in the two MEN mutated genes and RNA sequencing of the tumour tissue may explain the genetic phenomenon. The latter two events suggest that the RET mutations in MEN1 may not be an innocent bystander.

Predicted loss and gain of function mutations in ACO1 are associated with erythropoiesis

Hemoglobin is the essential oxygen-carrying molecule in humans and is regulated by cellular iron and oxygen sensing mechanisms. To search for novel variants associated with hemoglobin concentration, we performed genome-wide association studies of hemoglobin concentration using a combined set of 684,122 individuals from Iceland and the UK. Notably, we found seven novel variants, six rare coding and one common, at the ACO1 locus associating with either decreased or increased hemoglobin concentration. Of these variants, the missense Cys506Ser and the stop-gained Lys334Ter mutations are specific to eight and ten generation pedigrees, respectively, and have the two largest effects in the study (EffectCys506Ser = −1.61 SD, CI95 = [−1.98, −1.35]; EffectLys334Ter = 0.63 SD, CI95 = [0.36, 0.91]). We also find Cys506Ser to associate with increased risk of persistent anemia (OR = 17.1, P = 2 × 10−14). The strong bidirectional effects seen in this study implicate ACO1, a known iron sensing molecule, as a major homeostatic regulator of hemoglobin concentration.

CD20-positive extranodal NK/T cell lymphoma: clinicopathologic and prognostic features.

Extranodal natural killer (NK)/T cell lymphoma (ENKTCL) with aberrant CD20 expression is extremely rare. Here, we describe the clinicopathologic features of 11 CD20-positive ENKTCLs from three institutions in China along with a literature review. Membranous expression of CD20 was identified in 1.29% (11/851) of ENKTCLs. CD20-positive ENKTCLs primarily occurred in extra-nasal sites (72.2%, 13/18) rather than in the nasal cavity (27.8%, 5/18). Most evaluated patients (71.4%, 10/14) presented ENKTCL at advanced stage IV. The percentage of CD20-positive tumor cells ranged from 20 to 90%, and the CD20 staining intensity was dimmer in tumor cells than in normal B cells. Among four cases with multiple biopsies, three cases showed discordant expression of CD20 between the disseminated and primary lesions. All evaluated cases were negative for other B cell markers, including PAX5, CD79a, and CD19, except for one case that showed focally positive for CD79a. Patients with CD20-positive ENKTCL more frequently had advanced diseases (stage III/IV: 70% vs 17%, p= 0.001), with older age (median age at diagnosis: 60years vs. 43.5years, p= 0.006) and had inferior outcome (median survival: 18.7moths vs 36.0moths, p= 0.017) compared with CD20-negative cases. Four nonsynonymous single nucleotide variants (C > T) and one stop-gain mutation (C > T) in the exonic region of CD20 gene (MS4A1) were detected in one of seven cases with target region next-generation sequencing. Thus, ENKTCL with aberrant CD20 expression is rare, tends to occur in older patients, and is characterized by a highly aggressive clinical course and poor outcomes. The mechanism underlying the expression of CD20 in ENKTC still remains unknown.

Molecular pathogenesis of progression to myeloid leukemia from TET-insufficient status

AbstractLoss-of-function mutations in ten-eleven translocation-2 (TET2) are recurrent events in acute myeloid leukemia (AML) as well as in preleukemic hematopoietic stem cells (HSCs) of age-related clonal hematopoiesis. TET3 mutations are infrequent in AML, but the level of TET3 expression in HSCs has been found to decline with age. We examined the impact of gradual decrease of TET function in AML development by generating mice with Tet deficiency at various degrees. Tet2f/f and Tet3f/f mice were crossed with mice expressing Mx1-Cre to generate Tet2f/wtTet3f/fMx-Cre+ (T2ΔT3), Tet2f/fTet3f/wtMx-Cre+ (ΔT2T3), and Tet2f/fTet3f/fMx-Cre+ (ΔT2ΔT3) mice. All ΔT2ΔT3 mice died of aggressive AML at a median survival of 10.7 weeks. By comparison, T2ΔT3 and ΔT2T3 mice developed AML at longer latencies, with a median survival of ∼27 weeks. Remarkably, all 9 T2ΔT3 and 8 ΔT2T3 mice with AML showed inactivation of the remaining nontargeted Tet2 or Tet3 allele, respectively, owing to exonic loss in either gene or stop-gain mutations in Tet3. Recurrent mutations other than Tet3 were not noted in any mice by whole-exome sequencing. Spontaneous inactivation of residual Tet2 or Tet3 alleles is a recurrent genetic event during the development of AML with Tet insufficiency.

Three Brothers With Autism Carry a Stop‐Gain Mutation in the HPA‐Axis Gene NR3C2

Whole exome sequencing and copy-number variant analysis was performed on a family with three brothers diagnosed with autism. Each of the siblings shares an alteration in the nuclear receptor subfamily 3 group C member 2 (NR3C2) gene that is predicted to result in a stop-gain mutation (p.Q919X) in the mineralocorticoid receptor (MR) protein. This variant was maternally inherited and provides further evidence for a connection between the NR3C2 and autism. Interestingly, the NR3C2 gene encodes the MR protein, a steroid hormone-regulated transcription factor that acts in the hypothalamic-pituitary-adrenal axis and has been connected to stress and anxiety, both of which are features often seen in individuals with autism. Autism Res 2020, 13: 523-531. © 2020 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: Given the complexity of the genetics underlying autism, each gene contributes to risk in a relatively small number of individuals, typically less than 1% of all autism cases. Whole exome sequencing of three brothers with autism identified a rare variant in the nuclear receptor subfamily 3 group C member 2 gene that is predicted to strongly interfere with its normal function. This gene encodes the mineralocorticoid receptor protein, which plays a role in how the body responds to stress and anxiety, features that are often elevated in people diagnosed with autism. This study adds further support to the relevance of this gene as a risk factor for autism.

NOX1 Regulates Collective and Planktonic Cell Migration: Insights From Patients With Pediatric-Onset IBD and NOX1 Deficiency.

Genetic defects of pediatric-onset inflammatory bowel disease (IBD) provide critical insights into molecular factors controlling intestinal homeostasis. NOX1 has been recently recognized as a major source of reactive oxygen species (ROS) in human colonic epithelial cells. Here we assessed the functional consequences of human NOX1 deficiency with respect to wound healing and epithelial migration by studying pediatric IBD patients presenting with a stop-gain mutation in NOX1. Functional characterization of the NOX1 variant included ROS generation, wound healing, 2-dimensional collective chemotactic migration, single-cell planktonic migration in heterologous cell lines, and RNA scope and immunohistochemistry of paraffin-embedded patient tissue samples. Using exome sequencing, we identified a stop-gain mutation in NOX1 (c.160C>T, p.54R>*) in patients with pediatric-onset IBD. Our studies confirmed that loss-of-function of NOX1 causes abrogated ROS activity, but they also provided novel mechanistic insights into human NOX1 deficiency. Cells that were NOX1-mutant showed impaired wound healing and attenuated 2-dimensional collective chemotactic migration. High-resolution microscopy of the migrating cell edge revealed a reduced density of filopodial protrusions with altered focal adhesions in NOX1-deficient cells, accompanied by reduced phosphorylation of p190A. Assessment of single-cell planktonic migration toward an epidermal growth factor gradient showed that NOX1 deficiency is associated with altered migration dynamics with loss of directionality and altered cell-cell interactions. Our studies on pediatric-onset IBD patients with a rare sequence variant in NOX1 highlight that human NOX1 is involved in regulating wound healing by altering epithelial cytoskeletal dynamics at the leading edge and directing cell migration.

Homozygous mutations in DZIP1 can induce asthenoteratospermia with severe MMAF

BackgroundAsthenoteratospermia, one of the most common causes for male infertility, often presents with defective sperm heads and/or flagella. Multiple morphological abnormalities of the sperm flagella (MMAF) is one of the...

Retinitis Pigmentosa Due to Rp1 Biallelic Variants

In the present study, we screened 529 Brazilian individuals affected by inherited retinal disorders. A total of seven unrelated and nonsyndromic patients with RP1 biallelic variants (OMIM # 180100) were diagnosed in our centre and included in the study. They had classic retinitis pigmentosa with diagnosis at the first decade of life. The visual acuities were severely affected at a young age. The fundus aspects were similar among all patients. An atrophic ring was present around the fovea in several cases. All patients had molecular diagnosis, with six different RP1 variants. This study reports two new pathogenic variants - two frameshift duplications (c.1234dupA p.Met412Asnfs*7 and c.1265dupC p.Ala423Cysfs*2) and reinforces other four known pathogenic variants – two frameshift deletions (c.469delG p.Val157Trpfs*16 and c.3843delT p.Pro1282Leufs*12) and two stop gain mutations (c.1186 C > T p.Arg396* and c.1625C > G p.Ser542*). These findings broaden the spectrum of RP1 variants. This study also reviewed the fundus characteristics that clinically could raise the hypothesis of a retinitis pigmentosa due to RP1 gene. It is worthwhile to try to identify the disease-causing variants in each patient since it can provide prognostic information and be useful in genetic consultation and diagnosis in the future.

Biallelic mutations in CFAP65 cause male infertility with multiple morphological abnormalities of the sperm flagella in humans and mice

BackgroundMale infertility is a prevalent issue worldwide, mostly due to the impaired sperm motility. Multiple morphological abnormalities of the sperm flagella (MMAF) present aberrant spermatozoa with absent, short, coiled, bent...

Targeted sequencing reveals the mutational landscape responsible for sorafenib therapy in advanced hepatocellular carcinoma.

Rationale: The existence of primary and acquired drug resistance is the main obstacle for the effect of multi-kinase inhibitor sorafenib and regorafenib in advanced hepatocellular carcinoma (HCC). However, plenty of patients did not significantly benefit from sorafenib treatment and little is known about the mechanism of drug resistance.Methods: Laser capture microdissection was used to acquire matched normal liver and tumor tissues on formalin-fixed paraffin-embedded specimens collected before sorafenib therapy from the first surgery of 119 HCC patients. Ultra-deep sequencing (~1000×) targeting whole exons of 440 genes in microdissected specimens and siRNA screen in 7 cell lines were performed to find mutations associated with differential responses to sorafenib. Patient-derived xenograft models were employed to determine the role of TP53 in response to sorafenib. Lentiviruses harboring wild-type and c.G52C-mutant OCT4 were applied to explore the function of OCT4 in resistance to sorafenib. ChIP-PCR assay for analysis of OCT4 transcriptional activity was performed to explore the affinity with the KITLG promoter. Statistical analyses were used to associate levels of p53 and OCT4 with tumor features and patient outcomes.Results: Total 1,050 somatic mutations and 26 significant driver genes were identified. SiRNA screening in 7 HCC cell lines was further performed to identify mutations associated with differential responses to sorafenib. A recurrent nonsynonymous mutation c.G52C in OCT4 (OCT4mut) was strongly associated with good response to sorafenib, whereas the stop-gain mutation in TP53 showed the opposite outcome both in vitro and in vivo. OCT4wt-induced stem cell factor (encoded by KITLG gene, SCF) expression and cross-activation of c-KIT/FLT3-BRAF signals were identified indispensably for sorafenib resistance, which could be reversed by the combination of c-KIT tyrosine kinase inhibitors or neutralizing antibody against SCF. Mechanistically, an OCT4 binding site in upstream of KITLG promoter was identified with a higher affinity to wildtype of OCT4 rather than G52C-mutant form, which is indispensable for OCT4-induced expression of KITLG and sorafenib resistance.Conclusion: Our study reported a novel somatic mutation in OCT4 (c.G52C) responsible for the sorafenib effect, and also shed new light on the treatment of HCC through the combination of specific tyrosine kinase inhibitors according to individual genetic patterns.

Homozygous Null TBX4 Mutations Lead to Posterior Amelia with Pelvic and Pulmonary Hypoplasia

The development of hindlimbs in tetrapod species relies specifically on the transcription factor TBX4. In humans, heterozygous loss-of-function TBX4 mutations cause dominant small patella syndrome (SPS) due to haploinsufficiency. Here, we characterize a striking clinical entity in four fetuses with complete posterior amelia with pelvis and pulmonary hypoplasia (PAPPA). Through exome sequencing, we find that PAPPA syndrome is caused by homozygous TBX4 inactivating mutations during embryogenesis in humans. In two consanguineous couples, we uncover distinct germline TBX4 coding mutations, p.Tyr113∗ and p.Tyr127Asn, that segregated with SPS in heterozygous parents and with posterior amelia with pelvis and pulmonary hypoplasia syndrome (PAPPAS) in one available homozygous fetus. A complete absence of TBX4 transcripts in this proband with biallelic p.Tyr113∗ stop-gain mutations revealed nonsense-mediated decay of the endogenous mRNA. CRISPR/Cas9-mediated TBX4 deletion in Xenopus embryos confirmed its restricted role during leg development. We conclude that SPS and PAPPAS are allelic diseases of TBX4 deficiency and that TBX4 is an essential transcription factor for organogenesis of the lungs, pelvis, and hindlimbs in humans.

Identifying genetic variants underlying medication-induced osteonecrosis of the jaw in cancer and osteoporosis: a case control study

BackgroundBisphosphonate-induced osteonecrosis of the jaw (BRONJ) presents with a typical pattern of jaw necrosis in patients who have been prescribed bisphosphonates (BPs) and other antiangiogenetic drugs to treat osteoporosis or bone-related complications of cancer.MethodsThis study divided 38 patients with BRONJ into two groups according to the prescribing causes: cancer (n = 13) and osteoporosis (n = 25), and underwent whole exome sequencing and compared them with normal controls (n = 90). To identify candidate genes and variants, we conducted three analyses: a traditional genetic model, gene-wise variant score burden, and rare-variant analysis methods.ResultsThe stop-gain mutation (rs117889746) of the PZP gene in the BRONJ cancer group was significantly identified in the additive trend model analysis. In the cancer group, ARIDS, HEBP1, LTBP1, and PLVAP were identified as candidate genes. In the osteoporosis group, VEGFA, DFFA, and FAM193A genes showed a significant association. No significant genes were identified in the rare-variant analysis pipeline. Biologically accountable functions related to BRONJ occurrence-angiogenesis-related signaling (VEGFA and PLVAP genes), TGF-β signaling (LTBP1 and PZP genes), heme toxicity (HEBP1) and osteoblast maturation (ARIDS)-were shown in candidate genes.ConclusionThis study showed that the candidate causative genes contributing to the development of BRONJ differ according to the BP dose and background disease.

Familial Clustering of Hematological Malignancies: Harbingers of Wider Germline Cancer Susceptibility

Introduction. The Australian Familial Haematological Cancer Study (AFHCS) was founded in 2004 when only one familial haematological malignancy (FHM) gene was known, RUNX1 causing thrombocytopenia and predominantly an MDS/AML HM phenotype. Today, there are over a dozen known FHM genes, mostly characterized as predisposing to myeloid malignancies. Within our AFHCS cohort of over 200 families, this is also true with a significant proportion of families with predisposition to myeloid malignancies solved with our identification of germline mutations in genes such as GATA2, RUNX1,CEBPA and DDX41. In contrast the majority of unsolved families have a predominance of lymphoid malignancies, most commonly non-Hodgkin lymphoma and chronic lymphocytic leukaemia. In several of these families we have found known pathogenic mutations in genes involved in regulation of the homologous recombination (HR) DNA damage repair (DDR) pathway (e.g. BRCA2 Y1710fs* and PALB2 K142*) that are previously characterised with regard to their known solid tumour predisposition. In the AFHCS families with these mutations we observe a mixture of hematological tumors of mostly lymphoid origin as well as non-hematological tumours. This led us to hypothesise that there is a subset of families for which the predisposition to malignancy includes a spectrum of different malignancies, i.e. pan-cancer predisposition. Further, we hypothesise that these are associated with mutations in genes with roles in HR DNA repair. In light of this we undertook a review of the phenotypic and genetic characteristics of families in our AFHCS cohort. Methods. Malignancy phenotype data, with regard to the different tumor types observed in each AFHCS family was annotated and aggregated. Covariance matrix analysis was then used to compare the number of times different tumor types were observed occurring together in a family pedigree. Genetic data: we curated whole exome sequence data for damaging mutations in genes with a known role in HR DNA damage repair. Results. A phenotype review of our cohort found 52% of assessable FHM families also had multiple types of solid tumour and/or individuals with diagnosis of multiple malignancies, indicative of a 'pan-cancer' phenotype. Covariance analysis showed that Hodgkin and non-Hodgkin lymphoma most often occurred together and also co-occurred with non-HM tumors breast, melanoma, colorectal, prostate and ovarian subtypes, implying a possible shared genetic etiology (Figure 1A). Assessment of AFHCS families for mutations in DDR genes including DNA repair (e.g. FANC/BRCA pathway genes) and chromosome cohesion (RAD21 and related) identified 18 variants segregating with malignancy including 5 frameshift or stopgain mutations. These high impact mutations included genes previously characterised in the context of autosomal recessive predisposition to hematological malignancy such as PALB2/BRCA2 family (Fanconi Anemia, see Figure 1B), NBN1 (Nijmegen Breakage Syndrome), DDX11 (Warsaw Syndrome) and others. A further 18 variants segregated in families where pan-cancer status is still under investigation. Conclusions. Phenotypic and genetic analysis of unsolved HM predisposed families have identified that familial clustering of lymphoma in actuality identifies families with pan-cancer germline genetic susceptibility, characterised by mutations in DNA damage response genes. Collectively these mutations may have a significant impact on our understanding of germline cancer predisposition, a finding supported by recent genetic population studies on sporadic cohorts, including pediatric cancer cohorts, opening the door for the application of rational therapies as evidenced by the BRCA/PARP inhibitor paradigm. However, as each individual gene mutation is rare, international collaborative studies will be essential for accurate measurements of risk and prognostication to assist individuals in the clinic. Disclosures Branford: Novartis: Consultancy, Honoraria, Research Funding, Speakers Bureau; Bristol-Myers Squibb: Honoraria, Speakers Bureau; Qiagen: Consultancy, Honoraria; Cepheid: Consultancy, Honoraria. Scott:Celgene: Honoraria.

Somatic Mutations Potentiating RAS-MAPK Signaling Confer Resistant Potential Against FLT3-Inhibitors to Acute Myelogenous Leukemia

Acute myeloid leukemia (AML) is one of the most common hematologic malignancies derived from a small number of self-renewing leukemic stem cells (LSCs). AML has various genetic abnormalities such as chromosomal aberration, single nucleotide variant and insertion/deletion. In particular, internal tandem duplication of FMS-like tyrosine kinase 3 (FLT3-ITD) is the most frequently found in ~ 25 % of AML cases, moreover, AML with FLT3-ITD is classified in unfavorable. FLT3 is fundamentally essential for survival of hematopoietic stem cells (HSCs) as well as LSCs, but once ITD is acquired, FLT3-ITD promotes the proliferation of AML by activating downstream enzymes. Various FLT3 inhibitors are now available as effective and promising drugs. On the other hand, the resistance against those inhibitors has been regarded as an emerging problem in clinics. To clarify the molecular machineries how AML cells acquire the resistance against FLT3 inhibitors, we compared the mutation status of paired AML samples consisted of diagnostic and relapsed samples. LSCs, which are quiescent and highly resistant against conventional chemotherapies, are considered to play a central role in recurrence. Since we and other group previously reported that TIM-3 clearly discriminates LSCs from residual normal HSCs, we purified and evaluated the mutations of CD34+CD38-TIM-3+ LSCs or CD34+ immature AML cells. The paired diagnostic and relapsed samples obtained from the identical 5 AML patient treated with Gilteritinib were subjected to whole exome sequencing (WES) analysis. CD3+ T cells were also purified from the diagnostic samples and used as a germ line control to detect somatic mutations acquired in AML cells. Libraries for WES were prepared using Sure Select XT HS and Human All Exon V6 Capture Kit in accordance with manufacturer's instructions. Then we performed WES using NextSeq 500 with 150bp pair-end read. Surprisingly, in all 5 cases examined, AML clones lost FLT3-ITD, whereas clones harboring mutations potentiating RAS-MAPK signaling became dominant at relapse: one case acquired the activated KRAS (Q61H) mutation and the remaining four cases newly acquired the previously-unidentified mutations in RAS-MAPK inhibitory genes. Such mutations in RAS-MAPK-inhibitory genes include DIRAS3 (W173X), RASA1 (E70G), RAP1GAP2 (K18X), RIN2 (S355fs), RASA4 (C655R), RASA4B (E141G), MAP2K7 (T66P) and PTPN7 (T14M). Of note, these genes belong to RAS-MAPK-inhibitory pathways and the encoded proteins are reported to suppress the activity of RAS-MAPK pathways. These RAS-MAPK-inhibitory mutations were exclusively detected in the relapsed AML clones, and contained stop-gain and frameshift mutations. We, therefore, hypothesized that RAS/MAPK activation driven by somatic mutations contributes to the acquisition of resistance against FLT3 inhibitors in LSCs. Consistent with such hypothesis, phosflow analysis revealed that basal ERK phosphorylation was retained or rather increased in the relapse CD34+ AML cells lacking FLT3-ITD, indicating that RAS-MAPK activation was maintained independent of FLT3-ITD. Furthermore, ASP2215 and AC220 inhibited ERK phosphorylation in the diagnostic CD34+ AML cells, whereas both inhibitors failed in the inhibition of ERK activation in the relapsed AML clones in all 3 cases analyzed. Gilteritinib also failed in inhibiting ERK in other relapsed AML cases, however, the combination of ASP2215 and MEK inhibitor efficiently suppressed ERK phosphorylation. All of relapse AML cases exhibited the emergence of AML clones harboring mutations associated with RAS-MAPK pathway genes, and therefore, the clinical sequence for detecting such mutations might be useful to assess the risk of FLT3-inhibitor treatment failure in clinics. Furthermore, our study showed the efficacy of MEK inhibitors to inhibit RAS-MAPK signaling activity even in the relapsed AML cells. Thus, the combination therapy consisted of FLT3-inhibitors and MEK inhibitors might be one of the promising therapeutic strategies to overcome FLT3-inhibitor resistance in AML. In summary, our study revealed that mutations potentiating RAS-MAPK pathway should play a central role in conferring the resistance against FLT3-inhibitors to AML. Disclosures Akashi: Sumitomo Dainippon, Kyowa Kirin: Consultancy; Celgene, Kyowa Kirin, Astellas, Shionogi, Asahi Kasei, Chugai, Bristol-Myers Squibb: Research Funding.

Circulating DNA for Molecular Response Prediction, Characterization of Resistance Mechanisms and Quantification of CAR T-Cells during Axicabtagene Ciloleucel Therapy

Circulating DNA for Molecular Response Prediction, Characterization of Resistance Mechanisms and Quantification of CAR T-Cells during Axicabtagene Ciloleucel Therapy

NGS-based multi-gene panel analysis in early-onset colorectal cancer patients

Abstract Background Colorectal cancer (CRC) keeps an upward incidence and rejuvenation trend in Kazakhstan, as well as worldwide, which is the motive for revising traditional risk factors and searching for cause-effective relationships at the genome level. Genetic nature of early-onset CRC is still unclear. The aim of this study was to determine the spectrum of cancer-related gene mutations among early-onset CRC patients. Methods The study included 125 CRC patients aged between 17 and 50 from Kazakhstan. DNAs were extracted from blood using the GeneJET Purification Kit. Next-generation sequencing (NGS) was done on the MiSeq using the TruSightCancer Kit. NGS data were analyzed by the MiSeq Reporter and Variant Studio. SIFT and PolyPhen-2 were used to predict potential pathogenic effects of missense variants on protein structure and function. Results We were able to detect 24 pathogenic/likely pathogenic mutations in 20 (16%) cases, out of which 8 were novel. Out of all mutations, five were detected in the APC gene, three in FANCI, three in BRCA2, two in BRCA1, two in MLH1, and one mutation each, in MSH6, MUTYH, BLM, NBN, ATM, BMPR1A, CHEK2, AIP, and DICER1 genes. The analysis of mutation type has revealed 10 frameshift mutations, 5 missense mutations, 5 stop-gain mutations, 1 in-frame deletion, and 3 mutations involving uncorrected splicing. All mutations were in the heterozygous state. Most of the mutations were not available in the 1000G, ESP6500 and ExAC databases. 5% were available in the dbSNP database, 29.1% in the COSMIC, and 38.4% in the ClinVar and/or LOVD. Pathogenic mutations in high penetrance CRC genes were higher in patients with family history of cancer (FHC) (21.1%, P = 0.0002) and in patients with primary multiple tumors (20.0 %, P = 0.0004) compared with patients without/unknown FHC (3.1%). Conclusions Molecular genetic study of CRC in young patients using NGS allows to identify CRC cases with syndromic and sporadic nature, to stratify the level of risk for a particular patient and his/her relatives, to influence on the diagnostic and therapeutic approaches and clinical examinations. The findings from this study show the diagnostic value of the detected pathogenic mutations in key CRC genes from the Kazakhstan population as promising biomarkers for CRC diagnosis in young people. Legal entity responsible for the study Institute of General Genetics and Cytology. Funding Ministry of Healthcare of the Republic of Kazakhstan. Disclosure All authors have declared no conflicts of interest.