scholarly journals The malaria-protective human glycophorin structural variant DUP4 shows somatic mosaicism and association with hemoglobin levels

2018 ◽  
Author(s):  
Walid Algady ◽  
Sandra Louzada ◽  
Danielle Carpenter ◽  
Paulina Brajer ◽  
Anna Färnert ◽  
...  
Keyword(s):  
Severe Malaria ◽  
Copy Number ◽  
Fusion Gene ◽  
Sub Saharan Africa ◽  
Glycophorin A ◽  
Fusion Genes ◽  
Somatic Variation ◽  
Structural Variant ◽  
Complex Structural ◽  
Glycophorin B

AbstractGlycophorin A and glycophorin B are red blood cell surface proteins that are both receptors for the parasite Plasmodium falciparum, which is the principal cause of malaria in sub-Saharan Africa. DUP4 is a complex structural genomic variant that carries extra copies of a glycophorin A - glycophorin B fusion gene, and has a dramatic effect on malaria risk by reducing the risk of severe malaria by up to 40%. Using fiber-FISH and Illumina sequencing, we validate the structural arrangement of the glycophorin locus in the DUP4 variant, and reveal somatic variation in copy number of the glycophorin A-glycophorin B fusion gene. By developing a simple, specific, PCR-based assay for DUP4 we show the DUP4 variant reaches a frequency of 13% in a village in south-eastern Tanzania. We genotype a substantial proportion of that village and demonstrate an association of DUP4 genotype with hemoglobin levels, a phenotype related to malaria, using a family-based association test. Taken together, we show that DUP4 is a complex structural variant that may be susceptible to somatic variation, and show that it is associated with a malarial-related phenotype in a non-hospitalized population.Significance statementPrevious work has identified a human complex genomic structural variant called DUP4, which includes two novel glycophorin A-glycophorin B fusion genes, is associated with a profound protection against severe malaria. In this study, we present data showing the molecular basis of this complex variant. We also show evidence of somatic variation in the copy number of the fusion genes. We develop a simple robust assay for this variant and demonstrate that DUP4 is at an appreciable population frequency in Tanzania and that it is associated with higher hemoglobin levels in a malaria-endemic village. We suggest that DUP4 is therefore protective against malarial anemia.

scholarly journals Structural variation of the malaria-associated human glycophorin A-B-E region

2019 ◽  
Author(s):  
Sandra Louzada ◽  
Walid Algady ◽  
Eleanor Weyell ◽  
Luciana W. Zuccherato ◽  
Paulina Brajer ◽  
...  
Keyword(s):  
Structural Variation ◽  
Fusion Gene ◽  
Glycophorin A ◽  
Structural Variants ◽  
Recombination Hotspot ◽  
Structural Variant ◽  
E Region ◽  
Complex Structural ◽  
Fibre Fish ◽  
Almost All

AbstractApproximately 5% of the human genome consists of structural variants, which are enriched for genes involved in the immune response and cell-cell interactions. A well-established region of extensive structural variation is the glycophorin gene cluster, comprising three tandemly-repeated regions about 120kb in length, carrying the highly homologous genes GYPA, GYPB and GYPE. Glycophorin A and glycophorin B are glycoproteins present at high levels on the surface of erythrocytes, and they have been suggested to act as decoy receptors for viral pathogens. They act as receptors for invasion of a causative agent of malaria, Plasmodium falciparum. A particular complex structural variant (DUP4) that creates a GYPB/GYPA fusion gene is known to confer resistance to malaria. Many other structural variants exist, and remain poorly characterised. Here, we analyse sequences from 6466 genomes from across the world for structural variation at the glycophorin locus, confirming 15 variants in the 1000 Genomes project cohort, discovering 9 new variants, and characterising a selection using fibre-FISH and breakpoint mapping. We identify variants predicted to create novel fusion genes and a common inversion duplication variant at appreciable frequencies in West Africans. We show that almost all variants can be explained by unequal cross over events (non-allelic homologous recombination, NAHR) and. by comparing the structural variant breakpoints with recombination hotspot maps, show the importance of a particular meiotic recombination hotspot on structural variant formation in this region.

scholarly journals Resistance to malaria through structural variation of red blood cell invasion receptors

2016 ◽  
Author(s):  
Ellen M. Leffler ◽  
Gavin Band ◽  
George B.J. Busby ◽  
Katja Kivinen ◽  
Quang Si Le ◽  
...  
Keyword(s):  
Blood Cell ◽  
Severe Malaria ◽  
Cell Invasion ◽  
Red Blood Cell ◽  
Structural Variation ◽  
Sub Saharan Africa ◽  
Natural Resistance ◽  
Cell Phenotype ◽  
Human Populations ◽  
Structural Variant

AbstractPlasmodium falciparuminvades human red blood cells by a series of interactions between host and parasite surface proteins. Here we analyse whole genome sequence data from worldwide human populations, including 765 new genomes from across sub-Saharan Africa, and identify a diverse array of large copy number variants affecting the host invasion receptor genesGYPAandGYPB. We find that a nearby reported association with severe malaria is explained by a complex structural variant that involves the loss ofGYPBand gain of two hybrid genes, each with a GYPB extracellular domain and GYPA intracellular domain. This variant reduces the risk of severe malaria by 40% and has recently risen in frequency in parts of Kenya. We show that the structural variant encodes the Dantu blood group antigen, and therefore a serologically distinct red cell phenotype. These findings demonstrate that structural variation of red blood cell invasion receptors is associated with natural resistance toP. falciparummalaria.

scholarly journals PATH-17. INTRAGENIC COPY NUMBER BREAKPOINT ANALYSIS OF METHYLATION DATA FROM CNS TUMOURS IDENTIFIES NOVEL SUBGROUP-SPECIFIC CANDIDATE FUSION GENE ENRICHMENTS

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii427-iii428
Author(s):  
Alan Mackay ◽  
Yura Grabovska ◽  
Matthew Clarke ◽  
Diana Carvalho ◽  
Sara Temelso ◽  
...  
Keyword(s):  
Copy Number ◽  
Fusion Gene ◽  
High Grade Glioma ◽  
Structural Variations ◽  
Methylation Array ◽  
Kinase Gene ◽  
Integrated Diagnosis ◽  
Cns Tumours ◽  
Breakpoint Analysis ◽  
Balanced Translocations

Abstract Methylation array-based molecular profiling has redefined the classification of brain tumours and now forms an important part of their integrated diagnosis, providing both subgroup assignment and genome wide DNA copy number profiles. These latter data can be used to identify intragenic breakpoints which are frequently associated with structural variations resulting in therapeutically targetable oncogenic fusion genes. To systematically assess the landscape of these alterations, we combined publicly available methylation datasets resulting in a total of 5660 CNS tumours, around half paediatric, and including >1000 high grade glioma and DIPG. These were analysed by standard methodology (MNP, conumee), and intragenic breakpoint enrichment was compared within methylation subgroups, superfamilies, and tumours with no high-scoring classification. Benchmarking included sequence-verified cases such as infant hemispheric gliomas (IHG) with ALK(15%) and ROS1(7%) fusions, and pathognomic alterations associated with specific entities such as RELA-EPN, MYB-LGG and HGNET-MN1. We identified previously unreported enrichments of well-recognised fusion targets such as NTRK2in GBM_MID and NTRK3in DMG_K27 (both 5%), METin A_IDH / A_IDH_HG (3–5%), and FGFR1/3in GBM_G34 (8–9%). Novel recurrent kinase gene candidates to be verified and explored further include IGF1Rin 2–12% cases spanning glioma subgroups, and TIE1in poorly classified tumours. This latter ‘NOS’ group were also enriched in various transcription factor targets of breakpoints, including TCF4and PLAGL2. Despite limitations due to sample quality, resolution or balanced translocations, breakpoint analysis of methylation copy number profiles provides simple screening for structural rearrangements which may directly influence targeted therapy in paediatric CNS tumours.

Expression of the angiotensinogen gene is synergistically stimulated by 8-BrcAMP and Dex in opossum kidney cells

1995 ◽  
Vol 268 (1) ◽  
pp. R105-R111 ◽  
Author(s):  
M. Ming ◽  
T. T. Wang ◽  
S. Lachance ◽  
A. Delalandre ◽  
S. Carriere ◽  
...  
Keyword(s):  
Fusion Gene ◽  
Dependent Manner ◽  
Fusion Genes ◽  
Opossum Kidney ◽  
Ok Cells ◽  
Angiotensinogen Gene ◽  
Opossum Kidney Cells ◽  
Dependent Protein ◽  
Flanking Region ◽  
Responsive Element

We transiently transfected fusion genes with the 5'-flanking region of the angiotensinogen gene linked to a bacterial chloramphenicol acetyltransferase (CAT) coding sequence as a reporter into opossum kidney (OK) cells. The addition of 8-bromoadenosine 3',5'-cyclic monophosphate (8-BrcAMP) (10(-3)-10(-7) M) or forskolin (10(-9)-10(-5) M) stimulated the expression of the plasmid pOCAT [angiotensinogen nucleotide (N) -1498/+18] fusion gene in OK cells in a dose-dependent manner. The addition of dexamethasone (Dex) (10(-6) M) further enhanced the stimulatory effect of 8-BrcAMP or forskolin, whereas the addition of (R)-p-adenosine 3',5'-cyclic monophosphorothioate [(Rp)-cAMP[S], an inhibitor of cAMP-dependent protein kinase A, I and II] blocked the stimulatory effect of 8-BrcAMP. Furthermore, the addition of 8-BrcAMP (10(-3) M) or Dex (10(-6) M) or a combination of both stimulated the expression of pOCAT (angiotensinogen N -1138/+18), pOCAT (angiotensinogen N -960/+18), pOCAT (angiotensinogen N -814/+18), and pOCAT (angiotensinogen N -688/+18), but had no effect on the expression of pOCAT (angiotensinogen N -280/+18), pOCAT (angiotensinogen N -198/+18), pOCAT (angiotensinogen N -110/+18), pOCAT (angiotensinogen N -53/+18), and pOCAT (angiotensinogen N -35/+18). To further localize the putative cAMP-responsive element (CRE) in the angiotensinogen gene, we constructed fusion genes by inserting the DNA fragments angiotensinogen N -814 to N -689, angiotensinogen N -814 to N -761, and angiotensinogen N -760 to N -689 of the 5'-flanking region of the angiotensinogen gene upstream of the thymidine kinase (TK) promoter fused to a CAT gene and introduced them into OK cells.(ABSTRACT TRUNCATED AT 250 WORDS)

scholarly journals Identification of a Novel Oncogenic Fusion Gene SPON1-TRIM29 in Clinical Ovarian Cancer That Promotes Cell and Tumor Growth and Enhances Chemoresistance in A2780 Cells

2022 ◽  
Vol 23 (2) ◽  
pp. 689
Author(s):  
Saya Nagasawa ◽  
Kazuhiro Ikeda ◽  
Daisuke Shintani ◽  
Chiujung Yang ◽  
Satoru Takeda ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Rna Sequencing ◽  
Anticancer Drugs ◽  
Fusion Gene ◽  
Xenograft Model ◽  
Fusion Transcript ◽  
Serous Carcinoma ◽  
Fusion Genes ◽  
Sequencing Data ◽  
Chromosome 11

Gene structure alterations, such as chromosomal rearrangements that develop fusion genes, often contribute to tumorigenesis. It has been shown that the fusion genes identified in public RNA-sequencing datasets are mainly derived from intrachromosomal rearrangements. In this study, we explored fusion transcripts in clinical ovarian cancer specimens based on our RNA-sequencing data. We successfully identified an in-frame fusion transcript SPON1-TRIM29 in chromosome 11 from a recurrent tumor specimen of high-grade serous carcinoma (HGSC), which was not detected in the corresponding primary carcinoma, and validated the expression of the identical fusion transcript in another tumor from a distinct HGSC patient. Ovarian cancer A2780 cells stably expressing SPON1-TRIM29 exhibited an increase in cell growth, whereas a decrease in apoptosis was observed, even in the presence of anticancer drugs. The siRNA-mediated silencing of SPON1-TRIM29 fusion transcript substantially impaired the enhanced growth of A2780 cells expressing the chimeric gene treated with anticancer drugs. Moreover, a subcutaneous xenograft model using athymic mice indicated that SPON1-TRIM29-expressing A2780 cells rapidly generated tumors in vivo compared to control cells, whose growth was significantly repressed by the fusion-specific siRNA administration. Overall, the SPON1-TRIM29 fusion gene could be involved in carcinogenesis and chemotherapy resistance in ovarian cancer, and offers potential use as a diagnostic and therapeutic target for the disease with the fusion transcript.

scholarly journals Clinical significance of recurrent copy number aberrations in B-lineage acute lymphoblastic leukaemia without recurrent fusion genes across age cohorts

2017 ◽  
Vol 178 (4) ◽  
pp. 583-587 ◽  
Author(s):  
Monica Messina ◽  
Sabina Chiaretti ◽  
Anna Lucia Fedullo ◽  
Alfonso Piciocchi ◽  
Maria Cristina Puzzolo ◽  
...  
Keyword(s):  
Acute Lymphoblastic Leukaemia ◽  
Clinical Significance ◽  
Lymphoblastic Leukaemia ◽  
Copy Number ◽  
Fusion Genes ◽  
Age Cohorts ◽  
Copy Number Aberrations ◽  
B Lineage

scholarly journals Analysis of NTRK mutation and clinicopathologic factors in lung cancer patients in northeast China

2020 ◽  
Vol 35 (3) ◽  
pp. 36-40
Author(s):  
Hui Li ◽  
Shi Yan ◽  
Ying Liu ◽  
Lixia Ma ◽  
Xianhong Liu ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Whole Blood ◽  
Copy Number ◽  
Northeast China ◽  
Fusion Gene ◽  
Gene Mutations ◽  
Driver Gene ◽  
Blood Samples ◽  
Clinicopathologic Factors ◽  
Whole Blood Samples

Objective: NTRK mutations and clinicopathological factors in patients with lung cancer in northeast China were analyzed by next-generation sequencing (NGS), and references were provided for patients with NTRK mutations undergoing targeted therapy in northeast China. Methods: A total of 224 specimens in 173 patients with lung cancer were collected. This included 51 patients with matched tissue and whole blood samples,133 tissue samples, 84 whole blood samples, and 7 pleural effusion samples. NGS (520 genes) was used to detected NTRK mutations and clinicopathologic factors. Results: NTRK mutation was detected in eight patients (8/173, 4.6%), including four NTRK missense mutations (4/173, 2.3%), two NTRK fusion gene mutations (2/173, 1.2%), and two NTRK copy number deletions (2/173, 1.2%). Among the eight patients with NTRK mutations, four were associated with lung cancer driver gene mutations (3/4 EGFR, 1/4ALK); NTRK in two patients was inconsistent in tissue and paired whole blood testing; NTRK missense mutation was detected in one patient, and NTRK copy number deletion was detected in the other; and NTRK wild type was detected in two patients. There was no correlation between NTRK mutation and clinicopathologic factors (including gender, age, pathological type, smoking status, metastasis site). Conclusion: NTRK mutation was only 4.6%, effective fusion gene mutation was 1.2%, and common driver gene mutation in lung cancer was evident in 50% of patients. The results of NTRK were inconsistent with matched tissues and whole blood. Therefore, patients with NTRK mutation should use a variety of specimen types and large target area sequencing (panel) analysis method to provide individualized treatment.

scholarly journals Studies on human red-cell membrane glycophorin A and glycophorin B genes in glycophorin-deficient individuals

1989 ◽  
Vol 263 (3) ◽  
pp. 993-996 ◽  
Author(s):  
C G Tate ◽  
M J A Tanner ◽  
P A Judson ◽  
D J Anstee
Keyword(s):  
Cell Membrane ◽  
Genomic Dna ◽  
Southern Blot Analysis ◽  
Glycophorin A ◽  
Red Cell ◽  
Red Cell Membrane ◽  
Single Deletion ◽  
The Individual ◽  
Glycophorin B ◽  
Human Red Cell Membrane

1. Genomic DNA derived from individuals who lack glycophorin A (GPA), glycophorin B (GPB) or both of these proteins was subjected to Southern-blot analysis using GPA and GPB cDNA probes. 2. Bands on the Southern blots were assigned to the GPA gene, GPB gene or to a putative pseudogene. 3. Genomic DNA derived from an individual of the Mk phenotype was shown to have deletions in the GPA and GPB genes. The simplest model for the results obtained is that a single deletion spans the GPA and GPB genes in the individual studied.

scholarly journals Severe Case of Plasmodium falciparum Malaria in a Pregnant Woman from Nigeria

2019 ◽  
Vol 2019 ◽  
pp. 1-3
Author(s):  
Kruti Yagnik ◽  
Bilal Farooqi ◽  
Molly W. Mandernach ◽  
Anthony P. Cannella ◽  
Gautam Kalyatanda
Keyword(s):  
Pregnant Women ◽  
Severe Malaria ◽  
Plasmodium Falciparum Malaria ◽  
Severe Case ◽  
Pregnant Patient ◽  
Sub Saharan Africa ◽  
Blood Parasites ◽  
Intrauterine Pregnancy ◽  
Drug Of Choice ◽  
Sub Saharan

Human malaria has arguably affected more of human history than any other pathogen. Pregnant women have a higher risk of developing severe malaria as well as the risk of severe complications. We present a case of severe malaria in a pregnant patient from sub-Saharan Africa who was treated successfully with artesunate. A 28-year-old Nigerian woman with a 20-week intrauterine pregnancy presented with a five-day history of fever and diffuse joint pains. Evaluation of peripheral thin blood smear demonstrated a parasitemia of 9.8%. The patient was admitted to the intensive care unit, and oral clindamycin/quinine was initiated until intravenous artesunate was obtained. The patient completed four doses of IV artesunate, and after the 4th dose of artesunate, no blood parasites were seen on peripheral smear. The patient was discharged home and, upon clinic follow-up, did not have any further complications associated with either her disease or therapy. A review on the treatment of severe malaria in all trimesters of pregnancy supports the WHO recommendation for intravenous artesunate as the drug of choice. This case illustrates the importance of recognizing malaria in pregnant women from endemic countries and shows that artesunate compounds can be used safely in pregnancy, particularly with high parasitemia.

scholarly journals Identification and Characterization of Novel Fusion Genes with Potential Clinical Applications in Mexican Children with Acute Lymphoblastic Leukemia

2019 ◽  
Vol 20 (10) ◽  
pp. 2394 ◽  
Author(s):  
Minerva Mata-Rocha ◽  
Angelica Rangel-López ◽  
Elva Jiménez-Hernández ◽  
Blanca Angélica Morales-Castillo ◽  
Carolina González-Torres ◽  
...  
Keyword(s):  
Acute Lymphoblastic Leukemia ◽  
Fusion Gene ◽  
Lymphoblastic Leukemia ◽  
Fusion Genes ◽  
Cancer Etiology ◽  
Mexican Children ◽  
Genes Encoding ◽  
Identification And Characterization ◽  
Current Risk

Acute lymphoblastic leukemia is the most common type of childhood cancer worldwide. Mexico City has one of the highest incidences and mortality rates of this cancer. It has previously been recognized that chromosomal translocations are important in cancer etiology. Specific fusion genes have been considered as important treatment targets in childhood acute lymphoblastic leukemia (ALL). The present research aimed at the identification and characterization of novel fusion genes with potential clinical implications in Mexican children with acute lymphoblastic leukemia. The RNA-sequencing approach was used. Four fusion genes not previously reported were identified: CREBBP-SRGAP2B, DNAH14-IKZF1, ETV6-SNUPN, ETV6-NUFIP1. Although a fusion gene is not sufficient to cause leukemia, it could be involved in the pathogenesis of the disease. Notably, these new translocations were found in genes encoding for hematopoietic transcription factors which are known to play an important role in leukemogenesis and disease prognosis such as IKZF1, CREBBP, and ETV6. In addition, they may have an impact on the prognosis of Mexican pediatric patients with ALL, with the potential to be included in the current risk stratification schemes or used as therapeutic targets.

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