The Prognostic Impact of MYC Gene-Related Abnormalities on Multiple Myeloma Outcome through Fluorescence in situ Hybridization Analysis

Introduction: Chromosomal abnormalities (CAs) have been identified as important factors in determining the biological features and prognostic value of multiple myeloma (MM). MYC gene-related abnormalities (MYC GAs) are one of the CAs, but its unfavorable impact has not been fully investigated in daily clinical practice. Methods: This study retrospectively analyzed the prognostic impact of MYC GAs on 81 patients through fluorescence in situ hybridization analysis in our institute. Results: MYC GAs were associated with poor overall survival (hazard ratio [HR], 3.08; 95% confidence interval [CI], 1.23–7.73; p = 0.017), progression-free survival (PFS) (HR, 2.96; 95% CI, 1.58–5.53; p < 0.001), and time to next treatment (TNT) (HR, 2.11; 95% CI, 1.13–3.93; p = 0.018) in the median follow-up of 34.7 months. Furthermore, MYC GAs with an additional chromosome 8 (MYC-Ch8(+)) were associated with shorter PFS (HR, 3.15; 95% CI, 1.38–7.2; p = 0.0064), whereas MYC GAs without an additional chromosome 8 (MYC-Ch8(−)) were associated with shorter PFS (HR, 3.62; 95% CI, 1.51–8.68; p = 0.004) and shorter TNT (HR, 3.72; 95% CI, 1.41–9.81; p = 0.0078). Conclusion: These findings could help identify high-risk patients with MM. Further prospective studies are needed to confirm the significance of MYC GAs for the MM prognostic effect.

Role of defensins in innate immunity

Immune system of living organisms ranging from fungi, plants, vertebrates and invertebrates are all aided by polypeptide chains like defensins and cathelicidins. In humans the defensisns are quite fundamental part of innate immune system in combating with day-to-day exposure to unknown pathogens. The defensins are classified as alpha beta and sigma defensins expressed at chromosome 8 at nearly same positions, the sigma defensin is however synthetically developed as reterocyclin, as it has been stopped producing because of evolutionary development of stop codon 7.5 million years ago. The expression of Defensins can be either constitutive or inducible through epithelial cells, Paneth cells or other respective immune cells to regulate the activation of the innate immune responses. These impart their role either by direct microbicidal action, antiviral activity, inactivation or neutralization of microbial products, mobilization or activation of phagocytes and mast cells. Further to this there is lot more to explore about the availability of similar genetic expressions as defensins with unclear functions and in vivo experimental models development.

Chromosome 8 Polysomy Accounting for MYC Over-Expression in Angiosarcoma Arising as Somatic-Type Malignancy in Metastatic Teratoma. Case Report

MYC over-expression by immunohistochemistry (IHC) is utilised in routine pathology practice as a surrogate marker for MYC amplification, which plays a key oncogenic role in post-irradiation and chronic lymphedema-associated angiosarcoma. We present the case of a 32-year old male, who presented with high-grade angiosarcoma arising in a background of metastatic testicular teratoma. IHC for MYC showed strong nuclear expression in the angiosarcoma cells prompting the consideration of post-irradiation-induced angiosarcoma but our patient did not undergo radiotherapy. Fluorescence in-situ hybridization (FISH) excluded MYC amplification and instead showed Chromosome 8 polysomy, which accounted for the strong MYC IHC expression present, not previously described in the context of germ cell tumours. The occurrence of MYC over-expression due to polysomy illustrates a novel clinical scenario (angiosarcoma arising as somatic malignancy) where strong MYC IHC expression can be found in the absence of underlying amplification or prior radiotherapy exposure.

LY6S, a New Interferon-Inducible Human Member of the Ly6a-Subfamily Expressed by Spleen Cells and Associated with Inflammation and Viral Resistance

Syntenic genomic loci on human chromosome 8 (hChr8) and mouse chromosome 15 (mChr15) code for LY6/Ly6 (lymphocyte antigen 6) family proteins. The 23 murine Ly6 family genes include eight genes that are flanked by the murine Ly6e and Ly6l genes and form an Ly6 subgroup referred to here as the Ly6a subfamily gene cluster. Ly6a, also known as Sca1 (Stem Cell Antigen-1) and TAP (T-cell activating protein), is a member of the Ly6a subfamily gene cluster. No LY6 genes have been annotated within the syntenic LY6E to LY6L human locus. We report here on LY6S, a solitary human LY6 gene that is syntenic with the murine Ly6a subfamily gene cluster, and with which it shares a common ancestry. LY6S codes for the interferon-inducible GPI-linked LY6S-iso1 protein that contains only 9 of the 10 consensus LY6 cysteine residues and is most highly expressed in a non-classical cell population. Its expression leads to distinct shifts in patterns of gene expression, particularly of genes coding for inflammatory and immune response proteins, and LY6S-iso1 expressing cells show increased resistance to viral infection. Our findings reveal the presence of a previously un-annotated human interferon-stimulated gene, LY6S, which has a one to eight ortholog relationship with the genes of the Ly6a subfamily gene cluster, is most highly expressed in spleen cells of a non-classical cell-lineage and whose expression induces viral resistance and is associated with an inflammatory phenotype and with the activation of genes that regulate immune responses.

Underestimation of Heritability across the Molecular Layers of the Gene Expression Process

We investigated the extent of the heritability underestimation for molecules from an infinitesimal model in mixed model analysis. To this end, we estimated the heritability of transcription, ribosome occupancy, and translation in lymphoblastoid cell lines from Yoruba individuals. Upon considering all genome-wide nucleotide variants, a considerable underestimation in heritability was observed for mRNA transcription (−0.52), ribosome occupancy (−0.48), and protein abundance (−0.47). We employed a mixed model with an optimal number of nucleotide variants, which maximized heritability, and identified two novel expression quantitative trait loci (eQTLs; p < 1.0 × 10−5): rs11016815 on chromosome 10 that influences the transcription of SCP2, a trans-eGene on chromosome 1—whose expression increases in response to MGMT downregulation-induced apoptosis, the cis-eGene of rs11016815—and rs1041872 on chromosome 11 that influences the ribosome occupancy of CCDC25 on chromosome 8 and whose cis-eGene encodes ZNF215, a transcription factor that potentially regulates the translation speed of CCDC25. Our results suggest that an optimal number of nucleotide variants should be used in a mixed model analysis to accurately estimate heritability and identify eQTLs. Moreover, a heterogeneous covariance structure based on gene identity and the molecular layers of the gene expression process should be constructed to better explain polygenic effects and reduce errors in identifying eQTLs.

Genome-wide association study of autopsy-confirmed Multiple System Atrophy identifies common variants near ZIC1 and ZIC4

Multiple System Atrophy is a rare neurodegenerative disease with alpha-synuclein aggregation in glial cytoplasmic inclusions and either predominant olivopontocerebellar atrophy or striatonigral degeneration, leading to dysautonomia, parkinsonism, and cerebellar ataxia. One prior genome-wide association study in mainly clinically diagnosed patients with Multiple System Atrophy failed to identify genetic variants predisposing for the disease. Since the clinical diagnosis of Multiple System Atrophy yields a high rate of misdiagnosis when compared to the neuropathological gold standard, we studied common genetic variation in only autopsy-confirmed cases (N = 731) and controls (N = 2,898). The most strongly disease-associated markers were rs16859966 on chromosome 3 (P = 8.6 * 10-7, odds ratio (OR) = 1.58, [95% confidence interval (CI) = 1.32-1.89]), rs7013955 on chromosome 8 (P = 3.7 * 10-6, OR = 1.8 [1.40-2.31]), and rs116607983 on chromosome 4 (P = 4.0 * 10-6, OR = 2.93 [1.86-4.63]), all of which were supported by at least one additional genotyped and several imputed single nucleotide polymorphisms with P-values below 5 * 10-5. The genes closest to the chromosome 3 locus are ZIC1 and ZIC4 encoding the zinc finger proteins of cerebellum 1 and 4 (ZIC1 and ZIC4). Since mutations of ZIC1 and ZIC4 and paraneoplastic autoantibodies directed against ZIC4 are associated with severe cerebellar dysfunction, we conducted immunohistochemical analyses in brain tissue of the frontal cortex and the cerebellum from 24 Multiple System Atrophy patients. Strong immunohistochemical expression of ZIC4 was detected in a subset of neurons of the dentate nucleus in all healthy controls and in patients with striatonigral degeneration, whereas ZIC4 positive neurons were significantly reduced in patients with olivopontocerebellar atrophy. These findings point to a potential ZIC4-mediated vulnerability of neurons in Multiple System Atrophy.

Identification of a Novel HOOK3-FGFR1 Fusion Gene Involved in Activation of The NF-kappaB Pathway

BackgroundRearrangements involving the fibroblast growth factor receptor 1 (FGFR1) gene result in 8p11 myeloproliferative syndrome (EMS), which is a rare and aggressive hematological malignancy that is often initially diagnosed as myelodysplastic syndrome (MDS). Clinical outcomes are typically poor due to relative resistance to tyrosine kinase inhibitors (TKIs) and rapid transformation to acute leukemia. Deciphering the transcriptomic signature of FGFR1 fusions may open new treatment strategies for FGFR1 rearrangement patients.MethodsDNA sequencing (DNA-seq) was performed for 20 MDS patients and whole exome sequencing (WES) was performed for one HOOK3-FGFR1 fusion positive patient. RNA sequencing (RNA-seq) was performed for 20 MDS patients and 8 healthy donors. Fusion genes were detected using the STAR-Fusion tool. Fluorescence in situ hybridization (FISH), quantitative real-time PCR (qRT-PCR), and Sanger sequencing were used to confirm the HOOK3-FGFR1 fusion gene. The phosphorylation antibody array was performed to validate the activation of nuclear factor-kappaB (NF-kappaB) signaling. ResultsWe identified frequently recurrent mutations of ASXL1 and U2AF1 in the MDS cohort, which is consistent with previous reports. We also identified a novel in-frame HOOK3-FGFR1 fusion gene in one MDS case with abnormal monoclonal B-cell lymphocytosis and ring chromosome 8. FISH analysis detected the FGFR1 break-apart signal in myeloid blasts only. qRT-PCR and Sanger sequencing confirmed the HOOK3-FGFR1 fusion transcript with breakpoints located at the 11th exon of HOOK3 and 10th exon of FGFR1, and Western blot detected the chimeric HOOK3-FGFR1 fusion protein that is presumed to retain the entire tyrosine kinase domain of FGFR1. The transcriptional feature of HOOK3-FGFR1 fusion was characterized by the significant enrichment of the NF-kappaB pathway by comparing the expression profiling of FGFR1 fusion positive MDS with 8 healthy donors and FGFR1 fusion negative MDS patients. Further validation by phosphorylation antibody array also showed NF-kappaB activation, as evidenced by increased phosphorylation of p65 (Ser 536) and of IKBalpha (Ser 32). ConclusionThe HOOK3-FGFR1 fusion gene may contribute to the pathogenesis of MDS and activate the NF-kappaB pathway. These findings highlight a potential novel approach for combination therapy for FGFR1 rearrangement patients.

PpMYB36 Encodes a MYB-Type Transcription Factor That Is Involved in Russet Skin Coloration in Pear (Pyrus pyrifolia)

Fruit color is one of the most important external qualities of pear (Pyrus pyrifolia) fruits. However, the mechanisms that control russet skin coloration in pear have not been well characterized. Here, we explored the molecular mechanisms that determine the russet skin trait in pear using the F1 population derived from a cross between russet skin (‘Niitaka’) and non-russet skin (‘Dangshansu’) cultivars. Pigment measurements indicated that the lignin content in the skin of the russet pear fruits was greater than that in the non-russet pear skin. Genetic analysis revealed that the phenotype of the russet skin pear is associated with an allele of the PpRus gene. Using bulked segregant analysis combined with the genome sequencing (BSA-seq), we identified two simple sequence repeat (SSR) marker loci linked with the russet-colored skin trait in pear. Linkage analysis showed that the PpRus locus maps to the scaffold NW_008988489.1: 53297-211921 on chromosome 8 in the pear genome. In the mapped region, the expression level of LOC103929640 was significantly increased in the russet skin pear and showed a correlation with the increase of lignin content during the ripening period. Genotyping results demonstrated that LOC103929640 encoding the transcription factor MYB36 is the causal gene for the russet skin trait in pear. Particularly, a W-box insertion at the PpMYB36 promoter of russet skin pears is essential for PpMYB36-mediated regulation of lignin accumulation and russet coloration in pear. Overall, these results show that PpMYB36 is involved in the regulation of russet skin trait in pear.

Cytogenetically cryptic TNIP1-PDGFRB and PCM1-FGFR1 fusion leading to myeloid/lymphoid neoplasms with eosinophilia (MLN-eo) in children

Introduction: MLN-eo associated with gene rearrangements of PDGFRA, PDGFRB, FGFR1, or PCM1-JAK2 are rare haematological neoplasms primarily affecting adults. Eosinophilia commonly occurs but may also be absent. The heterogeneous clinical picture and the rarity of the disease, especially in children, may delay an early diagnosis. MLN-eo are characterized by constitutive tyrosine kinase activity due to gene fusions. It is thus of prognostic importance to obtain a prompt genetic diagnosis to start a specific therapy. Here we report two female paediatric cases of MLN-eo (6 months and 13 years old at initial diagnosis). Methods: In both cases, bone marrow morphology, karyotyping, fluorescence in-situ hybridization analysis (FISH) via break apart probes (PDGFRB (5q32), FGFR1 (8p12), JAK2 (9p24), FIP1L1/CHIC2/PDGFRA (4q12)), targeted RNA sequencing and in one case array CGH were performed. Results: The 6 months old girl was admitted to hospital with a 3-month history of rash and leukocytosis with eosinophilia. The skin showed multiple purpuric lesions (Fig 1 A/B). Mild splenomegaly was noted. White blood count (WBC) was 48000/µl with 38% eosinophils. Bone marrow trephine showed hypercellular marrow with mild fibrosis and eosinophilia without increase in blasts. Biopsy of a skin nodule displayed a histological pattern of interface dermatitis with eosinophilic infiltrate. (Fig 1 C/D). Fluorescence R-banding showed a normal karyotype (46,XX) (Fig. 2 A). However, FISH and array CGH detected an interstitial deletion of 5` PDGFRB (5q32) in 61 % of interphase nuclei (Fig. 2 B-D). Targeted RNA sequencing (RNA-seq) confirmed, as the array CGH suggested, the suspected TNIP1/PDGFRB fusion. According to the WHO criteria, diagnosis of a myeloid neoplasia with PDGFRB rearrangement due to an interstitial deletion in 5q was made. Because of the PDGFRB rearrangement, imatinib (250 mg/m²/d) therapy was started. Leukocyte and eosinophil counts normalized within 4 days without signs of tumour lysis. Skin lesions disappeared within 2 weeks. After 4 weeks, the dose was reduced to 100 mg/m² 3 x/week. Now at 14 months of age, peripheral counts continue to be normal and the fusion transcript is not detectable in the peripheral blood. The 13 years old girl was admitted with severe tachypnoea due to pleural effusions, hepatosplenomegaly and lymphadenopathy. Echocardiography showed endocarditis, left ventricular fibrosis and mitral insufficiency. WBC was 112170 /µL with 39% eosinophils. Bone marrow aspirate and trephine showed a feature of myeloproliferative neoplasia (MPN) with eosinophilia. The karyotype was normal. A rearrangement involving the FGFR1 locus was detected by FISH (Fig. 3 B/C). Splitting of the probe signals indicated an inversion on chromosome 8. Targeted RNA sequencing revealed a PCM1-FGFR1 fusion transcript. Diagnosis of a MLN-eo with FGFR1 rearrangement and evidence of a PCM1-FGFR1 fusion, most likely caused by an inversion on chromosome 8, was made. The girl stabilized after therapy with prednisone, vincristine, hydroxycarbamide and anti-IL-5 antibody. Peripheral blood counts normalized within 2 weeks. Eight weeks after initial diagnosis she presented with signs of a transient ischemic attack, respiratory distress and arterial hypotension. At that time WBC was 139000/µl with 53% myeloid blasts and 5% eosinophils. Trisomy 8 was detected in all metaphases and 88% of cells in FISH (Fig.3 A-C). Diagnosis of a progression to a myeloid blast phase was made. Induction chemotherapy (cytarabine, idarubicin, etoposidphosphate) was administered. On day +22 bone marrow aspirates showed the persisting picture of MPN. Preparations for hematopoietic stem cell transplantation (HSCT) and ponatinib therapy were begun, but cardiac and respiratory insufficiency that developed during chemotherapy were fatal. Conclusion: As these two cases have shown, standard cytogenetic and molecular methods may not be sufficient to diagnose MLN-eo due to cytogenetically cryptic aberrations. Thus, genetic diagnosis must be precise and quick (e.g. break apart FISH, targeted RNA-seq) in order to initiate adequate therapies with tyrosine kinase inhibitors or HSCT. Patients with rearrangements of PDGFRA or PDGFRB usually respond well to imatinib, whereas patients with FGFR1 and JAK2 gene fusions exhibit more aggressive diseases with variable sensitivity to tyrosine kinase inhibitors and have an early indication for HSCT. Figure 1 Figure 1. Disclosures Reiter: Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel expenses, Research Funding; Blueprint Medicines: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel expenses; Incyte: Membership on an entity's Board of Directors or advisory committees, Other: Travel expenses; AOP Orphan Pharmaceuticals: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: travel support; Deciphera: Membership on an entity's Board of Directors or advisory committees, Other: Travel expenses; Abbvie: Membership on an entity's Board of Directors or advisory committees; Celgene/BMS: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: travel support.