scholarly journals Genetic alterations in main candidate genes during melanoma progression

Oncotarget ◽  
2018 ◽  
Vol 9 (9) ◽  
pp. 8531-8541 ◽  
Author(s):  
Maria Cristina Sini ◽  
Valentina Doneddu ◽  
Panagiotis Paliogiannis ◽  
Milena Casula ◽  
Maria Colombino ◽  
...  
Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 1596-1596
Author(s):  
Bin Yin ◽  
David A. Largaespada ◽  
James R. Downing

Abstract The AML1/ETO fusion gene is caused by chromosomal translocation t(8;21), which is among the most frequent chromosomal rearrangement seen in acute myeloid leukemia (AML). AML1/ETO functions in a dominant negative fashion to directly repress AML1-mediated transcriptional activation, and block the differentiation of myeloid progenitors. Notably, although it is oncogenic, AML1/ETO is not by itself sufficient to cause fully malignant AML, but can do so when there are concurrent oncogenic mutations (Higuchi 2002). This suggests that AML1/ETO requires cooperation with additional genetic alterations that are as yet largely unknown. The BXH-2 mouse strain is characterized by high frequency of spontaneous leukemia caused via insertional mutagenesis by a B-ecotropic murine leukemia virus. The proviral insertion site can then be used as a molecular tag, proviral insertion tag (PIT), to identify mutations/dysregulations of genes involved in leukemogenesis. Indeed, the BXH-2 strain has been utilized as a powerful forward genetic system to identify a number of leukemia-associated genes by our lab and collaborators. In this study, we have attempted to identify AML-related genes and pathways that could cooperate with AML1/ETO expression in development of AML. We have introduced the conditional AML1/ETO allele and Mx1-Cre, whose expression is induced by pIpC, into BXH-2 strain background to generate AEB mice after 4~6 consecutive backcrossing, and monitored daily these mice for sign of disease. Notably, the latency of leukemia in pIpC-injected AEB mice (mostly 5~8 months) is significantly shorter than that in saline-injected AEB control mice (mostly over one year). Immunophenotyping the tumor cells showed positivity for myeloid cell surface markers. Furthermore, leukemogenicity was tested and confirmed by transplanting the tumor cells generated from enlarged lymph nodes into B6C3F1 recipients. These data suggest that these mice developed a fatal, aggressive myeloid leukemia. Southern blot showed, that in these leukemic cells, the recombined allele of AML1/ETO was formed by Cre induction. Induced expression of AML1/ETO was not only detected in peripheral white blood cells but also in tumors. Importantly, these AML1/ETO AML also harbor clonal proviral insertions, indicating that AML1/ETO-initiated leukemia is dramatically accelerated by chronic retroviral infection in our model. To identify AML1/ETO-cooperative leukemia genes, we have isolated several PITs from AML1/ETO-accelerated leukemias. These PITs have also been mapped onto mouse genome using Celera and Ensembl mouse genome databases, and been found to target new candidate genes. Interestingly, we have discovered a new common PIT, which have not been reported in previous work which has identified over 2000 PITs. This common PIT targets a G-protein coupled receptor-like gene, a member of the GPCR family. We believe that these studies will provide important information for better understanding the mechanisms of development of leukemia with t(8;21), and reveal promising candidate genes or pathways serving as the potential therapeutic targets for improving AML treatment.


2014 ◽  
Vol 12 (1) ◽  
pp. 117 ◽  
Author(s):  
Maria Colombino ◽  
MariaCristina Sini ◽  
Amelia Lissia ◽  
Vincenzo De Giorgi ◽  
Ignazio Stanganelli ◽  
...  

2021 ◽  
Vol 11 ◽  
Author(s):  
Boram Lee ◽  
Hyunwoo Lee ◽  
Junhun Cho ◽  
Sang Eun Yoon ◽  
Seok Jin Kim ◽  
...  

Primary refractory/relapsed diffuse large B-cell lymphoma (rrDLBCL) is an unresolved issue for DLBCL treatment and new treatments to overcome resistance is required. To explore the genetic mechanisms underlying treatment resistance in rrDLBCL and to identify candidate genes, we performed targeted deep sequencing of 430 lymphoma-related genes from 58 patients diagnosed with rrDLBCL. Genetic alterations found between the initial biopsy and biopsy at recurrence or refractory disease were investigated. The genes most frequently altered (> 20%) were (in decreasing order of frequency) CDKN2A, PIM1, CD79B, TP53, MYD88, MYC, BTG2, BTG1, CDKN2B, DTX1, CD58, ETV6, and IRF4. Genes mutation of which in pretreatment sample were associated with poor overall survival included NOTCH1, FGFR2, BCL7A, BCL10, SPEN and TP53 (P < 0.05). FGFR2, BCL2, BCL6, BCL10, and TP53 were associated with poor progression-free survival (P < 0.05). Most mutations were truncal and were maintained in both the initial biopsy and post-treatment biopsy with high dynamics of subclones. Immune-evasion genes showed increased overall mutation frequency (CD58, B2M) and variant allele fraction (CD58), and decreased copy number (B2M, CD70) at the post-treatment biopsy. Using the established mutational profiles and integrative analysis of mutational evolution, we identified information about candidate genes that may be useful for the development of future treatment strategies.


Antibiotics ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 374
Author(s):  
Myeongjin Choi ◽  
Kwan Soo Ko

The present study was undertaken to find novel genes associated with colistin resistance in Klebsiella pneumoniae. Five colistin-resistant mutants were derived from four colistin-susceptible parental K. pneumoniae strains belonging to different clones. Whole-genome sequencing was performed for the nine K. pneumoniae strains to screen altered candidate genes. Expression levels of genes with amino acid alterations in derivative strains were determined using quantitative real-time Polymerase chain reaction (PCR). Colistin susceptibility was examined in a parental strain complemented with altered candidate genes. Overall, 13 genetic alterations were identified in five pairs of isogenic K. pneumoniae strains. Genetic alterations related to KP1_3468, including the insertion of an IS5-like element in an intergenic or coding region and amino acid substitutions, were identified in three separate derivative strains. Amino acid substitutions and deletion of PhoQ were determined in one derivative strain. With inactivation of CrrA and substituted CrrB, amino acid substitutions and deletion were identified in a repressor of galETK operon (KP1_0061) and hypothetical protein (KP1_3620), respectively. Decreased colistin susceptibility was observed in a parental strain complemented with KP1-0061, but not a KP1-3620 gene. This study demonstrated diverse genetic paths to colistin resistance in K. pneumoniae. Our results suggest that a repressor of galETK operon may play an important role in colistin resistance in K. pneumoniae.


2014 ◽  
Vol 12 (Suppl 1) ◽  
pp. O3
Author(s):  
Maria Colombino ◽  
Maria Sini ◽  
Amelia Lissia ◽  
Antonio Cossu ◽  
Vincenzo De Giorgi ◽  
...  

2014 ◽  
Vol 96 ◽  
Author(s):  
EITAN FRIEDMAN ◽  
DANIEL S. MORAN ◽  
DANNY BEN-AVRAHAM ◽  
RAN YANOVICH ◽  
GIL ATZMON

SummaryWhile genetic factors in all likelihood contribute to stress fracture (SF) pathogenesis, a few studies focusing on candidate genes have previously been reported. The objective of this study is to gain better understanding on the genetic basis of SF in a gene-naive manner. Exome sequence capture followed by massive parallel sequencing of two pooled DNA samples from Israeli combat soldiers was employed: cases with high grade SF and ethnically matched healthy controls. The resulting sequence variants were individually verified using the Sequenom™ platform and the contribution of the genetic alterations was validated in a second cohort of cases and controls. In the discovery set that included DNA pool of cases (n = 34) and controls (n = 60), a total of 1174 variants with >600 reads/variant/DNA pool were identified, and 146 (in 127 genes) of these exhibited statistically significant (P < 0·05) different rates between SF cases and controls after multiple comparisons correction. Subsequent validation of these 146 sequence variants individually in a total of 136 SF cases and 127 controls using the Sequenom™ platform validated 20/146 variants. Of these, three missense mutations (rs7426114, rs4073918, rs3752135 in the NEB, SLC6A18 and SIGLEC12 genes, respectively) and three synonymous mutations (rs2071856, rs2515941, rs716745 in the ELFN2, GRK4, LRRC55 genes) displayed significant different rates in SF cases compared with controls. Exome sequencing seemingly unravelled novel candidate genes as involved in SF pathogenesis and predisposition.


Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 994-994
Author(s):  
Violaine Havelange ◽  
Ivan Théate ◽  
Evelyne Callet-Bauchu ◽  
Francine Mugneret ◽  
Lucienne Michaux ◽  
...  

Abstract Burkitt lymphomas/leukemias (BL) are highly aggressive mature B-cell malignancies characterized by a constant MYC rearrangement. MYC deregulation is an oncogenic event known to be necessary but not sufficient in BL pathogenesis. Additional (epi)genetic alterations should cooperate, such as inactivation of the p14arf-MDM2-TP53 pathway which is frequently detected. We recently demonstrated the independent negative prognostic impact of specific chromosomal alterations, del(13q) and +7q, in childhood BL. We also showed by Multi-FISH that 13q abnormalities are more heterogeneous than expected and that13q gains are underestimated by conventional cytogenetics (CC). DNA from 30 BL (15 adults/15 children) was analyzed with 50K Xba single nucleotide polymorphisms (SNP) arrays (Affymetrix), in order to characterize additional allelic imbalances and losses of heterozygosity. 47 gains and 30 losses were found in 22 BL; 57 chromosomal imbalances were cryptic (not detected by CC). A recurring 13q amplification was detected in 6 BL. The minimal amplified region (MAR) of 4.35 Mb includes 3 candidate genes: C13orf25, GPC5 and GPC6. One C13orf25 transcripts contains a miRNA 17–92 cluster. The amplicon was unmasked with BAC probes in 2/8 other screened BL with 13q abnormalities. This amplification was associated with a terminal deletion (minimal size: 5Mb) in half cases. A recurring 11q abnormality was also assessed by FISH with a MAR of 3.2 Mb containing candidate genes such as CBL, BLR1. Acquired partial uniparental disomies (pUPD) are characterized by loss of heterozygosity without chromosomal deletion. 73 pUPD (>5 Mb) were found in 15 BL; 14 were telomeric and probably resulted from one mitotic recombination. The pathogenic role of pUPD remains unclear. Some of them may be polymorphisms also detected in healthy population. Other may reflect genomic instability but in our series, no higher incidence of pUPD was detected in BL with a complex karyotype. Thirdly, non random pUPD may render the neoplastic cell homozygous for a preexisting mutation leading to the activation of an oncogene or inactivation of a tumor suppressor gene (TSG). Four telomeric pUPD on 1p, 9p, 17p and 17q were found in at least 2 BL. We confirmed homozygous mutations of 2 TSG (TP53 and CDKN2A) located on 17p and 9p pUPD, respectively. These pUPD may be another way of p14arf-MDM2-TP53 inactivation. Moreover, these results suggest an involvement of the miR 17–92 cluster known to interact with the MYC oncogene in BL pathogenesis. The expression pattern of the different mature miR 17–92 in BL with and without 13q amplification will be presented at the meeting.


Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 2622-2622
Author(s):  
Esther Natalie Oliva ◽  
Maria Cuzzola ◽  
Roberto Latagliata ◽  
Francesca Ronco ◽  
D'Errigo Maria Grazia ◽  
...  

Abstract Abstract 2622 Poster Board II-598 Introduction: Genetic alterations reported in myelodysplastic syndromes (MDS) are not disease-specific and the underlying molecular causes of the disease remain poorly understood. It has been suggested that one or more of the genes mapping within the commonly deleted region of the 5q syndrome, together with other distant genes, may be critical to the development of the 5q syndrome. Potential candidate genes have been identified including the tumor suppressor gene SPARC, and the ribosomial protein gene, RPS14. Haploinsufficiency of RPS14 has been demonstrated and recent evidence indicates RPS14 as a causal gene for the 5q syndrome. Lenalidomide has proven efficacy in MDS patients with del(5q). Rapid and durable responses include transfusion-independence, with a rise in Hb, suppression of the 5q-deletion clone and improvement in bone marrow morphologic features. Methods: In a multicenter Italian phase II trial to evaluate safety, changes in quality of life and efficacy of lenalidomide in primary MDS patients with del(5q) and low or Int-1 risk IPSS, we investigate changes in bone marrow cytogenetics and gene expression patterns during treatment. The starting dose of lenalidomide is 10 mg p.o once daily on a continuous daily schedule for a maximum of 12 months. Dosing is based upon clinical and laboratory findings. Bone marrow cytogenetics and gene expression profiling are performed on study entry and every 12 weeks up to end of study (week 52). Gene expression assays of 51 candidate genes from the published literature and genomic databases have been selected and are carried out with TaqMan® Low Density Array Fluidic card (TaqMan® Human Array, Applied Biosystems, Foster City, CA, USA) based on Applied Biosystems PRISM® 7900HT comparative dd CT method, according to manufacturer's instructions. Using an 18S mRNA gene pre-designed assay from Applied Biosystems to detect the expression of the housekeeping gene 18S in each sample, target gene expression is normalized with 18S gene expression derived from a bone marrow pool of normal healthy subjects and for each sample the ratio between the target and 18S are expressed. Results: Baseline values for 23 patients (mean age 73 ± 10 years) are available and 16 have been re-evaluated after 12 weeks. Mean Hb was 8.6 ± 0.9 g/dL and 20 patients were transfusion-dependent. Seven patients had additional cytogenetic abnormalities. At baseline, RPS14 was under-expressed in 19 out of 21 patients evaluated. After 12 weeks RPS14 was re-evaluated in 13 patients: all had erythroid responses and RPS14 increased significantly from 0.07 (IQ Range 0.03–0.13) to 76.1 (0.73– 304.0, p=0.002). SPARC expression was under-expressed in 15/23 patients and variations during treatment were not significant. Baseline FAS gene was under-expressed in all patients and increased above reference values (p=0,006) after 12 weeks in 7/14 cases. IL7R was over-expressed in all patients at baseline (median 3263.3, IQ range 1998.3–5027.1) and was significantly reduced after 12 weeks (median 0.17, IQ range 0.05–2.20, p<0.0001). TINAGL1 gene expression was very high at baseline (mean 5214 ± 3661) and significantly reduced below normal values during treatment (0.63±0.87, p<0.0001). WTI was over-expressed in almost all patients (median 3246, IQ range 1590–7785) and, though reduced during treatment, still remained highly over reference values at 12 weeks (p=0.148). The expression of the other genes did not vary significantly during treatment. Conclusions: A preliminary study evaluating short-term effects of lenalidomide in low and Int-1 IPSS risk MDS and del(5q) demonstrates that gene expression is abnormal and varies during treatment. RPS14 is down-expressed and a significant increase in its expression is observed during treatment with lenalidomide in responsive patients. There is also an increase in FAS expression; the protein encoded by FAS gene is a member of the TNF-receptor superfamily and its interaction with its ligand leads to apoptosis.The IL7R gene on chromosome 5 (5p13) codifies for the IL7 receptor, which blocks apoptosis during differentiation and activation of T lymphocytes. TINAGL1 gene on chromosome 1 codifies for a Cathepsin B-like protein implicated in a number of human diseases such as cancer. During lenalidomide treatment, the expression of IL7R and TINAGL1 are reduced. Further results and repeated testing during this trial may develop new insights in the pathogenesis of MDS with del(5q) and in long-term effects of lenalidomide on bone marrow changes. Disclosures: Oliva: Celgene: Consultancy. Balleari:Celgene: Consultancy. Finelli:Celgene: Consultancy.


2007 ◽  
Vol 25 (18_suppl) ◽  
pp. 8522-8522
Author(s):  
G. Palmieri ◽  
C. Rozzo ◽  
A. Manca ◽  
A. Cossu ◽  
A. Lissia ◽  
...  

8522 Background: Cytogenetic and molecular studies indicated the chromosome 9p21 and its CDKN locus, with the p16/CDKN2A tumor suppressor genes, as the genomic regions involved into the pathogenesis of malignant melanoma (MM). To further elucidate the role of such regions in melanoma, we evaluated the 9p21-linked molecular alterations during the different phases of melanocytic tumorigenesis. Methods: Paraffin-embedded tissue sections from common nevi, dysplastic nevi, and melanomas, including primary and metastatic MM lesion, as well as melanoma cell lines were evaluated by both fluorescence in situ hybridization (FISH) using probes spanning the entire 9p21 region and immunohistochemistry (IHC) for p16/CDKN2A expression. Results: Allelic deletion at the CDKN locus and p16/CDKN2A gene silencing were both observed at increased rates moving from nevi to early or advanced primary melanomas and to correspondent metastases. Dysplastic nevi, primary and secondary melanomas were instead found to be heterozygously deleted at one or more loci within the 9p21 chromosome in a quite similar fraction (55–62%) of cases. Inactivation of the p16/CDKN2A gene was found at rates higher in melanoma cell lines (67%) than in vivo melanomas (62% secondary and 12.5% primary melanomas), with a normal p16/CDKN2A IHC staining in all analyzed nevi. Conclusions: Our findings indicate a model of sequential accumulation of genetic alterations from normal melanocytes to metastatic melanoma, with a) 9p21 allelic loss playing a role in melanocytic transformation and tumor initiation; b) deletions at CDKN locus and p16/ CDKN2A gene inactivation participating to tumor dissemination. Presence of such alterations could be further evaluated as markers of the different phases of melanoma progression. No significant financial relationships to disclose.


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