scholarly journals OA 10.05 Non-Invasive Molecular Profiling in NSCLC by Targeted and Whole Exome Analysis of Plasma cfDNA

2017 ◽  
Vol 12 (11) ◽  
pp. S1772
Author(s):  
M. Cheng ◽  
J. Yang ◽  
M. Shady ◽  
P. Ulz ◽  
E. Heitzer ◽  
...  
2021 ◽  
Vol 22 (7) ◽  
pp. 3667
Author(s):  
Chiara Degli Esposti ◽  
Barbara Iadarola ◽  
Simone Maestri ◽  
Cristina Beltrami ◽  
Denise Lavezzari ◽  
...  

Neuroblastoma (NB) is an aggressive infancy tumor, leading cause of death among preschool age diseases. Here we focused on characterization of exosomal DNA (exo-DNA) isolated from plasma cell-derived exosomes of neuroblastoma patients, and its potential use for detection of somatic mutations present in the parental tumor cells. Exosomes are small extracellular membrane vesicles secreted by most cells, playing an important role in intercellular communications. Using an enzymatic method, we provided evidence for the presence of double-stranded DNA in the NB exosomes. Moreover, by whole exome sequencing, we demonstrated that NB exo-DNA represents the entire exome and that it carries tumor-specific genetic mutations, including those occurring on known oncogenes and tumor suppressor genes in neuroblastoma (ALK, CHD5, SHANK2, PHOX2B, TERT, FGFR1, and BRAF). NB exo-DNA can be useful to identify variants responsible for acquired resistance, such as mutations of ALK, TP53, and RAS/MAPK genes that appear in relapsed patients. The possibility to isolate and to enrich NB derived exosomes from plasma using surface markers, and the quick and easy extraction of exo-DNA, gives this methodology a translational potential in the clinic. Exo-DNA can be an attractive non-invasive biomarker for NB molecular diagnostic, especially when tissue biopsy cannot be easily available.


2018 ◽  
Author(s):  
Jake R. Conway ◽  
David Liu ◽  
Stephanie Wankowicz ◽  
Amaro Taylor-Weiner ◽  
Felix Dietlein ◽  
...  

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 1022-1022
Author(s):  
Masatoshi Takagi ◽  
Kohsuke Imai ◽  
Jinhua Piao ◽  
Motoy Yamashita ◽  
Akihiro Hoshino ◽  
...  

Abstract ALPS is characterized by chronic lymphoproliferation in combination with autoimmunity; mutations of molecules involved in FAS-dependent pathways play causative roles in this syndrome. The hallmarks of ALPS are an elevated CD4/CD8 double-negative T (DNT) cell count and attenuated induction of apoptosis by FAS stimulation. Autoimmune thrombocytopenia and/or hemolytic anemia are common in cases of ALPS; the combination of autoimmune thrombocytopenia and hemolytic anemia is referred to as Evans syndrome. ALPS is diagnosed in 47% of patients who present with Evans syndrome. Some patients with ALPS-like syndromes harbor mutations in RAS or PRKCD. In this study, we performed whole-exome analysis of undiagnosed patients exhibiting autoimmunity in combination with lymphoproliferation. Fifteen pediatric patients presenting with autoimmunity were enrolled in this study. Although not all of them fulfilled the diagnostic criteria of ALPS, most of them exhibited an ALPS-like phenotype, an autoimmune hematological disorder such as Evans syndrome, or immune thrombocytopenia with hepatosplenomegaly. Elevated counts of DNT cells among TCRαβ-positive cells were observed in some cases. All of the subjects screened negative for mutations in FAS, FASL, KRAS, and NRAS. These patients were subjected to whole-exome analysis, which revealed several mutations with known disease associations. One patient carried a mutation in CASP10, a causative gene for ALPS-CSAP (ALPS 2). This patient exhibited a typical ALPS phenotype with an elevated DNT cell count. In addition, we identified CTLA4 mutations in two patients, one of whom was described as ALPS type V (ALPS 5) and the other as CTLA4 haploinsufficiency with autoimmune infiltration (CHAI). A mutation in STAT3 was present in one patient. Dominant-negative mutations in the STAT3 gene result in hyper-IgE syndrome. Recently, an activating mutation of STAT3 was reported in infantile-onset multisystem autoimmune disease (ADMIO). It should be noted that an activating mutation of STAT3 results in a phenotype very similar to that of ALPS. Intriguingly, two autoinflammatory associated genes, PSTPIP1 and RNASEH2B were identified. Mutations in RNASEH2B causes Aicardi-Goutière syndrome (AGS), which phenotypically overlaps with SLE. Typical AGS develops as a results of biallelic mutations in causative genes. In this case, a heterozygous frame shift mutation was identified. Further evaluation is required to confirm whether this heterozygous frame shift mutation RNASEH2B really causes SLE or ALPS like symptoms. PSTPIP1 mutation causes pyogenic Arthritis, pyoderma gangrenosum and acne (PAPA) syndrome. The identified E250K mutation was one of the typical mutation in this disease. This patient exhibited SLE like symptom with hepatosplenomegaly without typical PAPA syndrome like symptoms, such as acne or pyoderma of the skin. Sequencing of the remaining patients yielded inconclusive results. The classical ALPS diagnostic procedure is well designed and suitable for identification of FAS-dependent apoptotic dysregulation. However, the measurement of FAS-dependent apoptosis requires technical skill, and the data quality is therefore dependent on the investigator. Moreover, RAS-associated ALPS-like disease (RALD, ALPS 3) and ALPS 5 (CHAI) cannot be identified by conventional ALPS diagnostic procedures. Therefore, the methods for diagnostic classification of these diseases need to be updated. It is interesting that mutations of autoinflammatory associated genes are involved in ALPS or SLE like patients. Our results reveal that a comprehensive genomic approach is a powerful tool for the characterization of ALPS or ALPS-like diseases. Together with recent progress in genome analysis in the PID field, our analyses provide an updated list of genes for use in differential diagnosis of ALPS-like diseases. This update will facilitate convenient genomic approaches such as comprehensive targeted sequencing focusing on genes involved in ALPS or ALPS-like diseases. This approach can be directly applied in the clinic to yield diagnostic benefits. Disclosures No relevant conflicts of interest to declare.


Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 5266-5266
Author(s):  
Keisuke Kato ◽  
Ai Yoshimi ◽  
Satoru Matsushima ◽  
Chie Kobayashi ◽  
Kunio Fukuda ◽  
...  

Abstract [Introduction] Mechanism of recurrence is fully characterized and is significant to improve prognosis in childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL) and T lymphoblastic leukemia (T-ALL).. We have analyzed recurrent cases of childhood BCP-ALL and T-ALL. [Procedure] We analyzed clinical samples of 18 cases with BCP-ALL and 3 cases with T-ALL, who had been treated in our institution. We have investigated gene status of IKZF1, CRLF2, CDKN2A/2B, JAKs, IL7RA, and TP53 using RT-PCR and MLPA methods and IGH/TCR on genomic PCR. Whole exome analysis was done using Ion AmpliSeq Exome in seven cases. [Result] We analyzed clinical samples of 21 cases with ALL, who had been treated in our institution. The cases were 18 cases with BCP-ALL and 3 cases with T-ALL. We have investigated gene status of IKZF1, CRLF2, CDKN2A/2B,JAKs,IL7RA, NOTCH (for T-ALL), and TP53. Whole exome analysis was done in two cases, particularly for a case from which we have established cell line. < Result > Eight BCP-ALL cases with P2RY8-CRLF2 chimeric transcript: four cases of which had P2RY8-CRLF2 chimeric transcript only at initial diagnosis; two cases obtained transcript at recurrence. This was confirmed employing LD-PCR genomic analysis. Ten BCP-ALL cases had deletion of IKZF1; two showed deletion at relapse and a case demonstrated deletion at diagnosis only. Two BCP-ALL cases showed mutation of IL7RA. One of T-ALL cases from which we have established cell line showed mutation of MSH2 and more than 200 non-synonymous mutations on whole exome analysis. One T-ALL cases showed mutation of JAK3 at diagnosis. One BCP-ALL case had MLH1 mutation < Discussion > The present study has suggested acquisition of complex genetic change at different point of evolution may work in recurrence of ALL. The present study has indicated P2RY8-CRLF2 works not as simple growth advantage but rather as manifestation of genomic instability. This may be also illustrated by recurrent cases with T-ALL having mutation of MSH2 and BCP-ALL having mutation of MLH1. Mutation of mismatch repair gene may be driver of gene mutation acquisition and consequently alterations of CREBBP and RAS or IKZF1, TP53, mismatch repair genes, or emergence of P2RY-CRLF2 chimeric transcript may be prognostically relevant in childhood acute lymphoblastic leukemia. Disclosures No relevant conflicts of interest to declare.


2016 ◽  
Vol 150 (4) ◽  
pp. S1013
Author(s):  
Revital Kariv ◽  
Guy Rosner ◽  
Leon Raskin

2015 ◽  
Vol 79 (5) ◽  
pp. 350-356 ◽  
Author(s):  
Rehab Serafi ◽  
Musharraf Jelani ◽  
Mona M. Almramhi ◽  
Hussein S.A. Mohamoud ◽  
Saleem Ahmed ◽  
...  

2012 ◽  
Vol 22 ◽  
pp. S29
Author(s):  
A. Leidenroth ◽  
H. Sørmo Sorte ◽  
G. Gilfillan ◽  
M. Ehrlich ◽  
R. Lyle ◽  
...  
Keyword(s):  

2019 ◽  
Author(s):  
Bhavana V. Chapman ◽  
Tatiana Karpinets ◽  
Travis T. Sims ◽  
Greyson Biegert ◽  
Xiaogang Wu ◽  
...  

AbstractObjectiveThe aim of this study was to validate a whole exome sequencing approach to longitudinally characterize the tumor mutational profile of cervical cancer patients undergoing chemoradiation (CRT).Experimental DesignCervical cancer tumor specimens from twenty-seven patients undergoing chemoradiation were collected before and throughout CRT and whole exome sequencing (WES) was performed to characterize individual mutations and alterations in unique genes. WES data were analyzed from cervical cancer patients in The Cancer Genome Atlas (TCGA) as a comparison group.ResultsOver 93% of mutated genes detected at baseline were present in TCGA. Tumor purity from collected swabs correlated with MRI tumor volumes during the course of treatment (R2=0.969). CDK4/CDK6/cyclin D1-related gene mutations involved in the ERK1/2, p16INK4, and p53 pathway and G1/S checkpoint most commonly persisted at the end of CRT.ConclusionThis non-invasive swab technique to serially sample tumor during CRT will allow new discoveries of dynamic tumor mutational profile changes during chemoradiation for mucosal tumors. Mutations that survived or increased during the initial weeks of radiation treatment are potential drivers of radiation resistance including the CDL4/CDK6/cyclin D1-related pathway.Statement of Translational RelevanceThere are no established biomarkers to predict chemoradiation (CRT) response for cervical cancer patients. Serial biopsies cannot be performed due to risks of bleeding and fistula. We used a novel non-invasive swab-based biopsy technique to obtain serial samples from a cohort of twenty-seven patients through the course of treatment, and validated this approach to obtain whole exome sequencing data. We analyzed dynamic tumor mutation profiles during CRT. Results from this study show that mutations in CDK4/CDK6/cyclin D1-related genes increased at the end of CRT, suggesting this pathway as a potential driver of radiation resistance.


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