Real-life disease monitoring in follicular lymphoma patients using liquid biopsy ultra-deep sequencing and PET/CT

In the present study, we screened 84 Follicular Lymphoma patients for somatic mutations suitable as liquid biopsy MRD biomarkers using a targeted next-generation sequencing (NGS) panel. We found trackable mutations in 95% of the lymph node samples and 80% of the liquid biopsy baseline samples. Then, we used an ultra-deep sequencing approach with 2 · 10^-4 sensitivity (LiqBio-MRD) to track those mutations on 151 follow-up liquid biopsy samples from 54 treated patients. Positive LiqBio-MRD at first-line therapy correlated with a higher risk of progression both at the interim evaluation (HR_INT 11.0, 95% CI 2.10-57.7, p = 0.005) and at the end of treatment (HR_EOT, HR 19.1, 95% CI 4.10-89.4, p < 0.001). Similar results were observed by PET/CT Deauville score, with a median PFS of 19 months vs. NR (p < 0.001) at the interim and 13 months vs. NR (p < 0.001) at EOT. LiqBio-MRD and PET/CT combined identified the patients that progressed in less than two years with 88% sensitivity and 100% specificity. Our results demonstrate that LiqBio-MRD is a robust and non-invasive approach, complementary to metabolic imaging, for identifying FL patients at high risk of failure during the treatment and should be considered in future response-adapted clinical trials.

Detection of kinase domain mutations in BCR::ABL1 leukemia by ultra-deep sequencing of genomic DNA

The screening of the BCR::ABL1 kinase domain (KD) mutation has become a routine analysis in case of warning/failure for chronic myeloid leukemia (CML) and B-cell precursor acute lymphoblastic leukemia (ALL) Philadelphia (Ph)-positive patients. In this study, we present a novel DNA-based next-generation sequencing (NGS) methodology for KD ABL1 mutation detection and monitoring with a 1.0E-4 sensitivity. This approach was validated with a well-stablished RNA-based nested NGS method. The correlation of both techniques for the quantification of ABL1 mutations was high (Pearson r = 0.858, p < 0.001), offering DNA-DeepNGS a sensitivity of 92% and specificity of 82%. The clinical impact was studied in a cohort of 129 patients (n = 67 for CML and n = 62 for B-ALL patients). A total of 162 samples (n = 86 CML and n = 76 B-ALL) were studied. Of them, 27 out of 86 harbored mutations (6 in warning and 21 in failure) for CML, and 13 out of 76 (2 diagnostic and 11 relapse samples) did in B-ALL patients. In addition, in four cases were detected mutation despite BCR::ABL1 < 1%. In conclusion, we were able to detect KD ABL1 mutations with a 1.0E-4 sensitivity by NGS using DNA as starting material even in patients with low levels of disease.

Intrinsic variation in the vertically transmitted core virome of the mosquito Aedes aegypti

Virome studies among metazoans have revealed the ubiquity of RNA viruses in animals, contributing to a fundamental re-thinking of the relationships between organisms and their microbiota. Mosquito viromes, often scrutinized due to their public health relevance, may also provide insight into broadly applicable concepts, such as a "core virome," a set of viruses consistently associated with a host species or population that may fundamentally impact its basic biology. A subset of mosquito-associated viruses (MAVs) could comprise such a core, and MAVs can be categorized as (i) arboviruses, which alternate between mosquito and vertebrate hosts, (ii) insect-specific viruses, which cannot replicate in vertebrate cells, and (iii) viruses with unknown specificity. MAVs have been widely characterized in the disease vector Aedes aegypti, and the occurrence of a core virome in this species has been proposed but remains unclear. Using a wild population previously surveyed for MAVs and a common laboratory strain, we investigated viromes in reproductive tissue via metagenomic RNA sequencing. Virome composition varied across samples, but four groups comprised >97% of virus sequences: a novel partiti-like virus (Partitiviridae), a toti-like virus (Totiviridae), unclassified Riboviria, and four orthomyxo-like viruses (Orthormyxoviridae). Whole or partial genomes for the partiti-like virus, toti-like virus, and one orthomyxo-like virus were assembled and analyzed phylogenetically. Multigenerational maintenance of these MAVs was confirmed by RT-PCR, indicating vertical transmission as a mechanism for persistence. This study provides fundamental information regarding MAV ecology and variability in A. aegypti and the potential for vertically maintained core viromes at the population level.

Neoantigen prediction and computational perspectives towards clinical benefit: recommendations from the ESMO Precision Medicine Working Group

BACKGROUND

The use of next-generation sequencing technologies has enabled the rapid identification of non-synonymous somatic mutations in cancer cells. Neoantigens are mutated peptides derived from somatic mutations not present in normal tissues that may result in the presentation of tumour-specific peptides capable of eliciting antitumour T-cell responses. Personalised neoantigen-based cancer vaccines and adoptive T-cell therapies have been shown to prime host immunity against tumour cells and are under clinical trial development. However, the optimisation and standardisation of neoantigen identification, as well as its delivery as immunotherapy are needed to increase tumour-specific T-cell responses and, thus, the clinical efficacy of current cancer immunotherapies.

METHODS

In this recommendation article, launched by the European Society for Medical Oncology (ESMO), we outline and discuss the available framework for neoantigen prediction and present a systematic review of the current scientific evidence.

RESULTS

A number of computational pipelines for neoantigen prediction are available. Most of them provide peptide major histocompatibility complex (MHC) binding affinity predictions, but more recent approaches incorporate additional features like variant allele fraction, gene expression, and clonality of mutations. Neoantigens can be predicted in all cancer types with high and low tumour mutation burden, in part by exploiting tumour-specific aberrations derived from mutational frameshifts, splice variants, gene fusions, endogenous retroelements and other tumour-specific processes that could yield more potently immunogenic tumour neoantigens. Ongoing clinical trials will highlight those cancer types and combinations of immune therapies that would derive the most benefit from neoantigen-based immunotherapies.

CONCLUSIONS

Improved identification, selection and prioritisation of tumour-specific neoantigens are needed to increase the scope of benefit from cancer vaccines and adoptive T-cell therapies. Novel pipelines are being developed to resolve the challenges posed by high-throughput sequencing and to predict immunogenic neoantigens.

Gut T cell-independent IgA responses to commensal bacteria require engagement of the TACI receptor on B cells

The gut mounts secretory immunoglobulin A (SIgA) responses to commensal bacteria through nonredundant T cell-dependent (TD) and T cell-independent (TI) pathways that promote the establishment of mutualistic host-microbiota interactions. SIgAs from the TD pathway target penetrant bacteria, and their induction requires engagement of CD40 on B cells by CD40 ligand on T follicular helper cells. In contrast, SIgAs from the TI pathway bind a larger spectrum of bacteria, but the mechanism underpinning their production remains elusive. Here, we show that the intestinal TI pathway required CD40-independent B cell-activating signals from TACI, a receptor for the innate CD40 ligand-like factors BAFF and APRIL. TACI-induced SIgA responses targeted a fraction of the gut microbiota without shaping its overall composition. Of note, TACI was dispensable for TD induction of IgA in gut-associated lymphoid organs. Thus, BAFF/APRIL signals acting on TACI orchestrate commensal bacteria-specific SIgA responses through an intestinal TI program.

What Reasons Lead Spanish Medical Students Not to Be in Favor of Organ Donation?

INTRODUCTION

Despite sensitization of medical students toward the donation of organs, a non-negligible percentage of students are not in favor of donation.

OBJECTIVE

To analyze the reasons of Spanish medical students who do not have a favorable attitude toward the donation of their own organs after death.

METHOD

The population under study is medical students in Spanish universities, using the database of the International Donor Collaborative Project, stratified by geographic area and academic year. The questionnaire completion was anonymous and self-administered. The study group is medical students with an unfavorable attitude toward organ donation. The assessment instrument used is a validated questionnaire of attitude toward the donation of organs for transplant, "PCID-DTO-Ríos." The reasons against the donation are valued in the questionnaire through a question.

RESULTS

Of the participants included in the PCID, students who are not in favor of organ donation were selected (n = 1899). Of them, 8.1% (n = 154) are against and 91.1% (n = 1745) are doubtful. The main reasons indicated are the fear of apparent death in 11.4% of respondents, fear of possible mutilation after donation in 11.1%, and religious reasons in 2.6%. Of those, 6.9% indicate other reasons but do not clearly specify the reasons, using words such as "fear" (2.5%) or "doubts about the process" (4.1%); 66.2% (n = 1257) indicated an "assertive refusal" ("I don't want to express my reasons").

CONCLUSION

Twenty percent of Spanish medical students are not in favor of donating their organs and are not in favor of showing their reasons.

Factors Related to the Attitude Toward Living Kidney Donation of the Population of Havana

INTRODUCTION

Living kidney donation (LKD) is one of the most used alternatives in the field of organ transplantation.

OBJECTIVE

Analyze the attitude toward LKD among the population of Havana, Cuba.

METHODS

Population under study. Population resident in Havana, Cuba.

INCLUSION CRITERIA

Sample of population over 15 years stratified by age and sex.

INSTRUMENT

Validated questionnaire of attitude toward donation and transplant "PCID-DVR-Ríos," self-administered and anonymously filled out.

STATISTICS

χ², Student t test, and a logistic regression analysis.

RESULTS

A total of 920 respondents have been included in the study. A total of 85.5% (n = 787) are in favor of the related LKD. In our study, 26.5% (n = 244) would remain in favor of unrelated LKD. Regarding the related LKD, the following variables remain independent in the multivariate analysis: 1. having studies (odds ratio [OR] = 3.649; P = .018); 2. attitude toward cadaveric organ donation (OR = 8.547; P < .001); 3. religion (OR = 4.385; P = .001); 4. opinion of the couple (OR = 4.672; P = .028); and 5. risk with living donation (OR = 10.989; P = .003).

CONCLUSIONS

The population of Havana has a very favorable attitude toward related LKD. Only a quarter of respondents are in favor of unrelated LKD.

Are Medical Students of Non-Spanish Nationality Studying in Spain as Sensitized to Transplantation as Those of Spanish Nationality?

INTRODUCTION

Awareness of organ donation among Spanish doctors and medical students is very positive. However, the emerging group of professionals of non-Spanish nationality studying in Spain has not been analyzed.

OBJECTIVE

To analyze the differences in the attitudes toward the different types of donation among medical students, according to their nationality.

METHODS

The population under study is medical students in Spanish universities using the database of the International Collaborative Donor Project, stratified by geographic area and academic year. Groups under study include students of non-Spanish nationality as group 1 (n = 1570) and students of Spanish nationality as Group 2 (n = 7705). Instruments are validated questionnaires of attitude toward donation "PCID-DTO-Ríos," "PCID-DVR-Ríos," "PCID-DVH-Ríos," and "PCID-XenoTx-Ríos."

RESULTS

The attitude toward the donation of own organs after death is similar in both groups (P = .703). Non-Spaniards are 79.2% in favor compared to 79.6% of Spaniards. Living kidney donation, both unrelated (33.3% vs 29.3% in favor; P = .001) and related (91.2% vs 89, 6% in favor; P = .047), is more favorable among non-Spanish students. There are no differences regarding non-related living liver donation (29.7% vs 29.3% in favor; P = .063), but there are differences in the results for related living liver donation (94.1% vs 88%; P < .001). The attitude toward xenotransplantation of organs is similar (80.8% vs 80.8%; P = .999).

CONCLUSIONS

Awareness of the donation of organs among Spanish medical students is similar to non-Spanish students studying in Spain, except the attitude toward living donation.

Information About Donation and Organ Transplantation Among Spanish Medical Students

INTRODUCTION

Health professionals are asked to promote health, especially organ transplantation; however, they do not always have specific training.

OBJECTIVE

To analyze information about donation and organ transplantation among Spanish medical students.

METHOD

The population under study is medical students in Spanish universities using the database of the International Donor Collaborative Project, stratified by geographic area and academic year (n = 9275). The instrument used is the attitude questionnaire for organ donation for "PCID-DTO-Ríos" transplantation, validated with an explained variance of 63.203% and α = 0.834. The Student t test was applied together with the χ² test, complemented by an analysis of the remainders, and Fisher's exact test was applied.

RESULTS

Of the students, 74% indicate that they have received information from university professors about organ transplant. Concerning specific issues with the donation, it is notable that only 66.7% (n = 6190) know and accept the concept of brain death as the death of a person. However, only 22% consider themselves as having good information, and 35.3% indicate that their information is scarce or void. Students indicate having received information about transplant from other extra-university sources, such as television and Internet (80.9%), books and magazines (73.2%), and the press (66.9%). From the information obtained in the sociofamilial field, 60.7% have obtained information from the family and 58.1% from friends. Of this information, 9% has been negative from friends, 7.5% from family, 6% from the Internet and television, and 4% from university professors.

CONCLUSION

Spanish medical students believe they have little information about organ transplantation and have received negative information.

Genetic analyses of aplastic anemia and idiopathic pulmonary fibrosis patients with short telomeres, possible implication of DNA-repair genes

Background

Telomeres are nucleoprotein structures present at the terminal region of the chromosomes. Mutations in genes coding for proteins involved in telomere maintenance are causative of a number of disorders known as telomeropathies. The genetic origin of these diseases is heterogeneous and has not been determined for a significant proportion of patients.

Methods

This article describes the genetic characterization of a cohort of patients. Telomere length was determined by Southern blot and quantitative PCR. Nucleotide variants were analyzed either by high-resolution melting analysis and Sanger sequencing of selected exons or by massive sequencing of a panel of genes.

Results

Forty-seven patients with telomere length below the 10% of normal population, affected with three telomeropathies: dyskeratosis congenita (4), aplastic anemia (22) or pulmonary fibrosis (21) were analyzed. Eighteen of these patients presented known pathogenic or novel possibly pathogenic variants in the telomere-related genes TERT, TERC, RTEL1, CTC1 and ACD. In addition, the analyses of a panel of 188 genes related to haematological disorders indicated that a relevant proportion of the patients (up to 35%) presented rare variants in genes related to DNA repair or in genes coding for proteins involved in the resolution of complex DNA structures, that participate in telomere replication. Mutations in some of these genes are causative of several syndromes previously associated to telomere shortening.

Conclusion

Novel variants in telomere, DNA repair and replication genes are described that might indicate the contribution of variants in these genes to the development of telomeropathies. Patients carrying variants in telomere-related genes presented worse evolution after diagnosis than the rest of patients analyzed.

Electronic supplementary material

The online version of this article (10.1186/s13023-019-1046-0) contains supplementary material, which is available to authorized users.

Sensitization Toward Organ Donation Among Medical Students in Spanish Regions With More Than 50 Donors Per Million Population

The awareness of organ donation among health professionals is important at the time of transplant promotion. In this sense, the training and awareness of the professionals in training is fundamental.

OBJECTIVE

To analyze the differences in the attitude toward organ donation and the factors that condition it among medical students of regions with donation rates >50 donors per million population (pmp) with respect to those with rates <40 donor pmp.

METHOD

Population under study: medical students in Spanish universities. Database of the Collaborative International Donor Project, stratified by geographic area and academic course. The completion was anonymous and self-administered. Groups under study: Group 1 (n = 1136): students in universities of regions with >50 donors pmp. Group 2 (n = 2018): university students in regions with <40 donors pmp. Assessment instrument: attitude questionnaire for organ donation for transplant PCID-DTO-Ríos.

RESULTS

The attitude toward organ donation for transplantation is similar among students from the autonomous communities with >50 donors pmp and with <40 donors pmp. In group 1, 79% (n = 897) of students are in favor compared with 81% (n = 1625) of group 2 (P=.29). The psychosocial profile toward donation is similar in both groups relating to the following variables (P < .05): sex, having discussed transplantation with family and as a couple, considering the possibility of needing a transplant, involvement in prosocial activities, attitude toward the manipulation of corpses, knowledge of the brain death concept, and religion.

CONCLUSIONS

The awareness of organ donation in Spanish medical students is quite homogeneous and is not related to the local donation rates of each region.

Gypsy Population Presents a Favorable Attitude Toward Related Living Donation

INTRODUCTION

Negative organ donation rates among the Gypsies is much higher than that of any other social group in Spain. However, living donation rates have not been raised much in this social group, despite the existence of several Gypsy patients on the waiting list for transplantation.

OBJECTIVE

To analyze the attitude toward related living donation among the Gypsy population who reside in Spain.

METHODS

This type of study is an observational sociological study. The study consisted of the adult Gypsy population residing in Spain, and a random sampling of 230 adult gypsies was conducted. Attitude questionnaires for live donation, both hepatic PCID-DVH-Ríos and renal PCID-DVR-Ríos, were used, and random selection was based on stratification. Questionnaires were self-administered and completed anonymously. Student t test, χ2, Fisher, and a logistic regression analysis were used.

RESULTS

A sample of 206 Gypsies (52% women) with a mean age of 34 years is obtained. Seventy-two percent (n = 150) would donate an organ to a relative in life, 8% (n = 16) would not donate it, and 20% (n = 41) have doubts. Respondents with a favorable attitude toward living donation presented a more favorable attitude toward cadaveric organ donation (55% vs 0%, P < .001). The attitude toward living kidney donation was more favorable (81% in favor) than toward living liver donation (P < .001).

CONCLUSIONS

The Gypsy ethnic group is sensitized to live donor transplantation. The family and cultural roots of Gypsy people could condition this favorable attitude, a fact to be taken into account to sensitize this social group and promote donation campaigns with the aim of increasing donation rates.

GSE4 peptide suppresses oxidative and telomere deficiencies in ataxia telangiectasia patient cells

Ataxia telangiectasia (AT) is a genetic disease caused by mutations in the ATM gene but the mechanisms underlying AT are not completely understood. Key functions of the ATM protein are to sense and regulate cellular redox status and to transduce DNA double-strand break signals to downstream effectors. ATM-deficient cells show increased ROS accumulation, activation of p38 protein kinase, and increased levels of DNA damage. GSE24.2 peptide and a short derivative GSE4 peptide corresponding to an internal domain of Dyskerin have proved to induce telomerase activity, decrease oxidative stress, and protect from DNA damage in dyskeratosis congenita (DC) cells. We have found that expression of GSE24.2 and GSE4 in human AT fibroblast is able to decrease DNA damage, detected by γ-H2A.X and 53BP1 foci. However, GSE24.2/GSE4 expression does not improve double-strand break signaling and repair caused by the lack of ATM activity. In contrast, they cause a decrease in 8-oxoguanine and OGG1-derived lesions, particularly at telomeres and mitochondrial DNA, as well as in reactive oxygen species, in parallel with increased expression of SOD1. These cells also showed lower levels of IL6 and decreased p38 phosphorylation, decreased senescence and increased ability to divide for longer times. Additionally, these cells are more resistant to treatment with H₂0₂ and the radiomimetic-drug bleomycin. Finally, we found shorter telomere length (TL) in AT cells, lower levels of TERT expression, and telomerase activity that were also partially reverted by GSE4. These observations suggest that GSE4 may be considered as a new therapy for the treatment of AT that counteracts the cellular effects of high ROS levels generated in AT cells and in addition increases telomerase activity contributing to increased cell proliferation.

What Is the Attitude Toward Cadaveric Organ Donation of the Ghanian Residents in Spain?

INTRODUCTION

The Ghanaian population is migrating toward the European economic community, especially toward the southern countries.

OBJECTIVE

To analyze the attitude toward organ donation among the population born in Ghana but currently residing in Spain.

METHOD

The study included the population born in Ghana who are ≥ 15 years of age and residents of Spain, stratified by age and sex. The assessment instrument used is the donation and transplant attitude questionnaire of Proyecto Colaborativo Internacional Donante (PCID-DTO Ríos), which was self-administered and anonymously completed with verbal consent. The statistics used were descriptive, χ², Student t test, and a logistic regression analysis.

RESULTS

The questionnaire was completed by 237 Ghanaians. Forty-three percent (n = 102) are in favor of cadaveric organ donation, 35% (n = 83) are against donating their own organs, and 20% (n = 48) are undecided. In the multivariate analysis, the association was maintained at the level of the primary studies (P < .001, OR = 25), not being afraid of possible mutilation after donating (P < .001, OR = 76.923), religion (P < .001; OR = 27.777), performing prosocial activities (P = .016, OR = 12.048), and having previously commented on the issue of organ donation and transplantation in the family setting (P = .012, OR = 4.878).

CONCLUSIONS

The Ghanaian immigrant population in Spain has an unfavorable attitude toward the donation of their own organs at death, which is conditioned by multiple psychosocial factors.

Are Senegalese Immigrants Residing in Spain in Favor of Organ Donation?

The Senegalese population is an emerging group in Europe. The number of foreign residents in Spain, France, and Italy has increased significantly. However, there are no studies that analyze their awareness of organ donation and transplantation.

OBJECTIVE

To analyze the attitude toward organ donation among the population born in Senegal residing in Spain.

METHODS

The study population was born in Senegal and resides in Spain. A sample of the population older than 15 years was obtained randomly and stratified by age and sex according to census data and immigrant support associations. Attitude was assessed using a validated questionnaire on psychosocial aspects toward organ donation (PCID-DTO Rios). A random selection of people to be surveyed was carried out. Assistance from African immigration support associations in Spain was needed to advise on the location of potential respondents. The survey was self-administered and completed anonymously.

RESULTS

A sample of 295 respondents was included in the study. Attitude toward deceased donation was favorable in 37% (n = 109) of respondents; 35% (n = 104) were against and 28% (n = 82) were undecided. Several variables were associated with having a more favorable attitude (P < .05): sex, having discussed donation with the family, not being concerned about the possible mutilation of the body after donation, the respondent's religion, and knowledge of one's partner's attitude in favor of organ donation.

CONCLUSIONS

The attitude toward organ donation among the population born in Senegal and residing in Spain is unfavorable, and it is associated with psychosocial factors.

Guinean Population Emigrant to Spain Has Very Little Awareness of the Donation and Transplantation of Organs

INTRODUCTION

The Guinean population is an emerging group in Europe, but the group's awareness of organ donation and transplantation has not been studied.

OBJECTIVE

To analyze the attitude toward organ donation among the population born in Guinea living in Spain.

METHODS

The population older than 15 years, born in Guinea, and resident in Spain was studied, stratified by age and sex, according to census data and immigrant assistance associations. The valuation tool used was the attitude questionnaire toward organ donation PCID-DTO RIOS (questionnaire on "Donor International Collaborative Project" on organ donation and transplantation developed by Dr Ríos). A random selection of people to survey was based on stratification. Support from African immigration support associations was needed to advise on the location of potential respondents. The completion was anonymous and self-administered. A descriptive statistic was performed, and Student t, χ², and Fisher tests and a logistic regression analysis were applied.

RESULTS

In all, 181 Guineans were surveyed, of whom 32% (n = 58) were in favor of the donation of their own organs after death, 32% (n = 57) were against, and 36% (n = 66) were undecided. The variables that are associated with attitude toward donation are separated mainly into 4 large groups (P < .001): (1) knowledge about the process of donation and organ transplantation; (2) attitude toward the manipulation of the body; (3) religious variables; and (4) sociofamily variables, especially in relation to the couple.

CONCLUSIONS

The Guinean population emigrant to Spain has an unfriendly attitude toward organ donation.

A new diagnostic method based on RT-PCR and CLART technology for non-small cell lung cancer (NSCLC) to detect major EML4-ALK and ROS.1 translocations: CLART CMA ALK and ROS.1

e20045

Background: EML4-ALK and ROS1 translocations represent 3-6% and 1-2% of NSCLC patients, respectively. These patients would benefit for a tyrosine kinase inhibitor therapies. Currently, the gold standard for ALK and ROS.1 detection are break-apart fluorescence in situ hybridization (FISH) or inmunodetection (IHC) of the chimeric fusion proteins. FISH has both high sensitivity and specificity, although often present technical interpretation problems due to signal instability and scoring. IHC is a rapid and low cost technique; however it presents several challenges regarding sensitivity and reproducibility. CLART CMA ALK & ROS.1 kit is based RT-PCR and detection of the amplified product was carried out by a low-density microarray platform: CLART (Clinical Arrays Technology) of major fusion transcripts of EML4-ALK and ROS.1 translocations ( V1: E13;A20 , V6: E13; ins69;A20 , V2: E20;A20 , V3a: E6:A20 , V3b: E6;ins33 A20 ,V5a: E2;A20 and V5b: E2;ins117A20 for EML4-ALK and SDC4-ROS1 S2;R32/ S2;R34, CD74-ROS1 C6;R34 and SLC34A2-ROS1 S4;R32/S4;R34). Methods: The translocations analysis was performed with CLART CMA ALK & ROS.1 kit. Clinical testing was performed using the RNA extracted from 115 samples of NSCLC patients being 34 patients with translocations detected in ALK or ROS.1 genes and 81 patients without any translocations. The results were cross-checked by comparison to Next GenerationS methodology performed on the PGM platform with the Ion Ampliseq Panel Oncomide Solid Tumor Fusion and the concordance was 95.6%. Results: Analytical sensitivity was assessed using fusion transcripts cloned in recombinant plasmids. Results ranged from 10 to 100 copies/5µl of recombinant plasmids. The analysis of 115 clinical samples allowed establishing the diagnostic sensitivity and specificity in 90.9-100% and 99-100% respectively. Conclusions: CLART CMA ALK & ROS.1 emerges as a suitable alternative of FISH/IHQ for diagnosis of the most common translocations in EML4-ALK and ROS.1 genes in NSCLC samples and therefore selecting patients that would best benefit from a target therapy.

Noninvasive EGFR testing in plasma circulating free DNA (cfDNA) by a new diagnostic method to detect point mutations, deletions and insertions associated to non small cell lung cancer: CLART CMA EGFR LB

e20008

Background: Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) are current treatments for advanced non-small cell lung cancer (NSCLC) with activating EGFR gene mutations. Histological samples are the standard tumor materials for EGFR mutation analysis. However, the accessibility of tumor samples is not always possible in advanced NSCLC patients. Moreover, a high percentage of EGFR mutated NSCLC patients will develop resistance to EGFR-TKIs such as T790M mutation. CLART CMA EGFR LB is a novel diagnostic assay able to detect 39 high-prevalence mutations associated with sensitivity or resistance to tyrosine kinase inhibitor treatment. Methods: A highly sensitive and specific method was developed for detection of EGFR mutations (G719X, T790M, L858R, L861Q, insertions in exon 20, and deletions in exon 19) in plasma samples (cfDNA). CLART CMA EGFR LB is based on a preamplification step with a multiplex ARMS-PCR and microarray detection system. Clinical testing was performed using 51 clinical plasma samples: 27 contained L858R, T790M, and deletions in exon 19; 24 contained wild type alleles. 20 samples were cross checked by next generation sequencing performed on the PGM platform (Ion Ampliseq™ Custom, deep-coverage 15000x). Results: Analytical sensitivity was assessed using recombinant plasmids, results ranged between 10-1000 copies/5µl for all mutations. cfDNA from cell lines with the mutations L858R, T790M and deletions in exon 19 at different frequencies (cfDNA Reference Standard, Horizon) were assessed. The system was able to detect the mutations present in a frequency of 2%. The analysis of 51 samples allowed establishing the diagnostic sensitivity and specificity in 93.33% and 100% respectively. CLART CMA EGFR LB showed similar analytical and diagnostic sensitivity than NGS for detecting L858R, T790M and deletions in exon 19. Conclusions: Our data support the use of CLART CMA EGFR LB for clinical testing prior to the selection of the appropriate treatment in NSCLC, monitoring the patient evolution and the emergence of resistance mutations such as T790M in plasma samples.

A mutation in the POT1 gene is responsible for cardiac angiosarcoma in TP53-negative Li-Fraumeni-like families

Cardiac angiosarcoma (CAS) is a rare malignant tumour whose genetic basis is unknown. Here we show, by whole-exome sequencing of a TP53-negative Li-Fraumeni-like (LFL) family including CAS cases, that a missense variant (p.R117C) in POT1 (protection of telomeres 1) gene is responsible for CAS. The same gene alteration is found in two other LFL families with CAS, supporting the causal effect of the identified mutation. We extend the analysis to TP53-negative LFL families with no CAS and find the same mutation in a breast AS family. The mutation is recently found once in 121,324 studied alleles in ExAC server but it is not described in any other database or found in 1,520 Spanish controls. In silico structural analysis suggests how the mutation disrupts POT1 structure. Functional and in vitro studies demonstrate that carriers of the mutation show reduced telomere-bound POT1 levels, abnormally long telomeres and increased telomere fragility.

Impact of chemotherapy on telomere length in sporadic and familial breast cancer patients

Recently, we observed that telomeres of BRCA1/2 mutation carriers were shorter than those of controls or sporadic breast cancer patients, suggesting that mutations in these genes might be responsible for this event. Given the contradictory results reported in the literature, we tested whether other parameters, such as chemotherapy, could be modifying telomere length (TL). We performed a cross-sectional study measuring leukocyte TL of 266 sporadic breasts cancer patients treated with first-line chemotherapy, with a median follow-up of 240 days. Additionally, we performed both cross-sectional and longitudinal studies in a series of 236 familial breast cancer patients that included affected and non-affected BRCA1/2 mutation carriers. We have measured in leukocytes from peripheral blood: the TL, percentage of short telomeres (<3 kb), telomerase activity levels and the annual telomere shortening speed. In sporadic cases we found that chemotherapy exerts a transient telomere shortening effect (around 2 years) that varies depending on the drug combination. In familial cases, only patients receiving treatment were associated with telomere shortening but they recovered normal TL after a period of 2 years. Chemotherapy affects TL and should be considered in the studies that correlate TL with disease susceptibility.

Expression of the genetic suppressor element 24.2 (GSE24.2) decreases DNA damage and oxidative stress in X-linked dyskeratosis congenita cells

The predominant X-linked form of Dyskeratosis congenita results from mutations in DKC1, which encodes dyskerin, a protein required for ribosomal RNA modification that is also a component of the telomerase complex. We have previously found that expression of an internal fragment of dyskerin (GSE24.2) rescues telomerase activity in X-linked dyskeratosis congenita (X-DC) patient cells. Here we have found that an increased basal and induced DNA damage response occurred in X-DC cells in comparison with normal cells. DNA damage that is also localized in telomeres results in increased heterochromatin formation and senescence. Expression of a cDNA coding for GSE24.2 rescues both global and telomeric DNA damage. Furthermore, transfection of bacterial purified or a chemically synthesized GSE24.2 peptide is able to rescue basal DNA damage in X-DC cells. We have also observed an increase in oxidative stress in X-DC cells and expression of GSE24.2 was able to diminish it. Altogether our data indicated that supplying GSE24.2, either from a cDNA vector or as a peptide reduces the pathogenic effects of Dkc1 mutations and suggests a novel therapeutic approach.

p53 pathway activation by telomere attrition in X-DC primary fibroblasts occurs in the absence of ribosome biogenesis failure and as a consequence of DNA damage

BACKGROUND

Dyskeratosis congenita (DC) is a rare inherited bone marrow failure syndrome with high clinical heterogeneity. Various mutations have been reported in DC patients, affecting genes that code for components of H/ACA ribonucleoproteins, proteins of the telomerase complex and components of the shelterin complex.

OBJECTIVES

We aim to clarify the role of ribosome biogenesis failure in senescence induction in X-DC since some studies in animal models have reported a decrease in ribosome biogenesis as a major role in the disease.

METHODS

Dyskerin was depleted in normal human fibroblasts by expressing two DKC1 shRNAs. Common changes in gene expression profile between these dyskerin-depleted cells and X-DC fibroblasts were analyzed.

RESULTS

Dyskerin depletion induced early activation of the p53 pathway probably secondary to ribosome biogenesis failure. However, the p53 pathway in the fibroblasts from X-DC patients was activated only after an equivalent number of passes to AD-DC fibroblasts, in which telomere attrition in each division rendered shorter telomeres than control fibroblasts. Indeed, no induction of DNA damage was observed in dyskerin-depleted fibroblasts in contrast to X-DC or AD-DC fibroblasts suggesting that DNA damage induced by telomere attrition is responsible for p53 activation in X-DC and AD-DC fibroblasts. Moreover, p53 depletion in senescent DC fibroblasts rescued their proliferative capacity and reverted the morphological changes produced after prolonged culture.

CONCLUSIONS

Our data indicate that ribosome biogenesis do not seem to play an important role in dyskeratosis congenita, conversely increasing DNA damage and activation of p53 pathway triggered by telomere shortening is the main activator of cell senescence.

Salmeterol/Fluticasone combination inhaler: a new, effective and well tolerated treatment for asthma

OBJECTIVE

The efficacy and tolerability of a new combination inhaler containing both salmeterol 50mg and fluticasone 100mg in a single device was compared with the delivery of the two drugs via two separate inhalers in a multicentre, double-blind, double-dummy study.

PATIENTS

244 symptomatic asthma patients (age range 12 to 78 years) were randomised to a 12-week treatment period with either salmeterol/fluticasone (50/100mg twice daily) via a single inhaler (combination) and placebo twice daily via another, or salmeterol 50mg twice daily via one inhaler and fluticasone 100mg twice daily via another (concurrent).

RESULTS

Morning peak expiratory flow rate (PEFR), symptoms and tolerability were collected throughout the treatment period. Adjusted mean improvements in morning PEFR were 42 and 33 L/min for combination and concurrent therapies, respectively, over the 12-week treatment period. Adjusted mean improvements in forced expiratory volume in 1 second (FEV(1)) from baseline at week 12 were 0.20 and 0.17L for combination and concurrent therapies, respectively. 60% of patients receiving combination inhaler and 64% of those receiving concurrent therapy had a mean daytime symptom score of zero over the treatment period compared with 17 and 15%, respectively, at baseline. Both treatments were well tolerated. Geometric mean morning serum cortisol levels were similar and no differences in the frequency of abnormal results were noted between the two groups.

CONCLUSION

This was the first study reporting the control of asthma by administration of salmeterol and fluticasone in combination via a single inhaler. The new combination inhaler was as effective and well tolerated as the two drugs administered individually and has potential advantages in terms of convenience.

The response of the different soybean metallothionein isoforms to cadmium intoxication

Cadmium is a highly toxic heavy metal for both plants and animals. The presence of Cd in agricultural soils is of major concern regarding its entry into the food chain, since Cd compounds are readily taken up by plants, and accumulated in edible parts due to their high solubility. In this study, we first demonstrate the high capacity for Cd concentration of soybean grains. Consequently, we considered the study and characterization of the molecular determinants of Cd accumulation -such as metallothioneins (MT)- to be of major practical importance. We report here the first characterization of the soybean MT system, with the identification of nine genes (one of which is a truncated pseudogene), belonging to the four plant MT types. The most highly expressed of each type was chosen for further function analysis. All of them are expressed at high levels in soybean tissues: GmMT1, GmMT2 and GmMT3 in roots, shoots and seeds, and GmMT4 only in seeds. The corresponding recombinant soybean MTs, synthesized in Escherichia coli cells cultured in metal supplemented media, exhibit greater cadmium than zinc binding capacity. These results suggest a definite role of GmMTs in Cd(II) accumulation as one of the main responses of soybean to an overload of this metal.

Immune correlates of HIV control

The development of an effective HIV vaccine is still hampered by the lack of clearly defined immune correlates of HIV control. Although a number of immune markers have been associated over last years with relative viral control and slower HIV disease progression, these associations are oftentimes complicated by the causality dilemma that does not allow to directly assign cause or effect to the identified parameters. In addition, many of these immune markers may act in concert or represent surrogate makers for otherwise controlled HIV infection. This review will revisit the current knowledge of host genetic and immune markers and their associations with HIV control, particularly examining the roles of virus-specific T cells and humoral immune responses and testing their role as direct correlates of control.

Defects in mTR stability and telomerase activity produced by the Dkc1 A353V mutation in dyskeratosis congenita are rescued by a peptide from the dyskerin TruB domain

BACKGROUND

The predominant X-linked form of dyskeratosis congenita results from mutations in dyskerin, a protein required for ribosomal RNA modification that is also a component of the telomerase complex. We have previously found that expression of an internal fragment of dyskerin (GSE24.2) rescues telomerase activity in X-linked dyskeratosis congenita (X-DC) patient cells.

MATERIALS AND METHODS

Here, we have generated F9 mouse cell lines expressing the most frequent mutation found in X-DC patients, A353V and study the effect of expressing the GSE24.2 cDNA or GSE24.2 peptide on telomerase activity by TRAP assay, and mTERT and mTR expression by Q-PCR. Point mutation in GSE24.2 residues were generated by site-directed mutagenesis.

RESULTS

Expression of GSE24.2 increases mTR and to a lesser extent mTERT RNA levels, and leads to recovery of telomerase activity. Point mutations in GSE24.2 residues known to be highly conserved and crucial for the pseudouridine-synthase activity of dyskerin abolished the effect of the peptide. Recovery of telomerase activity and increase in mTERT levels were found when the GSE24.2 peptide purified from bacteria was introduced into the cells. Moreover, mTR stability was also rescued by transfection of the peptide GSE24.2.

DISCUSSION

These data indicate that supplying GSE24.2, either from a cDNA vector, or as a peptide, can reduces the pathogenic effects of Dkc1 mutations and could form the basis of a novel therapeutic approach.