Germline mutations in ATM, CHEK2, and other known/potential breast cancer susceptibility genes among BRCA-negative Uruguayan patients with breast cancer

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Background: Breast cancer (BC) is the most frequent and the leading cause of death from cancer in Uruguayan women. In a previous study, we found BRCA1/2 germline mutations in less than 25% of the Uruguayan breast/ovarian cancer families studied. Due the impact and relevance of genetic testing in BC prevention and with the commitment to assure a wide accessibility, we developed genetic testing facilities at the University Hospital with the aim of analyzing and characterizing germline mutations in non BRCA known susceptibility and likely susceptibility genes. Methods: We studied 104 families who met the National Comprehensive Cancer Network (NCCN) criteria of hereditary BC. Analysis by next generation sequencing of BRCA1/2 genes revealed that 23 out of 104 cases studied (22%) carried pathogenic variants. Germline DNA from 42 cases BRCA negative was sequenced and analyzed for nine additional susceptibility genes (ATM, BARD1, CDH1, CHEK2, NBN, PALB2, PTEN, STK11 y TP53) included in a genetic panel. Also, in 24 cases negative for this panel we analyzed large deletions in BRCA1/2 by multiplex ligation-dependent probe amplification (MLPA) testing. In addition, to identify novel non-canonical causative genes, we extended our analysis to a complete exome sequencing of cases tested negative in genetic panels and MLPA analysis. Results: Among the 42 cases BRCA negative the sequencing of the extended genetic panel revealed 12 (28.8%) variants, 8 of uncertain significance (VUS) and 4 pathogenic, 2 novel (one in the ATM gene: NM_000051: c.614T > G and other in p53: NM_000546: c.245insT) and 2 previously reported (one in PALB2: NM_024675: c.2186insA and one in PALB2/1: NM_024675c.G7T genes). Regarding the VUS, it is worth highlighting the one found in exon 12 of CHEK2 (NM_007194: c.1333T > C) which was unusually frequent (16.7%) in our cohort when compared with public databases. Analysis of large deletions in BRCA1/2 in 24 cases without mutations in the genetic panel were negative for MLPA testing. Otherwise, complete exome sequencing of germline DNA from 22 cases negative for BRCA1/2 and for the genetic panel, revealed 18 variants, 16 that generate stop codons and 2 that generate loss of the termination codon (stoploss), suggesting a high potential for pathogenicity. Some striking examples are represented by the PSG2, CEP 135 y CEP 162, ZNF17 and ZNF260 genes. Conclusions: Of the 42 BRCA-negative cases, 4 (9.5%) carried a PV in a cancer susceptibility gene. The negative results obtained with MLPA in cases negative for BRCA and the extended genetic panel suggest that large deletions of BRCA are not a relevant cause of cancer susceptibility in this cohort. Otherwise, whole exome sequencing of 22 cases negatives for the previous genetic test showed pathogenic or probably PV in genes with no current evidence of association with breast and ovarian cancer.

Human endogenous retrovirus and multiple sclerosis: A review and transcriptome findings

Multiple Sclerosis is an autoimmune disease with an unknown etiology. Both genetic and environmental factors are believed to trigger MS autoimmunity. Among the environmental factors, infectious agents have been extensively investigated, and the Human Endogenous Retroviruses (HERVs), especially HERV-W, are believed to be associated with MS pathogenesis. HERVs are derived from ancestral infections and comprise around 8% of the human genome. Although most HERVs are silenced, retroviral genes may be expressed with virion formation. There is extensive evidence of the relationship between HERV-W and MS, including higher levels of HERV-W expression in MS patients, HERV-W protein detection in MS plaques, and the HERV-W env protein inducing an inflammatory response in in vitro and in vivo models. Here we discuss possible links of HERVs and the pathogenesis of MS and present new data regarding the diversity of HERVs expression in samples derived from MS patients.

Whole genome sequencing reveals a frameshift mutation and a large deletion in YY1AP1 in a girl with a panvascular artery disease

Background

Rare diseases are pathologies that affect less than 1 in 2000 people. They are difficult to diagnose due to their low frequency and their often highly heterogeneous symptoms. Rare diseases have in general a high impact on the quality of life and life expectancy of patients, which are in general children or young people. The advent of high-throughput sequencing techniques has improved diagnosis in several different areas, from pediatrics, achieving a diagnostic rate of 41% with whole genome sequencing (WGS) and 36% with whole exome sequencing, to neurology, achieving a diagnostic rate between 47 and 48.5% with WGS. This evidence has encouraged our group to pursue a molecular diagnosis using WGS for this and several other patients with rare diseases.

Results

We used whole genome sequencing to achieve a molecular diagnosis of a 7-year-old girl with a severe panvascular artery disease that remained for several years undiagnosed. We found a frameshift variant in one copy and a large deletion involving two exons in the other copy of a gene called YY1AP1. This gene is related to Grange syndrome, a recessive rare disease, whose symptoms include stenosis or occlusion of multiple arteries, congenital heart defects, brachydactyly, syndactyly, bone fragility, and learning disabilities. Bioinformatic analyses propose these mutations as the most likely cause of the disease, according to its frequency, in silico predictors, conservation analyses, and effect on the protein product. Additionally, we confirmed one mutation in each parent, supporting a compound heterozygous status in the child.

Conclusions

In general, we think that this finding can contribute to the use of whole genome sequencing as a diagnosis tool of rare diseases, and in particular, it can enhance the set of known mutations associated with different diseases.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40246-021-00328-1.

Whole transcriptome analysis of multiple Sclerosis patients reveals active inflammatory profile in relapsing patients and downregulation of neurological repair pathways in secondary progressive cases

BACKGROUND

Multiple sclerosis (MS) is an inflammatory autoimmune neurologic disease that causes progressive destruction of myelin sheath and axons. Affecting more than 2 million people worldwide, MS may presents distinct clinical courses. However, information regarding key gene expression and genic pathways related to each clinical form is still limited.

OBJECTIVE

To assess the whole transcriptome of blood leukocytes from patients with remittent-recurrent (RRMS) and secondary-progressive (SPMS) forms to explore the gene expression profile of each form.

METHODS

Total RNA was obtained and sequenced in Illumina HiSeq platform. Reads were aligned to human genome (GRCh38/hg38), BAM files were mapped and differential expression was obtained with DeSeq2. Up or downregulated pathways were obtained through Ingenuity IPA. Pro-inflammatory cytokines levels were also assessed.

RESULTS

The transcriptome was generated for nine patients (6 SPMS and 3 RRMS) and 5 healthy controls. A total of 731 and 435 differentially expressed genes were identified in SPMS and RRMS, respectively. RERE, IRS2, SIPA1L1, TANC2 and PLAGL1 were upregulated in both forms, whereas PAD2 and PAD4 were upregulated in RRMS and downregulated in SPMS. Inflammatory and neuronal repair pathways were upregulated in RRMS, which was also observed in cytokine analysis. Conversely, SPMS patients presented IL-8, IL-1, Neurothrophin and Neuregulin pathways down regulated.

CONCLUSIONS

Overall, the transcriptome of RRMS and SPMS clearly indicated distinct inflammatory profiles, where RRMS presented marked pro-inflammatory profile but SPMS did not. SPMS individuals also presented a decrease on expression of neuronal repair pathways.

Effects of PUMILIO1 and PUMILIO2 knockdown on cardiomyogenic differentiation of human embryonic stem cells culture

Posttranscriptional regulation plays a fundamental role in the biology of embryonic stem cells (ESCs). Many studies have demonstrated that multiple mRNAs are coregulated by one or more RNA-binding proteins (RBPs) that orchestrate mRNA expression. A family of RBPs, which is known as the Pumilio-FBF (PUF) family, is highly conserved among different species and has been associated with the undifferentiated and differentiated states of different cell lines. In humans, two homologs of the PUF family have been found: Pumilio 1 (PUM1) and Pumilio 2 (PUM2). To understand the role of these proteins in human ESCs (hESCs), we first assessed the influence of the silencing of PUM1 and PUM2 on pluripotency genes and found that the knockdown of Pumilio genes significantly decreased the OCT4 and NANOG mRNA levels and reduced the amount of nuclear OCT4, which suggests that Pumilio proteins play a role in the maintenance of pluripotency in hESCs. Furthermore, we observed that PUM1-and-PUM2-silenced hESCs exhibited improved efficiency of in vitro cardiomyogenic differentiation. Through an in silico analysis, we identified mRNA targets of PUM1 and PUM2 that are expressed at the early stages of cardiomyogenesis, and further investigation will determine whether these target mRNAs are active and involved in the progression of cardiomyogenesis. Our findings contribute to the understanding of the role of Pumilio proteins in hESC maintenance and differentiation.

Polysome-associated lncRNAs during cardiomyogenesis of hESCs

Long non-coding RNAs (lncRNAs) have been found to be involved in many biological processes, including the regulation of cell differentiation, but a complete characterization of lncRNA is still lacking. Additionally, there is evidence that lncRNAs interact with ribosomes, raising questions about their functions in cells. Here, we used a developmentally staged protocol to induce cardiogenic commitment of hESCs and then investigated the differential association of lncRNAs with polysomes. Our results identified lncRNAs in both the ribosome-free and polysome-bound fractions during cardiogenesis and showed a very well-defined temporal lncRNA association with polysomes. Clustering of lncRNAs was performed according to the gene expression patterns during the five timepoints analyzed. In addition, differential lncRNA recruitment to polysomes was observed when comparing the differentially expressed lncRNAs in the ribosome-free and polysome-bound fractions or when calculating the polysome-bound vs ribosome-free ratio. The association of lncRNAs with polysomes could represent an additional cytoplasmic role of lncRNAs, e.g., in translational regulation of mRNA expression.

Data describing the experimental design and quality control of RNA-Seq of human adipose-derived stem cells undergoing early adipogenesis and osteogenesis

An important tool to study the regulation of gene expression is the sequencing and the analysis of different RNA fractions: total, ribosome-free, monosomal and polysomal. By comparing these different populations, it is possible to identity which genes are differentially expressed and to get information on how transcriptional and translational regulation modulates cellular function. Therefore, we used this strategy to analyze the regulation of gene expression of human adipose-derived stem cells during the triggering of the adipogenic and osteogenic differentiation. Here, we have focused on analyzing the differential expression of mRNAs during early adipogenic and osteogenic differentiation, and presented the detailed data concerning the experimental design, the RNA-Seq quality data, the raw data obtained and the RT-qPCR validation data. This information is important to confirm the accuracy of the data considering a future reuse of the data provided. Moreover, this study may be used as groundwork for future characterization of the transcriptome and the translatome regulation of different cell types.

Cell cycle genes are downregulated after adipogenic triggering in human adipose tissue-derived stem cells by regulation of mRNA abundance

The adipogenic process is characterized by the expression of adipocyte differentiation markers that lead to changes in cell metabolism and to the accumulation of lipid droplets. Moreover, during early adipogenesis, cells undergo a strong downregulation of translational activity with a decrease in cell size, proliferation and migration. In the present study, we identified that after 24 hours of adipogenic induction, human adipose tissue-derived stem cells (hASCs) undergo a G1-cell cycle arrest consistent with reduced proliferation, and this effect was correlated with a shift in polysome profile with an enrichment of the monosomal fraction and a reduction of the polysomal fraction. Polysome profiling analysis also revealed that this change in the monosomal/polysomal ratio was related to a strong downregulation of cell cycle and proliferation genes, such as cyclins and cyclin-dependent kinases (CDKs). Comparing total and polysome-associated mRNA sequencing, we also observed that this downregulation was mostly due to a reduction of cell cycle and proliferation transcripts via control of total mRNA abundance, rather than by translational control.

Cardiomyogenic differentiation is fine-tuned by differential mRNA association with polysomes

BACKGROUND

Cardiac cell fate specification occurs through progressive steps, and its gene expression regulation features are still being defined. There has been an increasing interest in understanding the coordination between transcription and post-transcriptional regulation during the differentiation processes. Here, we took advantage of the polysome profiling technique to isolate and high-throughput sequence ribosome-free and polysome-bound RNAs during cardiomyogenesis.

RESULTS

We showed that polysome-bound RNAs exhibit the cardiomyogenic commitment gene expression and that mesoderm-to-cardiac progenitor stages are strongly regulated. Additionally, we compared ribosome-free and polysome-bound RNAs and found that the post-transcriptional regulation vastly contributes to cardiac phenotype determination, including RNA recruitment to and dissociation from ribosomes. Moreover, we found that protein synthesis is decreased in cardiomyocytes compared to human embryonic stem-cells (hESCs), possibly due to the down-regulation of translation-related genes.

CONCLUSIONS

Our data provided a powerful tool to investigate genes potentially controlled by post-transcriptional mechanisms during the cardiac differentiation of hESC. This work could prospect fundamental tools to develop new therapy and research approaches.

Predicting suicidal ideation by interpersonal variables, hopelessness and depression in real-time. An ecological momentary assessment study in psychiatric inpatients with depression

OBJECTIVE

To extend evidence on the short-term variability of passive and active suicidal ideation (SI) and the association with suggested proximal risk factors such as interpersonal variables (perceived burdensomeness [PB], thwarted belongingness [TB], hopelessness, and depression) in real-time.

METHODS

This is an observational study using a prospective design applying ecological momentary assessments (EMA). Eligible for study inclusion were inpatients with unipolar depression, current or lifetime suicidal ideation, and fluent German. Over six days, 74 participants rated their momentary level of passive and active SI, PB, TB, depressiveness, and hopelessness up to 10 times per day on smartphones. Data was collected from August 2015 to July 2017. Compliance was excellent (89.7%).

RESULTS

Mean squared successive differences supported temporal instability for all variables. According intra-class correlations, between 25% and 47% of variance was accounted for by within-person variability. Multilevel analysis demonstrated significant positive associations between hopelessness, depressiveness, PB, and TB with passive SI. Prospectively, hopelessness and PB remained predictors of passive SI. For active SI, hopelessness, depression, PB, and TB were significantly associated cross-sectionally. Prospectively, hopelessness, PB, and the interaction PBxTB predicted active SI. All models were controlled for previous level of SI.

CONCLUSIONS

This study provides further evidence on the short-term variability of SI in very short time frames implying the need of assessing SI repeatedly in clinical and research settings. The associations between interpersonal variables and passive and active SI were only partial in line with assumptions of the Interpersonal Theory of Suicide. Overall, the effects were small warranting further investigation.

Gene expression analysis of human adipose tissue-derived stem cells during the initial steps of in vitro osteogenesis

Mesenchymal stem cells (MSCs) have been widely studied with regard to their potential use in cell therapy protocols and regenerative medicine. However, a better comprehension about the factors and molecular mechanisms driving cell differentiation is now mandatory to improve our chance to manipulate MSC behavior and to benefit future applications. In this work, we aimed to study gene regulatory networks at an early step of osteogenic differentiation. Therefore, we analyzed both the total mRNA and the mRNA fraction associated with polysomes on human adipose tissue-derived stem cells (hASCs) at 24 h of osteogenesis induction. The RNA-seq results evidenced that hASC fate is not compromised with osteogenesis at this time and that 21 days of continuous cell culture stimuli are necessary for full osteogenic differentiation of hASCs. Furthermore, early stages of osteogenesis induction involved gene regulation that was linked to the management of cell behavior in culture, such as the control of cell adhesion and proliferation. In conclusion, although discrete initial gene regulation related to osteogenesis occur, the first 24 h of induction is not sufficient to trigger and drive in vitro osteogenic differentiation of hASCs.

“Mit Computern kenne ich mich eigentlich nicht aus …”

Objective: Self-report data is increasingly gathered by electronic devices. The present study aimed at testing usability and patient acceptance of two administration modes (tablet vs. paper-pencil) in primary care patients _ 60 years. Material and methods: Two depression instruments were administered using a randomized crossover design (n = 193). Results: Patients positively evaluated the usability of the tablet (clear presentation, well manageable). Additionally, the majority of patients preferred the tablet over the paper-pencil mode (more suitable, less stressful and difficult). Tablet mode and increasing age were associated with increased response time. Age, somatic morbidity and formal education showed only weak associations with usability and acceptance. Conclusion: Socio-demographic variables such as increasing age and formal education and somatic morbidity do not lead to limitations of use. Clinical relevance: The study demonstrates high usability and acceptance of depression assessment by tablets in elderly patients.

Polysome profiling shows the identity of human adipose-derived stromal/stem cells in detail and clearly distinguishes them from dermal fibroblasts

Although fibroblasts and multipotent stromal/stem cells, including adipose-derived stromal cells (ADSCs), have been extensively studied, they cannot be clearly distinguished from each other. We, therefore, investigated the cellular and molecular characteristics of ADSCs and fibroblasts. ADSCs and fibroblasts share several morphological similarities and surface markers, but were clearly found to be different types of cells. Contrary to previous reports, fibroblasts were not able to differentiate into adipocytes, osteoblasts, or chondrocytes. Polysome-bound mRNA profiling revealed that ∼ 1,547 genes were differentially expressed (DE) in the two cell types; the genes were related to cell adhesion, the extracellular matrix, differentiation, and proliferation. These findings were confirmed by functional analyses showing that ADSCs had a greater adhesion capacity than fibroblasts; the proliferation rate of fibroblasts was also higher than that of ADSCs. Importantly, 185 DE genes were integral to the plasma membrane and, thus, candidate markers for ADSC isolation and manipulation. We also observed that an established marker of fibroblasts and ADSCs, CD105, was overexpressed in ADSCs at both mRNA and protein levels. CD105 expression seemed to be related to differentiation capacity, at least for adipogenesis. This study shows that ADSCs and fibroblasts are distinct cell types. These findings should be taken into account when using these two cell types in basic and therapeutic studies.

Polysome profiling shows extensive posttranscriptional regulation during human adipocyte stem cell differentiation into adipocytes

Adipocyte stem cells (hASCs) can proliferate and self-renew and, due to their multipotent nature, they can differentiate into several tissue-specific lineages, making them ideal candidates for use in cell therapy. Most attempts to determine the mRNA profile of self-renewing or differentiating stem cells have made use of total RNA for gene expression analysis. Several lines of evidence suggest that self-renewal and differentiation are also dependent on the control of protein synthesis by posttranscriptional mechanisms. We used adipogenic differentiation as a model, to investigate the extent to which posttranscriptional regulation controlled gene expression in hASCs. We focused on the initial steps of differentiation and isolated both the total mRNA fraction and the subpopulation of mRNAs associated with translating ribosomes. We observed that adipogenesis is committed in the first days of induction and three days appears as the minimum time of induction necessary for efficient differentiation. RNA-seq analysis showed that a significant percentage of regulated mRNAs were posttranscriptionally controlled. Part of this regulation involves massive changes in transcript untranslated regions (UTR) length, with differential extension/reduction of the 3'UTR after induction. A slight correlation can be observed between the expression levels of differentially expressed genes and the 3'UTR length. When we considered association to polysomes, this correlation values increased. Changes in the half lives were related to the extension of the 3'UTR, with longer UTRs mainly stabilizing the transcripts. Thus, changes in the length of these extensions may be associated with changes in the ability to associate with polysomes or in half-life.

[Use of family resources in future need of care. Care preferences and expected willingness of providing care among relatives: a population-based study]

The family is an important resource in elderly care. It is of great interest if persons who might be in need of care in the future would use this resource. Our study assessed wishes and expectations regarding family care in a representative sample of the general population (≥ 45 years, N = 1,445) using questionnaires. Logistic regressions were performed to analyze the potential impact on the willingness to use or provide family care. One quarter of the participants reported experience in family care. In case of own need 62.9% of participants would prefer care provided by relatives and 56.7% would prefer professional care. Participants are more likely to use family care if they report having relatives, are experienced in care of relatives or do not associate old age with being a burden, e.g. report low values in the image of age "being a burden/demanding". Perceived willingness of the relatives to provide care is more likely if there is little regional distance to the relatives, in male participants and if participants talked about future care with their relatives. Besides structural factors, negative images of old age might have a negative influence on the willingness to use family care. Talking about care in old age seems to have a positive impact.

Latitudinal patterns in rodent metabolic flexibility

Macrophysiology is defined as the study of variation in physiological traits-including physiological trait flexibility-over large geographical and temporal scales, and the ecological implications of this variation. A classic example of a macrophysiological trend is the one emerging from the climatic variability hypothesis, which states that as the range of climatic fluctuation experienced by terrestrial animals increases with latitude, individuals at higher latitudes should be more plastic than individuals inhabiting lower latitudes. In this context, we evaluate the correlation between absolute metabolic scope during cold exposure (an instantaneous measure of metabolic flexibility) and different geographic and climatic variables for 48 rodent species. Conventional and phylogenetic informed analyses indicated a positive correlation between metabolic scope and geographic latitude. These findings, together with previous reports on latitudinal pattern in phenotypic flexibility, suggest that an increase in physiological flexibility with latitude may hold for many phenotypic traits.