The long noncoding RNA landscape of neuroendocrine prostate cancer and its clinical implications

Background

Treatment-induced neuroendocrine prostate cancer (tNEPC) is an aggressive variant of late-stage metastatic castrate-resistant prostate cancer that commonly arises through neuroendocrine transdifferentiation (NEtD). Treatment options are limited, ineffective, and, for most patients, result in death in less than a year. We previously developed a first-in-field patient-derived xenograft (PDX) model of NEtD. Longitudinal deep transcriptome profiling of this model enabled monitoring of dynamic transcriptional changes during NEtD and in the context of androgen deprivation. Long non-coding RNA (lncRNA) are implicated in cancer where they can control gene regulation. Until now, the expression of lncRNAs during NEtD and their clinical associations were unexplored.

Results

We implemented a next-generation sequence analysis pipeline that can detect transcripts at low expression levels and built a genome-wide catalogue (n = 37,749) of lncRNAs. We applied this pipeline to 927 clinical samples and our high-fidelity NEtD model LTL331 and identified 821 lncRNAs in NEPC. Among these are 122 lncRNAs that robustly distinguish NEPC from prostate adenocarcinoma (AD) patient tumours. The highest expressed lncRNAs within this signature are H19, LINC00617, and SSTR5-AS1. Another 742 are associated with the NEtD process and fall into four distinct patterns of expression (NEtD lncRNA Class I, II, III, and IV) in our PDX model and clinical samples. Each class has significant (z-scores >2) and unique enrichment for transcription factor binding site (TFBS) motifs in their sequences. Enriched TFBS include (1) TP53 and BRN1 in Class I, (2) ELF5, SPIC, and HOXD1 in Class II, (3) SPDEF in Class III, (4) HSF1 and FOXA1 in Class IV, and (5) TWIST1 when merging Class III with IV. Common TFBS in all NEtD lncRNA were also identified and include E2F, REST, PAX5, PAX9, and STAF. Interrogation of the top deregulated candidates (n = 100) in radical prostatectomy adenocarcinoma samples with long-term follow-up (median 18 years) revealed significant clinicopathological associations. Specifically, we identified 25 that are associated with rapid metastasis following androgen deprivation therapy (ADT). Two of these lncRNAs (SSTR5-AS1 and LINC00514) stratified patients undergoing ADT based on patient outcome.

Discussion

To date, a comprehensive characterization of the dynamic landscape of lncRNAs during the NEtD process has not been performed. A temporal analysis of the PDX-based NEtD model has for the first time provided this dynamic landscape. TFBS analysis identified NEPC-related TF motifs present within the NEtD lncRNA sequences, suggesting functional roles for these lncRNAs in NEPC pathogenesis. Furthermore, select NEtD lncRNAs appear to be associated with metastasis and patients receiving ADT. Treatment-related metastasis is a clinical consequence of NEPC tumours. Top candidate lncRNAs FENDRR, H19, LINC00514, LINC00617, and SSTR5-AS1 identified in this study are implicated in the development of NEPC. We present here for the first time a genome-wide catalogue of NEtD lncRNAs that characterize the transdifferentiation process and a robust NEPC lncRNA patient expression signature. To accomplish this, we carried out the largest integrative study that applied a PDX NEtD model to clinical samples. These NEtD and NEPC lncRNAs are strong candidates for clinical biomarkers and therapeutic targets and warrant further investigation.

Computational identification of micro-structural variations and their proteogenomic consequences in cancer

Motivation

Rapid advancement in high throughput genome and transcriptome sequencing (HTS) and mass spectrometry (MS) technologies has enabled the acquisition of the genomic, transcriptomic and proteomic data from the same tissue sample. We introduce a computational framework, ProTIE, to integratively analyze all three types of omics data for a complete molecular profile of a tissue sample. Our framework features MiStrVar, a novel algorithmic method to identify micro structural variants (microSVs) on genomic HTS data. Coupled with deFuse, a popular gene fusion detection method we developed earlier, MiStrVar can accurately profile structurally aberrant transcripts in tumors. Given the breakpoints obtained by MiStrVar and deFuse, our framework can then identify all relevant peptides that span the breakpoint junctions and match them with unique proteomic signatures. Observing structural aberrations in all three types of omics data validates their presence in the tumor samples.

Results

We have applied our framework to all The Cancer Genome Atlas (TCGA) breast cancer Whole Genome Sequencing (WGS) and/or RNA-Seq datasets, spanning all four major subtypes, for which proteomics data from Clinical Proteomic Tumor Analysis Consortium (CPTAC) have been released. A recent study on this dataset focusing on SNVs has reported many that lead to novel peptides. Complementing and significantly broadening this study, we detected 244 novel peptides from 432 candidate genomic or transcriptomic sequence aberrations. Many of the fusions and microSVs we discovered have not been reported in the literature. Interestingly, the vast majority of these translated aberrations, fusions in particular, were private, demonstrating the extensive inter-genomic heterogeneity present in breast cancer. Many of these aberrations also have matching out-of-frame downstream peptides, potentially indicating novel protein sequence and structure.

Availability and implementation

MiStrVar is available for download at https://bitbucket.org/compbio/mistrvar, and ProTIE is available at https://bitbucket.org/compbio/protie.

Contact

cenksahi@indiana.edu.

Supplementary information

Supplementary data are available at Bioinformatics online.

[Diagnosis and Therapeutic Interventions in Autism Spectrum Disorders in Adulthood]

Autism spectrum disorders (ASD) are characterized by disturbed social interaction and communication as well as stereotyped or repetitive behaviors and interests. Although adults with ASD often acquire complex compensatory strategies that help them master social situations in a rule-based fashion, they still show impairments in intuitive processing of social signals and especially nonverbal communication in complex everyday situations. This constitutes a particular challenge for the psychotherapy of ASD. Psychotherapists are required to explicitly inform and act as an agent of the non-autistic world to enable patients to acquire the ability to take different perspectives. The overall aim of cognitive behavioral therapy interventions addressing ASD in adulthood is to extend the patients' behavioral repertoire to improve their quality of life. Thus, besides psychoeducation on ASD and its frequently associated comorbidities, psychotherapy for adults with ASD should focus on the training and development of social-communicative skills. Furthermore, dealing with stress in everyday situations is an important aspect of psychotherapy of these patients.

Toward the development of a supported employment program for individuals with high-functioning autism in Germany

Human-human interactions are of central relevance for the success in professional and occupational environments, which also substantially influence quality of life. This is especially true in the case of individuals with high-functioning autism (HFA), who experience deficits in social cognition that often lead to social exclusion and unemployment. Despite good education and high motivation, individuals with HFA do not reach employment rates that are substantially higher than 50 %. This is an alarmingly high rate of unemployment considering that the United Nations have recently emphasized the inclusion of handicapped persons as a mandatory human right. To date, the specific needs of autistic persons with respect to their working environment are largely unexplored. It remains moreover an open question how support systems and activities, including newly developed communication devices for professional environments of individuals with HFA, should look like. The German health and social care systems are not adequately prepared for the proper support of this population. This leads us to suggest that supported employment programs should be developed for adults with HFA that specifically address their needs and requirements. Such programs should comprise (1) the adequate assessment of HFA, including a neuropsychological profile and an individual matching of persons' preferences with requirements of the working place, (2) on-the-job coaching activities that include systematic communication and interaction training, and (3) instruction of non-autistic peers, including colleagues and supervisors, about weaknesses and strengths of HFA.

[Psychosocial functioning of adults with late diagnosed autism spectrum disorders--a retrospective study]

BACKGROUND

The first time diagnosis of autism spectrum disorder (ASD) after passing childhood and adolescence is still considered a rare event. However, in recent years an increasing demand for diagnostic clarifications with suspected ASD in adulthood challenges this view. There is insufficient knowledge about the neuropsychological characterisation and psychosocial outcome of this adult subgroup in the autistic spectrum.

AIM

To determine the psychosocial functioning (living status, partnerships, level of education, psychiatric history) of adult patients with late diagnosed ASD.

METHODS

In a retrospective study, a chart review was conducted on 178 consecutively diagnosed individuals at a specialised outpatient clinic for adults with ASD. Global ratings of psychosocial functioning, assessment of psychiatric history and neuropsychological and psychopathological investigations were evaluated.

RESULTS

The majority of patients (92 %) diagnosed with ASD suffered from high-functioning autism (HFA)/Asperger syndrome (AS) according to the criteria of ICD-10 (F84.5). The gender ratio was 2:1 favouring males. Mean age at diagnosis (34.1 ± 9.5 years), general intelligence (HAWIE-R, global-IQ 115 ± 20) and self-rated autistic symptoms (autism spectrum quotient [AQ] 39 ± 6) were not discriminative to gender. The psychiatric history revealed a lifetime consultation rate of 78 %, most frequently with depression (50 %). The self-report instrument Beck depression inventory (BDI) identified 30 % of individuals presenting with depressive symptoms in clinical relevant intensity (BDI > 17). Achievement of an independent living status was reported by 68 % of individuals, 58 % reported about current or past intimate partnerships and almost two-thirds of the patients had achieved a higher educational status.

DISCUSSION

The majority of ASD diagnosed late in lifetime turned out to be HFA/AS, presenting with high psychosocial adjustment with regard to independent living, educational status and partnerships. The high level of global intelligence supports the hypothesis of cognitively compensated autistic disturbances leading to the diagnosis comparably late in lifetime. The lifetime rate of psychiatric consultations is high, reflecting the importance to consider a diagnosis of ASD even late in life.

GOAL: a software tool for assessing biological significance of genes groups

BACKGROUND

Modern high throughput experimental techniques such as DNA microarrays often result in large lists of genes. Computational biology tools such as clustering are then used to group together genes based on their similarity in expression profiles. Genes in each group are probably functionally related. The functional relevance among the genes in each group is usually characterized by utilizing available biological knowledge in public databases such as Gene Ontology (GO), KEGG pathways, association between a transcription factor (TF) and its target genes, and/or gene networks.

RESULTS

We developed

GOAL

Gene Ontology AnaLyzer, a software tool specifically designed for the functional evaluation of gene groups. GOAL implements and supports efficient and statistically rigorous functional interpretations of gene groups through its integration with available GO, TF-gene association data, and association with KEGG pathways. In order to facilitate more specific functional characterization of a gene group, we implement three GO-tree search strategies rather than one as in most existing GO analysis tools. Furthermore, GOAL offers flexibility in deployment. It can be used as a standalone tool, a plug-in to other computational biology tools, or a web server application.

CONCLUSION

We developed a functional evaluation software tool, GOAL, to perform functional characterization of a gene group. GOAL offers three GO-tree search strategies and combines its strength in function integration, portability and visualization, and its flexibility in deployment. Furthermore, GOAL can be used to evaluate and compare gene groups as the output from computational biology tools such as clustering algorithms.

The primary structure of Harpalus rufipes 5S ribosomal RNA: a contribution for understanding insect evolution

The nucleotide sequence of 5S ribosomal RNA from the beetle Harpalus rufipes was determined and compared with primary structures of other insect 5S rRNAs. Sequence differences between two beetle 5S rRNAs may represent phylogenetic markers specific for two groups of Coleoptera - Adephaga and Polyphaga. Analysis of all insect sequences using parsimony allowed us to infer a phylogenetic tree of insects, which is consistent with morphological and paleobiological data.