Application of annotation-agnostic RNA sequencing data analysis tools for biomarker discovery in liquid biopsy

RNA sequencing analysis is an important field in the study of extracellular vesicles (EVs), as these particles contain a variety of RNA species that may have diagnostic, prognostic and predictive value. Many of the bioinformatics tools currently used to analyze EV cargo rely on third-party annotations. Recently, analysis of unannotated expressed RNAs has become of interest, since these may provide complementary information to traditional annotated biomarkers or may help refine biological signatures used in machine learning by including unknown regions. Here we perform a comparative analysis of annotation-free and classical read-summarization tools for the analysis of RNA sequencing data generated for EVs isolated from persons with amyotrophic lateral sclerosis (ALS) and healthy donors. Differential expression analysis and digital-droplet PCR validation of unannotated RNAs also confirmed their existence and demonstrates the usefulness of including such potential biomarkers in transcriptome analysis. We show that find-then-annotate methods perform similarly to standard tools for the analysis of known features, and can also identify unannotated expressed RNAs, two of which were validated as overexpressed in ALS samples. We demonstrate that these tools can therefore be used for a stand-alone analysis or easily integrated into current workflows and may be useful for re-analysis as annotations can be integrated post hoc.

Patient Reported Outcome Measures in Adult Spinal Muscular Atrophy: A Scoping Review and Graphical Visualization of the Evidence

BACKGROUND

Spinal Muscular Atrophy (SMA) is a hereditary neuromuscular disease with an estimated prevalence of 1/10 000 births. SMA is increasingly recognized as a multi-system disease with a need to study additional under-recognized health domains such as quality of life, fatigue, bulbar function, respiratory function, and independence.

OBJECTIVE

Identify and assess reported evidence from the literature investigating Patient Reported Outcome Measures (PROMs) in adults with SMA. Develop a novel method drawing from network theory to graphically depict the literature, PROMs, and supporting psychometric evidence.

METHODS

A scoping review was completed following PRISM-ScR, COSMIN and JBI scoping review guidelines. Literature investigating PROMs in adult SMA or neuromuscular disease was identified from peer-reviewed and grey databases. A network graph was derived from extracted data.

RESULTS

5292 articles were retrieved, 81 articles met inclusion criteria; corresponding to 31 unique PROMs. Only two PROMs were developed specifically for SMA. Few PROMs covered multiple domains of health. Most PROMs were incompletely validated, focusing on concurrent validity, and few assessed responsiveness or internal consistency.

CONCLUSIONS

PROMs are emerging tools for monitoring and assessing adults with SMA. Despite their potential benefits, additional validation studies should be completed prior to their use for clinical decision-making. Network graphics may represent a technique to aid in the visualization of evidence supporting a scoping review.

An international survey of the structure and process of care for traumatic spinal cord injury in acute and rehabilitation facilities: lessons learned from a pilot study

BACKGROUND

To describe the key findings and lessons learned from an international pilot study that surveyed spinal cord injury programs in acute and rehabilitation facilities to understand the status of spinal cord injury care.

METHODS

An online survey with two questionnaires, a 74-item for acute care and a 51-item for rehabilitation, was used. A subset of survey items relevant to the themes of specialized care, timeliness, patient-centeredness, and evidence-based care were operationalized as structure or process indicators. Percentages of facilities reporting the structure or process to be present, and percentages of indicators met by each facility were calculated and reported separately for facilities from high-income countries (HIC) and from low and middle-income countries (LMIC) to identify "hard to meet" indicators defined as those met by less than two-thirds of facilities and to describe performance level.

RESULTS

A total of 26 acute and 26 rehabilitation facilities from 25 countries participated in the study. The comparison of the facilities based on the country income level revealed three general observations: 1) some indicators were met equally well by both HIC and LMIC, such as 24-hour access to CT scanners in acute care and out-patient services at rehabilitation facilities; 2) some indicators were hard to meet for LMIC but not for HIC, such as having a multidisciplinary team for both acute and rehabilitation settings; and 3) some indicators were hard to meet by both HIC and LMIC, including having peer counselling programs. Variability was also observed for the same indicator between acute and rehabilitation facilities, and a wide range in the total number of indicators met among HIC facilities (acute 59-100%; rehabilitation 36-100%) and among LMIC facilities (acute: 41-82%; rehabilitation: 36-93%) was reported.

CONCLUSIONS

Results from this international pilot study found that the participating acute and rehabilitation facilities on average adhered to 74% of the selected indicators, suggesting that the structure and processes to provide ideal traumatic spinal cord injury care were broadly available. Recruiting a representative sample of SCI facilities and incorporating regional attributes in future surveys will be helpful to examine factors affecting adherence to indicators.

Characteristics of phantom limb pain in U.S. civilians and service members

OBJECTIVES

The population of Americans with limb loss is on the rise, with a different profile than in previous generations (e.g., greater incidence of amputation due to diabetes). This study aimed to identify the key characteristics of phantom limb sensation (PLS) and pain (PLP) in a current sample of Americans with limb loss.

METHODS

This cross-sectional study is the first large-scale (n=649) study on PLP in the current population of Americans with limb loss. A convenience sample of military and civilian persons missing one or more major limbs was surveyed regarding their health history and experience with phantom limb phenomena.

RESULTS

Of the participants surveyed, 87% experienced PLS and 82% experienced PLP. PLS and PLP typically first occurred immediately after amputation (47% of cases), but for a small percentage (3-4%) onset did not occur until over a year after amputation. Recent PLP severity decreased over time (β=0.028, 95% CI: -0.05-0.11), but most participants reported PLP even 10 years after amputation. Higher levels of recent PLP were associated with telescoping (β=0.123, 95% CI: 0.04-0.21) and higher levels of pre-amputation pain (β=0.104, 95% CI: 0.03-0.18). Those with congenitally missing limbs experienced lower levels of recent PLP (t (37.93)=3.93, p<0.01) but there were no consistent differences in PLP between other amputation etiologies.

CONCLUSIONS

Phantom limb phenomena are common and enduring. Telescoping and pre-amputation pain are associated with higher PLP. Persons with congenitally missing limbs experience lower levels of PLP than those with amputation(s), yet PLP is common even in this subpopulation.

Consensus-based recommendations for titrating cannabinoids and tapering opioids for chronic pain control

AIMS

Opioid misuse and overuse have contributed to a widespread overdose crisis and many patients and physicians are considering medical cannabis to support opioid tapering and chronic pain control. Using a five-step modified Delphi process, we aimed to develop consensus-based recommendations on: 1) when and how to safely initiate and titrate cannabinoids in the presence of opioids, 2) when and how to safely taper opioids in the presence of cannabinoids and 3) how to monitor patients and evaluate outcomes when treating with opioids and cannabinoids.

RESULTS

In patients with chronic pain taking opioids not reaching treatment goals, there was consensus that cannabinoids may be considered for patients experiencing or displaying opioid-related complications, despite psychological or physical interventions. There was consensus observed to initiate with a cannabidiol (CBD)-predominant oral extract in the daytime and consider adding tetrahydrocannabinol (THC). When adding THC, start with 0.5-3 mg, and increase by 1-2 mg once or twice weekly up to 30-40 mg/day. Initiate opioid tapering when the patient reports a minor/major improvement in function, seeks less as-needed medication to control pain and/or the cannabis dose has been optimised. The opioid tapering schedule may be 5%-10% of the morphine equivalent dose (MED) every 1 to 4 weeks. Clinical success could be defined by an improvement in function/quality of life, a ≥30% reduction in pain intensity, a ≥25% reduction in opioid dose, a reduction in opioid dose to <90 mg MED and/or reduction in opioid-related adverse events.

CONCLUSIONS

This five-stage modified Delphi process led to the development of consensus-based recommendations surrounding the safe introduction and titration of cannabinoids in concert with tapering opioids.

Development of an implementation-focused network to improve healthcare delivery as informed by the experiences of the SCI knowledge mobilization network

Context: Implementing research findings into clinical practice is challenging. This manuscript outlines the experiences and key learnings from a network that operated as a community of practice across seven Canadian Spinal Cord Injury (SCI) rehabilitation centers. These learnings are being used to inform a new implementation-focused network involving SCI rehabilitation programs based in Ontario, Canada. Methods: The SCI KMN adapted and applied implementation science principles based on the National Implementation Research Network's (NIRN) Active Implementation Frameworks in the implementation of best practices in pressure injury and pain prevention and management. Results: The SCI KMN was successful in implementing best practices in both pressure ulcer and pain prevention and management across the various participating sites. Other key objectives met were building capacity in implementation methods in site personnel so that project scaling could occur with these skills and expertise applied to numerous other initiatives. Additionally, various papers, abstracts and conference presentation as well as an implementation guide were disseminated to inform the field of implementation science. Conclusion: The key lessons learned from this experience are being used to develop a new implementation-focused network. Features felt to be especially important for the SCI KMN includes a highly representative governance structure, the use of indicators within an overall evaluation framework and the systematic application of implementation processes with shared learnings supporting each site.

Conception and development of Sexual Health indicators to advance the quality of spinal cord injury rehabilitation: SCI-High Project

Context: Although spinal cord injury or disease (SCI/D) results in complex biological and psychosocial impairments that adversely impact an individual's overall quality of sexual life, sexual health is poorly integrated into the current rehabilitation processes. Therefore, it is vital to promote sexual health as a rehabilitation priority. Herein, we describe the selection of Sexual Health structure, process and outcome indicators for adults with SCI/D in the first 18 months after rehabilitation admission. Methods: Experts in sexual health and the SCI-High team identified key factors that influence the sexual health outcomes of rehabilitation interventions to inform Driver diagram development. This diagram informed the selection and development of indicators to promote a permissive environment for discussion of sexual health issues among regulated health care professionals (HCPs). A review of literature and psychometric properties of measurement tools facilitated final indicators selection. Results: The structure indicator is the proportion of rehabilitation HCPs who have completed annual preliminary sexual health training. The process indicator is the proportion of SCI/D inpatients that have a documented introduction to available local sexual health resources. The outcome indicator is a sexual health patient questionnaire used to assess sexual health patient outcomes and sexual health information/educational needs. Rapid-cycle piloting verified that the indicator tools developed are feasible for implementation. Conclusion: Successful implementation of the Sexual Health structure, process and outcome indicators will promote a permissive environment to enable open discussion, and lead to provision of equitable and optimal care related to sexual health following SCI/D. This will ultimately advance sexual health rehabilitation across the nation.

Implementation of pain best practices as part of the spinal cord injury knowledge mobilization network

Context/objective: The spinal cord injury (SCI) knowledge mobilization network (KMN) is a community of practice formed in 2011 as part of a national best practice implementation (BPI) effort to improve SCI care. This study objective was to determine whether completion and documentation of pain practices could be improved in a neurorehabilitation setting using the KMN implementation approach. Design: Single site, pre-post intervention study. Setting: Neurorehabilitation hospital. Participants: Twenty sequential consenting inpatients with SCI, with retrospective comparative analysis of 50 sequential SCI admissions pre-KMN. Interventions: A local Site Implementation Team (SIT) was formed to develop an implementation plan, including acceptable timeframes for completion and documentation of four specific pain best practices: (1) pain assessment on admission, (2) development of an Inter-Professional Pain Treatment Plan (IPTP), (3) pain monitoring throughout admission, and (4) a pain discharge plan. Outcomes: Provider adherences to pain best practices were the primary outcomes. The secondary outcome was patient satisfaction. Results: Provider adherence for most outcomes exceeded 70% completion within acceptable timeframes, with improvements found for all outcomes as compared to the retrospective cohort. Notably, pain education as part of the IPTP improved from 12% completion to 74%, documenting pain onset from 4.5% to 80% and pain discharge plan from 40% to 74%. Overall, participants were satisfied with their pain management. Conclusions: Pain best practices were more consistently documented after the KMN implementation. Pain practices in all four areas have now been expanded to all inpatient diagnoses using the same forms and framework created in the implementation process.

The Management of Incidental Prostate Cancer Following TURP

Aims The aim of this study was to assess the incidence, management and outcomes of incidentally diagnosed prostate cancer following TURP. Methods A retrospective review was performed using the histopathological departments’ database of all patients who underwent a TURP across two university teaching hospitals over a ten year period. Results During the study period, a total of 826 patients underwent a TURP. 72 (10.3%) had an incidental diagnosis of CaP following TURP. 46 (63.9%) were managed expectantly while 26 (36.1%) underwent active treatment. Overall mortality was 29.2% (n=21) while cancer specific mortality was 6.9% (n=5). All these patients were in the hormonal treatment sub-group. Conclusion Our study demonstrates an expectant approach is favourable in low risk disease. Curative treatment does need to be considered for younger patients with a long life expectancy or patients with higher risk disease.

Home mechanical ventilation: a Canadian Thoracic Society clinical practice guideline

Increasing numbers of patients are surviving episodes of prolonged mechanical ventilation or benefitting from the recent availability of userfriendly noninvasive ventilators. Although many publications pertaining to specific aspects of home mechanical ventilation (HMV) exist, very few comprehensive guidelines that bring together all of the current literature on patients at risk for or using mechanical ventilatory support are available. The Canadian Thoracic Society HMV Guideline Committee has reviewed the available English literature on topics related to HMV in adults, and completed a detailed guideline that will help standardize and improve the assessment and management of individuals requiring noninvasive or invasive HMV. The guideline provides a disease-specific review of illnesses including amyotrophic lateral sclerosis, spinal cord injury, muscular dystrophies, myotonic dystrophy, kyphoscoliosis, post-polio syndrome, central hypoventilation syndrome, obesity hypoventilation syndrome, and chronic obstructive pulmonary disease as well as important common themes such as airway clearance and the process of transition to home. The guidelines have been extensively reviewed by international experts, allied health professionals and target audiences. They will be updated on a regular basis to incorporate any new information.

Activity of patupilone for the treatment of recurrent or progressive brain metastases in patients (pts) with non-small cell lung cancer (NSCLC): An open-label, multicenter, phase II study

18058

Background: Advances in systemic chemotherapy have improved overall survival for patients with advanced NSCLC; unfortunately, CNS metastasis is common and limits survival benefits with current therapies. Unlike taxanes, preclinical findings suggest that the novel epothilone, patupilone, crosses the blood-brain barrier in 3 animal species and also has antitumor effects in brain tumor models. Results of an ongoing phase I/II study of patupilone as second-line therapy in pts with NSCLC are encouraging. The present study is evaluating the efficacy of patupilone in pts with brain metastases from NSCLC who have failed or recurred after previous chemotherapy, surgery, and/or radiation to the brain. Methods: This open-label, single-arm, multicenter, phase II study has a 2-stage design (25 pts per stage). Eligible pts have histologically confirmed NSCLC and = 1 recurrent, bidimensionally measurable intracranial lesion = 2 cm. Patupilone was administered IV at 10 mg/m2 as a single 20-min IV infusion every 3 weeks until disease progression, satisfactory response, or unacceptable toxicity. The primary multinomial endpoint was a combination of early progression (disease progression or death before cycle 1, day 21) and response rate (alive without progression at cycle 4, day 1). Results: An interim analysis of 13 pts with a median age of 62 years (range, 40–67 years) is reported. The most common adverse events (AEs) related to study drug were NCI CTC grade 1/2 diarrhea in 7 (54%) pts, nausea in 3 (23%), and fatigue in 2 (15%). Only 2 serious AEs (grade 4 colitis and grade 3 diarrhea) and 2 additional grade 3 AEs (diarrhea, neutropenia) were reported in 1 pt each. Three (23%) pts experienced early disease progression. Five (38%) pts responded, receiving a median 10 cycles (range, 5 to 12 cycles) and were alive without progression on cycle 4, day 1. Conclusions: Patupilone has activity in patients with CNS metastases from advanced NSCLC and is well tolerated. Additional investigation of patupilone as a treatment for brain metastases from NSCLC is warranted.

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