Adaptive immune responses to two-dose COVID-19 vaccine series in healthy Canadian adults ≥ 50 years: a prospective, observational cohort study.

To evaluate immune responses to COVID-19 vaccines in adults aged 50 years and older, spike protein (S)-specific antibody concentration, avidity, and function (via angiotensin-converting enzyme 2 (ACE2) inhibition surrogate neutralization and antibody dependent cellular phagocytosis (ADCP)), as well as S-specific T cells were quantified via activation induced marker (AIM) assay in response to two-dose series. Eighty-four adults were vaccinated with either: mRNA/mRNA (mRNA-1273 and/or BNT162b2); ChAdOx1-S/mRNA; or ChAdOx1-S/ChAdOx1-S. Anti-S IgG concentrations, ADCP scores and ACE2 inhibiting antibody concentrations were highest at one-month post-second dose and declined by four-months post-second dose for all groups. mRNA/mRNA and ChAdOx1-S/mRNA schedules had significantly higher antibody responses than ChAdOx1-S/ChAdOx1-S. CD8+ T-cell responses one-month post-second dose were associated with increased ACE2 surrogate neutralization. Antibody avidity (total relative avidity index) did not change between one-month and four-months post-second dose and did not significantly differ between groups by four-months post-second dose. In determining COVID-19 correlates of protection, a measure that considers both antibody concentration and avidity should be considered.

Factors associated with SARS-CoV-2 infection in unvaccinated children and young adults.

BACKGROUND AND OBJECTIVES: Pediatric COVID-19 cases are often mild or asymptomatic, which has complicated estimations of disease burden using existing testing practices. We aimed to determine the age-specific population seropositivity and risk factors of SARS-CoV-2 seropositivity among children and young adults during the pandemic in British Columbia (BC). METHODS: We conducted two cross-sectional serosurveys: phase 1 enrolled children and adults < 25 years between November 2020-May 2021 and phase 2 enrolled children < 10 years between June 2021-May 2022 in BC. Participants completed electronic surveys and self-collected finger-prick dried blood spot (DBS) samples. Samples were tested for immunoglobulin G antibodies against ancestral spike protein (S). Descriptive statistics from survey data were reported and two multivariable analyses were conducted to evaluate factors associated with seropositivity. RESULTS: A total of 2864 participants were enrolled, of which 95/2167 (4.4%) participants were S-seropositive in phase 1 across all ages, and 61/697 (8.8%) unvaccinated children aged under ten years were S-seropositive in phase 2. Overall, South Asian participants had a higher seropositivity than other ethnicities (13.5% vs. 5.2%). Of 156 seropositive participants in both phases, 120 had no prior positive SARS-CoV-2 test. Young infants and young adults had the highest reported seropositivity rates (7.0% and 7.2% respectively vs. 3.0-5.6% across other age groups). CONCLUSIONS: SARS-CoV-2 seropositivity among unvaccinated children and young adults was low in May 2022, and South Asians were disproportionately infected. This work demonstrates the need for improved diagnostics and reporting strategies that account for age-specific differences in pandemic dynamics and acceptability of testing mechanisms.

The success of publicly funded rotavirus vaccine programs for preventing community- and hospital-acquired rotavirus infections in Canadian pediatric hospitals: an observational study.

BACKGROUND: Canadian immunization programs for rotavirus started in 2011. We sought to determine their effect on the burden of community-acquired admissions and hospital-acquired rotavirus at pediatric hospitals. METHODS: The Canadian Immunization Monitoring Program Active (IMPACT) network conducted active surveillance for rotavirus-positive hospital admissions between 2005 and 2020 at 12 pediatric hospitals. We used yearly rates of community-acquired rotavirus per 10 000 admissions and hospital-acquired rotavirus infections per 1000 patient-days to determine changes in the pre- and post-vaccine program periods. RESULTS: During the 15-year study period, 5691 rotavirus hospital admissions and hospital-acquired infections were detected, including 4323 (76%) community-acquired infections and 1368 (24%) hospital-acquired infections. The average community-acquired rate in the pre-vaccine period was 60.3 (95% confidence interval [CI] 53.7-68.3) per 10 000 admissions, with a decline to 11.0 (95% CI 7.5-15.1) per 10 000 admissions in the post-vaccine period, resulting in an average reduction of 81.7% (95% CI 74.4%-87.8%). The rate of hospital-acquired rotavirus declined from 0.35 (95% CI 0.29-0.41) per 1000 patient-days in the pre-vaccine period to 0.05 (95% CI 0.03-0.07) per 1000 patient-days in the post-vaccine period, resulting in an 85.3% (95% CI 77.7%-91.9%) average decline. Herd protection was present among children aged 2-16 years. INTERPRETATION: Although start dates of rotavirus vaccine programs across provinces varied, there was around an 80% average decrease in both community-acquired and hospital-acquired rotavirus infections at pediatric hospitals in Canada in the 1- to 9-year interval after implementation of rotavirus vaccine programs. Herd protection is an important aspect of rotavirus vaccines for other children who are not vaccine eligible, and rotavirus vaccines continue to provide important benefits both for children and health care systems.

Adverse Events Following Immunization With mRNA and Viral Vector Vaccines in Individuals With Previous Severe Acute Respiratory Syndrome Coronavirus 2 Infection From the Canadian National Vaccine Safety Network.

BACKGROUND: Adults previously infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) develop short-term immunity and may have increased reactogenicity to coronavirus disease 2019 (COVID-19) vaccines. This prospective, multicenter, active-surveillance cohort study examined the short-term safety of COVID-19 vaccines in adults with a prior history of SARS-CoV-2. METHODS: Canadian adults vaccinated between 22 December 2020 and 27 November 2021 were sent an electronic questionnaire 7 days post-dose 1, dose 2, and dose 3 vaccination. The main outcome was health events occurring in the first 7 days after each vaccination that prevented daily activities, resulted in work absenteeism, or required a medical consultation, including hospitalization. RESULTS: Among 684 998 vaccinated individuals, 2.6% (18 127/684 998) reported a prior history of SARS-CoV-2 infection a median of 4 (interquartile range: 2-6) months previously. After dose 1, individuals with moderate (bedridden) to severe (hospitalized) COVID-19 who received BNT162b2, mRNA-1273, or ChAdox1-S vaccines had higher odds of a health event preventing daily activities, resulting in work absenteeism or requiring medical consultation (adjusted odds ratio [95% confidence interval]: 3.96 [3.67-4.28] for BNT162b2, 5.01 [4.57-5.50] for mRNA-1273, and 1.84 [1.54-2.20] for ChAdox1-S compared with no infection). Following dose 2 and 3, the greater risk associated with previous infection was also present but was attenuated compared with dose 1. For all doses, the association was lower or absent after mild or asymptomatic infection. CONCLUSIONS: Adults with moderate or severe previous SARS-CoV-2 infection were more likely to have a health event sufficient to impact routine activities or require medical assessment in the week following each vaccine dose.

Safety of COVID-19 vaccines in pregnancy: a Canadian National Vaccine Safety (CANVAS) network cohort study.

BACKGROUND: Pregnant individuals have been receiving COVID-19 vaccines following pre-authorisation clinical trials in non-pregnant people. This study aimed to determine the frequency and nature of significant health events among pregnant females after COVID-19 vaccination, compared with unvaccinated pregnant controls and vaccinated non-pregnant individuals. METHODS: We did an observational cohort study, set in seven Canadian provinces and territories including Ontario, Quebec, British Columbia, Alberta, Nova Scotia, Yukon, and Prince Edward Island. Eligibility criteria for vaccinated individuals were a first dose of a COVID-19 vaccine within the previous 7 days; an active email address and telephone number; ability to communicate in English or French; and residence in the aforementioned provinces or territories. Study participants were pregnant and non-pregnant females aged 15-49 years. Individuals were able to participate as controls if they were unvaccinated and fulfilled the other criteria. Data were collected primarily by self-reported survey after both vaccine doses, with telephone follow-up for those reporting any medically attended event. Participants reported significant health events (new or worsening of a health event sufficient to cause work or school absenteeism, medical consultation, or prevent daily activities) occurring within 7 days of vaccination or within the past 7 days for unvaccinated individuals. We employed multivariable logistic regression to examine significant health events associated with mRNA vaccines, adjusting for age group, previous SARS-CoV-2 infection, and trimester, as appropriate. FINDINGS: As of Nov 4, 2021, 191 360 women aged 15-49 years with known pregnancy status had completed the first vaccine dose survey and 94 937 had completed the second dose survey. 180 388 received one dose and 94 262 received a second dose of an mRNA vaccine, with 5597 pregnant participants receiving dose one and 3108 receiving dose two, and 174 765 non-pregnant participants receiving dose one and 91 131 receiving dose two. Of 6179 included unvaccinated control participants, 339 were pregnant and 5840 were not pregnant. Overall, 226 (4·0%) of 5597 vaccinated pregnant females reported a significant health event after dose one of an mRNA vaccine, and 227 (7·3%) of 3108 after dose two, compared with 11 (3·2%) of 339 pregnant unvaccinated females. Pregnant vaccinated females had an increased odds of a significant health event within 7 days of the vaccine after dose two of mRNA-1273 (adjusted odds ratio [aOR] 4·4 [95% CI 2·4-8·3]) compared with pregnant unvaccinated controls within the past 7 days, but not after dose one of mRNA-1273 or any dose of BNT162b2. Pregnant vaccinated females had decreased odds of a significant health event compared with non-pregnant vaccinated females after both dose one (aOR 0·63 [95% CI 0·55-0·72]) and dose two (aOR 0·62 [0·54-0·71]) of any mRNA vaccination. There were no significant differences in any analyses when restricted to events which led to medical attention. INTERPRETATION: COVID-19 mRNA vaccines have a good safety profile in pregnancy. These data can be used to appropriately inform pregnant people regarding reactogenicity of COVID-19 vaccines during pregnancy, and should be considered alongside effectiveness and immunogenicity data to make appropriate recommendations about best use of COVID-19 vaccines in pregnancy. FUNDING: Canadian Institutes of Health Research, Public Health Agency of Canada.

Child transmission of SARS-CoV-2: a systematic review and meta-analysis.

BACKGROUND: Understanding of the role of children in COVID-19 transmission has significant implications for school and childcare policies, as well as appropriate targeting of vaccine campaigns. The objective of this systematic review was to identify the role of children in SARS-CoV-2 transmission to other children and adults. METHODS: MEDLINE, EMBASE, CINAHL, Cochrane Central Register of Controlled Trials, and Web of Science were electronically searched for articles published before March 31, 2021. Studies of child-to-child and child-to-adult transmission and quantified the incidence of index and resulting secondary attack rates of children and adults in schools, households, and other congregate pediatric settings were identified. All articles describing confirmed transmission of SARS-CoV-2 from a child were included. PRISMA guidelines for data abstraction were followed, with each step conducted by two reviewers. RESULTS: 40 of 6110 articles identified met inclusion criteria. Overall, there were 0.8 secondary cases per primary index case, with a secondary attack rate of 8.4% among known contacts. The secondary attack rate was 26.4% among adult contacts versus 5.7% amongst child contacts. The pooled estimate of a contact of a pediatric index case being infected as secondary case was 0.10 (95% CI 0.03-0.25). CONCLUSIONS: Children transmit COVID-19 at a lower rate to children than to adults. Household adults are at highest risk of transmission from an infected child, more so than adults or children in other settings.

Risk of active tuberculosis in migrants diagnosed with cancer: a retrospective cohort study in British Columbia, Canada.

OBJECTIVES: To describe the association between types of cancer and active tuberculosis (TB) risk in migrants. Additionally, in order to better inform latent TB infection (LTBI) screening protocols, we assessed proportion of active TB cases potentially preventable through LTBI screening and treatment in migrants with cancer. DESIGN: Population-based, retrospective cohort study. SETTING: British Columbia (BC), Canada. PARTICIPANTS: 1 000 764 individuals who immigrated to Canada from 1985 to 2012 and established residency in BC at any point up to 2015. PRIMARY AND SECONDARY OUTCOME MEASURES: Using linked health administrative databases and disease registries, data on demographics, comorbidities, cancer type, TB exposure and active TB diagnosis were extracted. Primary outcomes included: time to first active TB diagnoses, and risks of active TB following cancer diagnoses which were estimated using Cox extended hazard regression models. Potentially preventable TB was defined as active TB diagnosed >6 months postcancer diagnoses. RESULTS: Active TB risk was increased in migrants with cancer ((HR (95% CI)) 2.5 (2.0 to 3.1)), after adjustment for age, sex, TB incidence in country of origin, immigration classification, contact status and comorbidities. Highest risk was observed with lung cancer (HR 11.2 (7.4 to 16.9)) and sarcoma (HR 8.1 (3.3 to 19.5)), followed by leukaemia (HR 5.6 (3.1 to 10.2)), lymphoma (HR 4.9 (2.7 to 8.7)) and gastrointestinal cancers (HR 2.7 (1.7 to 4.4)). The majority (65.9%) of active TB cases were diagnosed >6 months postcancer diagnosis. CONCLUSION: Specific cancers increase active TB risk to varying degrees in the migrant population of BC, with approximately two-thirds of active TB cases identified as potentially preventable.

Non-medical prescription opioid use and in-hospital illicit drug use among people who use drugs.

INTRODUCTION: Illicit drug use while admitted to hospital is common amongst people who use drugs. Furthermore, non-medical prescription opioid use (NMPOU) is increasingly being used by this population. This study was undertaken to investigate the relationship between NMPOU and having ever reported using illicit drugs in the hospital. METHODS: This study was a cross-sectional study design based on data derived from participants enrolled in three Canadian prospective cohort studies between December 2011 and November 2016. Using bivariable and multivariable logistic regression analyses, we examined the relationship between NMPOU and having ever reported illicit drug use in the hospital. RESULTS: Among the 1865 participants (951 male, 471 female) enrolled in the studies, 1422 (76.25%) met the inclusion criteria of having ever been hospitalised. Of these, 436 (30.7%) had used illicit drugs while in the hospital. In multivariable analyses, after adjusting for various confounders, we found a positive relationship between the percentage of reporting at least daily NMPOU in the past 6 months during the cohort study period and illicit drug use in the hospital (adjusted odds ratio 3.42; 95% confidence interval 1.46-8.02). DISCUSSION AND CONCLUSIONS: Among our sample, more persistent NMPOU was positively associated with having reported in-hospital illicit drug use. Our findings point to the need for better identification and management of opioid use disorder in acute care settings to reduce in-hospital illicit drug use, and to offer evidence-based medical treatments to achieve the most optimal outcomes for patients.

How Well Does TSTin3D Predict Risk of Active Tuberculosis in the Canadian Immigrant Population? An External Validation Study.

BACKGROUND: The online Tuberculin Skin Test/Interferon Gamma Release Assay (TST/IGRA) Interpreter V3.0 (TSTin3D), a tool for estimating the risk of active tuberculosis (TB) in individuals with latent TB infection (LTBI), has been in use for more than a decade, but its predictive performance has never been evaluated. METHODS: People with a positive TST or IGRA result from 1985 to 2015 were identified using a health data linkage that involved migrants to British Columbia, Canada. Comorbid conditions at the time of LTBI testing were identified from physician claims, hospitalizations, vital statistics, outpatient prescriptions, and kidney and HIV databases. The risk of developing active TB within 2 and 5 years was estimated using TSTin3D. The discrimination and calibration of these estimates were evaluated. RESULTS: A total of 37 163 individuals met study inclusion criteria; 10.4% were tested by IGRA. Generally, the TSTin3D algorithm assigned higher risks to demographic and clinical groups known to have higher active TB risks. Concordance estimates ranged from 0.66 to 0.68 in 2- and 5-year time frames. Comparing predicted to observed counts suggests that TSTin3D overestimates active TB risks and that overestimation increases over time (with relative bias of 3% and 12% in 2- and 5-year periods, respectively). Calibration plots also suggest that overestimation increases toward the upper end of the risk spectrum. CONCLUSIONS: TSTin3D can discriminate adequately between people who developed and did not develop active TB in this linked database of migrants with predominately positive skin tests. Further work is needed to improve TSTin3D's calibration.

The Impact of Childhood Emotional Abuse on Pain Interference Among People with Chronic Pain who Inject Drugs in Vancouver, Canada.

OBJECTIVE: High levels of chronic pain interference with daily activities are known to negatively impact quality of life. Although mental health conditions have been associated with pain interference and child abuse, research has been mixed regarding it acting as a mediator, with even less known among people who inject drugs. Therefore, we sought to explore childhood emotional abuse and pain interference among this population. METHODS: Data were derived from two prospective cohort studies of community-recruited people who inject drugs in Vancouver, Canada, between June 2014 and November 2016. We employed multivariable generalized estimating equations to examine the relationship between childhood emotional abuse and pain interference in the past six months. We also conducted a mediation analysis to examine whether mental health disorder diagnoses mediated this association. RESULTS: Among 822 eligible participants, 341 (41.5%) reported childhood emotional abuse. In a multivariable analysis, experiencing childhood emotional abuse remained independently associated with pain interference (adjusted odds ratio = 1.33, 95% confidence interval [CI] = 1.05-1.70) after adjusting for a range of confounders. Results from the mediation analysis yielded a statistically significant positive average causal mediation effect (ß = 0.01, 95% CI = 0.001-0.02). Approximately 12% of the effect was due to mediation. CONCLUSIONS: Our results demonstrate among people who inject drugs with chronic pain, those who experienced childhood emotional abuse were more likely to report pain interference, which was partially mediated by mental health disorder diagnosis history. These findings highlight the importance of incorporating screening and appropriate treatment for mental illness into chronic pain treatment.

TMEM30A loss-of-function mutations drive lymphomagenesis and confer therapeutically exploitable vulnerability in B-cell lymphoma.

Transmembrane protein 30A (TMEM30A) maintains the asymmetric distribution of phosphatidylserine, an integral component of the cell membrane and 'eat-me' signal recognized by macrophages. Integrative genomic and transcriptomic analysis of diffuse large B-cell lymphoma (DLBCL) from the British Columbia population-based registry uncovered recurrent biallelic TMEM30A loss-of-function mutations, which were associated with a favorable outcome and uniquely observed in DLBCL. Using TMEM30A-knockout systems, increased accumulation of chemotherapy drugs was observed in TMEM30A-knockout cell lines and TMEM30A-mutated primary cells, explaining the improved treatment outcome. Furthermore, we found increased tumor-associated macrophages and an enhanced effect of anti-CD47 blockade limiting tumor growth in TMEM30A-knockout models. By contrast, we show that TMEM30A loss-of-function increases B-cell signaling following antigen stimulation-a mechanism conferring selective advantage during B-cell lymphoma development. Our data highlight a multifaceted role for TMEM30A in B-cell lymphomagenesis, and characterize intrinsic and extrinsic vulnerabilities of cancer cells that can be therapeutically exploited.

Initiation into heroin use among street-involved youth in a Canadian setting: A longitudinal cohort study.

BACKGROUND: Emerging evidence suggests that non-medical prescription opioid (NMPO) use may be a risk factor for initiating heroin use; however, pathways from PO to heroin use among youth remain underexplored. We sought to examine the association between NMPO use and heroin initiation. METHODS: Between September 2005 and June 2017 data were derived from an open prospective cohort of street-involved youth aged 14-28 who use illegal drugs in Vancouver, Canada. The study included 526 youth who had never used non-injection heroin, and 652 youth who had never used injection heroin at baseline. We used Cox proportional hazards regressions to examine the association between NMPO use - in addition to other substance use patterns - and subsequent initiation into non-injection and injection heroin use. RESULTS: Among those who had never used non-injection heroin at baseline, 133 (25.3%) initiated non-injection heroin use during the study period. Among those who had never injected heroin at baseline, 137 (21.0%) initiated heroin injection during the study period. In multivariable analyses, NMPO use, crack use, and crystal methamphetamine use predicted non-injection heroin initiation (all p < 0.05). In separate multivariable analyses, non-injection heroin and crystal methamphetamine predicted heroin injection initiation (all p < 0.05). CONCLUSIONS: Among street-involved youth in this setting, NMPO use predicted initiation into non-injection heroin use but not initiation into heroin injection. Interestingly, crack cocaine and crystal methamphetamine use were stronger predictors of heroin initiation than NMPO use was, suggesting that stimulant use may carry greater risks for heroin initiation than NMPO use.

Characterising the association between positive hepatitis C virus antibody and pain among people who inject drugs.

INTRODUCTION AND AIMS: People who inject drugs (PWID) are a key group within the hepatitis C virus (HCV) pandemic. Chronic pain is a common condition among PWID as these individuals are often exposed to soft tissue infections due to injections and violence. This study aims to characterise the relationship between HCV exposure and pain among PWID. DESIGN AND METHODS: Data were derived from three prospective cohorts of PWID in Vancouver, Canada, between December 2011 and November 2016. The primary outcome was pain severity, which was defined based on the Euroqol EQ-5D-3L pain subscale. A bivariable and multivariable ordinal generalised estimating equations model was used to quantify the association between HCV exposure and pain among participants. RESULTS: One thousand and twelve of 2038 participants (50%) reported moderate/extreme pain at baseline. In total, 1473 (72%) participants were HCV-antibody positive. In unadjusted analyses, HCV exposure was positively associated with increased pain [odds ratio (OR) = 1.47; 95% confidence interval (CI): 1.20-1.81]. However, once adjusted for known confounders in multivariable analyses, HCV exposure did not remain significantly associated with increased pain (adjusted OR = 1.00; 95%CI: 0.78-1.28). DISCUSSION AND CONCLUSIONS: In this sample of PWID, HCV exposure was not significantly associated with pain once other factors were considered. These various factors may explain the elevated risk of pain among PWID and should be addressed in future initiatives when managing pain among PWID with HCV exposure. Future studies should also examine whether pain changes with changes in HCV status (i.e. active vs. cleared infection).

Characterizing Men Who Have Sex with Men and Use Injection Drugs in Vancouver, Canada.

We examined factors associated with reporting sex with men among men who inject drugs in Vancouver, Canada. Data were drawn from three open prospective cohorts of people who use drugs between 2005 and 2014. Generalized estimating equations were used to identify factors associated with reporting non-transactional sex with men (MSM) in the previous 6 months. Of 1663 men who used injection drugs, 225 (13.5%) were MSM over the study period. Sex with men was independently associated with younger age [Adjusted Odds Ratio (AOR) = 0.96], childhood sexual abuse (AOR = 2.65), sex work (AOR = 3.33), crystal methamphetamine use (AOR = 1.30), borrowing used syringes (AOR = 1.39), inconsistent condom use (AOR = 1.76), and HIV seropositivity (AOR = 3.82). MSM were less likely to be Hepatitis C-positive (AOR = 0.43) and to have accessed addiction treatment in the previous 6 months (AOR = 0.83) (all p < 0.05). Findings highlight vulnerabilities and resiliencies among MSM-PWID and indicate a need for trauma-informed and affirming harm reduction and substance use treatment services for MSM-PWID.

The relationship between childhood emotional abuse and chronic pain among people who inject drugs in Vancouver, Canada.

BACKGROUND: People who inject drugs (PWID) often contend with chronic pain as a result of illness and trauma, and such pain is known to have significant impacts on mental health, quality of life, and substance use behaviours. Although PWID are also known to have high rates of childhood trauma, little is known about how childhood emotional abuse may be associated with chronic pain in this population. OBJECTIVE: We undertook this study to explore emotional abuse and chronic pain among PWID. PARTICIPANTS AND SETTING: This study comprised a total of 1459 participants in Vancouver, Canada between June 2014 and November 2016. METHODS: We employed multivariable generalized estimating equations with data derived from two prospective cohort studies of community-recruited PWID to examine the relationship between childhood emotional abuse and chronic pain in the past six months. RESULTS: Among eligible participants, 591 (40.5%) reported childhood emotional abuse, and 760 (52.1%) reported chronic pain in the previous six months. In a multivariable analysis, experiencing childhood emotional abuse remained independently associated with chronic pain (adjusted odds ratio: 1.25; 95% confidence interval: 1.01-1.53) after adjustment for a range of socio-demographic and drug use confounders. CONCLUSIONS: Our findings suggest that childhood emotional abuse may have lasting relationships with chronic pain among PWID, potentially through established physiological and psychological mechanisms. Current chronic pain treatment may benefit from the evaluation of life course vulnerabilities that may be amenable to earlier interventions. Further, increased availability of effective trauma-informed chronic pain treatment is needed among this vulnerable population.

High-intensity cannabis use is associated with retention in opioid agonist treatment: a longitudinal analysis.

BACKGROUND AND AIMS: Cannabis use is common among people on opioid agonist treatment (OAT), causing concern for some care providers. However, there is limited and conflicting evidence on the impact of cannabis use on OAT outcomes. Given the critical role of retention in OAT in reducing opioid-related morbidity and mortality, we aimed to estimate the association of at least daily cannabis use on the likelihood of retention in treatment among people initiating OAT. As a secondary aim we tested the impacts of less frequent cannabis use. DESIGN: Data were drawn from two community-recruited prospective cohorts of people who use illicit drugs (PWUD). Participants were followed for a median of 81 months (interquartile range = 37-130). SETTING: Vancouver, Canada. PARTICIPANTS: This study comprised a total of 820 PWUD (57.8% men, 59.4% of Caucasian ethnicity, 32.2% HIV-positive) initiating OAT between December 1996 and May 2016. The proportion of women was higher among HIV-negative participants, with no other significant differences. MEASUREMENTS: The primary outcome was retention in OAT, defined as remaining in OAT (methadone or buprenorphine/naloxone-based) for two consecutive 6-month follow-up periods. The primary explanatory variable was cannabis use (at least daily versus less than daily) during the same 6-month period. Confounders assessed included: socio-demographic characteristics, substance use patterns and social-structural exposures. FINDINGS: In adjusted analysis, at least daily cannabis use was positively associated with retention in OAT [adjusted odds ratio (aOR) = 1.21, 95% confidence interval (CI) = 1.04-1.41]. Our secondary analysis showed that compared with non-cannabis users, at least daily users had increased odds of retention in OAT (aOR = 1.20, 95% CI = 1.02-1.43), but not less than daily users (aOR = 1.00, 95% CI = 0.87-1.14). CONCLUSIONS: Among people who use illicit drugs initiating opioid agonist treatment in Vancouver, at least daily cannabis use was associated with approximately 21% greater odds of retention in treatment compared with less than daily consumption.

Transcriptome-wide Interrogation of the Functional Intronome by Spliceosome Profiling.

Full understanding of eukaryotic transcriptomes and how they respond to different conditions requires deep knowledge of all sites of intron excision. Although RNA sequencing (RNA-seq) provides much of this information, the low abundance of many spliced transcripts (often due to their rapid cytoplasmic decay) limits the ability of RNA-seq alone to reveal the full repertoire of spliced species. Here, we present "spliceosome profiling," a strategy based on deep sequencing of RNAs co-purifying with late-stage spliceosomes. Spliceosome profiling allows for unambiguous mapping of intron ends to single-nucleotide resolution and branchpoint identification at unprecedented depths. Our data reveal hundreds of new introns in S. pombe and numerous others that were previously misannotated. By providing a means to directly interrogate sites of spliceosome assembly and catalysis genome-wide, spliceosome profiling promises to transform our understanding of RNA processing in the nucleus, much as ribosome profiling has transformed our understanding mRNA translation in the cytoplasm.

Assessment of Capture and Amplicon-Based Approaches for the Development of a Targeted Next-Generation Sequencing Pipeline to Personalize Lymphoma Management.

Targeted next-generation sequencing panels are increasingly used to assess the value of gene mutations for clinical diagnostic purposes. For assay development, amplicon-based methods have been preferentially used on the basis of short preparation time and small DNA input amounts. However, capture sequencing has emerged as an alternative approach because of high testing accuracy. We compared capture hybridization and amplicon sequencing approaches using fresh-frozen and formalin-fixed, paraffin-embedded tumor samples from eight lymphoma patients. Next, we developed a targeted sequencing pipeline using a 32-gene panel for accurate detection of actionable mutations in formalin-fixed, paraffin-embedded tumor samples of the most common lymphocytic malignancies: chronic lymphocytic leukemia, diffuse large B-cell lymphoma, and follicular lymphoma. We show that hybrid capture is superior to amplicon sequencing by providing deep more uniform coverage and yielding higher sensitivity for variant calling. Sanger sequencing of 588 variants identified specificity limits of thresholds for mutation calling, and orthogonal validation on 66 cases indicated 93% concordance with whole-genome sequencing. The developed pipeline and assay identified at least one actionable mutation in 91% of tumors from 219 lymphoma patients and revealed subtype-specific mutation patterns and frequencies consistent with the literature. This pipeline is an accurate and sensitive method for identifying actionable gene mutations in routinely acquired biopsy materials, suggesting further assessment of capture-based assays in the context of personalized lymphoma management.

Somatic IL4R mutations in primary mediastinal large B-cell lymphoma lead to constitutive JAK-STAT signaling activation.

Primary mediastinal large B-cell lymphoma (PMBCL) is a distinct subtype of diffuse large B-cell lymphoma thought to arise from thymic medullary B cells. Gene mutations underlying the molecular pathogenesis of the disease are incompletely characterized. Here, we describe novel somatic IL4R mutations in 15 of 62 primary cases of PMBCL (24.2%) and in all PMBCL-derived cell lines tested. The majority of mutations (11/21; 52%) were hotspot single nucleotide variants in exon 8, leading to an I242N amino acid change in the transmembrane domain. Functional analyses establish this mutation as gain of function leading to constitutive activation of the JAK-STAT pathway and upregulation of downstream cytokine expression profiles and B cell-specific antigens. Moreover, expression of I242N mutant IL4R in a mouse xenotransplantation model conferred growth advantage in vivo. The pattern of concurrent mutations within the JAK-STAT signaling pathway suggests additive/synergistic effects of these gene mutations contributing to lymphomagenesis. Our data establish IL4R mutations as novel driver alterations and provide a strong preclinical rationale for therapeutic targeting of JAK-STAT signaling in PMBCL.