Standardization of flow cytometry and cell sorting to enable a transcriptomic analysis in a multi-site sarcoidosis study

The contribution and regulation of various CD4+ T cell lineages that occur with remitting vs progressive courses in sarcoidosis are poorly understood. We developed a multiparameter flow cytometry panel to sort these CD4+ T cell lineages followed by measurement of their functional potential using RNA-sequencing analysis at six-month intervals across multiple study sites. To obtain good quality RNA for sequencing, we relied on chemokine receptor expression to identify and sort lineages. To minimize gene expression changes induced by perturbations of T cells and avoid protein denaturation caused by freeze/thaw cycles, we optimized our protocols using freshly isolated samples at each study site. To accomplish this study, we had to overcome significant standardization challenges across multiple sites. Here, we detail standardization considerations for cell processing, flow staining, data acquisition, sorting parameters, and RNA quality control analysis that were performed as part of the NIH-sponsored, multi-center study, BRonchoscopy at Initial sarcoidosis diagnosis Targeting longitudinal Endpoints (BRITE). After several rounds of iterative optimization, we identified the following aspects as critical for successful standardization: 1) alignment of PMT voltages across sites using CS&T/rainbow bead technology; 2) a single template created in the cytometer program that was used by all sites to gate cell populations during data acquisition and cell sorting; 3) use of standardized lyophilized flow cytometry staining cocktails to reduce technical error during processing; 4) development and implementation of a standardized Manual of Procedures. After standardization of cell sorting, we were able to determine the minimum number of sorted cells necessary for next generation sequencing through analysis of RNA quality and quantity from sorted T cell populations. Overall, we found that implementing a multi-parameter cell sorting with RNA-seq analysis clinical study across multiple study sites requires iteratively tested standardized procedures to ensure comparable and high-quality results.

Defining CD4 T helper and T regulatory cell endotypes of progressive and remitting pulmonary sarcoidosis (BRITE): protocol for a US-based, multicentre, longitudinal observational bronchoscopy study

INTRODUCTION

Sarcoidosis is a multiorgan granulomatous disorder thought to be triggered and influenced by gene-environment interactions. Sarcoidosis affects 45-300/100 000 individuals in the USA and has an increasing mortality rate. The greatest gap in knowledge about sarcoidosis pathobiology is a lack of understanding about the underlying immunological mechanisms driving progressive pulmonary disease. The objective of this study is to define the lung-specific and blood-specific longitudinal changes in the adaptive immune response and their relationship to progressive and non-progressive pulmonary outcomes in patients with recently diagnosed sarcoidosis.

METHODS AND ANALYSIS

The BRonchoscopy at Initial sarcoidosis diagnosis Targeting longitudinal Endpoints study is a US-based, NIH-sponsored longitudinal blood and bronchoscopy study. Enrolment will occur over four centres with a target sample size of 80 eligible participants within 18 months of tissue diagnosis. Participants will undergo six study visits over 18 months. In addition to serial measurement of lung function, symptom surveys and chest X-rays, participants will undergo collection of blood and two bronchoscopies with bronchoalveolar lavage separated by 6 months. Freshly processed samples will be stained and flow-sorted for isolation of CD4 +T helper (Th1, Th17.0 and Th17.1) and T regulatory cell immune populations, followed by next-generation RNA sequencing. We will construct bioinformatic tools using this gene expression to define sarcoidosis endotypes that associate with progressive and non-progressive pulmonary disease outcomes and validate the tools using an independent cohort.

ETHICS AND DISSEMINATION

The study protocol has been approved by the Institutional Review Boards at National Jewish Hospital (IRB# HS-3118), University of Iowa (IRB# 201801750), Johns Hopkins University (IRB# 00149513) and University of California, San Francisco (IRB# 17-23432). All participants will be required to provide written informed consent. Findings will be disseminated via journal publications, scientific conferences, patient advocacy group online content and social media platforms.

Comparative Profiling of the Immune System in Sarcoidosis via CITE-Seq and Flow Cytometry

CITE-Seq enables simultaneous single cell transcriptome and proteome analysis via combining single cell RNA-seq with oligo-labeled antibodies. Conventional techniques such as flow or mass cytometry have caveats including the number of epitopes accurately detected or an inability to recover samples for transcriptome analysis. These limitations are prohibitive for multivariate analysis of limited clinical samples. We developed a CITE-seq assay that enables comprehensive immune cell profiling of Sarcoidosis. Sarcoidosis is a granulomatous lung disease characterized by abnormal CD4+ T cell Th1 activity. However, the disease etiology and course are variable and the underlying molecular drivers remain unknown. The long-term goal of this study is to utilize CITE-seq to identify immune molecular pathways of Sarcoidosis pathogenesis. In our initial studies, we analyzed PBMC’s by CITE-seq vs. flow cytometry and observed similar cell profiles. However, the synergy of protein detection coupled with transcriptome analysis via CITE-seq enhanced cell subset identification vs. flow or scRNA-seq alone. We utilized CITE-seq in an ongoing longitudinal study of Sarcoidosis subjects to enhance resolution of the immune components contributing to disease. We compared CITE-seq to a flow cytometry panel analyzing the differential contributions of various CD4+ T cell lineages. The enhanced granularity provided by CITE-seq elucidated molecular pathways associated with disease pathogenesis. Thus, moving forward CITE-seq can provide the resolution and multivariate data collection required to identify the inflammatory drivers of Sarcoidosis.

Hepatitis B and C Viruses and Biologics

Hepatitis B virus (HBV) and hepatitis C virus (HCV) are common, worldwide viral illnesses that potentially impact the clinician's ability to manage patients with immunosuppressive medications such as biological therapy. In light of recent literature reviews, patients with HBV and HCV should be referred to a hepatologist or infectious disease expert prior to initiation of biological therapy.

High baseline bilirubin and low albumin predict liver decompensation and serious adverse events in HCV-infected patients treated with sofosbuvir-containing regimens

To conduct surveillance and determine the safety profile of new hepatitis C virus treatments in real-world clinical practice. Hepatic decompensation and other serious adverse events were investigated in an observational cohort study of 511 patients treated with regimens containing sofosbuvir, December 2013-June 2014. Among 499 previously stable patients (no history of hepatic decompensation during the previous 12 months), a nested case-control study was performed to identify predictors of decompensation/serious adverse event. Cases and controls were matched 1:5 based on treatment regimen and duration. Matched conditional logistic regression was used for analysis. Providers scored the likelihood that events were treatment-related (scale = 0-4). The cumulative incidence of decompensation/events was 6.4% for the total cohort. Among 499 previously stable patients, the incidence of decompensation/events was 4.5%; the mortality rate was 0.6%. Sixteen of the 499 experienced one or more serious complications considered to be at least potentially treatment-related, and the sustained virological response rate was 7/16 (44%). Two cases, both on sofosbuvir/simeprevir (without interferon or ribavirin), had complications consistent with autoimmune events (score 3, 'likely treatment-related'), and one experienced a flare of autoimmune hepatitis. Compared to controls, cases had higher baseline median model for end-stage liver disease scores (14 vs 8, P < 0.01). Decompensation/events was independently associated with lower baseline albumin (OR = 0.12/g/dL, P = 0.01) and higher total bilirubin (OR = 4.31/mg/dL, P = 0.01). Reduced hepatic function at baseline increased the risk of liver decompensation/events.

Treatment of severe recurrent hepatitis C after liver transplantation in HIV infected patients using sofosbuvir-based therapy

BACKGROUND

For liver transplant recipients with hepatitis C virus (HCV) and human immunodeficiency virus (HIV) co-infection, recurrence after LT is associated with a higher risk of graft loss than for HCV mono-infected patients. Prior HCV treatment options were limited by side effects and drug-drug interactions.

AIM

To evaluate treatment outcomes with sofosbuvir (SOF)-based therapy among HIV/HCV coinfected liver transplant recipients.

METHODS

Access to SOF and ribavirin (RBV) prior to regulatory approval was attained via an international compassionate access program for transplant recipients with a life expectancy of 1 year or less in the absence of HCV treatment. This report focuses on the short and longer term outcomes in HCV-HIV co-infected liver transplant recipients.

RESULTS

Twenty patients were treated, nine with early severe recurrence and 11 with cirrhosis. Eleven patients received SOF and RBV, one SOF, RBV and Peg-interferon, three SOF, RBV and simeprevir and five SOF, RBV and daclatasvir. Of the 18 patients who completed treatment, 16 (89%) achieved sustained virological response 12 weeks after the end of treatment (SVR12). Liver function tests (including bilirubin and albumin) improved significantly over time. Nineteen serious adverse events occurred in eight (40%) patients, none of them related to SOF. Two patients died during treatment and another, 1 year after the end of therapy, due to progressive end-stage liver disease. Importantly, HIV suppression was not compromised. No significant drug-drug interactions were reported.

CONCLUSIONS

Sofosbuvir-based regimens are safe, well-tolerated and provide high rates of SVR in HCV-HIV co-infected patients with severe recurrence after-liver transplant.

Adolescents with severe obesity: outcomes of participation in an intensive obesity management programme

BACKGROUND

Most interventions for childhood obesity are randomized controlled studies. Less is known about the effectiveness of clinical obesity programmes.

OBJECTIVE

To assess outcomes in adolescents participating in the SickKids Team Obesity Management Program (STOMP) vs. a comparison group of obese adolescents.

METHODS

Severely obese adolescents (n = 75) in STOMP (15.1 ± 1.8 years, body mass index [BMI] 44.8 ± 7.8 kg m(-2) ) were compared with adolescents (n = 41) not in the programme (14.9 ± 2.0 years, BMI 34.5 ± 8.0 kg m(-2) ). Outcomes were change in BMI, cardiometabolic, psychological and health behaviour measures.

RESULTS

At 6 months, STOMP patients' BMI was unchanged (0.08 ± 0.3; P = 0.79) and they reported improvements in quality of life and depression (-3.6 ± 1.4; P = 0.009), and increases in measures of readiness to change (RTC). Between-group differences in change between 0 and 6 months, in favour of STOMP patients, were observed for homeostatic measurement assessment-insulin resistance (HOMA-IR; -2.7 ± 1.0; P = 0.007), depression scores (-3.5 ± 1.7; P = 0.04), diet-RTC (0.6 ± 0.2; P < 0.001) and physical activity (1.7 ± 0.9; P = 0.05). At 12 months, STOMP patients increased BMI (0.8 ± 0.5; P = 0.07), but they exhibited decreased waist circumference (-7.4 ± 2.1 cm; P = 0.001) and HOMA-IR (-1.9 ± 0.6; P = 0.002). Between-group differences in change between 0 and 12 months, in favour of STOMP patients, were observed for waist circumference (-5.9 ± 2.4 cm; P = 0.01), HOMA-IR (-2.9 ± 0.7; P < 0.001) and diet-RTC (0.9 ± 0.2; P < 0.001).

CONCLUSIONS

STOMP participants did not experience a significant reduction in BMI but did have improvements in cardiometabolic, psychological and health behaviour outcomes. Evaluation of paediatric clinical obesity programmes using multiple measures is essential to understanding real-world outcomes.

Transmission of methicillin-resistant Staphylococcus aureus via deceased donor liver transplantation confirmed by whole genome sequencing

Donor-derived bacterial infection is a recognized complication of solid organ transplantation (SOT). The present report describes the clinical details and successful outcome in a liver transplant recipient despite transmission of methicillin-resistant Staphylococcus aureus (MRSA) from a deceased donor with MRSA endocarditis and bacteremia. We further describe whole genome sequencing (WGS) and complete de novo assembly of the donor and recipient MRSA isolate genomes, which confirms that both isolates are genetically 100% identical. We propose that similar application of WGS techniques to future investigations of donor bacterial transmission would strengthen the definition of proven bacterial transmission in SOT, particularly in the presence of highly clonal bacteria such as MRSA. WGS will further improve our understanding of the epidemiology of bacterial transmission in SOT and the risk of adverse patient outcomes when it occurs.

The Self-Injury Questionnaire: evaluation of the psychometric properties in a clinical population

This paper presents the findings, from a clinical study, on the reliability and validity of a new measure for intentions in self-harm behaviour, the Self-Injury Questionnaire (SIQ). Eighty-three patients, who had presented to an emergency department with an episode of self-harm/suicidal behaviour, were given the SIQ as part of a battery of measures to evaluate differentiation in self-harm intentions based upon a history of childhood physical and/or sexual abuse. The internal consistency for the total scale was strong (alpha = 0.83). Construct validity demonstrated significant correlations with standardized measures. A principle component analysis of responses yielded a five-factor solution with 'affect regulation' items loading on the first factor. Cronbach's alphas were adequate for each subscale (alpha = 0.72-0.77). These preliminary findings indicate that the SIQ is a valid and reliable measure for research in an acute self-harming population.

Processes and challenges: how the Sri Lankan health system managed the integration of leprosy services

At the end of 1999, the Ministry of Health in Sri Lanka took the bold decision to integrate its Leprosy Services within the country's general health system. The integration was completed in February 2001 and is already starting to bear fruit, but implementing the necessary changes has been a challenging task. Many new procedures had to be established, logistics improved, attitudes changed and health workers trained. A broad bridge between curative and preventative health services needed to be built. Integration efforts were supported by an advertising campaign to inform people that leprosy, like any other illness, can be treated at all health facilities. Contrary to the expectation that quality of service would drop following integration, more cases are now detected and an extensive network of government doctors is able to diagnose, treat and manage leprosy patients more efficiently. Prevalence has increased by 36% and the new case load by 41%. A few areas still need more attention, such as integrating MDT supplies within existing systems and improving the flow of information, but nonetheless the ownership of leprosy is shifting rapidly to local health services.

Surgical repair of type B aortic dissection complicated by early postoperative lung vein and artery thrombosis

A 24-year old man with Marfan syndrome previously operated for abdominal aortic aneurysm and type A dissection sustained a type B dissection. He underwent graft replacement of the descending and upper abdominal aorta, complicated by infarction of the left upper lobe and lobectomy was carried out. The postoperative course was uneventful. The mechanism for this rare complication is discussed.

Two new cases of FMR1 deletion associated with mental impairment

Screening of families clinically ascertained for the fragile X syndrome phenotype revealed two mentally impaired males who were cytogenetically negative for the fragile X chromosome. In both cases, screening for the FMR1 trinucleotide expansion mutation revealed a rearrangement within the FMR1 gene. In the first case, a 660-bp deletion is present in 40% of peripheral lymphocytes. PCR and sequence analysis revealed it to include the CpG island and the CGG trinucleotide repeat, thus removing the FMR1 promoter region and putative mRNA start site. In the second case, PCR analysis demonstrated that a deletion extended from a point proximal to FMR1 to 25 kb into the gene, removing all the region 5' to exon 11. The distal breakpoint was confirmed by Southern blot analysis and localized to a 600-bp region, and FMR1-mRNA analysis in a cell line established from this individual confirmed the lack of a transcript. These deletion patients provide further confirmatory evidence that loss of FMR1 gene expression is indeed responsible for mental retardation. Additionally, these cases highlight the need for the careful examination of the FMR1 gene, even in the absence of cytogenetic expression, particularly when several fragile X-like clinical features are present.

Pasteurella ureae meningitis and septicaemia

A 55-year-old male diabetic admitted with deafness, nystagmus, headache and vomiting was found to have meningitis due to Pasteurella ureae and responded to treatment with ampicillin. The P. ureae was unusual in showing X dependency. The family's dogs had had ear infections but no P. ureae were recovered from them when cultured three months later.