scHLAcount: allele-specific HLA expression from single-cell gene expression data

Summary

Bulk RNA sequencing studies have demonstrated that human leukocyte antigen (HLA) genes may be expressed in a cell type-specific and allele-specific fashion. Single-cell gene expression assays have the potential to further resolve these expression patterns, but currently available methods do not perform allele-specific quantification at the molecule level. Here, we present scHLAcount, a post-processing workflow for single-cell RNA-seq data that computes allele-specific molecule counts of the HLA genes based on a personalized reference constructed from the sample’s HLA genotypes.

Availability and implementation

scHLAcount is available under the MIT license at https://github.com/10XGenomics/scHLAcount.

Supplementary information

Supplementary data are available at Bioinformatics online.

A school outbreak of Norwalk-like virus: evidence for airborne transmission

An outbreak of gastroenteritis affected a school attended by children aged 4-11 years. Epidemiological features suggested this was due to Norwalk-like virus (NLV) and this was confirmed by polymerase chain reaction (PCR). Nucleotide sequence analysis of the PCR amplicons revealed identical strains in all five positive stool samples. Pupils were significantly more likely to become ill following an episode of vomiting within their classroom (adjusted odds ratio 4.1, 95% CI 1.8-9.3). The times from exposure to illness were consistent with direct infection from aerosolized viral particles where exposure to vomiting was high. Cleaning with quaternary ammonium preparations made no impact on the course of the outbreak. However, the outbreak stopped after the school closed for 4 days and was cleaned using chlorine-based agents. This study confirms the importance of vomiting in the transmission of NLV and provides evidence that direct infection with aerosolized viral particles occurs.

Factors influencing hepatitis B vaccine uptake in injecting drug users

BACKGROUND

Hepatitis B infection in injecting drug users is an important public health problem. Active immunization against hepatitis B is immunogenic and safe, but uptake rates in targeted vaccination programmes are low. This study was undertaken to identify factors associated with the uptake of hepatitis B vaccination in injecting drug users attending a needle exchange service.

METHODS

A retrospective cross-sectional survey of case-note data of injecting drug users who had no markers of hepatitis B infection or immunity was undertaken within a drop-in needle exchange service for injecting drug users in a large urban area in England. A qualitative study using semi-structured interviews with needle exchange staff was also conducted.

RESULTS

Of 207 injecting drug users, 180 (87 per cent) had been offered vaccine, 123 (59 per cent) accepted at least one dose and 55 (27 per cent) received three or more doses. Vaccine was less likely to be offered to those sharing injecting equipment or known to have hepatitis C. Needle sharing was also associated with failure to accept vaccine, as was increasing age and the length of contact with the service.

CONCLUSIONS

Those who are most at risk are least likely to be offered vaccine and accept it. This calls into doubt the effectiveness of hepatitis B vaccination strategies targeted at high-risk groups and adds weight to arguments for universal vaccination.

Emergency (999) calls to the ambulance service that do not result in the patient being transported to hospital: an epidemiological study

OBJECTIVE

To describe the demographic and clinical characteristics of patients who are not transported to hospital after an emergency (999) call to the East Midlands Ambulance Service, the reason for non-transportation, and the priority assigned when the ambulance is dispatched.

METHODS

The first 500 consecutive non-transported patients from 1 March 2000 were identified from the ambulance service command and control data. Epidemiological and clinical data were then obtained from the patient report form completed by the attending ambulance crew and compared with the initial priority dispatch (AMPDS) code that determined the urgency of the ambulance response.

RESULTS

Data were obtained for 498 patients. Twenty six per cent of these calls were assigned an AMPDS delta code (the most urgent category) at the time the call was received. Falls accounted for 34% of all non-transported calls. This group of patients were predominantly elderly people (over 70 years old) and the majority (89%) were identified as less urgent (coded AMPDS alpha or bravo) at telephone triage. The mean time that an ambulance was committed to each non-transported call was 34 minutes.

CONCLUSIONS

This study shows that falls in elderly people account for a significant proportion of non-transported 999 calls and are often assigned a low priority when the call is first received. There could be major gains if some of these patients could be triaged to an alternative response, both in terms of increasing the ability of the ambulance service to respond faster to clinically more urgent calls and improving the cost effectiveness of the health service. The AMPDS priority dispatch system has been shown to be sensitive but this study suggests that its specificity may be poor, resulting in rapid responses to relatively minor problems. More research is required to determine whether AMPDS prioritisation can reliably and safely identify 999 calls where an alternative to an emergency ambulance would be a more appropriate response.

Use of hygiene advice and active immunisation to control an outbreak of hepatitis A

A community outbreak of at least 16 cases of hepatitis A is described. Salivary antibody testing of 126 children within a school in that community showed only one case of undiagnosed previous infection. Three other children had received hepatitis A vaccine previously, and this was reflected in their antibody titres. For the schools serving the community control measures included advice on good hygiene (supervised handwashing and additional cleaning in the schools). All close contacts of cases (household and childminding contacts and all staff in one school) were given active immunisation, though two subsequently developed hepatitis A, 17 and 27 days after vaccination. The use of human normal immunoglobulin (HNIG) was fully discussed with contacts, but was declined in all cases. The low prevalence of previous infection found in the schoolchildren implies that, in future, few adults will be immune. Public concern about blood products after the recent Department of Health decision to stop using British-sourced plasma may be a factor in limiting the uptake of HNIG, especially as there is now a perceived safer alternative, namely hepatitis A vaccine. Lack of evidence of spread of disease within the schools involved demonstrates that good hygiene, especially handwashing, remains the most important element in the control of hepatitis A.

Endemic melioidosis in tropical northern Australia: a 10-year prospective study and review of the literature

In a prospective study of melioidosis in northern Australia, 252 cases were found over 10 years. Of these, 46% were bacteremic, and 49 (19%) patients died. Despite administration of ceftazidime or carbapenems, mortality was 86% (43 of 50 patients) among those with septic shock. Pneumonia accounted for 127 presentations (50%) and genitourinary infections for 37 (15%), with 35 men (18%) having prostatic abscesses. Other presentations included skin abscesses (32 patients; 13%), osteomyelitis and/or septic arthritis (9; 4%), soft tissue abscesses (10; 4%), and encephalomyelitis (10; 4%). Risk factors included diabetes (37%), excessive alcohol intake (39%), chronic lung disease (27%), chronic renal disease (10%), and consumption of kava (8%). Only 1 death occurred among the 51 patients (20%) with no risk factors (relative risk, 0.08; 95% confidence interval, 0.01-0.58). Intensive therapy with ceftazidime or carbapenems, followed by at least 3 months of eradication therapy with trimethoprim-sulfamethoxazole, was associated with decreased mortality. Strategies are needed to decrease the high mortality with melioidosis septic shock. Preliminary data on granulocyte colony-stimulating factor therapy are very encouraging.

Evidence for airborne transmission of Norwalk-like virus (NLV) in a hotel restaurant

An outbreak of gastroenteritis followed a meal in a large hotel during which one of the diners vomited. The clinical features of the illness suggested Norwalk-like virus (NLV, small round structured virus) infection, and this was confirmed by electron microscopy and reverse transcriptase polymerase chain reaction (RT-PCR) of stool samples. Further characterization of the virus by nucleotide sequence analysis of the PCR amplicons revealed identical strains in all the affected individuals. The foods served at the meal could not be demonstrated to be the cause of the outbreak. Analysis of attack rates by dining table showed an inverse relationship with the distance from the person who vomited. No one eating in a separate restaurant reported illness. Transmission from person-to-person or direct contamination of food seems unlikely in this outbreak. However, the findings are consistent with airborne spread of NLV with infection by inhalation with subsequent ingestion of virus particles.

Strategies for the analysis of oncogene overexpression. Studies of the neu oncogene in breast carcinoma

The development of a consistent strategy for the analysis of oncogene expression at the cellular level is essential for understanding the roles of these genes in the development and progression of human neoplasia. Detection of the neu oncogene products in breast carcinoma was selected as a model for analysis of oncogene expression. Fifty-two primary human breast carcinomas were evaluated by quantitation of neu DNA amplification and mRNA expression and by localization of neu mRNA and protein (p 185) at the cellular level by in situ hybridization (ISH) and immunohistochemistry (IHC). The specificity and sensitivity of the molecular and immunologic probes for neu were established with the use of genetically engineered cell lines that overexpressed either neu or epidermal growth factor receptor (EGFR). Twenty-nine percent of breast carcinomas demonstrated neu DNA amplification and mRNA overexpression, and there was close correlation between the level of neu mRNA expression and detection of neu gene products by ISH and IHC. Thirty-two percent of carcinomas demonstrated neu mRNA overexpression by ISH. The immunohistochemical method using TA1 monoclonal antibody for p185 was exquisitely sensitive in acetone-fixed frozen sections and provided an excellent approach for judging overexpression as confirmed by the various molecular analyses. All areas of nonmalignant breast epithelium stained weakly, and a wide range of staining intensity was observed in malignant breast epithelium, with 31% of carcinomas judged to be p185 overexpressors. Heterogeneous expression of p185 was seen in some carcinomas. This study provides a strategic approach for the evaluation of oncogene expression in human tumors.

neu oncogene protein and epidermal growth factor receptor are independently expressed in benign and malignant breast tissues

The neu oncogene protein, p185, and epidermal growth factor receptor (EGFR) were localized immunohistochemically in benign and malignant human breast tissues using monoclonal antibodies. Both benign and malignant epithelial cells were positive for these oncogene proteins in acetone-postfixed frozen sections. Stromal cells were negative for p185, but occasionally positive for EGFR. Myoepithelial cells were consistently positive for EGFR, and p185 was localized predominantly in duct-lining cells, where the basolateral plasma membrane was the normal expression site of both substances. Paraformaldehyde-prefixed frozen sections were less sensitive for antigen demonstration. Based on the intensity of immunoreactivity, 11 of 37 acetone-postfixed breast carcinomas (30%) were judged neu overexpressors, while none of 24 benign tissues overexpressed neu. Epidermal growth factor receptor was demonstrated in 18 of 36 acetone-postfixed cancer tissues (50%) and was overexpressed in three (8%). At the cellular level, heterogenous expression of p185 and EGFR was occasionally observed in both benign and malignant tissues, and a single case of cancer overexpressing both neu and EGFR showed reciprocal patterns of staining, indicating their independent expression. In some carcinomas, EGFR was localized only in stromal cells. Our findings confirmed mutually independent expression of the two closely related protooncogenes in benign and malignant breast tissues.

Analysis of c-erbB-2 expression in breast carcinomas with clinical follow-up

Various monoclonal antibodies reactive with protooncogene products or tumor-associated antigens have been utilized to investigate breast carcinoma biology or antigen expression with potential prognostic relevance. Murine monoclonal antibody TA1, generated by immunization of BALB/c mice with whole c-erbB-2 (neu) transformed NIH/3T3 cells, recognizes the extracellular domain of the c-erbB-2 protein and binds a Mr 185,000 protein by immunoprecipitation. Using avidin-biotin-peroxidase techniques and monoclonal antibody TA1, 313 archival primary adenocarcinomas of the breast were evaluated for c-erbB-2 overexpression; 290 of these were used for multiparametric statistical analysis. Historical, clinical (age, laterality), histological (nuclear grade, tumor size, lymph node status, lymphatic or blood invasion), and hormone receptor data as well as clinical outcome (minimal follow-up, 6 years; median follow-up, 8.5 years) were compared to TA1 staining. For these 290 patients Cox regression multivariate analysis showed the strongest correlation between lymph node status or estrogen receptor status and overall survival (P = 0.0001 and 0.049, respectively). TA1 staining did not significantly correlate with survival (P = 0.395). However, univariate analysis of certain patient subpopulations showed a significant correlation if the examined tumors were subdivided into negative or focally reactive and those with greater than or equal to 40% cellular reactivity. For T3, T4 patients, strong TA1 immunoreactivity correlated with a shortened disease-free survival (log rank P = 0.0018; Wilcoxon p = 0.0078) and overall survival (log rank P = 0.0002; Wilcoxon P = 0.0013). For these patients the overall survival at 6 years was markedly different between the strongly reactive tumors (0%) and the negative to weakly reactive tumors (55%). In lymph node-positive patients a trend between high TA1 reactivity and a worse overall survival was also noted (log rank P = 0.128; Wilcoxon P = 0.054), with a 6-year survival of 42% in the strongly reactive tumors (n = 16) and 65% in the negative to weakly reactive carcinomas (n = 105). No correlation between TA1 immunoreactivity and other historical, clinical, and histological features were noted. c-erbB-2 overexpression as measured by immunohistochemical techniques, therefore, may have clinical significance in certain patient subpopulations.

Generation and characterization of monoclonal antibodies specific for the human neu oncogene product, p185

A series of monoclonal antibodies specific for the extracellular domain of the human neu gene product (p185) have been produced. The generation of these monoclonal antibodies, and their biochemical and immunological characterization is described. The immunization protocol utilized a series of injections of NIH3T3 cells, cyclophosphamide, and a neu transfected NIH3T3 cell line (designated 18-3-7) which expressed the full length human neu-encoded protein. This immunization regimen induced an immune response to the extracellular portion of p185 on the 18-3-7 cells. A panel of ten hybridomas were identified which secreted monoclonal antibodies with a variety of epitope specificities, and reacted with p185 in a number of different experimental formats. As the neu gene product has been associated with human breast cancers, a series of monoclonal antibodies such as these could prove useful in the diagnosis, prognosis and/or treatment of these human malignancies.