Abstract 3044: The unexplored immune landscape of high-risk pediatric cancers

In adult cancer, immune signatures such as the T cell-inflamed gene expression profile (GEP) have been developed to predict which patients are likely to respond to immune checkpoint inhibitors (ICIs) beyond high tumor mutation burden (TMB) and PD-L1 expression. The GEP infers T cell infiltration and activation in the tumor microenvironment (TME) from transcriptomic data. However, it is not known whether tools such as GEP are applicable in pediatric cancer, as the TME in childhood cancers is largely unexplored and response to ICIs are rare. We have undertaken an integrated analysis of the pediatric TME using RNA-sequencing (RNA-seq) and immunohistochemistry (IHC). Our goal is to identify patients with T cell-inflamed or “hot” tumors who may benefit from ICIs. Through Australia's ZERO childhood cancer precision medicine program we performed RNA-seq on 347 high-risk pediatric cancers (estimated <30% chance of survival) and performed IHC for CD4, CD8, CD45 and PD-L1 on 112 matching samples. Using both informatic assessments and IHC as independent measures of immune infiltration, we mapped the immune landscape of the TME across a broad range of high-risk pediatric cancers. As RNA-seq is increasingly used in the analysis of patient tumors, we investigated numerous molecular correlates of immune infiltration, tailored specifically to pediatric patients. RNA-seq was used to generate the GEP and map expression profiles of immune checkpoint genes, and deconvolution algorithms were used to extract the immune cell composition for every tumor. The correlation analysis between IHC, deconvolution of cell mixture composition and GEP were assessed, including PD-L1 protein and mRNA expression. We observed significant correlation between PD-L1 protein and mRNA expression and a weak correlation of CD8+ T cells with GEP. Deconvoluted TME estimates were most tightly correlated with the presence of T cell infiltrates (CD4 and CD8) with IHC. TMB and tumor purity estimates were derived from whole genome sequencing for each case. No correlation was observed between TMB and immune infiltration, however, tumor purity was negatively correlated with immune infiltration. Using IHC as an independent marker of a T cell-inflamed TME, we have identified a novel pediatric immune signature that includes markers of CD4 and CD8 T cells, T cell cytotoxicity, T and NK cell recruitment and activation, MHC Class II molecules and immune checkpoints. This is the first study to comprehensively analyze the pediatric TME in a cohort of this size and diversity, with matching IHC for orthogonal validation. Through the combination of RNA-seq and IHC, we have devised a novel immune signature specific to pediatrics and these techniques have identified a subset of patients that are immune “hot” and may potentially respond to ICIs. Conversely, we also highlight the potential of identifying immune “cold” patients who may need immunomodulatory combination strategies to maximize immune response.

Citation Format: Chelsea Mayoh, Rachael L. Terry, Marie Wong, Loretta M. Lau, Dong Anh Khuong-Quang, Marion K. Mateos, Vanessa Tyrrell, Michelle Haber, David S. Ziegler, Mark J. Cowley, Joseph A. Trapani, Paul J. Neeson, Paul G. Ekert. The unexplored immune landscape of high-risk pediatric cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 3044.

The C-Circle Assay for alternative-lengthening-of-telomeres activity

The C-Circle Assay has satisfied the need for a rapid, robust and quantitative ALT assay that responds quickly to changes in ALT activity. The C-Circle Assay involves (i) extraction or simple preparation (Quick C-Circle Preparation) of the cell's DNA, which includes C-Circles (ii) amplification of the self-primed C-Circles with a rolling circle amplification reaction and (iii) sequence specific detection of the amplification products by native telomeric DNA dot blot or telomeric qPCR. Here we detail the protocols and considerations required to perform the C-Circle Assay and its controls, which include exonuclease removal of linear telomeric DNA, production of the synthetic C-Circle C96 and modulation of ALT activity by γ-irradiation.

HPV vaccination in Hong Kong: implications for medical education

OBJECTIVE

To explore the experience and attitudes of physicians in clinics, and to facilitate physicians' promotion of HPV vaccination.

DATA SOURCES

Primary data collected from conducting semi-structural in-depth interviews from May to June 2010 with 12 physicians in one district in Hong Kong to understand their experience of providing HPV vaccines, the difficulties in promoting HPV vaccines, and their attitudes towards HPV vaccination.

STUDY DESIGN

Physicians identified 4 categories of factors related to their experiences of and attitudes to providing HPV vaccination: (a) background information on HPV vaccination provided by physicians, (b) factors influencing women to receive vaccination, (c) physicians' recommendations to the public on HPV vaccines, and (d) physicians' perspectives on HPV vaccine promotion.

CONCLUSIONS

Our findings show that public knowledge on HPV and cervical cancer is insufficient and the role of government in vaccine promotion is unclear. Promotion strategies such as physicians' recommendation, financial assistance and health education provided by the government will influence HPV vaccination and its promotion.

A method for the automated mapping of laboratory results to LOINC

LOINC is emerging as the standard for laboratory result names, and there is great interest in mapping legacy terms from laboratory systems to it. However, the mapping task is non-trivial, requiring significant resource commitment and a good understanding of the LOINC identifying attributes for the laboratory result names. Because the number of results in a laboratory system may range from around 500 to 2000 or more, manual, one-by-one matching, even with the aid of the RELMA matching tool provided by LOINC, is time consuming and laborious. Moreover, human variation may introduce mapping inconsistencies or errors. Through our experience mapping the results from a variety of laboratory systems to LOINC, an automated mapping method has been developed and is described in this paper. This method allows for data from the laboratory information system to be provided in a manner familiar to the submitting technician, and makes use of parsing and logic rules, combined with synonyms, attribute relationships and mapping frequency data, to perform automated matching to LOINC.

Applying the desiderata for controlled medical vocabularies to drug information databases

Medication history has always been an integral part of the patient's medical record. With the advent of the computerized medical record and the longitudinal clinical data repository, having the medication history has enabled the development of clinical decision support system that alerts for drug to drug interactions and drug allergies. Furthermore, medication data is increasingly being analyzed from a utilization and clinical outcomes standpoint. For these activities to occur, a controlled pharmacy vocabulary akin to a controlled medical vocabulary is essential. Drug information databases are well-established sources of information for pharmacy-related data and products. However, do they measure up as a controlled vocabulary? Recent experience reviewing drug information databases and integrating pharmacy-related information into a data dictionary in real-time clinical use at multiple health care institutions have revealed several challenges and issues. These are discussed according to Cimino's desiderata for controlled medical vocabularies.

Molecular systematics of the Canidae

Despite numerous systematic studies, the relationships among many species within the dog family, Canidae, remain unresolved. Two problems of broad evolutionary significance are the origins of the taxonomically rich canidae fauna of South America and the development in three species of the trenchant heel, a unique meat-cutting blade on the lower first molar. The first problem is of interest because the fossil record provides little evidence for the origins of divergent South American species such as the maned wolf and the bush dog. The second issue is problematic because the trenchant heel, although complex in form, may have evolved independently to assist in the processing of meat. We attempted to resolve these two issues and five other specific taxonomic controversies by phylogenetic analysis of 2,001 base pairs of mitochondrial DNA (mtDNA) sequence data from 23 canidae species. The mtDNA tree topology, coupled with data from the fossil record, and estimates of rates of DNA sequence divergence suggest at least three and possibly four North American invasions of South America. This result implies that an important chapter in the evolution of modern canids remains to be discovered in the fossil record and that the South American canidae endemism is as much the result of extinction outside of South America as it is due to speciation within South America. The origin of the trenchant heel is not well resolved by our data, although the maximum parsimony tree is weakly consistent with a single origin followed by multiple losses of the character in several extant species. A combined analysis of the mtDNA data and published morphological data provides unexpected support for a monophyletic South American canidae clade. However, the homogeneity partition tests indicate significant heterogeneity between the two data sets.

Quality assessment and patient participation in care by means of a touch-screen computer

Hospital characteristics vary greatly across a geographic area such as a state. Hospital peer groups internally exhibit similar characteristics and can be used as a basis for the analysis of data, the dissemination of information, and the adoption of continuous quality improvement project results. This paper reflects the efforts made toward the identification of hospital peer groups within the state of Michigan. Hospital characteristics data for fiscal year 1992 were obtained from the American Hospital Association's Annual Survey of Hospitals and the Health Care Financing Administration's MEDPRO database. Thirteen peer group clusters have been identified, reviewed, and commented on by the state's hospital association and have met general approval by hospital administrators across the state. The established peer groups are being used to identify the differences in patterns of care among hospitals in the state. The peer groups also are being used for the feedback of comparable data and the identification of hospitals for participation in continuous quality improvement projects. The next research objective is to experiment with other clustering techniques and other inpatient populations. The consistency of the peer groupings across all clustering techniques and across both Medicare and total inpatient populations will be studied.

Research review: a computer-based diagnostic model for individual case review

A previous study found that Iliad, a diagnostic expert system, detects diagnostic errors missed by peer review organization (PRO) review. That study used volunteer physicians from an institution as gold standard reviewers, however. The article discusses a second experiment employing Utah PRO (UPRO) review physicians as gold standards. Iliad was compared with the Unified Clinical Data Set used by the UPRO and was found to detect otherwise unsuspected diagnostic errors. The confirmation rate of Iliad flags was much higher in the earlier study, however. No agreement was found between institution and UPRO physicians, but there was agreement between a unique physician (who was both an institution and UPRO physician) and each of the two groups. Because Iliad screens for potential diagnostic errors to be confirmed or denied by gold standard physician review, the different types of physicians in the two experiments might have been the cause.

Experience with a mixed semantic/syntactic parser

The value of the computerized medical record is derived in part from the availability of medical information in a coded form accessible to manipulation by processes designed for automated decision support, medical research, and computer assistance in the management of health care delivery. To meet these needs medical reports captured and stored as natural language documents must be encoded. Below we discuss an ongoing formative process aimed at developing a natural language understanding system for chest x-ray reports. Comparative data showing the progress of this process is presented.

A natural language understanding system combining syntactic and semantic techniques

A large proportion of the medical record currently available in computerized medical information systems is in the form of free text reports. While the accessibility of this source of data is improved through inclusion in the computerized record, it remains unavailable for automated decision support, medical research, and management of medical delivery systems. Natural language understanding systems (NLUS) designed to encode free text reports represent one approach to making this information available for these uses. Below we describe an experimental NLUS designed to parse the reports of chest radiographs and store the clinical data extracted in a medical data base.

Molecular genetic and morphological analyses of the African wild dog (Lycaon pictus)

African wild dog populations have declined precipitously during the last 100 years in eastern Africa. The possible causes of this decline include a reduction in prey abundance and habitat; disease; and loss of genetic variability accompanied by inbreeding depression. We examined the levels of genetic variability and distinctiveness among populations of African wild dogs using mitochondrial DNA (mtDNA) restriction site and sequence analyses and multivariate analysis of cranial and dental measurements. Our results indicate that the genetic variability of eastern African wild dog populations is comparable to that of southern Africa and similar to levels of variability found in other large canids. Southern and eastern populations of wild dogs show about 1% divergence in mtDNA sequence and form two monophyletic assemblages containing three mtDNA genotypes each. No genotypes are shared between the two regions. With one exception, all wild dogs examined from zoos had southern African genotypes. Morphological analysis supports the distinction of eastern and southern African wild dog populations, and we suggest they should be considered separate subspecies. An eastern African wild dog breeding program should be initiated to ensure preservation of the eastern African form and to slow the loss of genetic variability that, while not yet apparent, will inevitably occur if wild populations continue to decline. Finally, we examined the phylogenetic relationships of wild dogs to other wolf-like canids through analysis of 736 base pairs (bp) of cytochrome b sequence and showed wild dogs to belong to a phylogenetically distinct lineage of the wolf-like canids.

Performance of a diagnostic system (Iliad) as a tool for quality assurance

Quality assurance improves health care through detection of quality problems and feedback to the care giver. Current review procedures employed by the Peer Review Organizations (PROs), however, appear to underdetect quality problems, particularly those arising from diagnostic errors. We studied the use of an expert diagnostic system, Iliad, to detect quality problems arising from diagnostic errors. One hundred cases were selected from among those Medicare cases reviewed by the Utah PRO (UPRO) and which contained diagnoses recognized by Iliad. Iliad flagged 28 cases out of the 100 as containing diagnostic errors, and a gold standard physician review confirmed quality problems in 17 cases (60.7%). The UPRO review found 28 cases with quality problems, mostly treatment and documentation errors. The quality problems detected by Iliad appeared to be more serious than those detected by the UPRO review. Among the six cases with quality problems detected by both the UPRO and the Iliad review, there was none for which the same quality problem was detected by the two procedures. The two review procedures were therefore complementary.

Performance of a diagnostic system (Iliad) as a tool for quality assurance

Quality Assurance improves health care through detection of quality problems and feedback to the care giver. Current review procedures employed by the Peer Review Organizations (PROs), however, appear to under-detect quality problems, particularly those arising from diagnostic errors. We studied the use of an expert diagnostic system, Iliad, to detect quality problems arising from diagnostic errors. 100 cases were selected from among those Medicare cases reviewed by the Utah PRO (UPRO) and which contained diagnoses recognized by Iliad. Iliad flagged 28 cases out of the 100 as containing diagnostic errors, and a gold standard physician review confirmed quality problems in 17 cases (60.7%). The UPRO review found 28 cases with quality problems, mostly treatment and documentation errors. The quality problems detected by Iliad appeared to be more serious than those detected by the UPRO review. Among the six cases with quality problems detected by both the UPRO and Iliad review, there was none for which the same quality problem was detected by the two procedures. The two review procedures were therefore complementary.

Performance of a diagnostic system (Iliad) as a tool for quality assurance

Quality Assurance improves health care through detection of quality problems and feedback to the care giver. Current review procedures employed by the Peer Review Organizations (PROs), however, appear to underdetect quality problems, particularly those arising from diagnostic errors. We studied the use of an expert diagnostic system, Iliad, to detect quality problems arising from diagnostic errors. 100 cases were selected from among those Medicare cases reviewed by the Utah PRO (UPRO) and which contained diagnoses recognized by Iliad. Iliad flagged 28 cases out of the 100 as containing diagnostic errors, and a gold standard physician review confirmed quality problems in 17 cases (60.7%). The UPRO review found 28 cases with quality problems, mostly treatment and documentation errors. The quality problems detected by Iliad appeared to be more serious than those detected by the UPRO review. Among the six cases with quality problems detected by both the UPRO and Iliad review, there was none for which the same quality problem was detected by the two procedures. The two review procedures were therefore complementary.

Inability of polyglycolic acid mesh to inhibit immediate post-radical pelvic surgery adhesions

The ability of a polyglycolic acid (PGA)-derived mesh to limit the formation of immediate postoperative pelvic adhesions after radical resection of the pelvic viscera and peritoneum was investigated. Twenty female canines underwent total abdominal hysterectomy, bilateral salpingo-oophorectomy, and infracolonic omentectomy. The entire peritoneum of the pelvis and lower abdomen also was removed. In ten animals, a single layer of PGA mesh, tailored to cover the deperitonealized area, was sutured in place. Reperitonealization was not performed in control animals. Four weeks after initial surgery, animals were reexplored and killed. Adhesions to the anterior abdominal wall and pelvis were quantified and graded: (Table: See Text) These data indicate that the placement of a PGA mesh induces significant pelvic adhesions and potentiates the formation of pelvic abscesses.