Revealing the role of SPP1+ macrophages in glioma prognosis and therapeutic targeting by investigating tumor-associated macrophage landscape in grade 2 and 3 gliomas.

BACKGROUND: Glioma is a highly heterogeneous brain tumor categorized into World Health Organization (WHO) grades 1-4 based on its malignancy. The suppressive immune microenvironment of glioma contributes significantly to unfavourable patient outcomes. However, the cellular composition and their complex interplays within the glioma environment remain poorly understood, and reliable prognostic markers remain elusive. Therefore, in-depth exploration of the tumor microenvironment (TME) and identification of predictive markers are crucial for improving the clinical management of glioma patients. RESULTS: Our analysis of single-cell RNA-sequencing data from glioma samples unveiled the immunosuppressive role of tumor-associated macrophages (TAMs), mediated through intricate interactions with tumor cells and lymphocytes. We also discovered the heterogeneity within TAMs, among which a group of suppressive TAMs named TAM-SPP1 demonstrated a significant association with Epidermal Growth Factor Receptor (EGFR) amplification, impaired T cell response and unfavourable patient survival outcomes. Furthermore, by leveraging genomic and transcriptomic data from The Cancer Genome Atlas (TCGA) dataset, two distinct molecular subtypes with a different constitution of TAMs, EGFR status and clinical outcomes were identified. Exploiting the molecular differences between these two subtypes, we developed a four-gene-based prognostic model. This model displayed strong associations with an elevated level of suppressive TAMs and could be used to predict anti-tumor immune response and prognosis in glioma patients. CONCLUSION: Our findings illuminated the molecular and cellular mechanisms that shape the immunosuppressive microenvironment in gliomas, providing novel insights into potential therapeutic targets. Furthermore, the developed prognostic model holds promise for predicting immunotherapy response and assisting in more precise risk stratification for glioma patients.

A review on trends in development and translation of omics signatures in cancer.

The field of cancer genomics and transcriptomics has evolved from targeted profiling to swift sequencing of individual tumor genome and transcriptome. The steady growth in genome, epigenome, and transcriptome datasets on a genome-wide scale has significantly increased our capability in capturing signatures that represent both the intrinsic and extrinsic biological features of tumors. These biological differences can help in precise molecular subtyping of cancer, predicting tumor progression, metastatic potential, and resistance to therapeutic agents. In this review, we summarized the current development of genomic, methylomic, transcriptomic, proteomic and metabolic signatures in the field of cancer research and highlighted their potentials in clinical applications to improve diagnosis, prognosis, and treatment decision in cancer patients.

Revealing parental mosaicism: the hidden answer to the recurrence of apparent de novo variants.

Mosaicism refers to the presence of two or more populations of genetically distinct cells within an individual, all of which originate from a single zygote. Previous literature estimated the percentage of parental mosaicism ranged from 0.33 to 25.9%. In this study, parents whose children had previously been diagnosed with developmental disorders with an apparent de novo variant were recruited. Peripheral blood, buccal and semen samples were collected from these parents if available for the detection of potential parental mosaicism using droplet digital PCR, complemented with the method of blocker displacement amplification. Among the 20 families being analyzed, we report four families with parental mosaicism (4/20, 20%). Two families have maternal gonosomal mosaicism (EYA1 and EBF3) and one family has paternal gonadal mosaicism (CHD7) with a pathogenic/ likely pathogenic variant. One family has a paternal gonosomal mosaicism with a variant of uncertain significance (FLNC) with high clinical relevance. The detectable variant allele frequency in our cohort ranged from 8.7-35.9%, limit of detection 0.08-0.16% based on our in-house EBF3 assay. Detecting parental mosaicism not only informs family with a more accurate recurrence risk, but also facilitates medical teams to create appropriate plans for pregnancy and delivery, offering the most suitable care.

Genome-Wide DNA Methylation Profiling as Frontline Diagnostics for Central Nervous System Embryonal Tumors in Hong Kong.

This paper examines the link between CNS tumor biology and heterogeneity and the use of genome-wide DNA methylation profiling as a clinical diagnostic platform. CNS tumors are the most common solid tumors in children, and their prognosis remains poor. This study retrospectively analyzed pediatric patients with CNS embryonal tumors in Hong Kong between 1999 and 2017, using data from the territory-wide registry and available formalin-fixed paraffin-embedded tumor tissue. After processing archival tumor tissue via DNA extraction, quantification, and methylation profiling, the data were analyzed by using the web-based DKFZ classifier (Molecular Neuropathology (MNP) 2.0 v11b4) and t-SNE analysis. Methylation profiles were deemed informative in 85 samples. Epigenetic data allowed molecular subgrouping and confirmed diagnosis in 65 samples, verified histologic diagnosis in 8, and suggested an alternative diagnosis in 12. This study demonstrates the potential of DNA methylation profiling in characterizing pediatric CNS embryonal tumors in a large cohort from Hong Kong, which should enable regional and international collaboration in future pediatric neuro-oncology research.

Socio-economic costs of rare diseases and the risk of financial hardship: a cross-sectional study.

Background: To achieve universal healthcare coverage (UHC), the rare disease (RD) population must also receive quality healthcare without financial hardship. This study evaluates the impact of RDs in Hong Kong (HK) by estimating cost from a societal perspective and investigating related risk of financial hardship. Methods: A total of 284 RD patients and caregivers covering 106 RDs were recruited through HK's largest RD patient group, Rare Disease Hong Kong, in 2020. Resource use data were collected using the Client Service Receipt Inventory for Rare disease population (CSRI-Ra). Costs were estimated using a prevalence-based, bottom-up approach. Risk of financial hardship was estimated using catastrophic health expenditure (CHE) and impoverishing health expenditure (IHE) indicators. Multivariate regression was performed to identify potential determinants. Findings: Annual total RD costs in HK were estimated at HK$484,256/patient (United States (US) $62,084). Direct non-healthcare cost (HK$193,555/US$24,814) was the highest cost type, followed by direct healthcare (HK$187,166/US$23,995), and indirect (HK$103,535/US$13,273) costs. CHE at the 10% threshold was estimated at 36.3% and IHE at the $3.1 poverty line was 8.8%, both significantly higher than global estimates. Pediatric patients reported higher costs than adult patients (p < 0.001). Longer years since genetic diagnosis was the only factor significantly associated with both total costs (p = 0.026) and CHE (p = 0.003). Interpretation: This study serves as the first in the Asia Pacific region to simultaneously assess the societal costs and financial hardship related to RDs and highlights the importance of an early genetic diagnosis. These results contribute to existing evidence on the globally ubiquitous high costs of RDs, warranting collaboration between different stakeholders to include RD population in UHC planning. Funding: Health and Medical Research Fund, and the Society for the Relief of Disabled Children.

Meta-analysis of the diagnostic and clinical utility of exome and genome sequencing in pediatric and adult patients with rare diseases across diverse populations.

PURPOSE: This meta-analysis aims to compare the diagnostic and clinical utility of exome sequencing (ES) vs genome sequencing (GS) in pediatric and adult patients with rare diseases across diverse populations. METHODS: A meta-analysis was conducted to identify studies from 2011 to 2021. RESULTS: One hundred sixty-one studies across 31 countries/regions were eligible, featuring 50,417 probands of diverse populations. Diagnostic rates of ES (0.38, 95% CI 0.36-0.40) and GS (0.34, 95% CI 0.30-0.38) were similar (P = .1). Within-cohort comparison illustrated 1.2-times odds of diagnosis by GS over ES (95% CI 0.79-1.83, P = .38). GS studies discovered a higher range of novel genes than ES studies; yet, the rate of variant of unknown significance did not differ (P = .78). Among high-quality studies, clinical utility of GS (0.77, 95% CI 0.64-0.90) was higher than that of ES (0.44, 95% CI 0.30-0.58) (P < .01). CONCLUSION: This meta-analysis provides an important update to demonstrate the similar diagnostic rates between ES and GS and the higher clinical utility of GS over ES. With the newly published recommendations for clinical interpretation of variants found in noncoding regions of the genome and the trend of decreasing variant of unknown significance and GS cost, it is expected that GS will be more widely used in clinical settings.

Neuroimaging in Primary Coenzyme-Q10-Deficiency Disorders.

Coenzyme Q10 (CoQ10) is an endogenously synthesized lipid molecule. It is best known for its role as a cofactor within the mitochondrial respiratory chain where it functions in electron transfer and ATP synthesis. However, there are many other cellular pathways that also depend on the CoQ10 supply (redox homeostasis, ferroptosis and sulfide oxidation). The CoQ10 biosynthesis pathway consists of several enzymes, which are encoded by the nuclear DNA. The majority of these enzymes are responsible for modifications of the CoQ-head group (benzoquinone ring). Only three enzymes (PDSS1, PDSS2 and COQ2) are required for assembly and attachment of the polyisoprenoid side chain. The head-modifying enzymes may assemble into resolvable domains, representing COQ complexes. During the last two decades, numerous inborn errors in CoQ10 biosynthesis enzymes have been identified. Thus far, 11 disease genes are known (PDSS1, PDSS2, COQ2, COQ4, COQ5, COQ6, COQ7, COQ8A, COQ8B, COQ9 and HPDL). Disease onset is highly variable and ranges from the neonatal period to late adulthood. CoQ10 deficiency exerts detrimental effects on the nervous system. Potential consequences are neuronal death, neuroinflammation and cerebral gliosis. Clinical features include encephalopathy, regression, movement disorders, epilepsy and intellectual disability. Brain magnetic resonance imaging (MRI) is the most important tool for diagnostic evaluation of neurological damage in individuals with CoQ10 deficiency. However, due to the rarity of the different gene defects, information on disease manifestations within the central nervous system is scarce. This review aims to provide an overview of brain MRI patterns observed in primary CoQ10 biosynthesis disorders and to highlight disease-specific findings.

Evaluating High-Confidence Genes in Conotruncal Cardiac Defects by Gene Burden Analyses.

Background In nonsyndromic conotruncal cardiac defects, the use of next-generation sequencing for clinical diagnosis is increasingly adopted, but gene-disease associations in research are only partially translated to diagnostic panels, suggesting a need for evidence-based consensus. Methods and Results In an exome data set of 245 patients with conotruncal cardiac defects, we performed burden analysis on a high-confidence congenital heart disease gene list (n=132) with rare (<0.01%) and ultrarare (absent in the Genome Aggregation Database) protein-altering variants. Overall, we confirmed an excess of rare variants compared with ethnicity-matched controls and identified 2 known genes (GATA6, NOTCH1) and 4 candidate genes supported by the literature (ANKRD11, DOCK6, NPHP4, and STRA6). Ultrarare variant analysis was performed in combination with 3 other published studies (n=1451) and identified 3 genes (FLT4, NOTCH1, TBX1) to be significant, whereas a subgroup analysis involving 391 Chinese subjects identified only GATA6 as significant. Conclusions We suggest that these significant genes in our rare and ultrarare burden analyses warrant prioritization for clinical testing implied for rare inherited and de novo variants. Additionally, associations on ClinVar for these genes were predominantly variants of uncertain significance. Therefore, a more stringent assessment of gene-disease associations in a larger and ethnically diverse cohort is required to be prudent for future curation of conotruncal cardiac defect genes.

Aberrant phase separation and nucleolar dysfunction in rare genetic diseases.

Thousands of genetic variants in protein-coding genes have been linked to disease. However, the functional impact of most variants is unknown as they occur within intrinsically disordered protein regions that have poorly defined functions1-3. Intrinsically disordered regions can mediate phase separation and the formation of biomolecular condensates, such as the nucleolus4,5. This suggests that mutations in disordered proteins may alter condensate properties and function6-8. Here we show that a subset of disease-associated variants in disordered regions alter phase separation, cause mispartitioning into the nucleolus and disrupt nucleolar function. We discover de novo frameshift variants in HMGB1 that cause brachyphalangy, polydactyly and tibial aplasia syndrome, a rare complex malformation syndrome. The frameshifts replace the intrinsically disordered acidic tail of HMGB1 with an arginine-rich basic tail. The mutant tail alters HMGB1 phase separation, enhances its partitioning into the nucleolus and causes nucleolar dysfunction. We built a catalogue of more than 200,000 variants in disordered carboxy-terminal tails and identified more than 600 frameshifts that create arginine-rich basic tails in transcription factors and other proteins. For 12 out of the 13 disease-associated variants tested, the mutation enhanced partitioning into the nucleolus, and several variants altered rRNA biogenesis. These data identify the cause of a rare complex syndrome and suggest that a large number of genetic variants may dysregulate nucleoli and other biomolecular condensates in humans.

Diagnostic potential of the amniotic fluid cells transcriptome in deciphering mendelian disease: a proof-of-concept.

RNA sequencing (RNA-seq) is emerging in genetic diagnoses as it provides functional support for the interpretation of variants of uncertain significance. However, the use of amniotic fluid (AF) cells for RNA-seq has not yet been explored. Here, we examined the expression of clinically relevant genes in AF cells (n = 48) compared with whole blood and fibroblasts. The number of well-expressed genes in AF cells was comparable to that in fibroblasts and much higher than that in blood across different disease categories. We found AF cells RNA-seq feasible and beneficial in prenatal diagnosis (n = 4) as transcriptomic data elucidated the molecular consequence leading to the pathogenicity upgrade of variants in CHD7 and COL1A2 and revising the in silico prediction of a variant in MYRF. AF cells RNA-seq could become a reasonable choice for postnatal patients with advantages over fibroblasts and blood as it prevents invasive procedures.

Rare coding variation provides insight into the genetic architecture and phenotypic context of autism.

Some individuals with autism spectrum disorder (ASD) carry functional mutations rarely observed in the general population. We explored the genes disrupted by these variants from joint analysis of protein-truncating variants (PTVs), missense variants and copy number variants (CNVs) in a cohort of 63,237 individuals. We discovered 72 genes associated with ASD at false discovery rate (FDR) ≤ 0.001 (185 at FDR ≤ 0.05). De novo PTVs, damaging missense variants and CNVs represented 57.5%, 21.1% and 8.44% of association evidence, while CNVs conferred greatest relative risk. Meta-analysis with cohorts ascertained for developmental delay (DD) (n = 91,605) yielded 373 genes associated with ASD/DD at FDR ≤ 0.001 (664 at FDR ≤ 0.05), some of which differed in relative frequency of mutation between ASD and DD cohorts. The DD-associated genes were enriched in transcriptomes of progenitor and immature neuronal cells, whereas genes showing stronger evidence in ASD were more enriched in maturing neurons and overlapped with schizophrenia-associated genes, emphasizing that these neuropsychiatric disorders may share common pathways to risk.

Evaluating the Health-Related Quality of Life of the Rare Disease Population in Hong Kong Using EQ-5D 3-Level.

OBJECTIVES: This study aimed to establish a normative profile of health-related quality of life (HRQOL) of the rare disease (RD) population in Hong Kong (HK) and identify potential predictors. METHODS: Between March 2020 and October 2020, patients with RD and caregivers were recruited through Rare Disease Hong Kong, the largest RD patient group alliance in HK. HRQOL was derived using the EQ-5D 3-Level with reference to the established HK value set. Utility scores were stratified according to demographics and disease-related information. Multiple linear regression was performed to explore the associations between patient characteristics and HRQOL. RESULTS: A total of 286 patients, covering 107 unique RDs, reported a mean utility score of 0.53 (SD 0.36). Thirty patients (10.5%) reported negative utility scores, indicating worse-than-death health states. More problems were recorded in the "usual activities" and "self-care" dimensions. Univariate analyses revealed that neurologic diseases, high out-of-pocket expenditure, home modification, and living in public housing or subdivided flats/units were significantly associated with lower HRQOL. A total of 99 caregivers reported a mean utility score of 0.78 (SD 0.17), which was significantly associated with the utility score of patients they took care of (r = 0.32; P = .001). CONCLUSIONS: The normative profile of the RD population was established, which revealed lower HRQOL in the RD population than other chronic disease groups and general population in HK. Findings were corroborated by evidence from other cohorts using EQ-5D, combined as part of a meta-analysis. Identifying predictors highlight areas that should be prioritized to improve HRQOL of RD population through clinical and psychosocial dimensions.

Prenatal presentation in two fetuses with features of Beckwith Wiedemann syndrome-An unexpected diagnosis of androgenetic chimera and its clinical implications.

Beckwith Wiedemann Syndrome (BWS, OMIM 130650) is an imprinting disorder that may present antenatally with a constellation of sonographic features namely polyhydramnios, macrosomia, macroglossia, omphalocele, placental mesenchymal dysplasia, cardiomegaly, nephromegaly, fetal hydrops, and other rare anomalies. Paternal uniparental disomy in chromosome 11p15 imprinting region accounts for 20% of all BWS, and 8% among those were due to genome-wide paternal uniparental disomy (GWpUPD). GWpUPD is a rare condition and usually results in prenatal lethality. The 31 liveborns reported in the literature demonstrate female predominance in surviving GWpUPD. Here, we reported two prenatal cases which initially presented with features suggestive of BWS, which subsequently were confirmed to have GWpUPD. Further trio SNP genotyping analysis using SNP-based chromosomal microarray revealed androgenetic biparental chimera as the underlying cause. Finally, we highlighted the importance of recognizing GWpUPD as a possible cause in a fetus presenting with BWS phenotype, as it carried a different disease prognosis, tumor predisposition, manifestations of other imprinting disorders, and possibility in unmasking autosomal recessive disorders from the paternal alleles.

O'Donnell-Luria-Rodan syndrome: description of a second multinational cohort and refinement of the phenotypic spectrum.

BACKGROUND: O'Donnell-Luria-Rodan syndrome (ODLURO) is an autosomal-dominant neurodevelopmental disorder caused by pathogenic, mostly truncating variants in KMT2E. It was first described by O'Donnell-Luria et al in 2019 in a cohort of 38 patients. Clinical features encompass macrocephaly, mild intellectual disability (ID), autism spectrum disorder (ASD) susceptibility and seizure susceptibility. METHODS: Affected individuals were ascertained at paediatric and genetic centres in various countries by diagnostic chromosome microarray or exome/genome sequencing. Patients were collected into a case cohort and were systematically phenotyped where possible. RESULTS: We report 18 additional patients from 17 families with genetically confirmed ODLURO. We identified 15 different heterozygous likely pathogenic or pathogenic sequence variants (14 novel) and two partial microdeletions of KMT2E. We confirm and refine the phenotypic spectrum of the KMT2E-related neurodevelopmental disorder, especially concerning cognitive development, with rather mild ID and macrocephaly with subtle facial features in most patients. We observe a high prevalence of ASD in our cohort (41%), while seizures are present in only two patients. We extend the phenotypic spectrum by sleep disturbances. CONCLUSION: Our study, bringing the total of known patients with ODLURO to more than 60 within 2 years of the first publication, suggests an unexpectedly high relative frequency of this syndrome worldwide. It seems likely that ODLURO, although just recently described, is among the more common single-gene aetiologies of neurodevelopmental delay and ASD. We present the second systematic case series of patients with ODLURO, further refining the mutational and phenotypic spectrum of this not-so-rare syndrome.

Client Service Receipt Inventory as a standardised tool for measurement of socio-economic costs in the rare genetic disease population (CSRI-Ra).

The measurement of costs is fundamental in healthcare decision-making, but it is often challenging. In particular, standardised methods have not been developed in the rare genetic disease population. A reliable and valid tool is critical for research to be locally meaningful yet internationally comparable. Herein, we sought to develop, contextualise, translate, and validate the Client Service Receipt Inventory for the RAre disease population (CSRI-Ra) to be used in cost-of-illness studies and economic evaluations for healthcare planning. Through expert panel discussions and focus group meetings involving 17 rare disease patients, carers, and healthcare and social care professionals from Hong Kong, we have developed the CSRI-Ra. Rounds of forward and backward translations were performed by bilingual researchers, and face validity and semantic equivalence were achieved through interviews and telephone communications with focus group participants and an additional of 13 healthcare professional and university students. Intra-class correlation coefficient (ICC) was used to assess criterion validity between CSRI-Ra and electronic patient record in a sample of 94 rare disease patients and carers, with overall ICC being 0.69 (95% CI 0.56-0.78), indicating moderate to good agreement. Following rounds of revision in the development, contextualisation, translation, and validation stages, the CSRI-Ra is ready for use in empirical research. The CSRI-Ra provides a sufficiently standardised yet adaptable method for collecting socio-economic data related to rare genetic diseases. This is important for near-term and long-term monitoring of the resource consequences of rare diseases, and it provides a tool for use in economic evaluations in the future, thereby helping to inform planning for efficient and effective healthcare. Adaptation of the CSRI-Ra to other populations would facilitate international research.

Understanding and perception of direct-to-consumer genetic testing in Hong Kong.

Direct-to-consumer genetic testing (DTCGT) is gaining popularity in Hong Kong (HK). As DTCGT forgoes specialist medical involvement, healthcare professionals have raised concerns regarding its validity, utility, and the public's ability to interpret DTCGT results. Thus, genetic counseling (GC) is recommended to facilitate understanding of DTCGT. This study aimed to investigate HK public's perception toward DTCGT and the importance of GC in DTCGT. A total of 304 HK adults were invited to complete a 37-item survey online. Participants' genomic literacy, understanding and attitude toward DTCGT and GC, and responses to a mock DTCGT scenario were assessed. 48% of participants were aware of DTCGT while 82% indicated an interest. 30% of participants were aware of GC services in HK; 49% were interested in GC services for understanding DTCGT results. Participants scored on average 7.6/11 in the genomic sequencing knowledge scale and were weak in limitations of genomic testing. In the mock DTCGT scenario, 73% of participants expressed concern with the positive results initially. After being explained limitations of DTCGT, 40% of participants reported decreased concern. Reduced perceived helpfulness in medical management and lifestyle modification were also reported by 35% and 27%, respectively. This HK population demonstrated a high level of awareness and interest in DTCGT. As potential DTCGT users, they might experience excess concern and overestimate the usefulness of positive DTCGT results, particularly in medical management. The importance of GC to educate and guide interpretation of DTCGT results is supported; yet the awareness and access of GC services is inadequate in HK.

Preparing genomic revolution: Attitudes, clinical practice, and training needs in delivering genetic counseling in primary care in Hong Kong and Shenzhen, China.

PURPOSE: The aim was to evaluate knowledge, attitudes, and clinical practice concerning medical genetics, genetic testing, and counseling among primary care physicians (PCPs) in Hong Kong and Shenzhen, China. METHODS: The University of Hong Kong (HKU), HKU-Shenzhen Hospital, and Shenzhen Health Capacity Building and Continuing Education Center invited PCPs from Hong Kong and Shenzhen to participate in an online survey. RESULTS: The survey was completed by 151 PCPs and 258 PCPs from Hong Kong and Shenzhen, respectively. The majority agreed it was important to keep current with genetics (91%) and that personalized medicine was the future of healthcare (86%), yet only 10% reported that they had postgraduate training in genomic medicine. Seventeen percent of Hong Kong and 40% of Shenzhen's PCPs encountered genetic-related cases in the past 6 months, and they identified insufficient knowledge, few training opportunities, and self-rated low confidence in their skillsets as main barriers. CONCLUSIONS: Our survey shows that Hong Kong and Shenzhen's PCPs are not yet fully utilizing potential benefits of genomic medicine in their clinical practice, which could be addressed with a combination of easily accessible educational resources, clear referral pathways and guidelines on genetic diseases, and cross-specialty collaboration between healthcare systems and professional bodies.

'Do language and culture really matter?': A trans-disciplinary investigation of cultural diversity in genetic counseling in Hong Kong.

In this paper, we present evidence that in counseling culturally diverse patients, differences in spoken language and cultural beliefs of the patients and genetic counseling professionals do not necessarily impede successful counseling. We also highlight sociocultural factors, including socioeconomic background and genetic literacy, that may impact communication in multicultural/ multilingual contexts or when languages other than English are used. While genetic counseling is not short of insights and practical guidelines on sociocultural and language issues, and increasingly, research that employs interviews and surveys, empirical research that draws on authentic interactional data (in the form of video- and audio-recorded interactions and their transcripts) is limited. Our goal here is to assess how needs are communicated among a diverse population using an innovative empirical approach that builds on the analysis of transcribed interactions as the primary data and optimizes trans-disciplinary expertise in linguistics, genetics and genetic counseling. We present data from 42 genetic counseling encounters addressing Sudden Arrhythmic Death Syndrome (SADS) in Hong Kong. We demonstrate the value of the situated analysis of genetic counseling, which focuses on those junctures in the interaction where participants orient to their different linguistic and/or cultural backgrounds as relevant to the ongoing interaction. We further show that participants draw on various interactional resources to negotiate and resolve possible differences or misunderstandings. We highlight the advantages of incorporating authentic (i.e., non-simulated) data into the training of genetic counselors to increase cultural awareness and to provide communication tools (i.e., interactional strategies) they can draw on in their counseling practice.