Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing.

Accurate measurement of clonal genotypes, mutational processes, and replication states from individual tumor-cell genomes will facilitate improved understanding of tumor evolution. We have developed DLP+, a scalable single-cell whole-genome sequencing platform implemented using commodity instruments, image-based object recognition, and open source computational methods. Using DLP+, we have generated a resource of 51,926 single-cell genomes and matched cell images from diverse cell types including cell lines, xenografts, and diagnostic samples with limited material. From this resource we have defined variation in mitotic mis-segregation rates across tissue types and genotypes. Analysis of matched genomic and image measurements revealed correlations between cellular morphology and genome ploidy states. Aggregation of cells sharing copy number profiles allowed for calculation of single-nucleotide resolution clonal genotypes and inference of clonal phylogenies and avoided the limitations of bulk deconvolution. Finally, joint analysis over the above features defined clone-specific chromosomal aneuploidy in polyclonal populations.

Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer.

High-grade serous ovarian cancer (HGSC) exhibits extensive malignant clonal diversity with widespread but non-random patterns of disease dissemination. We investigated whether local immune microenvironment factors shape tumor progression properties at the interface of tumor-infiltrating lymphocytes (TILs) and cancer cells. Through multi-region study of 212 samples from 38 patients with whole-genome sequencing, immunohistochemistry, histologic image analysis, gene expression profiling, and T and B cell receptor sequencing, we identified three immunologic subtypes across samples and extensive within-patient diversity. Epithelial CD8+ TILs negatively associated with malignant diversity, reflecting immunological pruning of tumor clones inferred by neoantigen depletion, HLA I loss of heterozygosity, and spatial tracking between T cell and tumor clones. In addition, combinatorial prognostic effects of mutational processes and immune properties were observed, illuminating how specific genomic aberration types associate with immune response and impact survival. We conclude that within-patient spatial immune microenvironment variation shapes intraperitoneal malignant spread, provoking new evolutionary perspectives on HGSC clonal dispersion.

Single-cell genomic variation induced by mutational processes in cancer.

How cell-to-cell copy number alterations that underpin genomic instability1 in human cancers drive genomic and phenotypic variation, and consequently the evolution of cancer2, remains understudied. Here, by applying scaled single-cell whole-genome sequencing3 to wild-type, TP53-deficient and TP53-deficient;BRCA1-deficient or TP53-deficient;BRCA2-deficient mammary epithelial cells (13,818 genomes), and to primary triple-negative breast cancer (TNBC) and high-grade serous ovarian cancer (HGSC) cells (22,057 genomes), we identify three distinct 'foreground' mutational patterns that are defined by cell-to-cell structural variation. Cell- and clone-specific high-level amplifications, parallel haplotype-specific copy number alterations and copy number segment length variation (serrate structural variations) had measurable phenotypic and evolutionary consequences. In TNBC and HGSC, clone-specific high-level amplifications in known oncogenes were highly prevalent in tumours bearing fold-back inversions, relative to tumours with homologous recombination deficiency, and were associated with increased clone-to-clone phenotypic variation. Parallel haplotype-specific alterations were also commonly observed, leading to phylogenetic evolutionary diversity and clone-specific mono-allelic expression. Serrate variants were increased in tumours with fold-back inversions and were highly correlated with increased genomic diversity of cellular populations. Together, our findings show that cell-to-cell structural variation contributes to the origins of phenotypic and evolutionary diversity in TNBC and HGSC, and provide insight into the genomic and mutational states of individual cancer cells.

Clonal fitness inferred from time-series modelling of single-cell cancer genomes.

Progress in defining genomic fitness landscapes in cancer, especially those defined by copy number alterations (CNAs), has been impeded by lack of time-series single-cell sampling of polyclonal populations and temporal statistical models1-7. Here we generated 42,000 genomes from multi-year time-series single-cell whole-genome sequencing of breast epithelium and primary triple-negative breast cancer (TNBC) patient-derived xenografts (PDXs), revealing the nature of CNA-defined clonal fitness dynamics induced by TP53 mutation and cisplatin chemotherapy. Using a new Wright-Fisher population genetics model8,9 to infer clonal fitness, we found that TP53 mutation alters the fitness landscape, reproducibly distributing fitness over a larger number of clones associated with distinct CNAs. Furthermore, in TNBC PDX models with mutated TP53, inferred fitness coefficients from CNA-based genotypes accurately forecast experimentally enforced clonal competition dynamics. Drug treatment in three long-term serially passaged TNBC PDXs resulted in cisplatin-resistant clones emerging from low-fitness phylogenetic lineages in the untreated setting. Conversely, high-fitness clones from treatment-naive controls were eradicated, signalling an inversion of the fitness landscape. Finally, upon release of drug, selection pressure dynamics were reversed, indicating a fitness cost of treatment resistance. Together, our findings define clonal fitness linked to both CNA and therapeutic resistance in polyclonal tumours.

TAILS Identifies Candidate Substrates and Biomarkers of ADAMTS7, a Therapeutic Protease Target in Coronary Artery Disease.

Loss-of-function mutations in the secreted enzyme ADAMTS7 (a disintegrin and metalloproteinase with thrombospondin motifs 7) are associated with protection for coronary artery disease. ADAMTS7 catalytic inhibition has been proposed as a therapeutic strategy for treating coronary artery disease; however, the lack of an endogenous substrate has hindered the development of activity-based biomarkers. To identify ADAMTS7 extracellular substrates and their cleavage sites relevant to vascular disease, we used TAILS (terminal amine isotopic labeling of substrates), a method for identifying protease-generated neo-N termini. We compared the secreted proteome of vascular smooth muscle and endothelial cells expressing either full-length mouse ADAMTS7 WT, catalytic mutant ADAMTS7 E373Q, or a control luciferase adenovirus. Significantly enriched N-terminal cleavage sites in ADAMTS7 WT samples were compared to the negative control conditions and filtered for stringency, resulting in catalogs of high confidence candidate ADAMTS7 cleavage sites from our three independent TAILS experiments. Within the overlap of these discovery sets, we identified 24 unique cleavage sites from 16 protein substrates, including cleavage sites in EFEMP1 (EGF-containing fibulin-like extracellular matrix protein 1/Fibulin-3). The ADAMTS7 TAILS preference for EFEMP1 cleavage at the amino acids 123.124 over the adjacent 124.125 site was validated using both endogenous EFEMP1 and purified EFEMP1 in a binary in vitro cleavage assay. Collectively, our TAILS discovery experiments have uncovered hundreds of potential substrates and cleavage sites to explore disease-related biological substrates and facilitate activity-based ADAMTS7 biomarker development.

Identifying the nature of episodic memory deficits in Major Depressive Disorder using a Real-World What-Where-When task.

ABSTRACTDeficits in episodic memory have been reported in various psychiatric conditions, including Major Depressive Disorder (MDD). Many widely used episodic memory tests do not have the ability to distinguish between impaired memory of separate components of a real-life event (e.g., what happened, where it happened and when), and impaired binding of such real-life features. To address this issue, a naturalistic, real-world What-Where-When memory task was employed to assess the nature of episodic memory impairments in MDD. A validation study established that the task is sensitive to age-related episodic memory changes, and that intentional encoding does not invalidate the task. The main study then compared the performance of patients with depression and control participants on the intentionally encoded WWW task. Patients with MDD presented an overall episodic memory impairment arising from deficits in object memory and the ability to bind objects to temporal context. Taken together, our study confirms the episodic memory impairment in MDD, by providing evidence of deficient object memory and reduced ability to bind temporal context to objects in patients. Our naturalistic WWW task presents a promising approach for thorough identification of the nature of episodic memory impairments, under a real-world environment, in various conditions, including MDD.

Regulators of the secretory pathway have distinct inputs into single-celled branching morphogenesis and seamless tube formation in the Drosophila trachea.

Biological tubes serve as conduits through which gas, nutrients and other important fluids are delivered to tissues. Most biological tubes consist of multiple cells connected by epithelial junctions. Unlike these multicellular tubes, seamless tubes are unicellular and lack junctions. Seamless tubes are present in various organ systems, including the vertebrate vasculature, C.elegans excretory system, and Drosophila tracheal system. The Drosophila tracheal system is a network of air-filled tubes that delivers oxygen to all tissues. Specialized cells within the tracheal system, called terminal cells, branch extensively and form seamless tubes. Terminal tracheal tubes are polarized; the lumenal membrane has apical identity whereas the outer membrane exhibits basal characteristics. Although various aspects of membrane trafficking have been implicated in terminal cell morphogenesis, the precise secretory pathway requirements for basal and apical membrane growth have yet to be elucidated. In the present study, we demonstrate that anterograde trafficking, retrograde trafficking and Golgi-to-plasma membrane vesicle fusion are each required for the complex branched architecture of the terminal cell, but their inputs during seamless lumen formation are more varied. The COPII subunit, Sec31, and ER exit site protein, Sec16, are critical for subcellular tube architecture, whereas the SNARE proteins Syntaxin 5, Syntaxin 1 and Syntaxin 18 are more generally required for seamless tube growth and maintenance. These data suggest that distinct components of the secretory pathway have differential contributions to basal and apical membrane growth and maintenance during terminal cell morphogenesis.

Coronary Disease Association With ADAMTS7 Is Due to Protease Activity.

[Figure: see text].

Exposure to Violence in Social Unrest, Resilience, and Mental Health of Older People in Hong Kong.

OBJECTIVE: Older adults are prone to the negative effects of exposure to violence on their mental health. This study aimed to examine the impact of exposure to violence during social unrest and the role of resilience in the mental health of older people. DESIGN: A total of 1,203 people aged 65 years or older were randomly selected for a telephone survey using the random digit dialing numbering method in Hong Kong. MEASUREMENTS: A 13-item scale was developed to measure exposure to violence. The Chinese versions of the Connor-Davidson Resilience Scale and the Startle, Physiological Arousal, Anger, and Numbness scales for measuring mental health status were adopted in the survey. RESULTS: The results showed that the more frequently older people were exposed to information, the more negative mental health status they had. However, exposure to witnessing and experiencing violence was not significantly associated with mental health status. Older adults' level of resilience had a moderating effect between exposure to information and mental health, whereas the effect of exposure to information on mental health was stronger for respondents with lower resilience. CONCLUSION: This study showed that emotional problems caused by exposure to related information among older people should be properly addressed during massive social unrest and conflict. Their resilience capacity is an important moderating factor. Future interventions and support services should focus on enhancing the resilience of older people to better equip them with overcoming problems related to macro-social issues.

Trends in elder abuse and age discrimination during the COVID-19 pandemic in Hong Kong: Findings from a two-wave representative telephone survey study.

OBJECTIVES: Empirical evidence about the heightened risks of elder abuse and age discrimination during the COVID-19 pandemic is scarce. This study aimed to track the changes in rates of both, and investigated their associated factors in the community-dwelling older population in Hong Kong. METHODS: In this two-wave, cross-sectional telephone survey, we interviewed a population-based sample of individuals (≥55 years), and captured the situation of elder abuse and age discrimination before the COVID-19 outbreak (n = 1209, Wave 1: October-December 2019) and during the pandemic (n = 891, Wave 2: December 2020-January 2021). Participants reported their experiences of different types of abuse and discrimination, financial health, subjective well-being, satisfaction with environment, health and social services, and resilience. RESULTS: Abuse was reported by 20.2% of the sample before the outbreak and 17.8% during the pandemic; while discrimination was reported by 24.6% and 29.8% at the two time points, respectively. A drop in physical abuse was observed, but it was accompanied by a rise in discrimination in the form of harassment or refusal of services. Findings of logistic regression analysis show that abuse during the pandemic was associated with younger age, poorer subjective well-being, and lower resilience; while discrimination was associated with female gender, being married, and poorer subjective well-being. CONCLUSIONS: Elder abuse and discrimination were prevalent across time points. The pandemic has highlighted the marginalization of older persons in our communities. There is an urgent need for development of effective interventions to end abuse and discrimination.

Establishing community mental health facilities: a comparative review of Hong Kong and international jurisdictions.

BACKGROUND: The establishment of mental health facilities in the community has been hindered by opposition from local residents in Hong Kong. Through a comparative review, this study aimed to compare the issues related to the process of establishment of community-based mental health facilities between Hong Kong and selected overseas countries and regions. It will better inform the strategies and best practices that can be adopted for the establishment of mental health facilities in Hong Kong. METHODS: Three electronic databases (PubMed, Scopus, and PsycINFO) were used to examine literature on nine jurisdictions in Asia and western societies from 2005 to 2019. In addition, we conducted a number of in-depth interviews with overseas experts to gain in-depth insights and clarify information that was unavailable or unclear. A total of 19,248 articles were identified through the initial search. 71 of them met the inclusion criteria. In addition, 20 articles about the establishment of other types of community facilities or sensitive facilities were identified from supplementary sources. RESULTS: Most Western countries and Singapore have adopted regulations or laws to reduce public discrimination against particular groups, giving them corresponding human rights and legislating to demarcate the use of land in the community. Regions close to Hong Kong emphasize communication with community leaders to obtain support for sensitive services or facilities. CONCLUSIONS: Hong Kong may consider strengthening the land zoning ordinance in relation to community sensitive facilities, as well as increasing communication with the community and considering the possibility of locating facilities in government buildings.

Dementia literacy of racially minoritized people in a Chinese society: a qualitative study among South Asian migrants in Hong Kong.

OBJECTIVES: Research on dementia literacy in Chinese societies is still emerging, and this is especially the case among racially minoritized groups. The present study explored the knowledge, causal beliefs, and help-seeking behaviors of South Asian migrants in Hong Kong about dementia. It also investigated existing community barriers related to dementia knowledge and help-seeking. DESIGN: We conducted a qualitative study from a purposive sample of 38 older people and family caregivers from India, Pakistan, and Nepal who lived in Hong Kong. Focus groups and individual in-depth interviews were used to gather information, while thematic analysis was employed to analyze the data. RESULTS: Five main themes were identified: normalization with stigmatization of dementia; spiritual and psychosocial attributions of dementia; familial responsibility despite potential caregiving burden; uncertainties versus openness to professional care; and barriers and opportunities in dementia literacy. Ethnic minorities recognized dementia as a disease of normal aging or a mental disorder. They also perceived spiritual and psychosocial factors as their main causes. While participants recognized the potential burden of dementia caregiving, families were their first point of help-seeking, as many of them expressed contrasting feelings of confidence or doubt toward professional services. Utilization of health education strategies, together with collaboration with community leaders, could address the barriers to dementia literacy. CONCLUSIONS: This is the first study to explore how ethnic minorities in Asia perceive dementia and its related help-seeking behaviors in their communities. South Asian migrants in Hong Kong have a limited understanding of dementia and may experience delays in obtaining relevant community services. While culture influenced their knowledge, health education may address their misperceptions and help-seeking behaviors toward dementia. Culture- and language-specific programs could also improve dementia knowledge and health service access.

Intimate networks of care: Perceptions of intergenerational family care and experiences of ageing among Chinese midlife and older lesbians and gay men.

This article examines how lesbians and gay men imagine and build their 'intimate networks of care' and negotiate moral expectations towards intergenerational family care as they age. To date, little is known about the strength and complexities of different intimate ties or the role of intergenerational dynamics in shaping ageing sexual minority people's care needs and choices. Based on narrative interviews with ageing Chinese lesbians and gay men, the findings reveal their experiences of constantly juggling their ties with families of origin, moral values around intergenerational care and the urge to receive support from and offer support to chosen networks of people. Participants exercised agency in expanding their networks of care by building friendship and (online and offline) community networks for mutual care and support in later life. Nevertheless, as evidenced by the centrality of ageing with(out) children, and the moral obligation of caring for parents in participants' narratives, participants experienced tensions between enacting what was considered morally right/wrong and developing networks of care that were perceived as emotionally intimate. Linking relational sociology with the sociology of morality, we discuss the conceptual utility of 'intimate networks of care' for sociological theorising of the linkages between sexuality, care and relational lives.

Development and evaluation of an infusion active aging education (IAAE) model for university students.

This study proposed and evaluated an infusion active aging education (IAAE) model to help university students develop an age-friendly mind-set and the ability to empower older individuals through intergenerational learning. The IAAE model encompasses the (1) Identification of academic champions from various faculties, (2) Active infusion of cocreated intergenerational activities into discipline-specific curricula; (3) Activity implementation, and (4) Evaluation. In total, 511 students and 129 older adults participated in this study between 2018 and 2020. A mixed-method evaluation was conducted to compare the pretests and posttests results of the students in the intervention (n = 287) and comparison (n = 63) groups and to thematically analyze the data of qualitative in-depth interviews with 29 older adult participants. The results revealed that the intervention group students achieved significant improvements in aging-related knowledge, attitudes, skills, and professional interests, whereas the comparison group students achieved significant improvement only in aging-related knowledge. The older adult participants reported improvements in their understanding of young people, sense of self-worth, and generativity. The IAAE model can contribute to the growth of age-friendly practices by enriching university curricula with intergenerational interactions through a participatory and nonprescriptive approach.

Back to the campus: Lifelong experience of older learners in a university setting.

This study focuses on older participants' experiences of and views on a lifelong learning program at the Hong Kong Polytechnic University in Hong Kong. As many third age adults tend not to have the opportunity to receive tertiary education when they were young, this program aims to fulfil their dream of studying at a university and boost their self-esteem and self-confidence. Using qualitative research methods, this research was conducted after the MiniU program (supported by the Institute of Active Aging of the Hong Kong Polytechnic University). Semi-structured interviews were conducted with 32 participants after the program. While participants had acquired knowledge and experience of university life from the Mini-U program, they also reported concerns and difficulties with participation including difficulties in memorizing course content and financial difficulties. The program has offered a unique opportunity for enhancing participants' interpersonal relationships and wellbeing. The research also further informs the development of creative lifelong learning programs aimed at improving the well-being of older people.

Typology of family caregivers of older persons: A latent profile analysis using elder mistreatment risk and protective factors.

This study sought to identify subpopulations of caregivers of older persons based on their profiles of individual characteristics and caregiving contexts and aimed at examining the associations between caregiver profiles and elder mistreatment. A convenient sample of 600 adult caregivers of community-dwelling older people in Hong Kong participated. Results of latent profile analysis support a typology of 3 distinctive caregiver profiles: (a) non-vulnerable caregivers; (b) isolated, vulnerable caregivers; and (c) traumatized, vulnerable caregivers. Isolated and traumatized caregivers reported greater risk factors related to elder mistreatment: They had higher levels of caregiver stress and burden, lower levels of social support and resilience, greater neurotic personality orientation and problematic gambling behavior, and more severe childhood traumatic experiences. The two groups also display significantly higher level of abusive behaviors than non-vulnerable caregivers.

Social Workers' Involvement in Developing and Implementing Social Programs for Older Adults During the COVID-19 Pandemic in Nigeria: A Concept Paper and Suggestions for Action Plans.

Social workers, especially in the Global North/developed countries such as the United States of America, Australia, Canada, and the United Kingdom, have been actively involved in implementing social programs to improve the psychosocial, health, and wellbeing of older adults during the COVID-19 pandemic. However, this is not the case in the Global South/developing countries like Nigeria, Ghana, etc. This concept paper aims to describe the current state of Nigerian social workers' role in developing and implementing social programs for older adults during the COVID-19 pandemic and to identify action plans for further strengthening their involvement. We systematically reviewed the literature to identify Nigerian social workers' role in developing and implementing social programs for older adults during COVID-19. Our review reflected that social workers are rarely involved in developing and implementing social programs; when involved, their involvement is on a consultation basis, which limits their active involvement in multidisciplinary team of COVID-19 prevention and vaccination ad hoc committees in Nigeria.

Carbon Dot Therapeutic Platforms: Administration, Distribution, Metabolism, Excretion, Toxicity, and Therapeutic Potential.

Ultrasmall nanoparticles are often grouped under the broad umbrella term of "nanoparticles" when reported in the literature. However, for biomedical applications, their small sizes give them intimate interactions with biological species and endow them with unique functional physiochemical properties. Carbon quantum dots (CQDs) are an emerging class of ultrasmall nanoparticles which have demonstrated considerable biocompatibility and have been employed as potent theragnostic platforms. These particles find application for increasing drug solubility and targeting, along with facilitating the passage of drugs across impermeable membranes (i.e., blood brain barrier). Further functionality can be triggered by various environmental conditions or external stimuli (i.e., pH, temperature, near Infrared (NIR) light, ultrasound), and their intrinsic fluorescence is valuable for diagnostic applications. The focus of this review is to shed light on the therapeutic potential of CQDs and identify how they travel through the body, reach their site of action, administer therapeutic effect, and are excreted. Investigation into their toxicity and compatibility with larger nanoparticle carriers is also examined. The future of CQDs for theragnostic applications is promising due to their multifunctional attributes and documented biocompatibility. As nanomaterial platforms become more commonplace in clinical treatments, the commercialization of CQD therapeutics is anticipated.

Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling.

Single-cell RNA sequencing has enabled the decomposition of complex tissues into functionally distinct cell types. Often, investigators wish to assign cells to cell types through unsupervised clustering followed by manual annotation or via 'mapping' to existing data. However, manual interpretation scales poorly to large datasets, mapping approaches require purified or pre-annotated data and both are prone to batch effects. To overcome these issues, we present CellAssign, a probabilistic model that leverages prior knowledge of cell-type marker genes to annotate single-cell RNA sequencing data into predefined or de novo cell types. CellAssign automates the process of assigning cells in a highly scalable manner across large datasets while controlling for batch and sample effects. We demonstrate the advantages of CellAssign through extensive simulations and analysis of tumor microenvironment composition in high-grade serous ovarian cancer and follicular lymphoma.

FOXL2 in adult-type granulosa cell tumour of the ovary: oncogene or tumour suppressor gene?

A recurrent mutation in FOXL2 (c.402C>G; p.C134W) is present in over 95% of adult-type granulosa cell tumours (AGCTs). In contrast, various loss-of-function mutations in FOXL2 lead to the development of blepharophimosis, ptosis, and epicanthus inversus syndrome (BPES). BPES is characterised by an eyelid malformation often accompanied with primary ovarian insufficiency. Two recent studies suggest that FOXL2 C402G is a gain- or change-of-function mutation with altered DNA-binding specificity. Another study proposes that FOXL2 C402G is selectively targeted for degradation, inducing somatic haploinsufficiency, suggesting its role as a tumour suppressor. The latter study relies on data indicative of an FOXL2 allelic imbalance in AGCTs. Here we present RNA-seq data as genetic evidence that no real allelic imbalance is observed at the transcriptomic level in AGCTs. Additionally, there is no loss of protein expression in tumours harbouring the mutated allele. These data and other features of this mutation compared to other oncogenes and tumour suppressor genes argue strongly against FOXL2 being a tumour suppressor in this context. Given the likelihood that FOXL2 C402G is oncogenic, targeting the variant protein or its downstream consequences is the most viable path forward to identifying an effective treatment for this cancer. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.