Search

Whole-genome and transcriptome sequencing were performed to identify potential therapeutic strategies in the absence of viable treatment options for a patient initially diagnosed with vulvar adenocarcinoma. Genomic events were prioritized by comparison against variant distributions in the TCGA pan-cancer data set and complemented with detailed transcriptome sequencing and copy-number analysis. These findings were considered against published scientific literature in order to evaluate the functional effects of potentially relevant genomic events. Analysis of the transcriptome against a background of 27 TCGA cancer types led to reclassification of the tumor as a primary HER2+ mammary-like adenocarcinoma of the vulva. This revised diagnosis was subsequently confirmed by follow-up immunohistochemistry for a mammary-like adenocarcinoma. The patient was treated with chemotherapy and targeted therapies for HER2+ breast cancer. The detailed pathology and genomic findings of this case are presented herein.

IDH1 mutation is the earliest genetic alteration in low-grade gliomas (LGGs), but its role in tumor recurrence is unclear. Mutant IDH1 drives overproduction of the oncometabolite d-2-hydroxyglutarate (2HG) and a CpG island (CGI) hypermethylation phenotype (G-CIMP). To investigate the role of mutant IDH1 at recurrence, we performed a longitudinal analysis of 50 IDH1 mutant LGGs. We discovered six cases with copy number alterations (CNAs) at the IDH1 locus at recurrence. Deletion or amplification of IDH1 was followed by clonal expansion and recurrence at a higher grade. Successful cultures derived from IDH1 mutant, but not IDH1 wild type, gliomas systematically deleted IDH1 in vitro and in vivo, further suggestive of selection against the heterozygous mutant state as tumors progress. Tumors and cultures with IDH1 CNA had decreased 2HG, maintenance of G-CIMP, and DNA methylation reprogramming outside CGI. Thus, while IDH1 mutation initiates gliomagenesis, in some patients mutant IDH1 and 2HG are not required for later clonal expansions.

Comprehensive multiplatform analysis of 80 uveal melanomas (UM) identifies four molecularly distinct, clinically relevant subtypes: two associated with poor-prognosis monosomy 3 (M3) and two with better-prognosis disomy 3 (D3). We show that BAP1 loss follows M3 occurrence and correlates with a global DNA methylation state that is distinct from D3-UM. Poor-prognosis M3-UM divide into subsets with divergent genomic aberrations, transcriptional features, and clinical outcomes. We report change-of-function SRSF2 mutations. Within D3-UM, EIF1AX- and SRSF2/SF3B1-mutant tumors have distinct somatic copy number alterations and DNA methylation profiles, providing insight into the biology of these low- versus intermediate-risk clinical mutation subtypes.

Current therapies for medulloblastoma, a highly malignant childhood brain tumour, impose debilitating effects on the developing child, and highlight the need for molecularly targeted treatments with reduced toxicity. Previous studies have been unable to identify the full spectrum of driver genes and molecular processes that operate in medulloblastoma subgroups. Here we analyse the somatic landscape across 491 sequenced medulloblastoma samples and the molecular heterogeneity among 1,256 epigenetically analysed cases, and identify subgroup-specific driver alterations that include previously undiscovered actionable targets. Driver mutations were confidently assigned to most patients belonging to Group 3 and Group 4 medulloblastoma subgroups, greatly enhancing previous knowledge. New molecular subtypes were differentially enriched for specific driver events, including hotspot in-frame insertions that target KBTBD4 and 'enhancer hijacking' events that activate PRDM6. Thus, the application of integrative genomics to an extensive cohort of clinical samples derived from a single childhood cancer entity revealed a series of cancer genes and biologically relevant subtype diversity that represent attractive therapeutic targets for the treatment of patients with medulloblastoma.

Liver cancer has the second highest worldwide cancer mortality rate and has limited therapeutic options. We analyzed 363 hepatocellular carcinoma (HCC) cases by whole-exome sequencing and DNA copy number analyses, and we analyzed 196 HCC cases by DNA methylation, RNA, miRNA, and proteomic expression also. DNA sequencing and mutation analysis identified significantly mutated genes, including LZTR1, EEF1A1, SF3B1, and SMARCA4. Significant alterations by mutation or downregulation by hypermethylation in genes likely to result in HCC metabolic reprogramming (ALB, APOB, and CPS1) were observed. Integrative molecular HCC subtyping incorporating unsupervised clustering of five data platforms identified three subtypes, one of which was associated with poorer prognosis in three HCC cohorts. Integrated analyses enabled development of a p53 target gene expression signature correlating with poor survival. Potential therapeutic targets for which inhibitors exist include WNT signaling, MDM4, MET, VEGFA, MCL1, IDH1, TERT, and immune checkpoint proteins CTLA-4, PD-1, and PD-L1.

We performed genomic, epigenomic, transcriptomic, and proteomic characterizations of uterine carcinosarcomas (UCSs). Cohort samples had extensive copy-number alterations and highly recurrent somatic mutations. Frequent mutations were found in TP53, PTEN, PIK3CA, PPP2R1A, FBXW7, and KRAS, similar to endometrioid and serous uterine carcinomas. Transcriptome sequencing identified a strong epithelial-to-mesenchymal transition (EMT) gene signature in a subset of cases that was attributable to epigenetic alterations at microRNA promoters. The range of EMT scores in UCS was the largest among all tumor types studied via The Cancer Genome Atlas. UCSs shared proteomic features with gynecologic carcinomas and sarcomas with intermediate EMT features. Multiple somatic mutations and copy-number alterations in genes that are therapeutic targets were identified.

Cervical cancer remains one of the leading causes of cancer-related deaths worldwide. Here we report the extensive molecular characterization of 228 primary cervical cancers, one of the largest comprehensive genomic studies of cervical cancer to date. We observed notable APOBEC mutagenesis patterns and identified SHKBP1, ERBB3, CASP8, HLA-A and TGFBR2 as novel significantly mutated genes in cervical cancer. We also discovered amplifications in immune targets CD274 (also known as PD-L1) and PDCD1LG2 (also known as PD-L2), and the BCAR4 long non-coding RNA, which has been associated with response to lapatinib. Integration of human papilloma virus (HPV) was observed in all HPV18-related samples and 76% of HPV16-related samples, and was associated with structural aberrations and increased target-gene expression. We identified a unique set of endometrial-like cervical cancers, comprised predominantly of HPV-negative tumours with relatively high frequencies of KRAS, ARID1A and PTEN mutations. Integrative clustering of 178 samples identified keratin-low squamous, keratin-high squamous and adenocarcinoma-rich subgroups. These molecular analyses reveal new potential therapeutic targets for cervical cancers.

Informal urban communities (IUCs) in sub-Saharan Africa constitute some two-thirds of SSA cities. IUCs are often associated with lower-quality housing, low-income populations, low car ownership, and poor mobility infrastructure. As such, most IUC dwellers rely on shared mobility modes that are unsafe and inconvenient. The current study examines potential and perceived access in terms of travel distance and time to six selected socioeconomic activity types in selected IUCs in Kumasi-Ghana, and Dar es Salaam-Tanzania. This was underpinned by evaluating residents' perception of ease of access to workplace in relation to demographics, neighborhood characteristics, transport services characteristics, and travel characteristics. The applied multinomial logistic regression identified factors relating to age, education, income, travel time, road condition, access to major roads, travel modes, community location, inclusivity, safety, and affordability as strong indicators to enhance travel experiences. Across all activity types, the potential travel time underestimates the perceived travel time by 133% in Kumasi-Ghana, and 50% in Dar es Salaam-Tanzania. The overall access to socioeconomic activities based on travel distance and times was found to be relatively more favorable in Kumasi-Ghana than those in Dar es Salaam-Tanzania. [ABSTRACT FROM AUTHOR]

BackgroundDespite the rapid growth in the sophistication of research on bipolar disorder (BD), the field faces challenges in improving quality of life (QoL) and symptom outcomes, adapting treatments for marginalized communities, and disseminating research insights into real-world practice. Community-based participatory research (CBPR)-research that is conducted as a partnership between researchers and community members-has helped address similar gaps in other health conditions. This paper aims to improve awareness of the potential benefits of CBPR in BD research.MethodsThis paper is a product of the International Society for Bipolar Disorders (ISBD) Taskforce on Community Engagement which includes academic researchers, healthcare providers, people with lived experience of BD, and stakeholders from BD community agencies. Illustrative examples of CBPR in action are provided from two established centres that specialize in community engagement in BD research: the Collaborative RESearch Team to study psychosocial issues in BD (CREST.BD) in Canada, and the Spectrum Centre for Mental Health Research in the United Kingdom.Results and discussionWe describe the philosophy of CBPR and then introduce four core research areas the BD community has prioritized for research: new treatment approaches, more comprehensive outcome assessments, tackling stigma, and enhanced understanding of positive outcomes. We then describe ways in which CBPR is ideal for advancing each of these research areas and provide specific examples of ways that CBPR has already been successfully applied in these areas. We end by noting potential challenges and mitigation strategies in the application of CBPR in BD research.ConclusionsWe believe that CBPR approaches have significant potential value for the BD research community. The observations and concerns of people with BD, their family members, and supports clearly represent a rich source of information. CBPR approaches provide a collaborative, equitable, empowering orientation to research that builds on the diversity of strengths amongst community stakeholders. Despite the potential merits of this approach, CBPR is as yet not widely used in the BD research field, representing a missed opportunity.

The role of staff involved with undergraduate admissions and recruitment has changed since the turn towards marketisation in higher education. This article focuses on the system in England following both a sharp rise in student fees and an associated tendency for the public university agenda and related social priorities, such as widening participation, to come up against more private and commercial priorities, such as business engagement, league table performance and internationalisation. Drawing on evidence from detailed interviews with admissions personnel, both academic and non-academic, across three disciplines within one higher prestige university, we revisit the notion of selectivity and the practice of selection. Tensions are revealed between two opposing approaches: a more traditional model of university admissions, as based on local knowledge and sensitivity towards underrepresented groups, and a purportedly merit-driven model, as driven by perceived market position. We explore the intricate and often unexpected ways in which staff reconcile their professed beliefs with their professional practices, and the complex identity work needed to renegotiate personal values in light of shifting institutional needs. Findings are offered as a microcosm for broader trends in the higher education sector.

The calculus concepts of concavity and inflection points are critical for a complete understanding of quantities' behavior, making them important topics of research for those interested in the intersections of STEM disciplines. This study seeks to provide insight into this area by reporting on trends in students' concept projections of these concepts in a range of real-world contexts, including temperature, economics, human height, and the universe's expansion. While the students mostly thought of concavity and inflection points in pure mathematics as shapes associated with graphs, the projections with the real-world contexts were based much more on changing rates of change. Pedagogically important student confusions were also evident in their attempts at applying concavity and inflection points to the real-world contexts, and this paper uses the concept projection perspective to identify possible sources of these confusions.

The association of thyroid function with essential and non-essential amino acids is understudied, despite their common metabolic roles. Thus, our aim was to evaluate the association of thyroid function with the levels of branched-chain amino acids (BCAAs—leucine, isoleucine, and valine) and of alanine in the general population. We utilized data from the São Paulo research center of ELSA-Brasil, a longitudinal population-based cohort study. Thyroid parameters included thyroid stimulating hormone (TSH), free T4 and free T3 levels, and the FT4:FT3 ratio. BCAAs and alanine were analyzed on a fully automated NMR platform. The current analysis included euthyroid participants and participants with subclinical hyperthyroidism and hypothyroidism. We used Pearson's coefficient to quantify the correlation between thyroid-related parameters and amino acids. Linear regression models were performed to analyze whether thyroid parameters were associated with BCAAs and alanine levels. We included 4098 participants (51.3 ± 9.0 years old, 51.5% women) in this study. In the most adjusted model, higher levels of TSH were associated with higher levels of alanine, FT4 levels were inversely associated with isoleucine levels, FT3 levels were statistically significant and positively associated with valine and leucine, and the T3:T4 ratio was positively associated with all amino acids. We observed that subclinical hypothyroidism was positively associated with isoleucine and alanine levels in all models, even after full adjustment. Our findings highlight the association of subclinical hypothyroidism and thyroid-related parameters (including TSH, free T4, free T3, and FT4:FT3 ratio) with BCAAs and alanine. Further studies are needed to explore the mechanisms underlying this association. These insights contribute to our understanding of the influence of thyroid-related parameters on BCAA and alanine metabolism. [ABSTRACT FROM AUTHOR]