Translational Genomics Research Institute

Background As a member of the liprin‐α family of proteins, the functional relevance of PPFIA3 in cancer remains unclear. We aim to evaluate the role of PPFIA3 in pan‐cancer. Methods A large amount of RNA‐seq data was obtained from the TCGA and GTEx databases, using databases such as TISIDB, TIMER, cBioPortal, GEPIA2, HPA, CancerSEA, CellMiner, UALCAN, STRING, Sangerbox, Kaplan–Meier Plotter, and TISMO to analyze the correlation of PPFIA3 expression with tumor prognosis, immune infiltration levels, immune checkpoints, tumor mutational burden (TMB), microsatellite instability (MSI), methylation levels, immune therapy, drug sensitivity, and so forth. Results PPFIA3 expression is commonly elevated in most cancers and is associated with poor prognosis. Furthermore, high PPFIA3 expression significantly correlates with immune regulatory genes, immune checkpoints, TMB, MSI, and methylation status. Additionally, PPFIA3 expression is associated with immune cell composition and infiltration levels. Interestingly, in patients receiving anti‐PD‐L1 therapy, high PPFIA3 expression is associated with improved survival and prognosis. Further analysis suggests that PPFIA3 can serve as a predictive factor for responsiveness to immune checkpoint blockade therapy in breast cancer. Moreover, our results indicate a strong correlation between PPFIA3 and drug sensitivity. Conclusions This pan‐cancer study provides a comprehensive understanding of the critical role of PPFIA3 in human cancer and suggests that PPFIA3 may be a potential prognostic biomarker and therapeutic target for cancer immunotherapy.

Background Previous research has shown that in-lab motor skill acquisition (supervised by an experimenter) is sensitive to biomarkers of Alzheimer disease (AD). However, remote unsupervised screening of AD risk through a skill-based task via the web has the potential to sample a wider and more diverse pool of individuals at scale. Objective The purpose of this study was to examine a web-based motor skill game (“Super G”) and its sensitivity to risk factors of AD (eg, age, sex, APOE ε4 carrier status, and verbal learning deficits). Methods Emails were sent to 662 previous MindCrowd participants who had agreed to be contacted for future research and have their APOE ε4 carrier status recorded and those who were at least 45 years of age or older. Participants who chose to participate were redirected to the Super G site where they completed the Super G task using their personal computer remotely and unsupervised. Once completed, different Super G variables were derived. Linear and logistic multivariable regression was used to examine the relationship between available AD risk factors (age, sex, APOE ε4 carrier status, and verbal learning) and distinct Super G performance metrics. Results Fifty-four participants (~8% response rate) from the MindCrowd web-based cohort (mean age of 62.39 years; 39 females; and 23 APOE ε4 carriers) completed 75 trials of Super G. Results show that Super G performance was significantly associated with each of the targeted risk factors. Specifically, slower Super G response time was associated with being an APOE ε4 carrier (odds ratio 0.12, 95% CI 0.02-0.44; P =.006), greater Super G time in target (TinT) was associated with being male (odds ratio 32.03, 95% CI 3.74-1192,61; P =.01), and lower Super G TinT was associated with greater age ( β −3.97, 95% CI −6.64 to −1.30; P =.005). Furthermore, a sex-by-TinT interaction demonstrated a differential relationship between Super G TinT and verbal learning depending on sex (β male:TinT 6.77, 95% CI 0.34-13.19; P =.04). Conclusions This experiment demonstrated that this web-based game, Super G, has the potential to be a skill-based digital biomarker for screening of AD risk on a large scale with relatively limited resources.

Microneedle (MN) technology is gaining popularity as it offers many benefits and advantages over the conventional drug delivery methods. The transdermal drug delivery system (TDDS) with MNs offers painless, precise, and easy-to-use solutions that can be obtained using cost-effective technologies such as 3D printing. Numerous examples of microneedle applications have been reported for human use, especially given the context of the recent pandemic and the development of vaccination technologies. However, there is limited exploration of microneedles in veterinary medicine. In the following work, we presented a proposal for the efficient production of quickly dissolving microneedle patches from PVP (polyvinylpyrrolidone) and PVA (polyvinyl alcohol) polymers based on a model microneedle array printed using DLP (Digital Light Processing) technology. We have developed a repeatable process in which the obtained microneedles can easily penetrate the outer layers of skin and quickly deliver the model drug. Such a versatile platform can be used, among others, in the treatment of animal gingival diseases, which affect a significant amount of the cat and dog population. An important advantage of the presented solution is the possibility of implementing the whole technological process in a veterinary office in a short time and the possibility of easy adjusting the size of the patches to a specific animal.

Lewy body dementia (LBD) encompasses neurodegenerative dementias characterized by cognitive fluctuations, visual hallucinations, and parkinsonism. Clinical differentiation of LBD from Alzheimer’s disease (AD) remains complex due to symptom overlap, yet approximately 25% of dementia cases are diagnosed as LBD postmortem, primarily identified by the presence of α-synuclein aggregates, tau tangles, and amyloid plaques. These pathological features position LBD as a comorbid condition of both Parkinson’s disease (PD) and AD, with over 50% of LBD cases exhibiting co-pathologies. LBD’s mixed pathology complicates the development of comprehensive models that reflect the full spectrum of LBD’s etiological, clinical, and pathological features. While existing animal and cellular models have facilitated significant discoveries in PD and AD research, they lack specificity in capturing LBD’s unique pathogenic mechanisms, limiting the exploration of therapeutic avenues for LBD specifically. This review assesses widely used PD and AD models in terms of their relevance to LBD, particularly focusing on their ability to replicate human disease pathology and assess treatment efficacy. Furthermore, we discuss potential modifications to these models to advance the understanding of LBD mechanisms and propose innovative research directions aimed at developing models with enhanced etiological, face, predictive, and construct validity.

Background & Aims Epidemiological data suggest that participants with lower vs. higher body mass index (BMI) resist exposure to the obesogenic environment. To test this, we analyzed the relationship between overfeeding-induced weight and fat mass gains with baseline BMI and body fat percentage. Methods In this controlled intervention study, 34 men (age: 26±5 y old; BMI: 25.5±2.4 kg/m2, body fat [DXA]: 19.3±5.1%) consumed for 8 weeks 40% more energy than needed at weight maintenance. The energy costs of weight and fat mass gain were calculated as the 8-week excess energy consumed divided by weight or fat mass gain. Energy expenditure (baseline and after overfeeding) was determined using a metabolic chamber and doubly labeled water. Transcriptomic analysis was conducted from abdominal subcutaneous adipose tissue samples. Results Body weight increased 7.2±2.1 kg and fat mass 4.0±1.4 kg. There was no statistical association between baseline BMI and weight and fat mass gains. However, baseline body fat percentage was significantly associated with weight (r=0.57) and fat mass (r=0.59) gains. Body fat percentage was also statistically associated with energy cost of weight (r=-0.38) and fat mass (r=-0.40) gains. Metabolic adaptation in energy expenditure (adaptive thermogenesis) was unrelated to the energy cost of weight and fat mass gains. Transcriptomics analysis showed that high energy cost of weight gain was associated with up-regulation of inflammation-related pathways. Conclusion Body fat percentage at baseline was inversely associated with overfeeding-induced weight and fat gain resistance. The underlying compensatory response appears unrelated to changes in energy expenditure.

Background Genetic alteration of the MET receptor tyrosine kinase frequently occurs in glioblastoma (GBM). Clinically, bevacizumab treatment results in MET signaling activation, leading to GBM recurrence with a more malignant phenotype. While MET has been a promising therapeutic target, MET inhibitors have not been successful in treating GBM patients. MET-directed chimeric antigen receptor (CAR) T cells hold the promise of targeting MET-positive GBM regardless of genetic alterations or kinase activity. Methods GBM patient-derived xenografts (PDX) harboring MET amplification (METamp) or PTPRZ-MET fusion (ZM) were propagated in vivo followed by glioma stem cell (GSC) isolation. Cell-based assays were used for comparing GSC survival in response to MET inhibitors and CAR T cells. Multi-panel cytokine release was analyzed to profile MET-CAR T cell activation during co-culture with GBM. Orthotopic tumor growth and real-time imaging were performed to evaluate MET-CAR T cell therapeutic efficacy in vivo. Results Although GBM are heterogeneous tumors, neuro-sphere cells isolated from METamp or ZM fusion PDX tumors showed universal cognate genetic MET alteration along with GSC markers such as SOX2 and nestin. Both METamp and ZM fusion tumors showed MET overexpression but only the METamp cells presented activated MET signaling which was vulnerable to MET inhibitors. In contrast, MET-CAR T cells specifically inhibited all MET-positive tumor growth regardless of MET activation status. Conclusions Whereas MET inhibitors are effective in MET-active tumors, MET-CAR T cells eradicate MET-positive GBM growth in an antigen-dependent manner, demonstrating a promising therapeutic approach for treating MET-positive GBM. MET overexpression, especially METamp and ZM fusion may be used to predefine the GBM patients for treating with MET-CAR T cell therapy.

Multiple myeloma, a hematopoietic malignancy of terminally differentiated B cells, is the second most common hematological malignancy after leukemia. While patients have benefited from numerous advances in treatment in recent years resulting in significant increases to average survival time following diagnosis, myeloma remains incurable and relapse is common. To help identify novel therapeutic agents with efficacy against the disease and to search for biomarkers associated with differential response to treatment, a large-scale pharmacological screen was performed with 1,912 small molecule compounds tested at 11 doses for 47 human myeloma cell lines (HMCL). Raw and processed versions of the drug screen dataset are provided, as well as supportive information including drug and cell line metadata and high-level characterization of the most salient features of each. The dataset is publicly available at Zenodo and the workflow code used for data processing and generation of supporting figures and tables are available on GitHub.

Purpose It is recognized that disruptions in circadian behavior, such as with shift work or jet lag, are associated with diminished health. This known relationship implies that people with stronger indices of circadian behavior will exhibit improved physiology. To address the association between rhythmic activity behavior and physiology we proposed that metrics indicative of ‘more rhythmic’ rest-activity patterns would be associated with better cardiorespiratory fitness and walking energetics in a cohort of older adults. Methods Using baseline data from the Study of Muscle, Mobility and Aging (N = 799, Age: 76 ± 5 yrs, 58% female), we quantified metrics describing rhythmic aspects of rest-activity behavior (amplitude, robustness, time of peak activity, others) from continuous wrist-worn accelerometry. We used linear models to examine cross-sectional associations between rhythmic metrics with VO 2peak and walking energetics (cost-capacity ratio at slow and preferred walking speeds) adjusted for age, sex, race, height, health conditions, and other factors. Results Metrics that reflect more rhythmic behavior were associated with VO 2peak (higher amplitude: Q1: 18.4 vs. Q4: 22.0 mL·kg ⁻¹ ·min ⁻¹ ; p-trend <0.001, higher pseudo F-statistic/robustness Q1: 19.2 vs. Q4: 21.3 mL·kg ⁻¹ ·min ⁻¹ ; p-trend <0.001, and earlier time of peak activity (Q1 (earliest): 20.9 vs. Q4 (latest): 19.2 mL·kg ⁻¹ ·min ⁻¹ ; p-trend <0.001). Similar trends were observed with lower cost-capacity ratio at preferred and slow walking speeds (amplitude, pseudo F-statistic, acrophase: p-trend <0.001 for all). Conclusions More rhythmic activity behavior and earlier time of peak activity were associated with better cardiorespiratory fitness and walking energetics. These findings support the framework that rhythmic activity supports healthy physiology. Further investigations are warranted to determine if declines in rhythmicity of human behavior are predictive of disease.

OBJECTIVE Despite the use of multiple glucose-lowering medications, glycemic targets are not met in a significant fraction of people with type 2 diabetes. In this prospective, observational study we assessed the prevalence of hypercortisolism, a potential contributing factor to inadequate glucose control. RESEARCH DESIGN AND METHODS Individuals with type 2 diabetes and HbA1c 7.5%–11.5% (58–102 mmol/mol) on two or more glucose-lowering medications with or without micro-/macrovascular complications or taking multiple blood pressure–lowering medications were screened with a 1-mg dexamethasone suppression test. Common causes of false-positive DSTs were excluded. The primary end point was the prevalence of hypercortisolism, defined as post-DST cortisol >1.8 μg/dL (50 nmol/L). Characteristics associated with hypercortisolism were assessed with multiple logistic regression. The percentage and characteristics of participants with hypercortisolism and adrenal imaging abnormalities were also assessed. RESULTS Post-DST cortisol was unsuppressed in 252 of 1,057 participants (prevalence 23.8%; 95% CI 21.3, 26.5). Hypercortisolism prevalence was 33.3% among participants with cardiac disorders and 36.6% among those taking three or more blood pressure–lowering medications. Adrenal imaging abnormalities were reported in 34.7% of participants with hypercortisolism. Use of sodium–glucose cotransporter 2 inhibitors (odds ratio 1.558), maximum-dose glucagon-like peptide 1 receptor agonists (1.544), tirzepatide (1.981), or a higher number of blood pressure–lowering medications (1.390); older age (1.316); BMI <30 kg/m2 (1.639); non-Latino/Hispanic ethnicity (3.718); and use of fibrates (2.676) or analgesics (1.457) were associated with higher prevalence (all P < 0.03). CONCLUSIONS Hypercortisolism was associated with hyperglycemia in approximately one-quarter of individuals with inadequately controlled type 2 diabetes despite multiple medications.

A meaningful number of patients with PAH die suddenly, and there is little data to understand the events surrounding sudden death in PAH. We tested the hypothesis that sudden death is associated with pre‐mortem ECG or hemodynamics changes compared to those who died of RHF. We extracted data from the Vanderbilt University Medical Center Synthetic Derivative. Patients 18 years of age and older with Group 1 PAH secondary to any etiology who died between 2009 and 2017 with both ECG and RHC data from the inpatient and outpatient setting were included in the study. Continuous variables were compared using the Wilcoxon rank‐sum test while categorical variables were compared using the χ² test. Logistic regression models, adjusted for age and sex, were then used to evaluate the association between death and specific ECG or RHC measurements. Comparing the final ECG before death, those who died of SD had significantly shorter terminal 40 ms interval of the QRS than those who died of RHF, which became nonsignificant when adjusted for age and sex. We observed differences in baseline RHC data between SD and RHF including higher RV systolic pressure which remained significant when adjusted for age and sex. Using this data, we hope to find clinical data that can be used to predict increased risk of sudden death and aid in stratifying Group I PAH patients to earlier and more aggressive interventions.

Interpretation of variants identified during genetic testing is a significant clinical challenge. In this study, we developed a high-throughput CDKN2A functional assay and characterized all possible human CDKN2A missense variants. We found that 17.7% of all missense variants were functionally deleterious. We also used our functional classifications to assess the performance of in silico models that predict the effect of variants, including recently reported models based on machine learning. Notably, we found that all in silico models performed similarly when compared to our functional classifications with accuracies of 39.5–85.4%. Furthermore, while we found that functionally deleterious variants were enriched within ankyrin repeats, we did not identify any residues where all missense variants were functionally deleterious. Our functional classifications are a resource to aid the interpretation of CDKN2A variants and have important implications for the application of variant interpretation guidelines, particularly the use of in silico models for clinical variant interpretation.

Background Because implementation remains the biggest challenge to Ending the HIV Epidemic in the United States (EHE), since 2019, the National Institutes of Health (NIH) has funded 248 supplements to identify best practices for delivering evidence-based HIV interventions. NIH also funded a coordination center [Implementation Science (IS) Coordination Initiative “ISCI”] and 9 consultation hubs (“Hubs”) to provide technical assistance and cross-project information sharing, measure harmonization, and data synthesis. This article describes this unique capacity-building model, lessons learned from the first 5 years, and opportunities created by this infrastructure. Methods Beginning in FY20, Hubs were assigned 7–9 funded supplement projects in EHE priority jurisdictions. Primary Hub services included direct coaching, multiproject meetings, communities of practice, and technical webinars. ISCI and the Hubs met monthly to reflect on project support, discuss ways to enhance HIV IS broadly, and assess projects' use of Hub services. Findings Hub engagement strategies included grouping projects by HIV intervention type, setting data reporting expectations early, and tailoring engagement based on EHE team IS expertise. Support and coordination provided by the Hubs and ISCI have developed generalizable IS knowledge from local knowledge (e.g., publications and tools). The network of ISCI, the Hubs, and EHE projects have also led to infrastructure for conducting multisite HIV implementation research. Implications for D&I Science The Hub model is a novel, systemwide approach for rapidly improving IS capacity in a field. Implementation of this model will continue to be refined through an ongoing evaluation and as the funding transitions to regular, nonsupplement NIH funding mechanisms.

Background Rhipicephalus (Boophilus) microplus causes significant cattle production losses worldwide because it transmits Babesia bovis and B. bigemina, the causative agents of bovine babesiosis. Control of these ticks has primarily relied on treatment of cattle with chemical acaricides, but frequent use, exacerbated by the one-host lifecycle of these ticks, has led to high-level resistance to multiple classes of acaricides. Consequently, new approaches for control, such as anti-tick vaccines, are critically important. Key to this approach is targeting highly conserved antigenic epitopes to reduce the risk of vaccine escape in heterologous tick populations. Methods We evaluated amino acid conservation within 14 tick proteins across 167 R. microplus collected from geographically diverse locations in the Americas and Pakistan using polymerase chain reaction (PCR) amplicon sequencing and in silico translation of exons. Results We found that amino acid conservation varied considerably across these proteins. Only the voltage-dependent anion channel (VDAC) was fully conserved in all R. microplus samples (protein similarity 1.0). Four other proteins were highly conserved: the aquaporin RmAQP1 (0.989), vitellogenin receptor (0.985), serpin-1 (0.985), and subolesin (0.981). In contrast, the glycoprotein Bm86 was one of the least conserved (0.889). The Bm86 sequence used in the original Australian TickGARD vaccine carried many amino acid replacements compared with the R. microplus populations examined here, supporting the hypothesis that this vaccine target is not optimal for use in the Americas. By mapping amino acid replacements onto predicted three-dimensional (3D) protein models, we also identified amino acid changes within several small-peptide vaccines targeting portions of the aquaporin RmAQP2, chitinase, and Bm86. Conclusions These findings emphasize the importance of thoroughly analyzing protein variation within anti-tick vaccine targets across diverse tick populations before selecting candidate vaccine antigens. When considering protein conservation alone, RmAQP1, vitellogenin receptor, serpin-1, subolesin, and especially VDAC rank as high-priority anti-tick vaccine candidates for use in the Americas and perhaps globally.

The field of precision nutrition aims to develop dietary approaches based on individual biological factors such as genomics or the gut microbiota. The gut microbiota, which is the highly individualized and complex community of microbes residing in the colon, is a key contributor to human physiology. Although gut microbes play multiple roles in the metabolism of nutrients, their role in modulating the absorption of dietary energy from foods that escape digestion in the small intestine has the potential to variably affect energy balance and, thus, body weight. The fate of this energy, and its subsequent impact on body weight, is well described in rodents and is emerging in humans. This narrative review is focused on recent clinical evidence of the role of the gut microbiota in human energy balance, specifically its impact on energy available to the human host. Despite recent progress, remaining gaps in knowledge present opportunities for developing and implementing strategies to understand causal microbial mechanisms related to energy balance. We propose that implementing rigorous microbiota-focused measurements in the context of innovative clinical trial designs will elucidate integrated diet-host-gut microbiota mechanisms. These mechanisms are primed to be targets for precision nutrition interventions to optimize energy balance to achieve desired weight outcomes. Given the magnitude and impact of the obesity epidemic, implementing these interventions within comprehensive weight management paradigms has the potential to be of public health significance.

Functional CD8 ⁺ T cell immunity is essential for immune surveillance and host defense against infection and tumors. Epigenetic mechanisms, particularly RNA modification, in controlling CD8 ⁺ T cell immune response is not fully elucidated. Here, by T cell-specific deletion of fat mass and obesity-associated protein (FTO), a critical N6-methyladenosine (m ⁶ A) demethylase, we revealed that FTO was indispensable for adequate CD8 ⁺ T cell immune response and protective function. FTO ablation led to considerable cell death in activated CD8 ⁺ T cells, which was attributed to cell apoptosis. MeRIP-seq analysis revealed an increase in m ⁶ A methylation on Fas mRNA in FTO-deficient CD8 ⁺ T cells. The loss of FTO promoted Fas expression via enhancing the Fas mRNA stability, which depended on the m ⁶ A reader insulin-like growth factor-2 mRNA-biding proteins 3 (IGF2BP3). Mutation of the Fas m ⁶ A sites or knockdown IGF2BP3 could normalize the upregulated Fas expression and apoptosis levels caused by FTO ablation in CD8 ⁺ T cells. Our findings delineate a novel epigenetic regulatory mechanism of FTO-mediated m ⁶ A modification in supporting CD8 ⁺ T cell survival and effector responses, providing new insights into understanding the post-transcriptional regulation in CD8 ⁺ T cell immunological functions and the potential therapeutic intervention.

Hypertrophic cardiomyopathy (HCM) is the most common genetic myocardial disease, characterized by asymmetric left ventricular hypertrophy (LVH) due to sarcomeric mutations. Aortic stenosis (AS) results in concentric LVH, due to pressure overload. The aim of this study was to identify signaling pathways differentially regulated in HCM compared to AS, using plasma proteomic profiling. 76 HCM cases and 36 AS controls were matched by age and sex. A machine-learning (ML) model to predict HCM was built in the training set (70% cohort) and examined in the test set (30% cohort). Pathway analysis of proteins differentially expressed between HCM and AS was performed. The ML model accurately distinguished HCM from AS, with area under the receiver operating characteristic curve of 0.90 (95% CI: 0.79–1.00). Pathway analysis revealed differential regulation of Ras-MAPK, inflammatory and metabolic pathways. In conclusion, this study identified distinctive proteomic profiles and signaling pathways underlying LVH in HCM compared to AS. Graphical Abstract Comprehensive plasma proteomic profiling enables identification of distinctive proteomic profiles and signaling pathways underlying left ventricular hypertrophy in hypertrophic cardiomyopathy compared to aortic stenosis.

The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies1, 2–3. Consequently, our understanding of the evolution of our species is incomplete. Here we present haplotype-resolved reference genomes and comparative analyses of six ape species: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan and siamang. We achieve chromosome-level contiguity with substantial sequence accuracy (<1 error in 2.7 megabases) and completely sequence 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, to provide in-depth evolutionary insights. Comparative analyses enabled investigations of the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference genome. Such regions include newly minted gene families in lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes and subterminal heterochromatin. This resource serves as a comprehensive baseline for future evolutionary studies of humans and our closest living ape relatives.