Pan-cancer proteogenomics characterization of tumor immunity

Despite the successes of immunotherapy in cancer treatment over recent decades, less than <10%-20% cancer cases have demonstrated durable responses from immune checkpoint blockade. To enhance the efficacy of immunotherapies, combination therapies suppressing multiple immune evasion mechanisms are increasingly contemplated. To better understand immune cell surveillance and diverse immune evasion responses in tumor tissues, we comprehensively characterized the immune landscape of more than 1,000 tumors across ten different cancers using CPTAC pan-cancer proteogenomic data. We identified seven distinct immune subtypes based on integrative learning of cell type compositions and pathway activities. We then thoroughly categorized unique genomic, epigenetic, transcriptomic, and proteomic changes associated with each subtype. Further leveraging the deep phosphoproteomic data, we studied kinase activities in different immune subtypes, which revealed potential subtype-specific therapeutic targets. Insights from this work will facilitate the development of future immunotherapy strategies and enhance precision targeting with existing agents.

The role community-based healthcare providers play in managing hard-to-heal wounds

It is common for community-based healthcare providers (CHPs)-many of whom have not received specialised training in wound care-to deliver initial and ongoing management for various wound types and diverse populations. Wounds in any setting can rapidly transition to a stalled, hard-to-heal wound (HTHW) that is not following a normal healing trajectory. Failure to recognise or address issues that cause delayed healing can lead to increased costs, healthcare utilisation and suffering. To encourage early intervention by CHPs, a panel of wound care experts developed actionable evidence-based recommendations for CHPs delineating characteristics and appropriate care in identifying and treating HTHWs. A HTHW is a wound that fails to progress towards healing with standard therapy in an orderly and timely manner and should be referred to a qualified wound care provider (QWCP) for advanced assessment and diagnosis if not healed or reduced in size by 40%-50% within 4 weeks. HTHWs occur in patients with multiple comorbidities, and display increases in exudate, infection, devitalised tissue, maceration or pain, or no change in wound size. CHPs can play an important initial role by seeing the individual's HTHW risk, addressing local infection and providing an optimal wound environment. An easy-to-follow one-page table was developed for the CHP to systematically identify, evaluate and treat HTHWs, incorporating a basic toolkit with items easily obtainable in common office/clinic practice settings. A flow chart using visual HTHW clinical cues is also presented to address CHPs with different learning styles. These tools encourage delivery of appropriate early interventions that can improve overall healthcare efficiency and cost.

A brief nonattachment intervention based on the three marks of existence: development, rationale, and initial evidence

BACKGROUND

The practices described in Buddhist philosophy are essentially a suite of non-theistic cognitive and behavioral interventions designed to induce nonattachment (N-A), which can be defined in terms of the absence of a need for one's personal reality to be other than it is. Although meditative practices have received attention in multiple literatures, the cognitive analogs to these behaviorally-oriented practices have not.

DESIGN

Two experiments involving undergraduate participants (total N = 239; M age = 19.04) investigated whether the provision of wisdom related to the Three Marks of Existence (i.e., some degree of suffering is inevitable, there is impermanence, and many events are not in our control) could result in (1) higher nonattachment attitudes, (2) lower threat appraisals, (3) lower stressor reactivity, and (4) shorter emotion reaction durations.

RESULTS

With moderate to large effect sizes, the Three Marks trainings (relative to placebo or control conditions) resulted in (1) higher nonattachment attitudes, (2) lower threat appraisals, (3) no differences in negative emotional intensity, but 4) shorter emotion durations.

CONCLUSIONS

These results provide preliminary evidence that enduring cognitive trainings such as the Three Marks can be an effective tool to increase acceptance-related attitudes while attenuating negative reactivity.

Genome-wide association study of prostate-specific antigen levels in 392,522 men identifies new loci and improves cross-ancestry prediction

We conducted a multi-ancestry genome-wide association study of prostate-specific antigen (PSA) levels in 296,754 men (211,342 European ancestry; 58,236 African ancestry; 23,546 Hispanic/Latino; 3,630 Asian ancestry; 96.5% of participants were from the Million Veteran Program). We identified 318 independent genome-wide significant (p≤5e-8) variants, 184 of which were novel. Most demonstrated evidence of replication in an independent cohort (n=95,768). Meta-analyzing discovery and replication (n=392,522) identified 447 variants, of which a further 111 were novel. Out-of-sample variance in PSA explained by our new polygenic risk score reached 16.9% (95% CI=16.1%-17.8%) in European ancestry, 9.5% (95% CI=7.0%-12.2%) in African ancestry, 18.6% (95% CI=15.8%-21.4%) in Hispanic/Latino, and 15.3% (95% CI=12.7%-18.1%) in Asian ancestry, and lower for higher age. Our study highlights how including proportionally more participants from underrepresented populations improves genetic prediction of PSA levels, with potential to personalize prostate cancer screening.

Proteogenomic data and resources for pan-cancer analysis

The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) investigates tumors from a proteogenomic perspective, creating rich multi-omics datasets connecting genomic aberrations to cancer phenotypes. To facilitate pan-cancer investigations, we have generated harmonized genomic, transcriptomic, proteomic, and clinical data for >1000 tumors in 10 cohorts to create a cohesive and powerful dataset for scientific discovery. We outline efforts by the CPTAC pan-cancer working group in data harmonization, data dissemination, and computational resources for aiding biological discoveries. We also discuss challenges for multi-omics data integration and analysis, specifically the unique challenges of working with both nucleotide sequencing and mass spectrometry proteomics data.

Dysregulated Emotion and Trying Substances in Childhood: Insights from a Large Nationally Representative Cohort Study

OBJECTIVE

Transdiagnostic perspectives on the shared origins of mental illness posit that dysregulated emotion may represent a key driving force behind multiple forms of psychopathology, including substance use disorders. The present study examined whether a link between dysregulated emotion and trying illicit substances could be observed in childhood.

METHOD

In a large (N = 7,418) nationally representative sample of children (Mage = 9.9), individual differences in emotion dysregulation were indexed using child and parent reports of frequency of children's emotional outbursts, as well as children's performance on the emotional N-Back task. Two latent variables, derived from either parental/child-report or performance-based indicators, were evaluated as predictors of having ever tried alcohol, tobacco, or marijuana.

RESULTS

Results showed that reports of dysregulated emotion were linked to a greater likelihood of trying both alcohol and tobacco products. These findings were also present when controlling for individual differences in executive control and socioeconomic status.

CONCLUSIONS

These results suggest that well-established links between dysregulated negative emotion and substance use may emerge as early as in childhood and also suggest that children who experience excessive episodes of uncontrollable negative emotion may be at greater risk for trying substances early in life.

Examination of fully automated mammographic density measures using LIBRA and breast cancer risk in a cohort of 21,000 non-Hispanic white women

BACKGROUND

Breast density is strongly associated with breast cancer risk. Fully automated quantitative density assessment methods have recently been developed that could facilitate large-scale studies, although data on associations with long-term breast cancer risk are limited. We examined LIBRA assessments and breast cancer risk and compared results to prior assessments using Cumulus, an established computer-assisted method requiring manual thresholding.

METHODS

We conducted a cohort study among 21,150 non-Hispanic white female participants of the Research Program in Genes, Environment and Health of Kaiser Permanente Northern California who were 40-74 years at enrollment, followed for up to 10 years, and had archived processed screening mammograms acquired on Hologic or General Electric full-field digital mammography (FFDM) machines and prior Cumulus density assessments available for analysis. Dense area (DA), non-dense area (NDA), and percent density (PD) were assessed using LIBRA software. Cox regression was used to estimate hazard ratios (HRs) for breast cancer associated with DA, NDA and PD modeled continuously in standard deviation (SD) increments, adjusting for age, mammogram year, body mass index, parity, first-degree family history of breast cancer, and menopausal hormone use. We also examined differences by machine type and breast view.

RESULTS

The adjusted HRs for breast cancer associated with each SD increment of DA, NDA and PD were 1.36 (95% confidence interval, 1.18-1.57), 0.85 (0.77-0.93) and 1.44 (1.26-1.66) for LIBRA and 1.44 (1.33-1.55), 0.81 (0.74-0.89) and 1.54 (1.34-1.77) for Cumulus, respectively. LIBRA results were generally similar by machine type and breast view, although associations were strongest for Hologic machines and mediolateral oblique views. Results were also similar during the first 2 years, 2-5 years and 5-10 years after the baseline mammogram.

CONCLUSION

Associations with breast cancer risk were generally similar for LIBRA and Cumulus density measures and were sustained for up to 10 years. These findings support the suitability of fully automated LIBRA assessments on processed FFDM images for large-scale research on breast density and cancer risk.

Genetically adjusted PSA levels for prostate cancer screening

Prostate-specific antigen (PSA) screening for prostate cancer remains controversial because it increases overdiagnosis and overtreatment of clinically insignificant tumors. Accounting for genetic determinants of constitutive, non-cancer-related PSA variation has potential to improve screening utility. In this study, we discovered 128 genome-wide significant associations (P < 5 × 10-8) in a multi-ancestry meta-analysis of 95,768 men and developed a PSA polygenic score (PGSPSA) that explains 9.61% of constitutive PSA variation. We found that, in men of European ancestry, using PGS-adjusted PSA would avoid up to 31% of negative prostate biopsies but also result in 12% fewer biopsies in patients with prostate cancer, mostly with Gleason score <7 tumors. Genetically adjusted PSA was more predictive of aggressive prostate cancer (odds ratio (OR) = 3.44, P = 6.2 × 10-14, area under the curve (AUC) = 0.755) than unadjusted PSA (OR = 3.31, P = 1.1 × 10-12, AUC = 0.738) in 106 cases and 23,667 controls. Compared to a prostate cancer PGS alone (AUC = 0.712), including genetically adjusted PSA improved detection of aggressive disease (AUC = 0.786, P = 7.2 × 10-4). Our findings highlight the potential utility of incorporating PGS for personalized biomarkers in prostate cancer screening.

Transcriptome-Wide Association Analysis Identifies Novel Candidate Susceptibility Genes for Prostate-Specific Antigen Levels in Men Without Prostate Cancer

Deciphering the genetic basis of prostate-specific antigen (PSA) levels may improve their utility to screen for prostate cancer (PCa). We thus conducted a transcriptome-wide association study (TWAS) of PSA levels using genome-wide summary statistics from 95,768 PCa-free men, the MetaXcan framework, and gene prediction models trained in Genotype-Tissue Expression (GTEx) project data. Tissue-specific analyses identified 41 statistically significant (p < 0.05/12,192 = 4.10e-6) associations in whole blood and 39 statistically significant (p < 0.05/13,844 = 3.61e-6) associations in prostate tissue, with 18 genes associated in both tissues. Cross-tissue analyses that combined associations across 45 tissues identified 155 genes that were statistically significantly (p < 0.05/22,249 = 2.25e-6) associated with PSA levels. Based on conditional analyses that assessed whether TWAS associations were attributable to a lead GWAS variant, we found 20 novel genes (11 single-tissue, 9 cross-tissue) that were associated with PSA levels in the TWAS. Of these novel genes, five showed evidence of colocalization (colocalization probability > 0.5): EXOSC9, CCNA2, HIST1H2BN, RP11-182L21.6, and RP11-327J17.2. Six of the 20 novel genes are not known to impact PCa risk. These findings yield new hypotheses for genetic factors underlying PSA levels that should be further explored toward improving our understanding of PSA biology.

Quantitative In Vivo Imaging of the Androgen Receptor Axis Reveals Degree of Prostate Cancer Radiotherapy Response

Noninvasive biomarkers for androgen receptor (AR) pathway activation are urgently needed to better monitor patient response to prostate cancer therapies. AR is a critical driver and mediator of resistance of prostate cancer but currently available noninvasive prostate cancer biomarkers to monitor AR activity are discordant with downstream AR pathway activity. External beam radiotherapy (EBRT) remains a common treatment for all stages of prostate cancer, and DNA damage induced by EBRT upregulates AR pathway activity to promote therapeutic resistance. [89Zr]11B6-PET is a novel modality targeting prostate-specific protein human kallikrein 2 (hK2), which is a surrogate biomarker for AR activity. Here, we studied whether [89Zr]11B6-PET can accurately assess EBRT-induced AR activity.Genetic and human prostate cancer mouse models received EBRT (2-50 Gy) and treatment response was monitored by [89Zr]11B6-PET/CT. Radiotracer uptake and expression of AR and AR target genes was quantified in resected tissue.EBRT increased AR pathway activity and [89Zr]11B6 uptake in LNCaP-AR and 22RV1 tumors. EBRT increased prostate-specific [89Zr]11B6 uptake in prostate cancer-bearing mice (Hi-Myc x Pb_KLK2) with no significant changes in uptake in healthy (Pb_KLK2) mice, and this correlated with hK2 protein levels.

IMPLICATIONS

hK2 expression in prostate cancer tissue is a proxy of EBRT-induced AR activity that can noninvasively be detected using [89Zr]11B6-PET; further clinical evaluation of hK2-PET for monitoring response and development of resistance to EBRT in real time is warranted.

Biochemical activity induced by a germline variation in KLK3 (PSA) associates with cellular function and clinical outcome in prostate cancer

Genetic variation at the 19q13.3 KLK locus is linked with prostate cancer susceptibility. The non-synonymous KLK3 SNP, rs17632542 (c.536T>C; Ile163Thr-substitution in PSA) is associated with reduced prostate cancer risk, however, the functional relevance is unknown. Here, we identify that the SNP variant-induced change in PSA biochemical activity as a previously undescribed function mediating prostate cancer pathogenesis. The 'Thr' PSA variant led to small subcutaneous tumours, supporting reduced prostate cancer risk. However, 'Thr' PSA also displayed higher metastatic potential with pronounced osteolytic activity in an experimental metastasis in-vivo model. Biochemical characterization of this PSA variant demonstrated markedly reduced proteolytic activity that correlated with differences in in-vivo tumour burden. The SNP is associated with increased risk for aggressive disease and prostate cancer-specific mortality in three independent cohorts, highlighting its critical function in mediating metastasis. Carriers of this SNP allele had reduced serum total PSA and a higher free/total PSA ratio that could contribute to late biopsy decisions and delay in diagnosis. Our results provide a molecular explanation for the prominent 19q13.3 KLK locus, rs17632542 SNP, association with a spectrum of prostate cancer clinical outcomes.

Germline rare deleterious variant load alters cancer risk, age of onset and tumor characteristics

Recent studies show that rare, deleterious variants (RDVs) in certain genes are critical determinants of heritable cancer risk. To more comprehensively understand RDVs, we performed the largest-to-date germline variant calling analysis in a case-control setting for a multi-cancer association study from whole-exome sequencing data of 20,789 participants, split into discovery and validation cohorts. We confirm and extend known associations between cancer risk and germline RDVs in specific gene-sets, including DNA repair (OR = 1.50; p-value = 8.30e-07; 95% CI: 1.28-1.77), cancer predisposition (OR = 1.51; p-value = 4.58e-08; 95% CI: 1.30-1.75), and somatic cancer drivers (OR = 1.46; p-value = 4.04e-06; 95% CI: 1.24-1.72). Furthermore, personal RDV load in these gene-sets associated with increased risk, younger age of onset, increased M1 macrophages in tumor and, increased tumor mutational burden in specific cancers. Our findings can be used towards identifying high-risk individuals, who can then benefit from increased surveillance, earlier screening, and treatments that exploit their tumor characteristics, improving prognosis.

MiXcan: a framework for cell-type-aware transcriptome-wide association studies with an application to breast cancer

Human bulk tissue samples comprise multiple cell types with diverse roles in disease etiology. Conventional transcriptome-wide association study approaches predict genetically regulated gene expression at the tissue level, without considering cell-type heterogeneity, and test associations of predicted tissue-level expression with disease. Here we develop MiXcan, a cell-type-aware transcriptome-wide association study approach that predicts cell-type-level expression, identifies disease-associated genes via combination of cell-type-level association signals for multiple cell types, and provides insight into the disease-critical cell type. As a proof of concept, we conducted cell-type-aware analyses of breast cancer in 58,648 women and identified 12 transcriptome-wide significant genes using MiXcan compared with only eight genes using conventional approaches. Importantly, MiXcan identified genes with distinct associations in mammary epithelial versus stromal cells, including three new breast cancer susceptibility genes. These findings demonstrate that cell-type-aware transcriptome-wide analyses can reveal new insights into the genetic and cellular etiology of breast cancer and other diseases.

Second-to-Second Affective Responses to Images Correspond With Affective Reactivity, Variability, and Instability in Daily Life

Two distinct literatures have evolved to study within-person changes in affect over time. One literature has examined affect dynamics with millisecond-level resolution under controlled laboratory conditions, and the second literature has captured affective dynamics across much longer timescales (e.g., hours or days) within the relatively uncontrolled but more ecologically valid conditions of daily life. Despite the importance of linking these literatures, very little research has been done so far. In the laboratory, peak affect intensities and reaction durations were quantified using a paradigm that captures second-to-second changes in subjective affect elicited by provocative images. In two studies, analyses attempted to link these micro-dynamic indexes to fluctuations in daily affect ratings collected via daily protocols up to 4 weeks later. Although peak intensity and reaction duration scores from the laboratory did not consistently relate to daily scores pertaining to affect variability or instability, the total magnitude of changes in affect following images did display relationships of this type. In addition, higher peaks in the laboratory predicted larger intensity reactions to salient daily events. Together, the studies provide insights into the mechanisms through which correspondences and noncorrespondences between laboratory reactivity indices and daily affect dynamic measures can be expected.

Adolescent Emotion Regulation and Future Psychopathology: A Prospective Transdiagnostic Analysis

Transdiagnostic frameworks posit a causal link between emotion regulation (ER) ability and psychopathology. However, there is little supporting longitudinal evidence for such frameworks. Among N = 1,262 adolescents, we examined the prospective bidirectional relationship between ER and future pathological anxiety, depression, and substance dependence symptoms in 10 assessment waves over 7 years. In Random-intercept cross-lagged panel models, within-person results do not reveal prospective lag-1 effects of either ER or symptoms. However, between-person analyses showed that dispositional ER ability at baseline predicted greater risk for developing clinically significant depression, anxiety, and substance dependence over the 7-year follow-up period. These findings provide some of the first direct evidence of prospective effects of ER on future symptom risk across affect-related disorders, and should strengthen existing claims that ER ability represents a key transdiagnostic risk factor.

A psychological flexibility perspective on well-being: Emotional reactivity, adaptive choices, and daily experiences

According to psychological flexibility theory, fully experiencing one's emotions, even when they involve negative reactions, can enhance psychological well-being. In pursuit of this possibility, procedures capable of disentangling reaction intensities from reaction durations, in response to affective images, were developed and variations of this paradigm were applied in understanding variations in happiness and adaptive behavior. Consistent with psychological flexibility theory, three studies showed that more intense emotional reactions, irrespective of valence, were associated with higher levels of well-being. Two additional studies showed that happy individuals, relative to less happy individuals, exhibited more functional approach/avoidance behavior in behavior-focused tasks. Together, the results are consistent with the idea that adaptive emotion generation systems are those that flexibly adapt emotion output to concurrent emotion-related stimulation. The program of research adds to our understanding of the relationship between emotion reactivity and well-being while highlighting specific processes through which emotion and well-being interact. (PsycInfo Database Record (c) 2022 APA, all rights reserved).

Germline Pathogenic Variants Impact Clinicopathology of Advanced Lung Cancer

BACKGROUND

The genetic factors that modulate risk for developing lung cancer have not been fully defined. Here, we sought to determine the prevalence and clinical significance of germline pathogenic/likely pathogenic variants (PV) in patients with advanced lung cancer.

METHODS

We studied clinical and tumor characteristics of germline PV in 5,118 patients who underwent prospective genomic profiling using paired tumor-normal tissue samples in 468 cancer genes.

RESULTS

Germline PV in high/moderate-penetrance genes were observed in 222 (4.3%) patients; of these, 193 patients had PV in DNA damage repair (DDR) pathway genes including BRCA2 (n = 54), CHEK2 (n = 30), and ATM (n = 26) that showed high rate of biallelic inactivation in tumors. BRCA2 heterozygotes with lung adenocarcinoma were more likely to be never smokers and had improved survival compared with noncarriers. Fourteen patients with germline PV in lung cancer predisposing genes (TP53, EGFR, BAP1, and MEN1) were diagnosed at younger age compared with noncarriers, and of tumor suppressors, 75% demonstrated biallelic inactivation in tumors. A significantly higher proportion of germline PV in high/moderate-penetrance genes were detected in high-risk patients who had either a family history of any cancer, multiple primary tumors, or early age at diagnosis compared with unselected patients (10.5% vs. 4.1%; P = 1.7e-04).

CONCLUSIONS

These data underscore the biological and clinical importance of germline mutations in highly penetrant DDR genes as a risk factor for lung cancer.

IMPACT

The family members of lung cancer patients harboring PV in cancer predisposing genes should be referred for genetic counseling and may benefit from proactive surveillance.

SNPs at SMG7 Associated with Time from Biochemical Recurrence to Prostate Cancer Death

BACKGROUND

A previous genome-wide association study identified several loci with genetic variants associated with prostate cancer survival time in two cohorts from Sweden. Whether these variants have an effect in other populations or if their effect is homogenous across the course of disease is unknown.

METHODS

These variants were genotyped in a cohort of 1,298 patients. Samples were linked with age, PSA level, Gleason score, cancer stage at surgery, and times from surgery to biochemical recurrence to death from prostate cancer. SNPs rs2702185 and rs73055188 were tested for association with prostate cancer-specific survival time using a multivariate Cox proportional hazard model. SNP rs2702185 was further tested for association with time to biochemical recurrence and time from biochemical recurrence to death with a multi-state model.

RESULTS

SNP rs2702185 at SMG7 was associated with prostate cancer-specific survival time, specifically the time from biochemical recurrence to prostate cancer death (HR, 2.5; 95% confidence interval, 1.4-4.5; P = 0.0014). Nine variants were in linkage disequilibrium (LD) with rs2702185; one, rs10737246, was found to be most likely to be functional based on LD patterns and overlap with open chromatin. Patterns of open chromatin and correlation with gene expression suggest that this SNP may affect expression of SMG7 in T cells.

CONCLUSIONS

The SNP rs2702185 at the SMG7 locus is associated with time from biochemical recurrence to prostate cancer death, and its LD partner rs10737246 is predicted to be functional.

IMPACT

These results suggest that future association studies of prostate cancer survival should consider various intervals over the course of disease.

Abstract 1441: Genetic determinants of PSA levels improve prostate cancer screening

Prostate-specific antigen (PSA) screening for prostate cancer (PCa) remains controversial due to poor sensitivity and specificity that lead to overdiagnosis and overtreatment. The aim of our study is to characterize genetic determinants of PSA levels in cancer-free men in order to personalize PCa screening. We hypothesize that test accuracy may be improved by accounting for PSA variation that is due to genetic factors and does not reflect PCa.

We conducted the largest ever genome-wide association study (GWAS) of PSA in men without PCa (N=95,768; 85,924 predominantly European ancestry) using data from the UK Biobank, BioVU, PLCO, and Kaiser Permanente cohorts. Our GWAS discovered 129 PSA-associated variants (P&lt;5×10-8), 82 of which were novel. A polygenic score (PGSPSA) comprised of these 129 variants was successfully validated in two cancer prevention trials: PCPT (n=5737) and SELECT (n=22,247). PGSPSA explained 7.3% (p=7.0×10-98) of variation in baseline PSA in PCPT and 8.7% (p=7.0×10-476) in SELECT. Importantly, PGSPSA was not associated with PCa status in PCPT (OR=0.98, p=0.71) or SELECT (OR=1.04, p=0.98), which confirms that it reflects benign PSA variation.

Potential clinical utility of PSA genetic adjustment was explored by examining reclassification at thresholds used for biopsy referrals in a real-world setting at Kaiser Permanente. We estimated that correction using PGSPSA would have avoided 21.2% of negative biopsies in non-cases. Reclassification below the biopsy referral threshold was also more common in cases, particularly with low-grade disease with Gleason score &lt;7 (7.3% below vs. 2.6% above). Overall, genetic correction of PSA appeared to improve the accuracy of referral decisions, with a Net Reclassification Index of 0.148.

Next, we evaluated genetically adjusted PSA in the context of detection of aggressive PCa, defined as Gleason score ≥7, PSA ≥10 ng/mL, T3-T4 stage, and/or distant or nodal metastases. Genetically adjusted baseline PSA was more robustly associated with aggressive PCa than observed PSA and yielded a higher area under the curve (AUC) in PCPT (OR=3.03, p=3.5×10-7; AUC: 0.72 vs. 0.68) and SELECT (OR=3.37, p=3.5×10-11; AUC: 0.78 vs. 0.74) when added to a baseline model with age and trial arm. Furthermore, genetically adjusted PSA provides complementary information to PCa risk variants. In PCPT, a logistic regression model that included genetically corrected PSA and the 269-variant PGSPCa achieved a significantly higher AUC than PGSPCa-269 alone for aggressive PCa (AUC: 0.73 vs. 0.65, p=3.3×10-4) and overall PCa (AUC=0.69 vs. 0.66, p=3.3×10-6).

Our work provides evidence that accounting for genetic determinants of PSA has the potential to reduce unnecessary testing and overdiagnosis of low-risk PCa, as well as increase detection of aggressive disease. Larger and more diverse study populations are required to fully characterize the genetic basis of PSA variation and optimize its clinical utility.

Citation Format: Linda Kachuri, Rebecca E. Graff, Sonja I. Berndt, Mitchell Machiela, Neal D. Freedman, Stephen J. Chanock, John P. Shelley, Kerry Schaffer, Jonathan D. Mosley, Phyllis J. Goodman, Cathee Till, Ian Thompson, Robert J. Klein, Stephen K. Van Den Eeden, Thomas J. Hoffmann, John S. Witte. Genetic determinants of PSA levels improve prostate cancer screening [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1441.

Association of Selective Serotonin Reuptake Inhibitor Use With Abnormal Physical Movement Patterns as Detected Using a Piezoelectric Accelerometer and Deep Learning in a Nationally Representative Sample of Noninstitutionalized Persons in the US

IMPORTANCE

Selective serotonin reuptake inhibitors (SSRIs) are a common first-line treatment for some psychiatric disorders, including depression and anxiety; although they are generally well tolerated, SSRIs have known adverse effects, including movement problems, sleep disruption, and gastrointestinal problems (eg, nausea and upset stomach). No large-scale studies using naturalistic, longitudinal, objective data have validated physical activity findings, and actigraphy data are well suited to address this task.

OBJECTIVES

To evaluate whether differences in physical movement exist among individuals treated with SSRIs compared with control participants and to identify the unique features of the movement of patients treated with SSRIs.

DESIGN, SETTING, AND PARTICIPANTS

This cross-sectional study examines longitudinally collected wearable movement data within a cross-sectional sample of 7162 participants from the 2005-2006 National Health and Nutrition Examination Survey (NHANES), a nationally representative population-based sample of noninstitutionalized persons in the US having both medication information and passive movement data. Statistical analysis was performed from April 1, 2021, to February 1, 2022.

EXPOSURES

The use of SSRIs (sertraline hydrochloride, escitalopram oxalate, fluoxetine hydrochloride, paroxetine hydrochloride, and citalopram hydrobromide), as reported by participants interviewed by NNHANES personnel, was the primary exposure, measured as a binary variable (taking an SSRI vs not taking an SSRI).

MAIN OUTCOMES AND MEASURES

The primary outcome was the intensity of body movement as recorded by a piezoelectric accelerometer worn on the right hip for more than 1 week.

RESULTS

Of the 7162 participants included in the study, the mean (SD) age was 33.7 (22.6) years, 266 (3.7%) were taking an SSRI, 3706 (51.7%) were female, 1934 (27.0%) were Black, 1823 (25.5%) were Mexican American, 210 (2.9%) were other Hispanic, 336 (4.7%) were other or multiracial, and 2859 (39.9%) were White (per the NHANES data collection protocol). A cross-validated, deep learning classifier was constructed that achieved fair performance predicting SSRI use (area under the curve, 0.67 [95% CI, 0.64-0.71] for the validation set and 0.66 [95% CI, 0.64-0.68] for the test set). To account for possible confounding by indication, we constructed a parallel model incorporating depression severity, finding only marginal performance improvement. When averaged across individuals and across 7 days, the results show less overall movement in the SSRI group (mean, 120.1 vertical acceleration counts/min [95% CI, 115.7-124.6 vertical acceleration counts/min]) compared with the non-SSRI control group (mean, 168.8 vertical acceleration counts/min [95% CI, 162.8-174.9 vertical acceleration counts/min]).

CONCLUSIONS AND RELEVANCE

This cross-sectional study found a moderate association between passive movement and SSRI use, as well as SSRI detection capacity of passive movement using time series deep learning models. The results support the use of passive sensors for exploration and characterization of psychotropic medication adverse effects.

The value of a biopsy in chronic ulcers: a case series

Chronic wounds affect millions of individuals in the United States. Chronic wounds of the lower extremity and foot are commonly associated with vascular insufficiency, diabetes, pressure, and neuropathy. Nonhealing wounds are at risk of severe complications, including infection, gangrene, amputation, and malignant transformation. Primary cutaneous malignancies may masquerade as nonhealing ulcers; thus, it can be challenging to differentiate between the malignant transformation of a chronic wound and a primary cutaneous malignancy with ulceration. A biopsy can be a safe, valuable tool in investigating underlying pathology in chronic wounds. Early biopsy diagnosis of malignant transformation can prevent diagnostic and treatment delays. Presented is a review of biopsy and its need and timing to identify malignant transformation in chronic wounds. The authors present 3 patient cases in which biopsies confirmed presence of malignancy in chronic ulcers.

Using negative pressure wound therapy with instillation and dwell time to create a path to closure for older patients with chronic wounds: a retrospective case series

BACKGROUND

Chronic podiatric wounds are common causes of morbidity and mortality in older patients. Negative pressure wound therapy with instillation and dwell time (NPWTi-d) has been recommended in wounds with high levels of exudate, contaminated wounds, and wounds in which healing progression has stalled.

PURPOSE

This retrospective case series describes the use of NPWTi-d to prepare 4 chronic wounds for closure in older patients with multiple comorbidities.

METHODS

Patients (N = 4) ranged in age from 65 to 95 years and had wounds present for at least 90 days. Previous treatments included conventional NPWT and debridement. NPWTi-d consisted of instillation of 10 to 20 mL normal saline, dwell time for 1 minute, followed by 3-hour cycles of -125 mm Hg. Antibiotics were administered as needed. Wounds included a 210-day Wagner grade 3 diabetic foot ulcer (3.2 × 1.8 × 0.3 cm³), a 90-day dehisced wound (9.5 × 2.6 × 0.4 cm³), a 300-day neuropathic ulcer (0.7 × 0.5 × 2.1 cm³), and a 150-day Wagner grade 2 diabetic foot ulcer (4.5 × 3.3 × 0.9 cm³). NPWTi-d was applied for 3 to 33 days, when care was transitioned to advanced wound dressings.

RESULTS

All 4 wounds responded positively to therapy, exhibiting reduced slough, growing granulation tissue, and size reduction. Closure was achieved in all cases.

CONCLUSION

In these 4 patients, NPWTi-d, used as part of a treatment regimen including debridement, antibiotics, and advanced wound dressings, was effective in creating an environment that promoted wound healing and prepared the wounds for eventual closure.

Managing Wound Dehiscence With Mechanical Negative Pressure Wound Therapy: A Case Report

Mechanical negative pressure wound therapy (mNPWT) is commonly used in the management of a variety of wounds, including diabetic foot ulcerations, surgical wounds, venous ulcerations, and wound dehiscence. This mechanically powered, disposable modality can be used to manage wounds in the outpatient setting and has been shown to be an effective wound care option when transitioning patients from the inpatient to outpatient setting and continuing NPWT for wound care. Mechanical NPWT helps promote wound healing by decreasing edema and via removal of tissue debris and exudate. Traditional NPWT is bulky, is often noisy, and requires a power source. A mechanically powered, disposable, easily applied, off-the-shelf mNPWT device is available for patients with small- to medium-sized wounds with mild to moderate exudate. The disposable mNPWT device provides -125 mm Hg pressure, is silent and small, can be worn under clothes, and allows the patient to be fully ambulatory, thus, more mobile. The mNPWT device tubing can be cut to fit to enable safer ambulation than the powered system and to enable the patient to work and enjoy social activities without a medical device showing. This single case study of a patient with chronic diabetic foot ulcerations of the medial first metatarsal head and dorsal proximal interphalangeal joints of the second and third toes of the left foot, which had not been successfully treated with conservative care and had been present for more than 1 year.

Attention to emotion and reliance on feelings in decision-making: Variations on a pleasure principle

Individuals are thought to differ in the extent to which they attend to and value their feelings, as captured by the construct of attention to emotion. The well-being correlates of attention to emotion have been extensively studied, but the decision-making correlates have not been. A three study program of research (total N = 328) sought to examine relationships between stimulus-specific feelings and decisions concerning those stimuli in the context of high levels of within-subject power. Evidence for the pleasure principle was robust, in that individuals placed a virtual self closer to stimuli that they found more pleasant (Study 1) and they wished to re-view such stimuli more frequently (Studies 2 & 3). These relationships, however, were more pronounced at higher levels of attention to emotion. The findings affirm the importance of feelings in decision-making while highlighting ways in which individual differences in attention to emotion operate.

Predicting acute suicidal ideation on Instagram using ensemble machine learning models

INTRODUCTION

Online social networking data (SN) is a contextually and temporally rich data stream that has shown promise in the prediction of suicidal thought and behavior. Despite the clear advantages of this digital medium, predictive modeling of acute suicidal ideation (SI) currently remains underdeveloped. SN data, in conjunction with robust machine learning algorithms, may offer a promising way forward.

METHODS

We applied an ensemble machine learning model on a previously published dataset of adolescents on Instagram with a prior history of lifetime SI (N = 52) to predict SI within the past month. Using predictors that capture language use and activity within this SN, we evaluated the performance of our out-of-sample, cross-validated model against previous efforts and leveraged a model explainer to further probe relative predictor importance and subject-level phenomenology.

RESULTS

Linguistic and SN data predicted acute SI with an accuracy of 0.702 (sensitivity = 0.769, specificity = 0.654, AUC = 0.775). Model introspection showed a higher proportion of SN-derived predictors with substantial impact on prediction compared with linguistic predictors from structured interviews. Further analysis of subject-specific predictor importance uncovered potentially informative trends for future acute SI risk prediction.

CONCLUSION

Application of ensemble learning methodologies to SN data for the prediction of acute SI may mitigate the complexities and modeling challenges of SI that exist within these time scales. Future work is needed on larger, more heterogeneous populations to fine-tune digital biomarkers and more robustly test external validity.

The momentary and the macro in action control: A motor control analysis of impulse control difficulties

According to cybernetic models of self-regulation, the success of one's overt behaviors may very well depend on how well one controls one's behaviors in more momentary terms. The present research applies such perspectives to the analysis of individual differences in impulse control difficulties, which are thought to constitute losses of control in responses to stressors or distress, representing a form of emotional impulsivity. In three studies (total N = 349), undergraduate participants were asked to perform motor control tasks involving stationary or moving targets, which permitted the computation of a tremor instability index that represented the extent to which movements were noisy or unpredictable (less controlled) from moment to moment. Study 1 found that individuals with higher levels of impulse control difficulties exhibited higher levels of tremor, Study 2 replicated this pattern, and Study 3 showed that the tremor instability index predicted similar contingencies in daily life. The findings, in total, identify a micromomentary signature of macrolevel tendencies toward emotional impulsivity. (PsycInfo Database Record (c) 2021 APA, all rights reserved).

Sequencing at lymphoid neoplasm susceptibility loci maps six myeloma risk genes

Inherited genetic risk factors play a role in multiple myeloma (MM), yet considerable missing heritability exists. Rare risk variants at genome-wide association study (GWAS) loci are a new avenue to explore. Pleiotropy between lymphoid neoplasms (LNs) has been suggested in family history and genetic studies, but no studies have interrogated sequencing for pleiotropic genes or rare risk variants. Sequencing genetically enriched cases can help discover rarer variants. We analyzed exome sequencing in familial or early-onset MM cases to identify rare, functionally relevant variants near GWAS loci for a range of LNs. A total of 149 distinct and significant LN GWAS loci have been published. We identified six recurrent, rare, potentially deleterious variants within 5 kb of significant GWAS single nucleotide polymorphisms in 75 MM cases. Mutations were observed in BTNL2, EOMES, TNFRSF13B, IRF8, ACOXL and TSPAN32. All six genes replicated in an independent set of 255 early-onset MM or familial MM or precursor cases. Expansion of our analyses to the full length of these six genes resulted in a list of 39 rare and deleterious variants, seven of which segregated in MM families. Three genes also had significant rare variant burden in 733 sporadic MM cases compared with 935 control individuals: IRF8 (P = 1.0 × 10-6), EOMES (P = 6.0 × 10-6) and BTNL2 (P = 2.1 × 10-3). Together, our results implicate six genes in MM risk, provide support for genetic pleiotropy between LN subtypes and demonstrate the utility of sequencing genetically enriched cases to identify functionally relevant variants near GWAS loci.

Dynamic negativity effects in emotional responding: Onsets, peaks, and influences from repetition

Emotional responses to aversive stimuli may be more mandatory than emotional responses to appetitive stimuli, and extant theorizing suggests that negative reactions may be more peaked at maximum intensity. Parameters of this type were investigated within two experiments (total N = 198) in which emotional images were presented and re-presented as participants indicated their moment-to-moment feeling changes in response to both appetitive and aversive images. Negative emotional reactions were more detectable, with more definitive onsets and peaks, and peak amplitudes were systematically higher in the context of aversive stimuli. Furthermore, stimulus repetition enhanced negative emotional responding in terms of both faster onset times and more pronounced peak amplitudes. Although behavioral activation and behavioral inhibition motivation modulated the emotional onset and peak reactivity metrics, such individual differences did not interact with the repetition effects that were observed. These results highlight several dynamic negativity effects that distinguish positive versus negative emotional reactivity processes. (PsycInfo Database Record (c) 2021 APA, all rights reserved).

Functional Common and Rare ERBB2 Germline Variants Cooperate in Familial and Sporadic Cancer Susceptibility

We investigated a Spanish and Catalan family in which multiple cancer types tracked across three generations, but for which no genetic etiology had been identified. Whole-exome sequencing of germline DNA from multiple affected family members was performed to identify candidate variants to explain this occurrence of familial cancer. We discovered in all cancer-affected family members a single rare heterozygous germline variant (I654V, rs1801201) in ERBB2/HER2, which is located in a transmembrane glycine zipper motif critical for ERBB2-mediated signaling and in complete linkage disequilibrium (D' = 1) with a common polymorphism (I655V, rs1136201) previously reported in some populations as associated with cancer risk. Because multiple cancer types occurred in this family, we tested both the I654V and the I655V variants for association with cancer across multiple tumor types in 6,371 cases of Northern European ancestry drawn from The Cancer Genome Atlas and 6,647 controls, and found that the rare variant (I654V) was significantly associated with an increased risk for cancer (OR = 1.40; P = 0.021; 95% confidence interval (CI), 1.05-1.89). Functional assays performed in HEK 293T cells revealed that both the I655V single mutant (SM) and the I654V;I655V double mutant (DM) stabilized ERBB2 protein and activated ERBB2 signaling, with the DM activating ERBB2 significantly more than the SM alone. Thus, our results suggest a model whereby heritable genetic variation in the transmembrane domain activating ERBB2 signaling is associated with both sporadic and familial cancer risk, with increased ERBB2 stabilization and activation associated with increased cancer risk. PREVENTION RELEVANCE: By performing whole-exome sequencing on germline DNA from multiple cancer-affected individuals belonging to a family in which multiple cancer types track across three generations, we identified and then characterized functional common and rare variation in ERBB2 associated with both sporadic and familial cancer. Our results suggest that heritable variation activating ERBB2 signaling is associated with risk for multiple cancer types, with increases in signaling correlated with increases in risk, and modified by ancestry or family history.

Novel ultra-rare exonic variants identified in a founder population implicate cadherins in schizophrenia

The identification of rare variants associated with schizophrenia has proven challenging due to genetic heterogeneity, which is reduced in founder populations. In samples from the Ashkenazi Jewish population, we report that schizophrenia cases had a greater frequency of novel missense or loss of function (MisLoF) ultra-rare variants (URVs) compared to controls, and the MisLoF URV burden was inversely correlated with polygenic risk scores in cases. Characterizing 141 "case-only" genes (MisLoF URVs in ≥3 cases with none in controls), the cadherin gene set was associated with schizophrenia. We report a recurrent case mutation in PCDHA3 that results in the formation of cytoplasmic aggregates and failure to engage in homophilic interactions on the plasma membrane in cultured cells. Modeling purifying selection, we demonstrate that deleterious URVs are greatly overrepresented in the Ashkenazi population, yielding enhanced power for association studies. Identification of the cadherin/protocadherin family as risk genes helps specify the synaptic abnormalities central to schizophrenia.

Are polygenic risk scores ready for the cancer clinic?—a perspective

To realize the goals of precision medicine in complex disease, discriminative clinical risk models are needed. One approach that has been proposed is polygenic risk scores (PRSs). PRSs incorporate information about inherited genetic risk for cancer, specifically those genetic variants that are common in the population. While PRSs are clearly associated with risk of cancer, there is an on-going debate on whether integrating PRSs into clinical practice have utility. Here, we present this important discussion to the cancer clinic. We argue that in cancer, the clinical utility of PRSs will depend on their actionability, or how such a score may guide clinical practice. In turn, the actionability depends on several factors. First, actionability depends on the discriminative power of the score, or how well it predicts who is at risk of the disease. Second, it depends on their comparative performance with respect to existing practice, as a score with good discriminative power will not be useful if there are better predictors used in the clinic. Finally, for a PRS to be useful there must also be available preventive actions. We discuss the strengths and challenges of utilizing a PRS in the context of each of these criteria, and provide insights on what is needed towards moving forward in translating PRSs into the cancer clinic. We further argue that in future studies, beyond predicting cancer risk, similarly developed PRS models may be of utility in predicting prognosis or treatment resistance.

Genome-wide association study identifies novel single nucleotide polymorphisms having age-specific effect on prostate-specific antigen levels

BACKGROUND

Testing for prostate-specific antigen (PSA) levels in blood are widely used and associated with prostate cancer risk and outcome. After puberty, PSA levels increase by age and multiple single nucleotide polymorphisms (SNPs) have been found to be associated with PSA levels. However, the relationship between the effects of SNPs and age on PSA remains unknown.

METHODS

To test for SNP × age interaction, we conducted a genome-wide association study using 2394 men without prostate cancer diagnosis from Malmö, Sweden as a discovery set and 2137 men from the eMERGE study (USA) for validation. Linear regression was used to identify significant interactions between SNP and age (p < 1 × 10^-4 for discovery, p < .05 for validation).

RESULTS

The 15 SNPs from three different loci (8p11.22, 8p12, 3q25.31) are found to have age-specific effect on PSA levels. Expression quantitative trait loci (eQTLs) analysis shows that 12 SNPs from 3q25.31 locus affect the expression level of three genes: KCNAB1, SLC33A1, PLCH1.

CONCLUSIONS

Our results suggest that SNPs may have age-specific effect on PSA levels, which provides new direction to study genetic markers for PSA.

Validation of prostate cancer risk variants rs10993994 and rs7098889 by CRISPR/Cas9 mediated genome editing

GWAS have identified numerous SNPs associated with prostate cancer risk. One such SNP is rs10993994. It is located in the β-microseminoprotein (MSMB) promoter region, mediates MSMB prostate secretion levels, and is linked to mRNA expression changes in both MSMB and the adjacent gene NCOA4. In addition, our previous work showed a second SNP, rs7098889, is in positive linkage disequilibrium with rs10993994 and associated with MSMB expression independent of rs10993994. Here, we generate a series of clones with single alleles removed by double guide RNA (gRNA) mediated CRISPR/Cas9 deletions, through which we demonstrate that each of these SNPs independently and greatly alters MSMB expression in an allele-specific manner. We further show that these SNPs have no substantial effect on the expression of NCOA4. These data demonstrate that a single SNP can have a large effect on gene expression and illustrate the importance of functional validation studies to deconvolute observed correlations. The method we have developed is generally applicable to test any SNP for which a relevant heterozygous cell line is available. AUTHOR SUMMARY: In pursuing the underlying biological mechanism of prostate cancer pathogenesis, scientists utilized the existence of common single nucleotide polymorphisms (SNPs) in the human genome as genetic markers to perform large scale genome wide association studies (GWAS) and have so far identified more than a hundred prostate cancer risk variants. Such variants provide an unbiased and systematic new venue to study the disease mechanism, and the next big challenge is to translate these genetic associations to the causal role of altered gene function in oncogenesis. The majority of these variants are waiting to be studied and lots of them may act in oncogenesis through gene expression regulation. To prove the concept, we took rs10993994 and its linked rs7098889 as an example and engineered single cell clones by allelic-specific CRISPR/Cas9 deletion to separate the effect of each allele. We observed that a single nucleotide difference would lead to surprisingly high level of MSMB gene expression change in a gene specific and cell-type specific manner. Our study strongly supports the notion that differential level of gene expression caused by risk variants and their associated genetic locus play a major role in oncogenesis and also highlights the importance of studying the function of MSMB encoded β-MSP in prostate cancer pathogenesis.

Identification of 31 loci for mammographic density phenotypes and their associations with breast cancer risk

Mammographic density (MD) phenotypes are strongly associated with breast cancer risk and highly heritable. In this GWAS meta-analysis of 24,192 women, we identify 31 MD loci at P < 5 × 10-8, tripling the number known to 46. Seventeen identified MD loci also are associated with breast cancer risk in an independent meta-analysis (P < 0.05). Mendelian randomization analyses show that genetic estimates of dense area (DA), nondense area (NDA), and percent density (PD) are all significantly associated with breast cancer risk (P < 0.05). Pathway analyses reveal distinct biological processes involving DA, NDA and PD loci. These findings provide additional insights into the genetic basis of MD phenotypes and their associations with breast cancer risk.

Inherited Rare, Deleterious Variants in ATM Increase Lung Adenocarcinoma Risk

INTRODUCTION

Lung cancer is the leading cause of cancer deaths in the world, and lung adenocarcinoma (LUAD) is its most prevalent subtype. Symptoms are often found in advanced disease in which treatment options are limited. Identifying genetic risk factors will enable better identification of high-risk individuals.

METHODS

To identify LUAD risk genes, we performed a case-control association study for gene-level burden of rare, deleterious variants (RDVs) in germline whole-exome sequencing data of 1083 patients with LUAD and 7650 controls, split into discovery and validation cohorts. Of these, we performed whole-exome sequencing on 97 patients and acquired the rest from multiple public databases. We annotated all rare variants for pathogenicity conservatively, using the guidelines of the American College of Medical Genetics and Genomics and ClinVar curation, and investigated gene-level RDV burden using penalized logistic regression. All statistical tests were two-sided.

RESULTS

We discovered and replicated the finding that the burden of germline ATM RDVs was significantly higher in patients with LUAD versus controls (combined cohort OR = 4.6; p = 1.7e-04; 95% confidence interval = 2.2-9.5; 1.21% of cases; 0.24% of controls). Germline ATM RDVs were also enriched in an independent clinical cohort of 1594 patients from the MSK-IMPACT study (0.63%). In addition, we observed that an Ashkenazi Jewish (AJ) founder ATM variant, rs56009889, was statistically significantly more frequent in AJ cases versus AJ controls in our cohort (combined AJ cohort OR = 2.7, p = 6.9e-03, 95% confidence interval = 1.3-5.3).

CONCLUSIONS

Our results indicate that ATM is a moderate-penetrance LUAD risk gene and that LUAD may be a part of the ATM-related cancer syndrome spectrum. Individuals with ATM RDVs are at an elevated LUAD risk and can benefit from increased surveillance (particularly computed tomography scanning), early detection, and chemoprevention programs, improving prognosis.

An integrative ENCODE resource for cancer genomics

ENCODE comprises thousands of functional genomics datasets, and the encyclopedia covers hundreds of cell types, providing a universal annotation for genome interpretation. However, for particular applications, it may be advantageous to use a customized annotation. Here, we develop such a custom annotation by leveraging advanced assays, such as eCLIP, Hi-C, and whole-genome STARR-seq on a number of data-rich ENCODE cell types. A key aspect of this annotation is comprehensive and experimentally derived networks of both transcription factors and RNA-binding proteins (TFs and RBPs). Cancer, a disease of system-wide dysregulation, is an ideal application for such a network-based annotation. Specifically, for cancer-associated cell types, we put regulators into hierarchies and measure their network change (rewiring) during oncogenesis. We also extensively survey TF-RBP crosstalk, highlighting how SUB1, a previously uncharacterized RBP, drives aberrant tumor expression and amplifies the effect of MYC, a well-known oncogenic TF. Furthermore, we show how our annotation allows us to place oncogenic transformations in the context of a broad cell space; here, many normal-to-tumor transitions move towards a stem-like state, while oncogene knockdowns show an opposing trend. Finally, we organize the resource into a coherent workflow to prioritize key elements and variants, in addition to regulators. We showcase the application of this prioritization to somatic burdening, cancer differential expression and GWAS. Targeted validations of the prioritized regulators, elements and variants using siRNA knockdowns, CRISPR-based editing, and luciferase assays demonstrate the value of the ENCODE resource.

Expanded encyclopaedias of DNA elements in the human and mouse genomes

The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.

Genetic signature of prostate cancer mouse models resistant to optimized hK2 targeted α-particle therapy

Hu11B6 is a monoclonal antibody that internalizes in cells expressing androgen receptor (AR)-regulated prostate-specific enzyme human kallikrein-related peptidase 2 (hK2; KLK2). In multiple rodent models, Actinium-225-labeled hu11B6-IgG1 ([225Ac]hu11B6-IgG1) has shown promising treatment efficacy. In the present study, we investigated options to enhance and optimize [225Ac]hu11B6 treatment. First, we evaluated the possibility of exploiting IgG3, the IgG subclass with superior activation of complement and ability to mediate FC-γ-receptor binding, for immunotherapeutically enhanced hK2 targeted α-radioimmunotherapy. Second, we compared the therapeutic efficacy of a single high activity vs. fractionated activity. Finally, we used RNA sequencing to analyze the genomic signatures of prostate cancer that progressed after targeted α-therapy. [225Ac]hu11B6-IgG3 was a functionally enhanced alternative to [225Ac]hu11B6-IgG1 but offered no improvement of therapeutic efficacy. Progression-free survival was slightly increased with a single high activity compared to fractionated activity. Tumor-free animals succumbing after treatment revealed no evidence of treatment-associated toxicity. In addition to up-regulation of canonical aggressive prostate cancer genes, such as MMP7, ETV1, NTS, and SCHLAP1, we also noted a significant decrease in both KLK3 (prostate-specific antigen ) and FOLH1 (prostate-specific membrane antigen) but not in AR and KLK2, demonstrating efficacy of sequential [225Ac]hu11B6 in a mouse model.

Prostate cancer risk SNP rs10993994 is a trans-eQTL for SNHG11 mediated through MSMB

How genome-wide association studies-identified single-nucleotide polymorphisms (SNPs) affect remote genes remains unknown. Expression quantitative trait locus (eQTL) association meta-analysis on 496 prostate tumor and 602 normal prostate samples with 117 SNPs revealed novel cis-eQTLs and trans-eQTLs. Mediation testing and colocalization analysis demonstrate that MSMB is a cis-acting mediator for SNHG11 (P < 0.01). Removing rs10993994 in LNCaP cell lines by CRISPR/Cas9 editing shows that the C-allele corresponds with an over 100-fold increase in MSMB expression and 5-fold increase in SNHG11 compared with the T-allele. Colocalization analysis confirmed that the same set of SNPs associated with MSMB expression is associated with SNHG11 expression (posterior probability of shared variants is 66.6% in tumor and 91.4% in benign). These analyses further demonstrate variants driving MSMB expression differ in tumor and normal, suggesting regulatory network rewiring during tumorigenesis.

Treatment of Deep Full-thickness Wounds Containing Exposed Muscle, Tendon, and/or Bone Using a Bioactive Human Skin Allograft: A Large Cohort Case Series

BACKGROUND

Deep wounds with exposed muscle, tendon, and/or bone structures are especially difficult to treat, often requiring a multifaceted approach. Bioactive human skin allograft (BSA) has been proven to be effective in the treatment of deep wounds, but the mechanism of action and clinical use in the real-world setting is not as well known.

OBJECTIVE

The aim of this case series is to study deep wounds treated with BSA to better understand how it is used in real-world patients and discuss its mechanism of action.

MATERIALS AND METHODS

A total of 51 deep wounds of various etiologies and locations were included from 10 sites across the United States. To be included, patients must have failed wound care without BSA for at least 30 days, with more than 50% reduction in size prior to BSA application.

RESULTS

The mean wound area was 50.37 cm2 and average wound duration was 3.67 months. The mean time to closure was 15.33 weeks, achieved with an average of 4.24 BSA applications. Many patients received adjunctive therapies either prior to or in combination with BSA.

CONCLUSIONS

This study demonstrates the effectiveness of BSA in the treatment of deep wounds of various etiologies. The authors provide clinical information on using BSA either alone or in conjunction with other advanced modalities and offer insight into the hypothesized mechanism of action in which these grafts become incorporated. Ultimately, this information can guide best practices in the treatment of full-thickness wounds to improve outcomes.

Use of Oxidized Regenerated Cellulose (ORC)/Collagen/Silver-ORC Dressings Alone or Subsequent to Advanced Wound Therapies in Complex Wounds

INTRODUCTION

Chronic or senescent wounds are difficult to heal and often require a multimodal treatment plan. Negative pressure wound therapy (NPWT) or advanced wound dressings, such as oxidized regenerated cellulose (ORC)/collagen/silver-ORC dressings, can be used to promote granulation tissue development and stimulate wound healing in these complex wounds.

OBJECTIVE

This article examines the use of ORC/collagen/silver-ORC dressings alone or subsequent to advanced wound therapies in a retrospective cohort of 24 patients.

MATERIALS AND METHODS

Wounds were assessed upon presentation. If necessary, oral and/or intravenous antibiotics were administered. Each wound underwent sharp debridement. Patients received either ORC/collagen/silver-ORC dressings with a secondary dressing alone or following NPWT. Skin substitutes and epidermal grafting also were utilized to promote wound healing and wound size reduction.

RESULTS

Twenty-four patients with an average age of 66.8 ± 12.7 years were treated. The most prevalent comorbidities were hypertension, diabetes, obesity, peripheral neuropathy, hyperlipidemia, coronary heart disease, and tobacco use. Wound types (N = 27) included diabetic foot ulcers, surgical wounds, traumatic wounds, an ulcer (secondary to chronic gout with tophi), and thermal burns. All 27 wounds fully closed, with an average time to heal of 65.5 ± 41.5 days.

CONCLUSIONS

Use of advanced treatment modalities including NPWT, epidermal grafting, and ORC/collagen/silver-ORC dressings contributed to wound healing in these patients with complex and/or chronic wounds.