Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity.

Defining cell types requires integrating diverse single-cell measurements from multiple experiments and biological contexts. To flexibly model single-cell datasets, we developed LIGER, an algorithm that delineates shared and dataset-specific features of cell identity. We applied it to four diverse and challenging analyses of human and mouse brain cells. First, we defined region-specific and sexually dimorphic gene expression in the mouse bed nucleus of the stria terminalis. Second, we analyzed expression in the human substantia nigra, comparing cell states in specific donors and relating cell types to those in the mouse. Third, we integrated in situ and single-cell expression data to spatially locate fine subtypes of cells present in the mouse frontal cortex. Finally, we jointly defined mouse cortical cell types using single-cell RNA-seq and DNA methylation profiles, revealing putative mechanisms of cell-type-specific epigenomic regulation. Integrative analyses using LIGER promise to accelerate investigations of cell-type definition, gene regulation, and disease states.

Posttranslational modifications of serine protease TMPRSS13 regulate zymogen activation, proteolytic activity, and cell surface localization.

TMPRSS13, a member of the type II transmembrane serine protease (TTSP) family, harbors four N-linked glycosylation sites in its extracellular domain. Two of the glycosylated residues are located in the scavenger receptor cysteine-rich (SRCR) protein domain, while the remaining two sites are in the catalytic serine protease (SP) domain. In this study, we examined the role of N-linked glycosylation in the proteolytic activity, autoactivation, and cellular localization of TMPRSS13. Individual and combinatory site-directed mutagenesis of the glycosylated asparagine residues indicated that glycosylation of the SP domain is critical for TMPRSS13 autoactivation and catalytic activity toward one of its protein substrates, the prostasin zymogen. Additionally, SP domain glycosylation-deficient TMPRSS13 displayed impaired trafficking of TMPRSS13 to the cell surface, which correlated with increased retention in the endoplasmic reticulum. Importantly, we showed that N-linked glycosylation was a critical determinant for subsequent phosphorylation of endogenous TMPRSS13. Taken together, we conclude that glycosylation plays an important role in regulating TMPRSS13 activation and activity, phosphorylation, and cell surface localization.

TMPRSS13 zymogen activation, surface localization, and shedding is regulated by proteolytic cleavage within the non-catalytic stem region.

TMPRSS13 is a member of the type II transmembrane serine protease (TTSP) family. Here we characterize a novel post-translational mechanism important for TMPRSS13 function: proteolytic cleavage within the extracellular TMPRSS13 stem region located between the transmembrane domain and the first site of N-linked glycosylation at asparagine (N)-250 in the scavenger receptor cysteine rich (SRCR) domain. Importantly, the catalytic competence of TMPRSS13 is essential for stem region cleavage, suggesting an autonomous mechanism of action. Site-directed mutagenesis of the 10 basic amino acids (four arginine and six lysine residues) in this region abrogated zymogen activation and catalytic activity of TMPRSS13, as well as phosphorylation, cell surface expression, and shedding. Mutation analysis of individual arginine residues identified R223, a residue located between the low-density lipoprotein receptor class A domain and the SRCR domain, as important for stem region cleavage. Mutation of R223 causes a reduction in the aforementioned functional processing steps of TMPRSS13. These data provide further insight into the roles of different post-translational modifications as regulators of the function and localization of TMPRSS13. Additionally, the data suggest the presence of complex interconnected regulatory mechanisms that may serve to ensure the proper levels of cell-surface and pericellular TMPRSS13-mediated proteolysis under homeostatic conditions.

Cell surface-anchored serine proteases in cancer progression and metastasis.

Over the last two decades, a novel subgroup of serine proteases, the cell surface-anchored serine proteases, has emerged as an important component of the human degradome, and several members have garnered significant attention for their roles in cancer progression and metastasis. A large body of literature describes that cell surface-anchored serine proteases are deregulated in cancer and that they contribute to both tumor formation and metastasis through diverse molecular mechanisms. The loss of precise regulation of cell surface-anchored serine protease expression and/or catalytic activity may be contributing to the etiology of several cancer types. There is therefore a strong impetus to understand the events that lead to deregulation at the gene and protein levels, how these precipitate in various stages of tumorigenesis, and whether targeting of selected proteases can lead to novel cancer intervention strategies. This review summarizes current knowledge about cell surface-anchored serine proteases and their role in cancer based on biochemical characterization, cell culture-based studies, expression studies, and in vivo experiments. Efforts to develop inhibitors to target cell surface-anchored serine proteases in cancer therapy will also be summarized.

Association between walnut consumption and diabetes risk in NHANES.

BACKGROUND: Dietary interventions and cohort studies relating tree nut consumption to blood glucose levels suggest a possible effect of walnuts. OBJECTIVE: To examine the associations between walnut consumption and diabetes risk using data from the National Health and Nutrition Examination Survey. METHODS: National Health and Nutrition Examination Survey data on adults conducting 24-hour dietary recall was pooled across the years 1999 through 2014. Diabetes status or risk was based on self-report, medication use, fasting plasma glucose levels, and haemoglobin A1c (HbA1c ) levels. Individuals were characterized based on reported consumption of walnuts, mixed-nuts, or no nuts. RESULTS: After adjustment for covariates, walnut consumers showed lower risk for diabetes compared with non-nut consumers based on self-report (odds ratio of 0.47, 95% confidence interval [CI] 0.31-0.72) as well as fasting blood glucose (relative risk ratio 0.32, CI 0.17-0.58) and HbA1c (relative risk ratio 0.51, CI 0.27-0.99). For each standard deviation of increase in walnut intake, prevalence of diabetes dropped 47%. The gender by walnut interaction suggests that the effect may be more potent among women than men (dose response P = .061). CONCLUSIONS: Both among individuals with known diabetes and those diagnosed based on elevated diabetes blood markers, the prevalence of individuals with diabetes was significantly lower among the walnut consumers. A possible gender-specific effect invites further attention.

Controlling Hypertension through Education and Coaching in Kidney Disease (CHECK-D): protocol of a cluster randomised controlled trial.

INTRODUCTION: Chronic kidney disease (CKD) affects 30 million Americans. Early management focused on blood pressure (BP) control decreases cardiovascular morbidity and mortality. Less than 40% of patients with CKD achieve recommended BP targets due to many barriers. These barriers include a lack of understanding of the implications of their diagnosis and how to optimise their health.This cluster randomised control trial hypothesises that the combination of early primary care CKD education, and motivational interviewing (MI)-based health coach support, will improve patient behaviours aligned with BP control by increasing patient knowledge, self-efficacy and motivation. The results will aid in sustainable interventions for future patient-centric education and coaching support to improve quality and outcomes in patients with CKD stages 3-5. Outcomes in patients with CKD stages 3-5 receiving the intervention will be compared with similar patients within a control group. Continuous quality improvement (CQI) and systems methodologies will be used to optimise resource neutrality and leverage existing technology to support implementation and future dissemination. The innovative approach of this research focuses on the importance of a multidisciplinary team, including off-site patient coaching, that can intervene early in the CKD care continuum by supporting patients with education and coaching. METHODS AND ANALYSIS: We will test impact of BP control when clinician-delivered education is followed by 12 months of MI-based health coaching. We will compare outcomes in 350 patients with CKD stages 3-5 between intervention and control groups in primary care. CQI and systems methodologies will optimise education and coaching for future implementation and dissemination. ETHICS AND DISSEMINATION: This study was approved by the University of Michigan Institutional Review Boards (IRBMED) HUM00136011, HUM00150672 and SITE00000092 and the results of the study will be published on ClinicalTrials.gov, in peer-reviewed journals, as well as conference abstracts, posters and presentations. TRIAL REGISTRATION NUMBER: NCT04087798.

"I'm Being Forced to Make Decisions I Have Never Had to Make Before": Oncologists' Experiences of Caring for Seriously Ill Persons With Poor Prognoses and the Dilemmas Created by COVID-19.

PURPOSE: The COVID-19 pandemic has created a new set of problems for clinicians. This study examines the experiences of oncologists providing care to seriously ill persons near the end of life in the context of the COVID-19 pandemic. METHODS: Between January 2020 and August 2020, we conducted semistructured, in-depth individual interviews with 22 purposefully sampled oncologists from practices enrolled in the Michigan Oncology Quality Consortium. Deidentified transcripts of the interviews were examined using thematic analysis. RESULTS: Our respondents described several novel problems created by the COVID-19 pandemic, including: (1) ethical challenges, (2) the need to manage uncertainty-physically and emotionally-on the part of both patients and oncologists, and (3) the difficulty of integrating technology and communication for seriously ill persons. These problems were made more complex by features of the pandemic: resource scarcity (and the need to fairly allocate poor resources), delays in care, high levels of fear, and the increased importance of advance care planning. Nonabandonment served as a way to cope with increased stress, and the use of telemedicine became an increasingly important medium of communication. CONCLUSION: This study offers an in-depth exploration of the problems faced by oncologists as a result of the COVID-19 pandemic and how they navigated them. Optimal decision making for seriously ill persons with cancer during the COVID-19 pandemic must include open acknowledgment of the ethical challenges involved, the emotions experienced by both patients and their oncologists, and the urgent need to integrate technology with compassionate communication in determining patient preferences.

The cell-surface anchored serine protease TMPRSS13 promotes breast cancer progression and resistance to chemotherapy.

Breast cancer progression is accompanied by increased expression of extracellular and cell-surface proteases capable of degrading the extracellular matrix as well as cleaving and activating downstream targets. The type II transmembrane serine proteases (TTSPs) are a family of cell-surface proteases that play critical roles in numerous types of cancers. Therefore, the aim of this study was to identify novel and uncharacterized TTSPs with differential expression in breast cancer and to determine their potential roles in progression. Systematic in silico data analysis followed by immunohistochemical validation identified increased expression of the TTSP family member, TMPRSS13 (transmembrane protease, serine 13), in invasive ductal carcinoma patient tissue samples compared to normal breast tissue. To test whether loss of TMPRSS13 impacts tumor progression, TMPRSS13 was genetically ablated in the oncogene-induced transgenic MMTV-PymT tumor model. TMPRSS13 deficiency resulted in a significant decrease in overall tumor burden and growth rate, as well as a delayed formation of detectable mammary tumors, thus suggesting a causal relationship between TMPRSS13 expression and the progression of breast cancer. Complementary studies using human breast cancer cell culture models revealed that siRNA-mediated silencing of TMPRSS13 expression decreases proliferation, induces apoptosis, and attenuates invasion. Importantly, targeting TMPRSS13 expression renders aggressive triple-negative breast cancer cell lines highly responsive to chemotherapy. At the molecular level, knockdown of TMPRSS13 in breast cancer cells led to increased protein levels of the tumor-suppressive protease prostasin. TMPRSS13/prostasin co-immunoprecipitation and prostasin zymogen activation experiments identified prostasin as a potential novel target for TMPRSS13. Regulation of prostasin levels may be a mechanism that contributes to the pro-oncogenic properties of TMPRSS13 in breast cancer. TMPRSS13 represents a novel candidate for targeted therapy in combination with standard of care chemotherapy agents in patients with hormone receptor-negative breast cancer or in patients with tumors refractory to endocrine therapy.

TMPRSS13 promotes cell survival, invasion, and resistance to drug-induced apoptosis in colorectal cancer.

Cancer progression is often accompanied by increased levels of extracellular proteases capable of remodeling the extracellular matrix and promoting pro-cancerous signaling pathways by activating growth factors and receptors. The type II transmembrane serine protease (TTSP) family encompasses several proteases that play critical roles in cancer progression; however, the expression or function of the TTSP TMPRSS13 in carcinogenesis has not been examined. In the present study, we found TMPRSS13 to be differentially expressed at both the transcript and protein levels in human colorectal cancer (CRC). Immunohistochemical analyses revealed consistent high expression of TMPRSS13 protein on the cancer cell surface in CRC patient samples; in contrast, the majority of normal colon samples displayed no detectable expression. On a functional level, TMPRSS13 silencing in CRC cell lines increased apoptosis and impaired invasive potential. Importantly, transgenic overexpression of TMPRSS13 in CRC cell lines increased tolerance to apoptosis-inducing agents, including paclitaxel and HA14-1. Conversely, TMPRSS13 silencing rendered CRC cells more sensitive to these agents. Together, our findings suggest that TMPRSS13 plays an important role in CRC cell survival and in promoting resistance to drug-induced apoptosis; we also identify TMPRSS13 as a potential new target for monotherapy or combination therapy with established chemotherapeutics to improve treatment outcomes in CRC patients.

Alternative Splicing of RAD6B and Not RAD6A is Selectively Increased in Melanoma: Identification and Functional Characterization.

Rad6B, a principal component of the translesion synthesis pathway, and activator of canonical Wnt signaling, plays an essential role in cutaneous melanoma development and progression. As Rad6 is encoded by two genes, namely, UBE2A (RAD6A) and UBE2B (RAD6B), in humans, we compared their expressions in melanomas and normal melanocytes. While both genes are weakly expressed in normal melanocytes, Rad6B is more robustly expressed in melanoma lines and patient-derived metastatic melanomas than RAD6A. The characterization of RAD6B transcripts revealed coexpression of various splice variants representing truncated or modified functional versions of wild-type RAD6B in melanomas, but not in normal melanocytes. Notably, two RAD6B isoforms with intact catalytic domains, RAD6BΔexon4 and RAD6Bintron5ins, were identified. We confirmed that RAD6BΔexon4 and RAD6Bintron5ins variants are expressed as 14 and 15 kDa proteins, respectively, with functional in vivo ubiquitin conjugating activity. Whole exome sequence analysis of 30 patient-derived melanomas showed RAD6B variants coexpressed with wild-type RAD6B in all samples analyzed, and RAD6Bintron5ins variants were found in half the cases. These variants constitute the majority of the RAD6B transcriptome in contrast to RAD6A, which was predominantly wild-type. The expression of functional RAD6B variants only in melanomas reveals RAD6B's molecular heterogeneity and its association with melanoma pathogenesis.

Prostate Tumor Cell-Derived IL1ß Induces an Inflammatory Phenotype in Bone Marrow Adipocytes and Reduces Sensitivity to Docetaxel via Lipolysis-Dependent Mechanisms.

Adipocyte-tumor cell cross-talk is one of the critical mediators of tumor progression and an emerging facilitator of therapy evasion. Tumor cells that metastasize to adipocyte-rich bone marrow take advantage of the interplay between metabolic and inflammatory pathways to activate prosurvival mechanisms that allow them to thrive and escape therapy. Using in vitro and in vivo models of marrow adiposity, we demonstrate that metastatic prostate carcinoma cells engage bone marrow adipocytes in a functional cross-talk that promotes IL1ß expression in tumor cells. Tumor-supplied IL1ß contributes to adipocyte lipolysis and regulates a proinflammatory phenotype in adipocytes via upregulation of COX-2 and MCP-1. We further show that the enhanced activity of the IL1ß/COX-2/MCP-1 axis and a resulting increase in PGE2 production by adipocytes coincide with augmented hypoxia signaling and activation of prosurvival pathways in tumor cells, revealing a potential mechanism of chemoresistance. The major consequence of this interplay is the reduced response of prostate cancer cells to docetaxel, a phenomenon sensitive to the inhibition of lipolysis. IMPLICATIONS: Studies presented herein highlight adipocyte lipolysis as a tumor-regulated metabolic event that engages proinflammatory cross-talk in the microenvironment to promote prostate cancer progression in bone. Understanding the impact of bone marrow adipose tissue on tumor adaptation, survival, and chemotherapy response is fundamentally important, as current treatment options for metastatic prostate cancer are palliative.

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution.

Spatial positions of cells in tissues strongly influence function, yet a high-throughput, genome-wide readout of gene expression with cellular resolution is lacking. We developed Slide-seq, a method for transferring RNA from tissue sections onto a surface covered in DNA-barcoded beads with known positions, allowing the locations of the RNA to be inferred by sequencing. Using Slide-seq, we localized cell types identified by single-cell RNA sequencing datasets within the cerebellum and hippocampus, characterized spatial gene expression patterns in the Purkinje layer of mouse cerebellum, and defined the temporal evolution of cell type-specific responses in a mouse model of traumatic brain injury. These studies highlight how Slide-seq provides a scalable method for obtaining spatially resolved gene expression data at resolutions comparable to the sizes of individual cells.

Vaxvec: The first web-based recombinant vaccine vector database and its data analysis.

A recombinant vector vaccine uses an attenuated virus, bacterium, or parasite as the carrier to express a heterologous antigen(s). Many recombinant vaccine vectors and related vaccines have been developed and extensively investigated. To compare and better understand recombinant vectors and vaccines, we have generated Vaxvec (http://www.violinet.org/vaxvec), the first web-based database that stores various recombinant vaccine vectors and those experimentally verified vaccines that use these vectors. Vaxvec has now included 59 vaccine vectors that have been used in 196 recombinant vector vaccines against 66 pathogens and cancers. These vectors are classified to 41 viral vectors, 15 bacterial vectors, 1 parasitic vector, and 1 fungal vector. The most commonly used viral vaccine vectors are double-stranded DNA viruses, including herpesviruses, adenoviruses, and poxviruses. For example, Vaxvec includes 63 poxvirus-based recombinant vaccines for over 20 pathogens and cancers. Vaxvec collects 30 recombinant vector influenza vaccines that use 17 recombinant vectors and were experimentally tested in 7 animal models. In addition, over 60 protective antigens used in recombinant vector vaccines are annotated and analyzed. User-friendly web-interfaces are available for querying various data in Vaxvec. To support data exchange, the information of vaccine vectors, vaccines, and related information is stored in the Vaccine Ontology (VO). Vaxvec is a timely and vital source of vaccine vector database and facilitates efficient vaccine vector research and development.

Medial and Lateral Heel Whips: Prevalence and Characteristics in Recreational Runners.

OBJECTIVE: To investigate the prevalence and characteristics of recreational runners with medial and lateral heel whips. DESIGN: Observational cohort study. SETTING: Clinical research laboratory. PARTICIPANTS: A total of 256 recreationally active runners and joggers participated. MAIN OUTCOME MEASURES: High-definition video was acquired from a posterior view while runners ran at a self-selected pace on a treadmill. Heel whips, defined as the medial or lateral rotation of the foot in the transverse plane during initial swing, were measured with Dartfish software. Subjects were stratified by direction (medial and lateral) and severity (W_5-10 = 5-10 degrees; W_10+ = >10 degrees) of heel whip. Body mass index and gender comparisons, as well as measurement reliability, also were explored. RESULTS: Mean heel whip angle across runners was 0.4 degrees (medial) with a standard deviation of 9.2 degrees. Of the 512 feet analyzed, 274 (54%) demonstrated a 5 degree whip or greater. There was a similar number of medial and lateral heel whips observed (27% each). Female runners were twice as likely to demonstrate a lateral heel whip of greater than 8.9 degrees. Overweight runners had more medially directed whips when compared with normal and underweight runners. CONCLUSIONS: More than half of the recreational runners studied were observed to have a medial or lateral heel whip of greater than 5 degrees. These data reveal the age, body mass index, and gender distribution of recreational runners with and without heel whips.