Type I Interferon Signaling on Antigen-Presenting Cells Blunts Cell-Mediated Immunity toward Listeria monocytogenes.

Listeria monocytogenes is a facultative intracellular pathogen that has been used for decades to understand mechanisms of bacterial pathogenesis and both innate and adaptive immunity. L. monocytogenes is a potent activator of CD8+ T-cell-mediated immunity, yet how the innate immune response to infection modulates CD8+ T-cell responses is incompletely understood. Here, we address how two innate immune pathways triggered by L. monocytogenes, type I interferon (IFN) production and inflammasome activation, impact the CD8+ T-cell response. We utilized a combination of mutant mice and genetically engineered L. monocytogenes to address this question. Mice lacking the type I IFN receptor (IFNAR-/-) had the most robust T-cell response, while caspase-1-/- mice were not different from wild type (WT). Caspase-1-/-/IFNAR-/- mice had fewer T-cells than IFNAR-/- mice, suggesting a role for inflammasome activation in the absence of type I IFN. IFNAR-/- had more than twice as many memory precursors promoting enhanced protection from rechallenge. Importantly, short-lived effectors were equivalent in all strains of mice. L. monocytogenes strains genetically modified to induce lower type I interferon production yielded enhanced T-cell responses. IFNAR-/- dendritic cells induced more T-cells to proliferate than WT in ex vivo T-cell proliferation assays, suggesting deficits from type I interferon signaling may be dendritic cell intrinsic, rather than acting on T-cells. Thus, modulating type I IFN signaling during vaccination may lead to more potent T-cell-based vaccines. Importantly, this suggests innate immune signaling significantly impacts the CD8+ T-cell response and suggests CD8+ T-cell quantity and quality are important factors to consider during rational vaccine design.

Stromal remodeling regulates dendritic cell abundance and activity in the tumor microenvironment.

Stimulatory type 1 conventional dendritic cells (cDC1s) engage in productive interactions with CD8+ effectors along tumor-stroma boundaries. The paradoxical accumulation of "poised" cDC1s within stromal sheets is unlikely to simply reflect passive exclusion from tumor cores. Drawing parallels with embryonic morphogenesis, we hypothesized that invasive margin stromal remodeling generates developmentally conserved cell fate cues that regulate cDC1 behavior. We find that, in human T cell-inflamed tumors, CD8+ T cells penetrate tumor nests, whereas cDC1s are confined within adjacent stroma that recurrently displays site-specific proteolysis of the matrix proteoglycan versican (VCAN), an essential organ-sculpting modification in development. VCAN is necessary, and its proteolytic fragment (matrikine) versikine is sufficient for cDC1 accumulation. Versikine does not influence tumor-seeding pre-DC differentiation; rather, it orchestrates a distinctive cDC1 activation program conferring exquisite sensitivity to DNA sensing, supported by atypical innate lymphoid cells. Thus, peritumoral stroma mimicking embryonic provisional matrix remodeling regulates cDC1 abundance and activity to elicit T cell-inflamed tumor microenvironments.

Interpolation Methods for Molecular Potential Energy Surface Construction.

The concept of a potential energy surface (PES) is one of the most important concepts in modern chemistry. A PES represents the relationship between the chemical system's energy and its geometry (i.e., atom positions) and can provide useful information about the system's chemical properties and reactivity. Construction of accurate PESs with high-level theoretical methodologies, such as density functional theory, is still challenging due to a steep increase in the computational cost with the increase of the system size. Thus, over the past few decades, many different mathematical approaches have been applied to the problem of the cost-efficient PES construction. This article serves as a short overview of interpolative methods for the PES construction, including global polynomial interpolation, trigonometric interpolation, modified Shepard interpolation, interpolative moving least-squares, and the automated PES construction derived from these.

A rare case of a novel coagulase negative Staphylococcus native valve endocarditis in a 28-year-old male.

Coagulase negative staphylococci (CoNS) are an emerging cause of native valve endocarditis in community and healthcare settings. We describe a case of a 28-year-old man with no significant risk factors who presented with Staphylococcus pettenkoferi native valve endocarditis. During our patient's initial hospitalization, he was treated for CoNS bacteraemia and subsequently discharged after a protracted hospital course with a transthoracic echocardiogram (TTE) showing no valvular vegetations. However, during the course of his second hospitalization, speciation identified S. pettenkoferi and transoesophageal echocardiogram (TEE) showed aortic valve perforations with new regurgitation raising concern for left sided endocarditis. We postulate that our patient may have been infected with the same CoNS species causing aortic valve endocarditis during his initial hospitalization. This case highlights the importance of recognizing CoNS as a possible causative bacterium in NVE, as well as the importance of obtaining a TEE when evaluating a patient for suspected endocarditis.

Reduced-dimensional surface hopping with offline-online computations.

Molecular dynamics simulations often classically evolve the nuclear geometry on adiabatic potential energy surfaces (PESs), punctuated by random hops between energy levels in regions of strong coupling, in an algorithm known as surface hopping. However, the computational expense of integrating the geometry on a full-dimensional PES and computing the required couplings can quickly become prohibitive as the number of atoms increases. In this work, we describe a method for surface hopping that uses only important reaction coordinates, performs all expensive evaluations of the true PESs and couplings only once before simulating dynamics (offline), and then queries the stored values during the surface hopping simulation (online). Our Python codes are freely available on GitHub. Using photodissociation of azomethane as a test case, this method is able to reproduce experimental results that have thus far eluded ab initio surface hopping studies.

Phagocytes produce prostaglandin E2 in response to cytosolic Listeria monocytogenes.

Listeria monocytogenes is an intracellular bacterium that elicits robust CD8+ T-cell responses. Despite the ongoing development of L. monocytogenes-based platforms as cancer vaccines, our understanding of how L. monocytogenes drives robust CD8+ T-cell responses remains incomplete. One overarching hypothesis is that activation of cytosolic innate pathways is critical for immunity, as strains of L. monocytogenes that are unable to access the cytosol fail to elicit robust CD8+ T-cell responses and in fact inhibit optimal T-cell priming. Counterintuitively, however, activation of known cytosolic pathways, such as the inflammasome and type I IFN, lead to impaired immunity. Conversely, production of prostaglandin E2 (PGE2) downstream of cyclooxygenase-2 (COX-2) is essential for optimal L. monocytogenes T-cell priming. Here, we demonstrate that vacuole-constrained L. monocytogenes elicit reduced PGE2 production compared to wild-type strains in macrophages and dendritic cells ex vivo. In vivo, infection with wild-type L. monocytogenes leads to 10-fold increases in PGE2 production early during infection whereas vacuole-constrained strains fail to induce PGE2 over mock-immunized controls. Mice deficient in COX-2 specifically in Lyz2+ or CD11c+ cells produce less PGE2, suggesting these cell subsets contribute to PGE2 levels in vivo, while depletion of phagocytes with clodronate abolishes PGE2 production completely. Taken together, this work demonstrates that optimal PGE2 production by phagocytes depends on L. monocytogenes access to the cytosol, suggesting that one reason cytosolic access is required to prime CD8+ T-cell responses may be to facilitate production of PGE2.

Efficient Approximation of Potential Energy Surfaces with Mixed-Basis Interpolation.

The potential energy surface (PES) describes the energy of a chemical system as a function of its geometry and is a fundamental concept in modern chemistry. A PES provides much useful information about the system, including the structures and energies of various stationary points, such as stable conformers (local minima) and transition states (first-order saddle points) connected by a minimum-energy path. Our group has previously produced surrogate reduced-dimensional PESs using sparse interpolation along chemically significant reaction coordinates, such as bond lengths, bond angles, and torsion angles. These surrogates used a single interpolation basis, either polynomials or trigonometric functions, in every dimension. However, relevant molecular dynamics (MD) simulations often involve some combination of both periodic and nonperiodic coordinates. Using a trigonometric basis on nonperiodic coordinates, such as bond lengths, leads to inaccuracies near the domain boundary. Conversely, polynomial interpolation on the periodic coordinates does not enforce the periodicity of the surrogate PES gradient, leading to nonconservation of total energy even in a microcanonical ensemble. In this work, we present an interpolation method that uses trigonometric interpolation on the periodic reaction coordinates and polynomial interpolation on the nonperiodic coordinates. We apply this method to MD simulations of possible isomerization pathways of azomethane between cis and trans conformers. This method is the only known interpolative method that appropriately conserves total energy in systems with both periodic and nonperiodic reaction coordinates. In addition, compared to all-polynomial interpolation, the mixed basis requires fewer electronic structure calculations to obtain a given level of accuracy, is an order of magnitude faster, and is freely available on GitHub.

Expression of NrasQ61R and MYC transgene in germinal center B cells induces a highly malignant multiple myeloma in mice.

NRAS Q61 mutations are prevalent in advanced/relapsed multiple myeloma (MM) and correlate with poor patient outcomes. Thus, we generated a novel MM model by conditionally activating expression of endogenous NrasQ61R and an MYC transgene in germinal center (GC) B cells (VQ mice). VQ mice developed a highly malignant MM characterized by a high proliferation index, hyperactivation of extracellular signal-regulated kinase and AKT signaling, impaired hematopoiesis, widespread extramedullary disease, bone lesions, kidney abnormalities, preserved programmed cell death protein 1 and T-cell immunoreceptor with immunoglobulin and immunoreceptor tyrosine-based inhibition motif domain immune-checkpoint pathways, and expression of human high-risk MM gene signatures. VQ MM mice recapitulate most of the biological and clinical features of human advanced/high-risk MM. These MM phenotypes are serially transplantable in syngeneic recipients. Two MM cell lines were also derived to facilitate future genetic manipulations. Combination therapies based on MEK inhibition significantly prolonged the survival of VQ mice with advanced-stage MM. Our study provides a strong rationale to develop MEK inhibition-based therapies for treating advanced/relapsed MM.

Pumilio response and AU-rich elements drive rapid decay of Pnrc2-regulated cyclic gene transcripts.

Vertebrate segmentation is regulated by the segmentation clock, a biological oscillator that controls periodic formation of somites, or embryonic segments, which give rise to many mesodermal tissue types. This molecular oscillator generates cyclic gene expression with the same periodicity as somite formation in the presomitic mesoderm (PSM), an area of mesenchymal cells that give rise to mature somites. Molecular components of the clock include the Hes/her family of genes that encode transcriptional repressors, but additional genes cycle. Cyclic gene transcripts are cleared rapidly, and clearance depends upon the pnrc2 (proline-rich nuclear receptor co-activator 2) gene that encodes an mRNA decay adaptor. Previously, we showed that the her1 3'UTR confers instability to otherwise stable transcripts in a Pnrc2-dependent manner, however, the molecular mechanism(s) by which cyclic gene transcripts are cleared remained largely unknown. To identify features of the her1 3'UTR that are critical for Pnrc2-mediated decay, we developed an array of transgenic inducible reporter lines carrying different regions of the 3'UTR. We find that the terminal 179 nucleotides (nts) of the her1 3'UTR are necessary and sufficient to confer rapid instability. Additionally, we show that the 3'UTR of another cyclic gene, deltaC (dlc), also confers Pnrc2-dependent instability. Motif analysis reveals that both her1 and dlc 3'UTRs contain terminally-located Pumilio response elements (PREs) and AU-rich elements (AREs), and we show that the PRE and ARE in the last 179 â€‹nts of the her1 3'UTR drive rapid turnover of reporter mRNA. Finally, we show that mutation of Pnrc2 residues and domains that are known to facilitate interaction of human PNRC2 with decay factors DCP1A and UPF1 reduce the ability of Pnrc2 to restore normal cyclic gene expression in pnrc2 mutant embryos. Our findings suggest that Pnrc2 interacts with decay machinery components and cooperates with Pumilio (Pum) proteins and ARE-binding proteins to promote rapid turnover of cyclic gene transcripts during somitogenesis.

Approximating Periodic Potential Energy Surfaces with Sparse Trigonometric Interpolation.

The potential energy surface (PES) describes the energy of a chemical system as a function of its geometry and is a fundamental concept in computational chemistry. A PES provides much useful information about the system, including the structures and energies of various stationary points, such as local minima, maxima, and transition states. Construction of full-dimensional PESs for molecules with more than 10 atoms is computationally expensive and often not feasible. Previous work in our group used sparse interpolation with polynomial basis functions to construct a surrogate reduced-dimensional PESs along chemically significant reaction coordinates, such as bond lengths, bond angles, and torsion angles. However, polynomial interpolation does not preserve the periodicity of the PES gradient with respect to angular components of geometry, such as torsion angles, which can lead to nonphysical phenomena. In this work, we construct a surrogate PES using trigonometric basis functions, for a system where the selected reaction coordinates all correspond to the torsion angles, resulting in a periodically repeating PES. We find that a trigonometric interpolation basis not only guarantees periodicity of the gradient but also results in slightly lower approximation error than polynomial interpolation.

Listeria monocytogenes cancer vaccines: bridging innate and adaptive immunity.

PURPOSE OF THE REVIEW: Immunotherapy has emerged as a promising cancer treatment, however success in only select clinical indications underscores the need for novel approaches. Recently Listeria monocytogenes-based vaccines have been developed to drive tumor specific T-cell responses. Here, we discuss recent preclinical studies using L. monocytogenes vaccines, innate immune pathways that influence T-cell priming, and new vaccine strategies in clinical trials. RECENT FINDINGS: Recent studies indicate that in addition to inducing antigen specific T-cell responses, L. monocytogenes vaccines remodel the TME. In addition, several innate immune pathways influence adaptive immune responses to L. monocytogenes and modulating these pathways holds promise to enhance anti-tumor T-cell responses. SUMMARY: The interplay between innate and adaptive immune responses to L. monocytogenes is poorly understood. Understanding these interactions will facilitate the design of better anti-cancer vaccines and improved use of combination therapies.

Tumor matrix remodeling and novel immunotherapies: the promise of matrix-derived immune biomarkers.

Recent advances in our understanding of the dynamics of cellular cross-talk have highlighted the significance of host-versus-tumor effect that can be harnessed with immune therapies. Tumors exploit immune checkpoints to evade adaptive immune responses. Cancer immunotherapy has witnessed a revolution in the past decade with the development of immune checkpoint inhibitors (ICIs), monoclonal antibodies against cytotoxic T lymphocyte antigen 4 (CTLA-4) and programmed cell death protein 1 (PD-1) or their ligands, such as PD1 ligand 1 (PD-L1). ICIs have been reported to have activity against a broad range of tumor types, in both solid organ and hematologic malignancy contexts. However, less than one-third of the patients achieve a durable and meaningful treatment response. Expression of immune checkpoint ligands (e.g., PD-L1), mutational burden and tumor-infiltrating lymphocytes are currently used as biomarkers for predicting response to ICIs. However, they do not reliably predict which patients will benefit from these therapies. There is dire need to discover novel biomarkers to predict treatment efficacy and to identify areas for development of combination strategies to improve response rates. Emerging evidence suggests key roles of tumor extracellular matrix (ECM) components and their proteolytic remodeling products in regulating each step of the cancer-immunity cycle. Here we review tumor matrix dynamics and matrix remodeling in context of anti-tumor immune responses and immunotherapy and propose the exploration of matrix-based biomarkers to identify candidates for immune therapy.

tbx6l and tbx16 are redundantly required for posterior paraxial mesoderm formation during zebrafish embryogenesis.

BACKGROUND: T-box genes encode a large transcription factor family implicated in many aspects of development. We are focusing on two related zebrafish T-box genes, tbx6l and tbx16, that are expressed in highly overlapping patterns in embryonic paraxial mesoderm. tbx16 mutants are deficient in trunk, but not tail, somites; we explored whether presence of tail somites in tbx16 mutants was due to compensatory function provided by the tbx6l gene. RESULTS: We generated two zebrafish tbx6l mutant alleles. Loss of tbx6l has no apparent effect on embryonic development, nor does tbx6l loss enhance the phenotype of two other T-box gene mutants, ta and tbx6, or of the mesp family gene mutant msgn1. In contrast, loss of tbx6l function dramatically enhances the paraxial mesoderm deficiency of tbx16 mutants. CONCLUSIONS: These data demonstrate that tbx6l and tbx16 genes function redundantly to direct tail somite development. tbx6l single mutants develop normally because tbx16 fully compensates for loss of tbx6l function. However, tbx6l only partially compensates for loss of tbx16 function. These results resolve the question of why loss of function of tbx16 gene, which is expressed throughout the ventral and paraxial mesoderm, profoundly affects somite development in the trunk but not the tail. Developmental Dynamics 246:759-769, 2017. © 2017 Wiley Periodicals, Inc.

Pnrc2 regulates 3'UTR-mediated decay of segmentation clock-associated transcripts during zebrafish segmentation.

Vertebrate segmentation is controlled by the segmentation clock, a molecular oscillator that regulates gene expression and cycles rapidly. The expression of many genes oscillates during segmentation, including hairy/Enhancer of split-related (her or Hes) genes, which encode transcriptional repressors that auto-inhibit their own expression, and deltaC (dlc), which encodes a Notch ligand. We previously identified the tortuga (tor) locus in a zebrafish forward genetic screen for genes involved in cyclic transcript regulation and showed that cyclic transcripts accumulate post-splicing in tor mutants. Here we show that cyclic mRNA accumulation in tor mutants is due to loss of pnrc2, which encodes a proline-rich nuclear receptor co-activator implicated in mRNA decay. Using an inducible in vivo reporter system to analyze transcript stability, we find that the her1 3'UTR confers Pnrc2-dependent instability to a heterologous transcript. her1 mRNA decay is Dicer-independent and likely employs a Pnrc2-Upf1-containing mRNA decay complex. Surprisingly, despite accumulation of cyclic transcripts in pnrc2-deficient embryos, we find that cyclic protein is expressed normally. Overall, we show that Pnrc2 promotes 3'UTR-mediated decay of developmentally-regulated segmentation clock transcripts and we uncover an additional post-transcriptional regulatory layer that ensures oscillatory protein expression in the absence of cyclic mRNA decay.

Satellite-like cells contribute to pax7-dependent skeletal muscle repair in adult zebrafish.

Satellite cells, also known as muscle stem cells, are responsible for skeletal muscle growth and repair in mammals. Pax7 and Pax3 transcription factors are established satellite cell markers required for muscle development and regeneration, and there is great interest in identifying additional factors that regulate satellite cell proliferation, differentiation, and/or skeletal muscle regeneration. Due to the powerful regenerative capacity of many zebrafish tissues, even in adults, we are exploring the regenerative potential of adult zebrafish skeletal muscle. Here, we show that adult zebrafish skeletal muscle contains cells similar to mammalian satellite cells. Adult zebrafish satellite-like cells have dense heterochromatin, express Pax7 and Pax3, proliferate in response to injury, and show peak myogenic responses 4-5 days post-injury (dpi). Furthermore, using a pax7a-driven GFP reporter, we present evidence implicating satellite-like cells as a possible source of new muscle. In lieu of central nucleation, which distinguishes regenerating myofibers in mammals, we describe several characteristics that robustly identify newly-forming myofibers from surrounding fibers in injured adult zebrafish muscle. These characteristics include partially overlapping expression in satellite-like cells and regenerating myofibers of two RNA-binding proteins Rbfox2 and Rbfoxl1, known to regulate embryonic muscle development and function. Finally, by analyzing pax7a; pax7b double mutant zebrafish, we show that Pax7 is required for adult skeletal muscle repair, as it is in the mouse.

Outcomes assessment in rotator cuff pathology: what are we measuring?

BACKGROUND: Assessments used to measure outcomes associated with rotator cuff pathology and after repair are varied. This lack of standardization leads to difficulty drawing comparisons across studies. We hypothesize that this variability in patient-reported outcome measures and objective metrics used in rotator cuff studies persists even in high-impact, peer reviewed journals. METHODS: All studies assessing rotator cuff tear and repair outcomes in 6 orthopedic journals with a high impact factor from January 2010 to December 2014 were reviewed. Cadaveric and animal studies and those without outcomes were excluded. Outcome measures included range of motion (forward elevation, abduction, external rotation, and internal rotation), strength (in the same 4 planes), tendon integrity imaging, patient satisfaction, and functional assessment scores. RESULTS: Of the 156 included studies, 63% documented range of motion measurements, with 18% reporting range of motion in all 4 planes. Only 38% of studies reported quantitative strength measurements. In 65% of studies, tendon integrity was documented with imaging (38% magnetic resonance imaging/magnetic resonance anrhrogram, 31% ultrasound, and 8% computed tomography arthrogram). Finally, functional score reporting varied significantly, with the 5 most frequently reported scores ranging from 16% to 61% in studies, and 15 of the least reported outcomes were each reported in ≤6% of studies. CONCLUSIONS: Significant variability exists in outcomes reporting after rotator cuff tear and repair, making comparisons between clinical studies difficult. Creating a uniformly accepted, validated outcomes tool that assesses pain, function, patient satisfaction, and anatomic integrity would enable consistent outcomes assessment after operative and nonoperative management and allow comparisons across the literature.

Arm pain in youth baseball players: a survey of healthy players.

BACKGROUND: Overuse injury in youth baseball players is increasing in prevalence, and these injuries have been correlated to pitching mechanics and pitch counts/types. Prior studies regarding arm pain in these athletes have focused simply on presence or absence of pain during the season rather than on detailed factors related to arm pain with respect to frequency, severity, and associated performance and psychosocial effect. HYPOTHESIS/PURPOSE: The goal of this study was to investigate frequency, quality, and effect of arm pain in healthy youth baseball players. The hypothesis was that arm pain will affect a majority of healthy baseball players and will be associated with adverse psychosocial effects. STUDY DESIGN: Descriptive epidemiological study. METHODS: A novel survey focusing on arm pain in youth baseball players was developed for the purpose of this study. Survey questions were formulated by a consortium of trainers, clinicians, and coaches. Surveys were administered to healthy youth baseball players throughout the states of New Jersey and New York. RESULTS: A total of 203 healthy players completed the survey; 23% of players (n=47) reported a prior overuse injury. Only 26% and 20% of players reported that their arm never hurt when throwing or the day after throwing, respectively; 30% of players reported that arm pain at least sometimes caused them to have less fun playing; and 46% of players reported at least once being encouraged to keep playing despite having arm pain. Pitchers were more likely to report arm pain while throwing and the day after throwing and to indicate that arm pain held them back from being a better player (all P<.05). Those with prior overuse injury were more likely to have arm pain while throwing, to have arm fatigue during a game or practice, and to be encouraged to keep playing despite having pain (all P<.05). CONCLUSION: A majority of healthy (actively competing) youth baseball players report at least some baseline arm pain and fatigue, and many players suffer adverse psychosocial effects from this pain.

Performance, Return to Competition, and Reinjury After Tommy John Surgery in Major League Baseball Pitchers: A Review of 147 Cases.

BACKGROUND: Pitching performance metrics, durability, and reinjury after Tommy John surgery in professional baseball players have not been well described. PURPOSE: The purpose of this study was to determine the likelihood of return to professional competition, reinjury rate, and change in performance after Tommy John surgery in Major League Baseball pitchers. The hypothesis was that performance metrics and durability will decline after surgery. STUDY DESIGN: Cohort study; Level of evidence, 3. METHODS: Publicly available records were accessed to generate a list of all Major League Baseball pitchers from 1999 to 2011 who had undergone ulnar collateral ligament reconstruction at any point in their careers; those with multiple reconstructive procedures were excluded. Return to active (≥1 game) or established (≥10 games) competition and/or placement on the disabled list was documented for each player. Among established players, pitching performance was compared pre- and postoperatively, as well as with age-matched control pitchers. RESULTS: Of 147 pitchers included, 80% returned to pitch in at least 1 Major League Baseball game. Only 67% of established pitchers returned to the same level of competition postoperatively, and 57% of established players returned to the disabled list because of injuries to the throwing arm. Finally, performance declined across several metrics after surgery compared with preinjury levels, such as earned run average, batting average against, walks plus hits per inning pitched, percentage of pitches thrown in the strike zone, innings pitched, percentage fastballs thrown, and average fastball velocity (P < .05 for all). However, these declines were not statistically different from similar declines found in age-matched controls who did not undergo Tommy John surgery. CONCLUSION: Return to the disabled list after Tommy John surgery is common among professional pitchers (>50%), and performance declines across several major metrics after surgery. Patients undergoing Tommy John surgery should be counseled appropriately regarding the likelihood of return to preinjury levels of competition and performance.