Proteomic Biomarkers of Survival in Idiopathic Pulmonary Fibrosis

Rationale: Idiopathic pulmonary fibrosis (IPF) causes progressive lung scarring and high mortality. Reliable and accurate prognostic biomarkers are urgently needed. Objectives: To identify and validate circulating protein biomarkers of IPF survival. Methods: High-throughput proteomic data were generated using prospectively collected plasma samples from patients with IPF from the Pulmonary Fibrosis Foundation Patient Registry (discovery cohort) and the Universities of California, Davis; Chicago; and Virginia (validation cohort). Proteins associated with three-year transplant-free survival (TFS) were identified using multivariable Cox proportional hazards regression. Those associated with TFS after adjustment for false discovery in the discovery cohort were advanced for testing in the validation cohort, with proteins maintaining TFS association with consistent effect direction considered validated. After combining cohorts, functional analyses were performed, and machine learning was used to derive a proteomic signature of TFS. Measurements and Main Results: Of 2,921 proteins tested in the discovery cohort (n = 871), 231 were associated with differential TFS. Of these, 140 maintained TFS association with consistent effect direction in the validation cohort (n = 355). After cohorts were combined, the validated proteins with the strongest TFS association were latent-transforming growth factor β-binding protein 2 (hazard ratio [HR], 2.43; 95% confidence interval [CI] = 2.09-2.82), collagen α-1(XXIV) chain (HR, 2.21; 95% CI = 1.86-2.39), and keratin 19 (HR, 1.60; 95% CI = 1.47-1.74). In decision curve analysis, a proteomic signature of TFS outperformed a similarly derived clinical prediction model. Conclusions: In the largest proteomic investigation of IPF outcomes performed to date, we identified and validated 140 protein biomarkers of TFS. These results shed important light on potential drivers of IPF progression.

Regulation of epithelial transitional states in murine and human pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a progressive scarring disease arising from impaired regeneration of the alveolar epithelium after injury. During regeneration, type 2 alveolar epithelial cells (AEC2s) assume a transitional state that upregulates multiple keratins and ultimately differentiate into AEC1s. In IPF, transitional AECs accumulate with ineffectual AEC1 differentiation. However, whether and how transitional cells cause fibrosis, whether keratins regulate transitional cell accumulation and fibrosis, and why transitional AECs and fibrosis resolve in mouse models but accumulate in IPF are unclear. Here, we show that human keratin 8 (KRT8) genetic variants were associated with IPF. Krt8-/- mice were protected from fibrosis and accumulation of the transitional state. Keratin 8 (K8) regulated the expression of macrophage chemokines and macrophage recruitment. Profibrotic macrophages and myofibroblasts promoted the accumulation of transitional AECs, establishing a K8-dependent positive feedback loop driving fibrogenesis. Finally, rare murine transitional AECs were highly senescent and basaloid and may not differentiate into AEC1s, recapitulating the aberrant basaloid state in human IPF. We conclude that transitional AECs induced and were maintained by fibrosis in a K8-dependent manner; in mice, most transitional cells and fibrosis resolved, whereas in human IPF, transitional AECs evolved into an aberrant basaloid state that persisted with progressive fibrosis.

Fatal COVID-19 and Non-COVID-19 Acute Respiratory Distress Syndrome Is Associated with Incomplete Alveolar Type 1 Epithelial Cell Differentiation from the Transitional State without Fibrosis

Acute respiratory distress syndrome (ARDS) due to coronavirus disease 2019 and other etiologies results from injury to the alveolar epithelial cell (AEC) barrier resulting in noncardiogenic pulmonary edema, which causes acute respiratory failure; recovery requires epithelial regeneration. During physiological regeneration in mice, type 2 AECs (AEC2s) proliferate, exit the cell cycle, transiently assume a transitional state, then differentiate into type 1 AECs (AEC1s); in humans, persistence of the transitional state is associated with pulmonary fibrosis. It is unknown whether transitional cells emerge and differentiate into AEC1s without fibrosis in human ARDS and why transitional cells differentiate into AEC1s during physiological regeneration but persist in fibrosis. We hypothesized that incomplete but ongoing AEC1 differentiation from transitional cells without fibrosis may underlie persistent barrier permeability and acute respiratory failure in ARDS. Immunostaining of postmortem ARDS lungs revealed abundant transitional cells without fibrosis. They were typically cuboidal or partially spread, sometimes flat, and occasionally expressed AEC1 markers. Immunostaining and/or single-cell RNA sequencing revealed that transitional cells in mouse models of physiological regeneration, ARDS, and fibrosis express markers of cell cycle exit but only in fibrosis express a specific senescence marker. Thus, in severe, fatal early ARDS, AEC1 differentiation from transitional cells is incomplete, underlying persistent barrier permeability and respiratory failure but ongoing without fibrosis; senescence of transitional cells may be associated with pulmonary fibrosis.

Fatal COVID-19 ARDS associated with incomplete AEC1 differentiation from the transitional state without senescence or fibrosis

COVID-19 ARDS is associated with prolonged respiratory failure and high mortality, but the underlying mechanisms are unknown. ARDS results from injury to the alveolar epithelial cell (AEC) barrier; clinical recovery requires epithelial regeneration. During physiologic regeneration, AEC2s proliferate, exit the cell cycle, and transiently assume a transitional state before differentiating into AEC1s; transitional cells persist with ineffectual AEC1 differentiation in pulmonary fibrosis. It is unknown why transitional cells differentiate into AEC1s during physiologic regeneration but persist with ensuing scar in fibrosis and whether incomplete AEC1 differentiation from transitional cells without fibrosis may underlie prolonged respiratory failure in COVID-19 ARDS. Immunostaining of postmortem COVID-19 ARDS lungs revealed abundant transitional cells. They were typically cuboidal or partially spread, occasionally flat, but rarely expressed AEC1 markers. They formed organized monolayers on alveolar septa without fibrosis. Immunostaining and/or meta-analysis of scRNAseq datasets revealed that transitional cells in two mouse models of physiologic regeneration, COVID-19 ARDS, and fibrosis express markers of cell cycle exit but only in fibrosis express a specific senescence marker. These data suggest that in COVID-19 ARDS, physiologic AEC1 differentiation from transitional cells is incomplete, thus underlying prolonged barrier permeability and respiratory failure, but as in physiologic regeneration, is ongoing without fibrosis.

Association of Regulatory Genetic Variants for Protein Kinase Cα with Mortality and Drug Efficacy in Patients with Heart Failure

PURPOSE

Protein kinase C alpha (gene: PRKCA) is a key regulator of cardiac contractility. Two genetic variants have recently been discovered to regulate PRKCA expression in failing human heart tissue (rs9909004 [T → C] and rs9303504 [C → G]). The association of those variants with clinical outcomes in patients with heart failure (HF), and their interaction with HF drug efficacy, is unknown.

METHODS

Patients with HF in a prospective registry starting in 2007 were genotyped by whole genome array (n = 951). The primary outcome was all-cause mortality. Cox proportional hazards models adjusted for established clinical risk factors and genomic ancestry tested the independent association of rs9909004 or rs9303504 and the variant interactions with cornerstone HF pharmacotherapies (beta-blockers or angiotensin-converting enzyme inhibitors/angiotensin receptor blockers) in additive genetic models.

RESULTS

The minor allele of rs9909004, but not of rs9303504, was independently associated with a decreased risk for all-cause mortality: adjusted HR = 0.81 (95% CI = 0.67-0.98), p = 0.032. The variants did not significantly interact with mortality benefit associated with cornerstone HF pharmacotherapies (p > 0.1 for all).

CONCLUSIONS

A recently discovered cardiac-specific regulatory variant for PRKCA (rs9909004) was independently associated with a decreased risk for all-cause mortality in patients with HF. The variant did not interact with mortality benefit associated with cornerstone HF pharmacotherapies.

Serine protease inhibitor-6 differentially affects the survival of effector and memory alloreactive CD8-T cells

The clonal expansion of effector T cells and subsequent generation of memory T cells are critical in determining the outcome of transplantation. While cytotoxic T lymphocytes induce direct cytolysis of target cells through secretion of Granzyme-B (GrB), they also express cytoplasmic serine protease inhibitor-6 (Spi6) to protect themselves from GrB that has leaked from granules. Here, we studied the role of GrB/Spi6 axis in determining clonal expansion of alloreactive CD8-T cells and subsequent generation of memory CD8-T cells in transplantation. CD8-T cells from Spi6(-/-) mice underwent more GrB mediated apoptosis upon alloantigen stimulation in vitro and in vivo following adoptive transfer into an allogeneic host. Interestingly, while OT1.Spi6(-/-) CD8 T cells showed significantly lower clonal expansion following skin transplants from OVA mice, there was no difference in the size of the effector memory CD8-T cells long after transplantation. Furthermore, lack of Spi6 resulted in a decrease of short-lived-effector-CD8-cells but did not impact the pool of memory-precursor-effector-CD8-cells. Similar results were found in heart transplant models. Our findings suggest that the final alloreactive CD8-memory-pool-size is independent from the initial clonal-proliferation as memory precursors express low levels of GrB and therefore are independent of Spi6 for survival. These data advance our understanding of memory T cells generation in transplantation and provide basis for Spi6 based strategies to target effector T cells.

Detection of the common resistance genes in Gram-negative bacteria using gene chip technology

OBJECTIVE

To design a resistance gene detection chip that could, in parallel, detect common clinical drug resistance genes of Gram-negative bacteria.

MATERIALS AND METHODS

Seventy clinically significant Gram-negative bacilli (Klebsiella pneumoniae, Escherichia coli, Enterobacter cloacae, Pseudomonas aeruginosa, Acinetobacter baumannii) were collected. According to the known resistance gene sequences, we designed and synthesized primers and probes, which were used to prepare resistance gene detection chips, and finally we hybridized and scanned the gene detection chips.

RESULTS

The results between the gene chip and polymerase chain reaction (PCR) were compared. The rate was consistently 100% in the eight kinds of resistance genes tested (TEM, SHV, CTX-M, DHA, CIT, VIM, KPC, OXA-23). One strain of Pseudomonas aeruginosa had the IMP, but it was not found by gene chip.

CONCLUSION

The design of Gram-negative bacteria-resistant gene detection chip had better application value.

Serine protease inhibitor 6 plays a critical role in protecting murine granzyme B-producing regulatory T cells

Regulatory T cells (Tregs) play a pivotal role in the maintenance of immune tolerance and hold great promise as cell therapy for a variety of immune-mediated diseases. However, the cellular mechanisms that regulate Treg maintenance and homeostasis have yet to be fully explored. Although Tregs express granzyme-B (GrB) to suppress effector T cells via direct killing, the mechanisms by which they protect themselves from GrB-mediated self-inflicted damage are unknown. To our knowledge, we show for the first time that both induced Tregs and natural Tregs (nTregs) increase their intracellular expression of GrB and its endogenous inhibitor, serine protease inhibitor 6 (Spi6) upon activation. Subcellular fractionation and measurement of GrB activity in the cytoplasm of Tregs show that activated Spi6(-/-) Tregs had significantly higher cytoplasmic GrB activity. We observed an increase in GrB-mediated apoptosis in Spi6(-/-) nTregs and impaired suppression of alloreactive T cells in vitro. Spi6(-/-) Tregs were rescued from apoptosis by the addition of a GrB inhibitor (Z-AAD-CMK) in vitro. Furthermore, adoptive transfer experiments showed that Spi6(-/-) nTregs were less effective than wild type nTregs in suppressing graft-versus-host disease because of their impaired survival, as shown in our in vivo bioluminescence imaging. Finally, Spi6-deficient recipients rejected MHC class II-mismatch heart allografts at a much faster rate and showed a higher rate of apoptosis among Tregs, as compared with wild type recipients. To our knowledge, our data demonstrate, for the first time, a novel role for Spi6 in Treg homeostasis by protecting activated Tregs from GrB-mediated injury. These data could have significant clinical implications for Treg-based therapy in immune-mediated diseases.

Impairment of immune systems in diabetes

Type 1 diabetes mellitus (T1DM) is an autoimmune disease that involves the progressive destruction of the insulin-producing beta cells in the islets of langerhans. It is a complex process that results from the loss of tolerance to insulin and other beta-cell-specific antigens. Various genetic and environmental factors have been studied so far, but precise causation has yet to be established. Numerous studies in rodents and human subjects have been performed in order to elucidate the role of B and T cells, which determine the risk of development and progression of diabetes. These studies have demonstrated that while T1DM is fundamentally a T-cell-mediated autoimmune response, the development of this disease results from complex interactions between the adaptive and innate immune systems, with numerous cell types thought to contribute to pathogenesis. Like any complex disease, the variation in severity and incidence of T1DM can be attributed to a combination of genetic and environmental factors.

Split-dose administration of thiopurine drugs: a novel and effective strategy for managing preferential 6-MMP metabolism

BACKGROUND

Mercaptopurine and azathioprine (AZA) are efficacious in treating IBD. 6-tioguanine (6-TGN) levels correlate with therapeutic efficacy, whereas high 6-methylmercaptopurine (6-MMP) levels are associated with hepatotoxicity and myelotoxicity. Some IBD patients exhibit dose-limiting preferential 6-MMP production, which may lead to undesired side effects and impact efficacy.

AIM

To review the outcomes of thiopurine split-dosing in patients with preferential 6-MMP metabolism.

METHODS

A retrospective chart review of 179 IBD patients treated at the Cedars-Sinai IBD Center with AZA or mercaptopurine was performed. Preferential 6-MMP metabolisers with 6-MMP levels greater than 7000 pmol/8 × 10(8) erythrocytes who underwent split-dosing were identified and assessed for biochemical and clinical responses to these dose modifications.

RESULTS

A total of 20 of 179 patients met the criteria for preferential 6-MMP metabolism and underwent thiopurine split-dosing. Dividing the total daily thiopurine dose led to a reduction in 6-MMP levels (11785 vs. 5324 pmol/8 × 10(8) erythrocytes; P < 0.0001) without negatively affecting clinical disease activity or 6-TGN levels (239 vs. 216 pmol/8 × 10(8) erythrocytes; P = N.S.) and led to resolution of 6-MMP associated side effects (elevated transaminases, leucopenia and flu-like symptoms) in all but two patients. After mean follow-up of 36 months, 12 patients remained in clinical remission on split-dose mercaptopurine. Five of the remaining eight patients escalated to anti-TNF therapy, two progressed to surgery, and one switched to tioguanine therapy.

CONCLUSION

Split-dose administration of mercaptopurine/AZA represents an alternative option in IBD patients with preferential 6-MMP metabolism who might otherwise require steroid exposure or escalation of therapy.

Genomic studies of GVHD-lessons learned thus far

GVHD remains the most significant complication of hematopoietic SCT, despite advances in HLA matching and the identification of risk various factors. To account for the variation in the incidence and severity of this disease, many genetic association studies have been performed in order to explore the role of immunoregulatory gene polymorphisms. These genes include those that encode cytokines, chemokines, and costimulatory molecules. Polymorphisms in other classes of genes such as those involved in drug metabolism, protein folding, and DNA replication have also been studied. In this review, we address the current knowledge of the role of genetic polymorphisms in GVHD. We also discuss the potential pitfalls inherent in genetic association testing and alternative strategies to address these problems.

The novel role of SERPINB9 in cytotoxic protection of human mesenchymal stem cells

Clinical trials using allogeneic mesenchymal stem cells (MSCs) are ongoing for the purpose of providing therapeutic benefit for a variety of human disorders. Pertinent to their clinical use are the accessibility to sufficient quantities of these cells allowing for repetitive administration, as well as a better understanding of the specific mechanisms by which allogeneic MSCs evade host immune responses that in turn influence their life span following administration. In this report, we sought to characterize and compare human peripheral blood MSCs (hPB-MSCs) with bone marrow-derived MSCs. hPB-MSCs met the established criteria to characterize this cellular lineage, including capacity for self-renewal, differentiation into tissues of mesodermal origin, and expression of phenotypic surface markers. In addition, hPB-MSCs suppressed alloreactive proliferation as well as the production of proinflammatory cytokines. Examination of the mechanisms by which allogeneic MSCs evade the host immune response, which is crucial for their therapeutic use, demonstrated that constitutive expression of serine protease inhibitor 9 (PI-9) on hPB-MSCs and bone marrow-derived MSCs is a major defense mechanism against granzyme B-mediated destruction by NK cells. Similarly, MSCs treated with small interfering RNA for PI-9 increased MSC cellular death, whereas expression of transgenic PI-9 following retroviral transduction protected MSCs. These data significantly advance our understanding of the immunomodulatory role for hPB-MSCs as well as the mechanisms by which they evade host immune responses. These findings contribute to the development of MSC-based therapies for diseases.

Chaotic resonance: two-state model with chaos-induced escape over potential barrier

We consider the resonant effects of chaotic fluctuations on a strongly damped particle in a bistable potential driven by weak sinusoidal perturbation. We derive analytical expressions of chaos-induced transition rate between the neighboring potential wells based on the inhomogeneous Smoluchowski equation. Our first-order analysis reveals that the transition rate has the form of the Kramers escape rate except for a perturbed prefactor. This modification to the prefactor is found to arise from the statistical asymmetry of the chaotic noise. By means of the two-state model and the chaos-induced transition rate, we arrive at an analytical expression of the signal-to-noise ratio (SNR). Our first-order SNR shows that chaotic resonance can correspond directly to stochastic resonance.

Chaos-induced escape over a potential barrier

We investigate the statistical parity of a class of chaos-generated noises on the escape of strongly damped particles out of a potential well. We show that statistical asymmetry in the chaotic fluctuations can lead to a skewed Maxwell-Boltzmann distribution in the well. Depending on the direction of skew, the Kramers escape rate is enhanced or suppressed accordingly. Based on the Perron-Frobenious equation, we determine an analytical expression for the escape rate's prefactor that accounts for this effect. Furthermore, our perturbative analysis proves that in the zeroth-order limit, the rate of particle escape converges to the Kramers rate.

Analysis on the origin of directed current from a class of microscopic chaotic fluctuations

We show that the Perron-Frobenius equation of microscopic chaos based on double symmetric maps leads to an inhomogeneous Smoluchowski equation with a source term. Our perturbative analysis reveals that the source term gives rise to a directed current for a strongly damped particle in a spatially periodic potential. In addition, our result proves that in the zeroth-order limit, the position distribution of the particle obeys the Smoluchowski equation even though the fluctuating force is deterministic.

Spectral broadening of sound scattered by advecting atmospheric turbulence

Scattering and spectral broadening of a monochromatic sound wave by atmospheric turbulence that is flowing with a uniform constant horizontal wind is considered. The acoustic source and a detector are at rest and at different positions in a ground-fixed frame. Analytic expressions are derived for the sound pressure scattered to the detector by a single eddy. Since distances and the scattering angle change with time as the eddy flows through the scattering volume, the detector signal has time-dependent amplitude and frequency, for which general formulas are derived. A computer code is developed that calculates the scattered signal and its Fourier transform from a single eddy, or from a steady-state collection of eddies of many different scale lengths that represents isotropic homogeneous turbulence flowing with the wind. The code utilizes a time-shift algorithm that reduces the calculation time substantially. Several numerical results from this code are presented, including simulations of a recent experiment. The predicted spectral shape, including peak width and jaggedness, are in good agreement with experiment.

In vitro and in vivo correlation of the effect of granulocytemacrophage colony-stimulating factor gene transfer on the tumorigenicity and immunogenicity of B16 melanoma

Transduction of murine B16 melanoma cells with a GM-CSF gene, the B16-MG tumor line, showed reduced tumorigenicity. In vitro studies demonstrated no remarkable difference between the parent and transduced tumor lines in their ability to induce secondary response to generate the anti-tumor killer cells (immunogenicity), or in their susceptibility to the killing by anti-tumor killer cells (immunosensitivity). Both CD4(+) and CD8(+) cells were required for the generation of the effecters. Nevertheless the effecters were determined to be Thy1.2(+), CD8(-), and NK1.1(-). At least two antigenic specificities could be defined in the cytolytic reactions. One was a broadly cross-reactive antigen shared by a variety of tumor cells, and the other apparently a tumor-specific antigen which was only present in B16 tumors. Cold target inhibition experiment confirmed these specificities. In the in vivo tumor transplantation study, the B16-MG cell line was not only more immunogenic but also was more immunosensitive than the parent line. More than 50% of the mice which were immunized with B16-MG remained tumor free after challenge with the parent tumor B16, indicating that GM-CSF gene transfer makes an effective tumor vaccine. The in vivo protective effect was specific for B16 tumor, thus only the tumor-specific antigen could function as transplantation antigen. Both CD4(+) and CD8(+) cells were required for providing the in vivo protection. Both the B16 and B16-MG tumor bearing hosts could generate anti-tumor killer cells, hence the development of progressive growth of B16 tumor was not due to the lack of anti-tumor immune response. It appears that the overall effect of in vivo tumor immunity is determined by a complex network of interactions among different compartments of host immune cells and different compartments of host immune cells and different immune-regulatory molecules derived from the host and from the tumor.

A theoretical analysis of a new drug delivery system: a cylindrical device with a vertical opening on its surface

A theoretical analysis of a proposed drug delivery device is presented. The device is of cylindrical shape with an opening on its side surface. Analytical expressions for the temporal variations in the amount of drug released and the size of the unreleased portion of the device are derived. The result of numerical simulation reveals that an approximately zero-order mechanism can be obtained, provided that the device is designed appropriately. The applicability of the analytical expressions derived is justified by examining the release of sodium salicylate embedded in polyethylene. The present work is a generalization of analyses suggested previously for some similar devices.

Evaluation of the quality of bedside monitoring of the blood glucose level in a teaching hospital

We evaluated the precision and accuracy of monitoring of the blood glucose level in the laboratory and at the bedside with one of four glucose meters by an experienced operator and by 39 nurses in a teaching hospital. For precision studies aqueous quality control materials were used. A total of 85 blood samples were tested. The precision of the glucose meters (expressed as the coefficient of variation [CV]) in the hands of the experienced operator ranged from 6.7% to 11.1%. The correlation between the values obtained by the experienced operator and the reference values obtained in the laboratory was high (0.95 to 0.98). The precision of the values obtained by the nurses using the meters ranged from 13.7% on medical wards to 45.7% in the intensive care unit (ICU). The correlation between these values and those obtained in the central laboratory ranged from 0.72 to 0.82. Twenty-four percent of the glucose values determined on medical wards and 62% of those determined in the ICU deviated from the reference value by at least 20%. Of the 85 patients 12 (14%) would have received different insulin dosages had the reference value been available at the same time as the glucose meter reading: in 3 of the patients the discrepancy was 6 units of insulin or greater. Continuous quality control of bedside monitoring of the blood glucose level is needed. In addition, personnel who use glucose meters should receive adequate training.

Inhibition of human monocyte antigen presentation, but not HLA-DR expression, by cyclosporine

The effects of cyclosporine (CsA) on antigen-dependent human T cell proliferation have been studied using tetanus toxoid as the antigen. CsA significantly inhibited antigen-dependent T cell proliferation at concentrations as low as 0.1 microgram/ml. In dissecting this system we found that preexposure of separated monocytes to CsA during the period of antigen processing led to a marked inhibition of proliferation of T cells added subsequently to the monocytes. We investigated whether this suppressive effect on monocyte antigen presentation was related to monocyte HLA-DR expression, interleukin 1 (IL-1) production, or prostaglandin (PG) secretion. None of these functions seemed to be affected by CsA. In particular, human monocyte HLA-DR expression was not inhibited by CsA, even at concentration of 10 micrograms/ml. The addition of exogenous IL-1 or indomethacin did not reverse the inhibitory effects of CsA. These experiments demonstrate that CsA inhibits antigen-dependent human T cell proliferation, at least in part by acting directly on human monocytes to inhibit antigen presentation. The mechanism of action seems to be independent of IL-1 production, PG secretion, and HLA-DR expression.