Anti-HEp-2 Autoantibodies in Trial Patients.

<p>A.) Indirect Immuno-fluorescence Assays (IFA). a.) Pretreatment anti-HEp-2 autoantibodies were present at plasma titrations of 1:80 in Subject #6. b.) Autoantibodies were diminished immediately following his TPE treatment (image here at 1:20 titration). c.) Normal plasma control specimen (1:20 titration). B.) IFA Titers. Anti-HEp-2 autoantibody titers were determined in the first eight subjects. Titers were reduced following the initial TPE series in all except Subject #1 (dotted line, solid circles), who was also the only subject among these that did not have a beneficial clinical response.</p

Additional file 2: of Measuring associations between the microbiota and repeated measures of continuous clinical variables using a lasso-penalized generalized linear mixed model

Figure S1. Additional OC-COPD associations between laboratory measurements and bacteria identified by LassoGLMM. Strong associations between bacteria and (a) percent neutrophils (O1), (b) partial pressure of oxygen PO2(O4) (c) SAT (O5), (d) alkaline phosphatase (O6), and (e) glucose (O10). Each horizontal grey line represents an individual. When a colored circle is located on the grey line, it is the relative abundance of that microbe for that subject. Perfect positive association between clinical variable and bacteria would form a line from the bottom-left to the top-right of the graph and would have a highly positive β coefficient in the LassoGLMM. Perfect negative association would form a line from the top-left to the bottom-right of the graph and would have a highly negative β coefficient. (PDF 287 kb

Flowchart of subject recruitments for these experimental trials.

<p>Original Regimen denotes the first series of subjects who were treated with the initial, relatively more conservative regimen (#1–7). Augmented Regimen denotes the most recent four subjects (#8–11) who received a more aggressive therapeutic course, based on interval results in the first cohort (see text for details). TPE = therapeutic plasma exchange; IVIG = intravenous immunoglobulin; * denotes oral consent of patients, under auspices of innovative clinical practice, that were given by these patients after being fully informed of potential risks and yet-unproven efficiencies of the novel treatments.</p

Additional file 4: of Measuring associations between the microbiota and repeated measures of continuous clinical variables using a lasso-penalized generalized linear mixed model

Figure S2. Wilcoxon p-values based on quartile cutoffs compared to LassoGLMM β coefficients for LHMP study. Each plot represents one LassoGLMM with non-zero coefficients. For each bacterial or fungal genera, the Wilcoxon p-value (before adjustment for multiple hypotheses testing) based on the first (a and c) or third quartile (b and d) is plotted on the X-axis and the LassoGLMM β coefficient is plotted on the Y-axis. Most β coefficients are equal to 0; those that are not are labeled with their lowest taxonomic assignment appearing horizontally. The dashed vertical line indicates nominal significance based on a Wilcoxon p-value of 0.05. The nominally significant genera that have a β coefficient of 0 are labeled with an arrow indicating their lowest taxonomic assignment, except in panel c where they would be, from smallest to largest p-value, Catonella, Actinomyces, Porphyromonas, Alicyclobacillus, Megasphaera, Ramularia, Prevotella, Ralstonia, Atopobium, and Veillonella. (PDF 246 kb

Radiographic Changes with Experimental Treatment.

<p>In addition to better lung function and gas exchange, experimental treatments frequently improved the chest radiographs (CXR) of these subjects. a) Pretreatment CXR of Subject #5 during relapse shows diffuse infiltrates; b.) Radiographic improvement (and extubation) of this subject to 2^nd TPE series. c.) CXR of Subject #7 immediately prior to treatment and d.) after first three TPE. These (and other) radiographic and clinical improvements in the subject population were not attributable to changes in intravascular volume status or infection.</p

Additional file 1: of Measuring associations between the microbiota and repeated measures of continuous clinical variables using a lasso-penalized generalized linear mixed model

Table S1. Correlations between bacteria and laboratory measurements in OC-COPD. Table displays the Spearman correlations between all bacteria-laboratory measurement pairs. P values were adjusted (AdjustedP) using the Bonferroni correction. The last column (NwithGenus) is a count of the number of samples that contained the genus in that correlation-pair. (XLSX 173 kb

Matrix Metalloproteinase 7 (MMP7).

<p>Plasma MMP7 levels did not appear to consistently decrease with TPE, nor correlate with clinical responses. In particular, three subjects (#3,4,7, open circles, dotted lines) had increases or no changes of MMP7 levels from pretreatment values despite having prolonged clinical remissions.</p

Clinical Responses to Experimental Therapy.

<p>A.) Decreases in Supplemental Oxygen Requirements. Oxygen requirements decreased in only one of the historical control subjects during their hospitalizations, whereas pulmonary gas exchange improved with experimental treatments among most of the trial cohort (see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0127771#pone.0127771.t002" target="_blank">Table 2</a>). B.) Changes in Abilities to Ambulate. Trial subjects who responded to experimental therapy reported improved exercise tolerance, but maximal walk distances were added as a formal outcome assessment in latest subjects, identified here by subject number (see Tables <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0127771#pone.0127771.t001" target="_blank">1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0127771#pone.0127771.t002" target="_blank">2</a>). With the exception of Subject #10 who showed no response to the experimental treatment, the walk distances of these later patients increased substantially. (Note: The post-treatment >2 mile distance of Subject #9 was limited by boredom rather than exercise capacity).</p

Survival Comparisons.

<p>A.) Survival in the aggregate trial subject population (n = 11) was greater than among historical control AE-IPF patients (n = 20). Cross hatches and numbers in parentheses denote censored observations. Lung transplantation censoring is denoted with “T”. B.) Clinical responses may be more durable and survival may be further enhanced among the later trial subjects (n = 4) treated with a more aggressive regimen of autoantibody-targeted modalities (9 initial TPE + rituximab + IVIG).</p

Autoantibody-Targeted Treatments for Acute Exacerbations of Idiopathic Pulmonary Fibrosis

<div><p>Background</p><p>Severe acute exacerbations (AE) of idiopathic pulmonary fibrosis (IPF) are medically untreatable and often fatal within days. Recent evidence suggests autoantibodies may be involved in IPF progression. Autoantibody-mediated lung diseases are typically refractory to glucocorticoids and nonspecific medications, but frequently respond to focused autoantibody reduction treatments. We conducted a pilot trial to test the hypothesis that autoantibody-targeted therapies may also benefit AE-IPF patients.</p><p>Methods</p><p>Eleven (11) critically-ill AE-IPF patients with no evidence of conventional autoimmune diseases were treated with therapeutic plasma exchanges (TPE) and rituximab, supplemented in later cases with intravenous immunoglobulin (IVIG). Plasma anti-epithelial (HEp-2) autoantibodies and matrix metalloproteinase-7 (MMP7) were evaluated by indirect immunofluorescence and ELISA, respectively. Outcomes among the trial subjects were compared to those of 20 historical control AE-IPF patients treated with conventional glucocorticoid therapy prior to this experimental trial.</p><p>Results</p><p>Nine (9) trial subjects (82%) had improvements of pulmonary gas exchange after treatment, compared to one (5%) historical control. Two of the three trial subjects who relapsed after only five TPE responded again with additional TPE. The three latest subjects who responded to an augmented regimen of nine TPE plus rituximab plus IVIG have had sustained responses without relapses after 96-to-237 days. Anti-HEp-2 autoantibodies were present in trial subjects prior to therapy, and were reduced by TPE among those who responded to treatment. Conversely, plasma MMP7 levels were not systematically affected by therapy nor correlated with clinical responses. One-year survival of trial subjects was 46+15% vs. 0% among historical controls. No serious adverse events were attributable to the experimental medications.</p><p>Conclusion</p><p>This pilot trial indicates specific treatments that reduce autoantibodies might benefit some severely-ill AE-IPF patients. These findings have potential implications regarding mechanisms of IPF progression, and justify considerations for incremental trials of autoantibody-targeted therapies in AE-IPF patients.</p><p>Trial Registration</p><p>ClinicalTrials.gov <a href="http://clinicaltrials.gov/ct2/results?term=NCT01266317" target="_blank">NCT01266317</a></p></div