Model Based Targeting of IL-6-Induced Inflammatory Responses in Cultured Primary Hepatocytes to Improve Application of the JAK Inhibitor Ruxolitinib

May combine two claims.

Abrogation of gp130-dependent signaling in hepatocytes prolongs survival and reduces liver damage in an in vivo sepsis model.

“Accordingly, abrogation of glycoprotein 130 (gp130)-dependent signaling in hepatocytes was shown to prolong survival and to reduce liver damage in an in vivo sepsis model (Klein et al., 2007).”

• cites Klein et al., 2007 sourceSupported

May combine two claims.

Late APP genes clustered and were mostly induced upon hIL-6 treatment.

“Hierarchical clustering of significantly regulated genes and further APP genes of interest (Heinrich et al., 1990) revealed that especially late APP genes clustered and were mostly induced upon hIL-6 treatment (Figure 2C).”

• cites Heinrich et al., 1990 sourceSupported

Probably not a substantial claim: may not pass S3 (load-bearing).

Serum amyloid P was suggested to contribute to the persistence of amyloid deposits.

“serum amyloid P, the major APP in mice, was suggested to contribute to the persistence of amyloid deposits (Tennent et al., 1995).”

• cites Tennent et al., 1995 sourceSupported

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Ruxolitinib has been internationally approved for therapy of myelofibrosis and polycythemia vera, which are frequently caused by the V617F gain-of-function mutation within JAK2.

“The JAK1/2 inhibitor Ruxolitinib/INCB018424 (Jakavi/Jakafi, Incyte Pharmaceuticals, Novartis; Lin et al., 2009; Quintas-Cardama et al., 2010) has been internationally approved for the therapy of myelofibrosis (Mesa et al., 2012; Verstovsek et al., 2012) and polycythemia vera (Vannucchi et al., 2015), which are frequently caused by the V617F gain-of-function mutation within JAK2 (Kralovics et al.,”

• cites Mesa et al., 2012; Verstovsek et al., 2012Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

• cites Vannucchi et al., 2015 sourcePartly supported

  The Abstract Background and Discussion report that ruxolitinib was studied and found effective for polycythemia vera, the condition for which this citation is offered. Our copy does not establish the claimed international approval; it describes the study as taking place when there were no approved alternatives for these patients. The myelofibrosis and JAK2-mutation portions are attached to other citations. (LLM, conf=0.83)

  Experimental — accuracy not yet measured
• cites Kralovics et al., 2005 sourceSupported

Probably not a substantial claim: may not pass S3 (load-bearing).

Stattic treatment inhibited IL-6-induced STAT3 phosphorylation and nuclear translocation in hepatocytes.

“Stattic treatment inhibited IL-6-induced STAT3 phosphorylation and nuclear translocation in hepatocytes (Schust et al., 2006).”

• cites Schust et al., 2006 sourcePartly supported

  The Results and Discussion report that Stattic reduced IL-6-induced STAT3 Tyr705 phosphorylation and inhibited cytokine-induced STAT3 nuclear translocation. However, these experiments used HepG2 liver carcinoma cells, not hepatocytes as the citing sentence states. (LLM, conf=0.87)

  Experimental — accuracy not yet measured

Probably not a substantial claim: may not pass S3 (load-bearing).

Increased apoptosis was observed in STAT3-dependent cancer cell lines upon Stattic treatment.

“Moreover, increased apoptosis was observed in STAT3-dependent cancer cell lines upon Stattic treatment (Schust et al., 2006).”

• cites Schust et al., 2006 sourceSupported

May combine two claims.

Stattic blocks activation and dimerization of STAT3.

“Stattic blocks activation and dimerization of STAT3 (Schust et al., 2006) and therefore in our model inhibits the respective conversion of STAT3 to pSTAT3.”

• cites Schust et al., 2006 sourceSupported

Probably not a substantial claim: may not pass S3 (load-bearing).

Target mRNA expression data were normalized to the geometric mean of Hprt and Tbp expression.

“Data were normalized to the geometric mean (Vandesompele et al., 2002) of Hprt and Tbp expression.”

• cites Vandesompele et al., 2002 sourceSupported

Probably not a substantial claim: may not pass S3 (load-bearing).

Deactivation of nuclear STAT3 is mediated by phosphatases.

“Deactivation of nuclear STAT3 was suggested to be mediated by phosphatases (Yamamoto et al., 2002).”

• cites Yamamoto et al., 2002 sourceSupported

Probably not a substantial claim: may not pass S3 (load-bearing).

In the context of hepatitis C virus infection, CXCL10 contributes to persistent liver inflammation and fibrosis.

“In the context of hepatitis C virus infection, CXCL10 was suggested to contribute to persistent liver inflammation and fibrosis”

• cites Zeremski et al., 2008, 2009Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

• cites Brownell and Polyak, 2013 sourceSupported

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

IL-33 is induced in fibrotic livers, and hepatic stellate cells are suggested as major IL-33 producers in this context.

“This IL-1-like cytokine (Schmitz et al., 2005) was described to be induced in fibrotic livers, and hepatic stellate cells were suggested as major IL-33 producer in this context (Marvie et al., 2010).”

• cites Marvie et al., 2010 sourceSupported

Probably not a substantial claim: may not pass S2 (checkable).

To obtain a predictive mathematical model, the relation of considered species and experimentally measured components as well as the amount of experimental data needs to be appropriate.

“To obtain a predictive mathematical model, the relation of considered species and experimentally measured components as well as the amount of experimental data needs to be appropriate”

• cites Aldridge et al., 2006 sourceNot checked — no full text of the source
• cites Bachmann et al., 2012 sourceSupported

May combine two claims.

Ren et al. reported no statistically significant increase of Il22 mRNA in response to hepatectomy, but an increase of IL-22 protein in serum at late time points starting at 6 h with peak at 12 h.

“These results are in line with the studies of Ren et al. reporting that there is no statistically significant increase of Il22 mRNA in response to hepatectomy, but rather an increase of IL-22 protein is observed in the serum at late time points post hepatectomy starting at 6 h post treatment with a peak at 12 h (Ren et al., 2010).”

• cites Ren et al., 2010 sourcePartly supported

  The Results report that hepatic IL-22 mRNA rose after partial hepatectomy without reaching statistical significance. They also report increased serum IL-22 from 6 through 48 hours, with statistical significance at 12 hours, but do not state that the serum level peaked at 12 hours. Page numbers are unavailable in our copy. (LLM, conf=0.86)

  Experimental — accuracy not yet measured

Probably not a substantial claim: may not pass S3 (load-bearing).

The measured STAT3 protein concentration in primary mouse hepatocytes is in good agreement with published data from primary human hepatocytes.

“The obtained value for STAT3 is in good agreement with recently published data from a mass spectrometry approach to determine molecules per cell in primary human hepatocytes (Wisniewski et al., 2016).”

• cites Wisniewski et al., 2016 sourcePartly supported

  Section 3.3 describes mass-spectrometry-based estimates of protein copies per cell in human hepatocytes, supporting the description of the cited dataset. The passages found do not give a STAT3 value or establish that it agrees with the citing paper’s mouse-hepatocyte measurement (searched: STAT3 and its full protein name). (LLM, conf=0.78)

  Experimental — accuracy not yet measured

Probably not a substantial claim: may not pass S3 (load-bearing).

A twice-daily dosing regimen has been successfully applied in treatment of myelofibrosis patients.

“A twice-daily dosing regimen was furthermore successfully applied in the treatment of myelofibrosis patients (Verstovsek et al., 2012).”

• cites Verstovsek et al., 2012 sourceSupported

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Primary mouse hepatocyte isolation was performed in a standardized way according to Klingmuller et al. (2006) or according to the refined protocol described by Huard et al. (2012).

“Primary mouse hepatocyte isolation was performed in a standardized way according to Klingmuller et al. (2006) or according to the refined protocol described by Huard et al. (2012).”

• cites Klingmuller et al. (2006) sourceNot checked — no full text of the source
• cites Huard et al. (2012) sourceSupported

Probably not a substantial claim: may not pass S3 (load-bearing).

Previous treatment planning was based on preclinical data and empirical results from clinical trials.

“Notably, previous treatment planning was based on preclinical data and empirical results from clinical trials (Quintas-Cardama et al., 2010; Shi et al., 2011).”

• cites Quintas-Cardama et al., 2010 sourcePartly supported

  The Results describe using preclinical whole-blood assay findings to guide dose selection in mouse studies, and the Abstract says preliminary clinical results supported the preclinical findings. Neither passage establishes that previous treatment planning was based on both preclinical data and empirical clinical-trial results. (LLM, conf=0.78)

  Experimental — accuracy not yet measured
• cites Shi et al., 2011 sourceNot checked — no full text of the source

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Microarray analysis used a linear regression model with Limma and a significance threshold of Benjamini-Hochberg adjusted p < 0.01.

“To analyze significant gene regulation, we applied a linear regression model with the Limma package (Ritchie et al., 2015). Gene expression values yi were modeled to be explained by time frames t (early, intermediate and late) and condition c (IL-6 and control). The significance threshold of Benjamini–Hochberg adjusted p < 0.01 was implemented.”

• cites Ritchie et al., 2015 sourceSupported

May combine two claims.

After peaking, the phospho-STAT3 signal decreased in PHx and LPS treated livers and returned to levels close to baseline at 24 h.

“After peaking, the phospho-STAT3 signal decreased likewise in PHx and LPS treated livers, and returned to levels close to baseline at 24 h.”

May combine two claims.

Based on extensive experimental data, the mathematical model describes pathway activation and key target gene induction during regenerative and inflammatory conditions, as well as the impact of Ruxolitinib and Stattic.

“Based on extensive experimental data, the mathematical model describes pathway activation and key target gene induction during regenerative and inflammatory conditions, as well as the impact of the pathway inhibitors Ruxolitinib and Stattic.”

• AssumptionThe authors state this as an assumption: Constant IL-6 concentrations and complete removal of ligand after stimulation pulses can be assumed in the model.
• AssumptionThe authors state this as an assumption: Dephosphorylation of gp130 and JAK1 is coupled.
• AssumptionThe authors state this as an assumption: The law of mass-action kinetics applies to the modeled reactions.
• AssumptionThe authors state this as an assumption: Stattic inhibition is irreversible and its concentrations can be modeled as constant.
• AssumptionThe authors state this as an assumption: A separate STAT3 dimerization step can be neglected because the oligomerization state of STAT3 was not assessed by experiments.

May combine two claims.

In PCA, samples were separated by time and condition, and biological duplicates clustered, indicating high reproducibility.

“In the two most relevant PCs the samples were separated by time and by condition (control vs. hIL-6) and biological duplicates were clustered (Figure 2A) indicating high reproducibility.”

May combine two claims.

The STAT3 signal detected after NaCl injection was out of range of the reference curve and corresponded to <0.1 ng/mL hIL-6.

“The STAT3 signal detected after NaCl injection was out of range of our reference curve and corresponded to <0.1 ng/mL hIL-6 (Figure 1C).”

May combine two claims.

Peak phospho-STAT3 levels were reached at 2 h following PHx and after 1 h following LPS injection.

“Peak levels were reached at 2 h following PHx and even earlier, after 1 h following LPS injection.”

Probably not a substantial claim: may not pass S3 (load-bearing).

CRP displayed a similar expression pattern as Apcs.

“Interestingly, the gene encoding the C reactive protein (CRP), displayed a similar expression pattern as Apcs.”

May combine two claims.

723, 779, and 694 genes were IL-6-regulated at early, intermediate, and late time points, respectively.

“In total 1,728 genes were significantly regulated upon hIL-6 stimulation (Appendix Figure S1A), while 723, 779, and 694 genes were IL-6-regulated at early, intermediate, and late time points, respectively.”

May combine two claims.

Sham surgery and NaCl injection caused serum IL-6 levels to increase only slightly; less than 0.4 ng/mL after sham surgery and <0.1 ng/mL after NaCl injection were measured.

“Less than 0.4 ng/mL IL-6 after sham surgery and <0.1 ng/mL IL-6 after NaCl injection were measured.”

May combine two claims.

Following the peak, IL-6 levels dropped quickly and returned to baseline levels at 8-24 h.

“Following the peak, IL-6 levels dropped quickly and returned to baseline levels at 8–24 h.”

May combine two claims.

STAT3 activation was detectable from 2.5 ng/mL hIL-6, then steeply increased and quickly reached saturation at 25-50 ng/mL.

“It was detectable from 2.5 ng/mL hIL-6 on, then steeply increased and quickly reached saturation at 25–50 ng/mL (Figure 1C).”

May combine two claims.

The corresponding mouse IL-6 concentrations were 1.8 and 50 ng/mL for PHx and LPS, respectively.

“This corresponds to a mouse IL-6 concentration of 1.8 and 50 ng/mL, respectively (Figure 1D).”

May combine two claims.

Cxcl10 responded at 25-50 ng/mL hIL-6 and did not reach saturation within the observed hIL-6 range.

“The other early-induced gene Cxcl10 responded at 25–50 ng/mL hIL-6, and did not reach saturation within the observed hIL-6 range.”

May combine two claims.

Export of phosphorylated STAT3 could be made arbitrarily small in identifiability analysis and was omitted from the final model.

“However, based on identifiability analysis (see Appendix Figure S15), we found that export of phosphorylated STAT3 could be made arbitrarily small and was therefore omitted from the final model.”

May combine two claims.

Socs3 expression at 1, 6, and 24 h was detectable from 1 ng/mL hIL-6, steadily increased, and reached saturation at 50 ng/mL hIL-6.

“Socs3 expression at 1, 6, and 24 h was detectable from 1 ng/mL hIL-6, steadily increased, and reached saturation at 50 ng/mL hIL-6.”

May combine two claims.

Inhibitor pre-treatment for 1 h caused reduced basal Socs3 mRNA and reduced sensitivity and peak magnitude of the dose-dependent Socs3 response upon IL-6 stimulation.

“Inhibitor pre-treatment for 1 h caused a reduced basal level of Socs3 mRNA and a reduced sensitivity and peak magnitude of the dose-dependent Socs3 response upon IL-6 stimulation (Figure 5).”

May combine two claims.

The crossing of heterozygous mKate2-STAT3 animals resulted in 66.8% WT and 33.2% heterozygous animals (n = 232), and heterozygous mice showed no phenotype concerning viability compared to WT.

“The crossing of the heterozygous animals resulted in 66.8% WT and 33.2% heterozygous animals (n = 232) and these heterozygous mice showed no phenotype, also concerning viability in comparison to WT animals.”

May combine two claims.

mKate2-STAT3 is expressed at a slightly lower level than endogenous STAT3, but its phosphorylation dynamics correlate with endogenous STAT3 phosphorylation dynamics.

“These studies showed that mKate2-STAT3 is expressed at a slightly lower level than the endogenous protein but the phosphorylation dynamics correlated with the phosphorylation dynamics of the endogenous STAT3.”

May combine two claims. The quote only partly states this claim.

All target genes showed sigmoidal dose response curves and saturation at high IL-6 concentrations (100-500 ng/mL).

“All showed sigmoidal dose response curves and saturation at high IL-6 concentrations (100–500 ng/mL).”

May combine two claims.

For the APP genes, Cxcl10 had the shortest delay, followed by Fgg; the other APP genes exhibited slower dynamics.

“For the APP genes, Cxcl10 had the shortest delay, followed by Fgg. The other APP genes exhibited slower dynamics (see Appendix Figure S24).”

May combine two claims.

Microarray analysis identified Socs3 to critically contribute to overall regulation and to be significantly IL-6-induced at all time points.

“This is consistent with our microarray analysis, which identified Socs3 to critically contribute to overall regulation (Figure 2B) and to be significantly IL-6-induced at all time points (Figure 2C).”

May combine two claims.

Fgg, Hamp, Il33, Apcs, Hp, and Hpx mRNAs were induced from 1 to 10 ng/mL hIL-6, with sensitivities similar to Socs3.

“In contrast, the sensitivities of intermediate and late APP genes were similar to that of Socs3—Fgg, Hamp, Il33, Apcs, Hp, and Hpx mRNAs were induced from 1 to 10 ng/mL hIL-6.”

May combine two claims.

After peak, Socs3 mRNA levels declined but stayed elevated throughout the observed time frame.

“Afterwards, Socs3 mRNA levels declined, but stayed elevated throughout the observed time frame.”

May combine two claims.

Socs3, Cxcl10, Fgg, Il33, Hp, and Hpx required an explicit delay in the model to describe the available data, while Apcs and Hamp did not.

“Based on repeated profile likelihood analysis, we concluded that Socs3, Cxcl10, Fgg, Il33, Hp, and Hpx required an explicit delay in the model to describe the available data, while Apcs and Hamp did not.”

• AssumptionThe authors state this as an assumption: Constant IL-6 concentrations and complete removal of ligand after stimulation pulses can be assumed in the model.
• AssumptionThe authors state this as an assumption: Dephosphorylation of gp130 and JAK1 is coupled.
• AssumptionThe authors state this as an assumption: The law of mass-action kinetics applies to the modeled reactions.
• AssumptionThe authors state this as an assumption: Stattic inhibition is irreversible and its concentrations can be modeled as constant.
• AssumptionThe authors state this as an assumption: A separate STAT3 dimerization step can be neglected because the oligomerization state of STAT3 was not assessed by experiments.

May combine two claims.

IL-6 treatment rescued the decrease and caused elevated Apcs expression at 24 h relative to untreated cells.

“IL-6 treatment rescued this decrease and caused elevated Apcs expression at 24 h relative to untreated cells (Figure 4 and Appendix Figure S10).”

May combine two claims.

Fgg, Hamp, and Il33 were induced by IL-6 and clearly detectable from 3 to 6 h on.

“The genes Fgg, Hamp, and Il33 were induced by IL-6 and were clearly detectable from 3 to 6 h on, as shown by qRT-PCR analysis.”

May combine two claims.

Socs3 levels declined but stayed elevated up to 24 h.

“Subsequently, its levels declined but stayed elevated up to 24 h.”

May combine two claims.

The mathematical model quantitatively links IL-6 levels to JAK1-STAT3 signaling dynamics and gene expression, and describes the impact of Ruxolitinib and Stattic on STAT3 and its target gene activation.

“We could quantitatively link these different levels by implementing a mathematical model, which not only described experimentally observed signaling dynamics, but also the impact of the pathway inhibitors Ruxolitinib and Stattic on STAT3 and its target gene activation.”

May combine two claims.

A very rapid induction of Il6 mRNA was detected in response to LPS injection, maximal after 1 h, coinciding with maximal STAT3 phosphorylation at 1 h post treatment.

“On the contrary a very rapid induction of Il6 mRNA was detected particularly in response to LPS injection that was already maximal after 1 h of LPS injection (Appendix Figure S14) and coincided with maximal STAT3 phosphorylation observed at 1 h post treatment (Figure 1B).”

May combine two claims.

The effect was most obvious for Socs3, and recognizable for all other genes, although error bars were partly overlapping for single and triple treatment.

“The effect was most obvious for Socs3, and also recognizable for all other genes, although error bars were partly overlapping for single and triple treatment.”

May combine two claims.

Comparing model predictions and experimental data for different Ruxolitinib regimens and IL-6 concentrations revealed good agreement; Ruxolitinib-mediated suppression of mKate2-STAT3 nuclear translocation was improved with triple treatment compared with single.

“Comparing model predictions and experimental data for the different Ruxolitinib treatment regimens and IL-6 concentrations revealed good agreement between model and experiment (Figure 7D and Appendix Figure S6): Ruxolitinib-mediated suppression of mKate2-STAT3 nuclear translocation was improved when the triple treatment regime was applied, compared with single treatment.”

May combine two claims.

Compared to single treatment, triple treatment induced a more sustained inhibitory effect, utilizing considerably lower doses for repetitive treatment after the initial bolus.

“Compared to the single treatment (q24h), the triple treatment (q8h) induced a more sustained inhibitory effect, utilizing considerably lower doses for the repetitive treatment after the initial bolus.”

May combine two claims.

Inhibiting production and activation of the receptor, inhibiting activation of STAT3, and reducing degradation of Socs3 mRNA are predicted to lead to additional attenuation of the APP response.

“Here we can observe that inhibiting production and activation of the receptor, inhibiting the activation of STAT3 and reducing the degradation of Socs3 (mRNA) are all predicted to lead to additional attenuation of the APP response.”

May combine two claims.

In primary mouse hepatocytes, Cxcl10 mRNA is selectively induced by inflammatory IL-6 concentrations, while all other analyzed target genes respond to both regenerative and inflammatory IL-6 stimuli.

“Cxcl10 mRNA was selectively induced by inflammatory IL-6 concentrations, while all other analyzed target genes responded to both, regenerative and inflammatory IL-6 stimuli (Figure 5).”

Probably not a substantial claim: may not pass S3 (load-bearing).

Principal component analysis showed first two principal components explained 68.1% of variance (PC1: 58.4%, PC2: 9.7%).

“The first two principal components explained most of the variance in the data set (PC1: 58.4%, PC2: 9.7%, 68.1% in total).”

May combine two claims.

A certain amount of IL-6 is required for efficient immune defense and liver regeneration.

“On the other hand, a certain amount of IL-6 is required for efficient immune defense (Kopf et al., 1994) and liver regeneration (Cressman et al., 1996; Sakamoto et al., 1999; Zimmers et al., 2003).”

• cites Kopf et al., 1994 sourceNot checked — no full text of the source
• cites Cressman et al., 1996; Sakamoto et al., 1999; Zimmers et al., 2003Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Probably not a substantial claim: may not pass S3 (load-bearing).

Increased IL-6 activity is associated with chronic inflammatory diseases including rheumatoid arthritis, multiple sclerosis, and Crohn's disease.

“Increased activity of interleukin (IL)-6 has been associated with chronic inflammatory diseases including rheumatoid arthritis (Hirano et al., 1988), multiple sclerosis (Frei et al., 1991; Navikas et al., 1996), and Crohn's disease (Ito, 2003).”

• cites Hirano et al., 1988 sourceNot checked — no full text of the source
• cites Frei et al., 1991; Navikas et al., 1996Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

• cites Ito, 2003 sourceNot checked — no full text of the source

May combine two claims.

In hepatocytes, IL-6 regulates acute phase protein production by activating the IL-6 receptor complex with gp130, and signals are transduced via JAK1 and STAT3.

“Central target cells of IL-6 are hepatocytes, where IL-6 regulates the production of acute phase proteins (APPs) by first activating the IL-6 receptor complex with the signal-transducing subunit gp130. Signals are further transduced via janus kinase 1 (JAK1) and signal transducer and activator of transcription 3 (STAT3; Bode and Heinrich, 2001).”

• cites Bode and Heinrich, 2001Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Persistent inflammation can initiate or promote malignant progression, and a pro-tumorigenic role of IL-6 has been suggested.

“Persistent inflammation can initiate or promote (Grivennikov and Karin, 2011) malignant progression and a pro-tumorigenic role of IL-6, which is elevated in many types of cancer, has been suggested (Heikkila et al., 2008).”

• cites Grivennikov and Karin, 2011 sourceNot checked — no full text of the source
• cites Heikkila et al., 2008 sourceNot checked — no full text of the source

May combine two claims.

Other cytokines OSM, IL-11, IL-10, and IL-22 also induce STAT3 phosphorylation and could contribute to regenerative and inflammatory signaling in the liver.

“However, other cytokines such as Oncostatin-M (OSM), IL-11, IL-10, and IL-22, also induce STAT3 phosphorylation (see Nakamura et al., 2004; Sabat et al., 2010; Nishina et al., 2012; Rao et al., 2014) and therefore could contribute to the complex regenerative and inflammatory signaling in the liver.”

• cites Nakamura et al., 2004; Sabat et al., 2010; Nishina et al., 2012; Rao et al., 2014Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

IL-22 is a mediator of cross-talk between immune cells and hepatocytes and contributes to efficient liver regeneration but potentially distinct from IL-6 primarily contributes to long-term recovery.

“Together these studies suggest that IL-22 is a mediator of the cross-talk between immune cells and hepatocytes and contributes to efficient liver regeneration but potentially distinct from IL-6 primarily contributes to long-term recovery.”

• cites Kudira et al., 2016 sourceNot checked — no full text of the source
• cites Wallace and Subramaniam, 2015 sourceNot checked — no full text of the source

May combine two claims.

High IL-6 levels are frequently found and correlate with poor outcome in patients with sepsis.

“High IL-6 levels are also frequently found and correlate with poor outcome in patients with sepsis, an acute systemic inflammatory response (Waage et al., 1989; Calandra et al., 1991; Damas et al., 1992; Norrby-Teglund et al., 1995).”

• cites Waage et al., 1989; Calandra et al., 1991; Damas et al., 1992; Norrby-Teglund et al., 1995Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Classified as probably not a substantial claim. May combine two claims.

Xu et al. predicted that IL-6 signaling could be best targeted at the receptor level, and that reduced inhibitor dose may be achievable by applying possible inhibitor combinations.

“These studies predicted that IL-6 signaling could be best targeted at the receptor level, and that reduced inhibitor dose may be achievable by applying possible inhibitor combinations (Xu et al., 2015).”

• cites Xu et al., 2015Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Guidelines recommend a repetitive, constant dose of Ruxolitinib 10 mg twice daily for polycythemia vera or 20 mg twice daily for myelofibrosis.

“According to the guidelines, the recommendation for Jakavi is a repetitive, constant dose of 10 mg twice daily (q12h) for polycythemia vera or 20 mg twice daily (q12h) for myelofibrosis (Rote, 2016).”

• cites Rote, 2016Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

APPs fulfill beneficial roles in host defense and tissue repair.

“Although, APPs fulfill beneficial roles in host defense and tissue repair (Bode et al., 2012), several adverse effects have been reported for different APPs.”

• cites Bode et al., 2012 sourceNot checked — no full text of the source

May combine two claims.

Model parameters were estimated by a maximum likelihood approach, and identifiability of the dynamic model parameters was ensured by Profile Likelihood.

“The mathematical model consists of coupled ordinary differential equations (ODE) and the model parameters were estimated by a maximum likelihood approach, whereas identifiability of the dynamic model parameters was ensured by the Profile Likelihood.”

Classified as probably not a substantial claim. May combine two claims.

ODE-based mathematical models are well-suited to study the dynamics of signal transduction and have enabled identification of therapeutic targets within signaling networks.

“Mathematical models based on ordinary differential equations (ODEs) are well-suited to study the dynamics of signal transduction and have enabled the identification of therapeutic targets within signaling networks (Schoeberl et al., 2009; Raia et al., 2011).”

• cites Schoeberl et al., 2009; Raia et al., 2011Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

May combine two claims.

Several ODE-based mathematical models of IL-6 signaling have been reported, but only Xu et al. tested potential effects of targeting selected pathway components on APP expression in silico.

“Although several ODE-based mathematical models of IL-6 signaling have been reported to date (Singh et al., 2006; Moya et al., 2011; Dittrich et al., 2012), only with a recently described mathematical model (Xu et al., 2015) potential effects of targeting selected pathway components on APP expression were tested in silico.”

• cites Singh et al., 2006; Moya et al., 2011; Dittrich et al., 2012Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

• cites Xu et al., 2015Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Probably not a substantial claim: may not pass S3 (load-bearing).

Hepcidin contributes to the development of anemia under inflammatory conditions.

“Hepcidin, for instance, a crucial regulator of iron homeostasis (Sakamori et al., 2010; Ganz and Nemeth, 2012), contributes to the development of anemia under inflammatory conditions (Weinstein et al., 2002; Kemna et al., 2005).”

• cites Weinstein et al., 2002; Kemna et al., 2005Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Probably not a substantial claim: may not pass S3 (load-bearing).

Elevated expression of fibrinogen is related to formation and progression of atherosclerotic plaques.

“Elevated expression of fibrinogen was related to formation and progression of atherosclerotic plaques (Levenson et al., 1995)”

• cites Levenson et al., 1995 sourceNot checked — no full text of the source

May combine two claims.

The model-based predictions reported by Xu et al. were not experimentally validated, limiting applicability to targeting IL-6 signaling in human disease.

“However, the model-based predictions reported by Xu et al. were not experimentally validated, thus limiting applicability to targeting IL-6 signaling in human disease.”

• cites Xu et al., 2015Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Probably not a substantial claim: may not pass S3 (load-bearing).

Ruxolitinib is also tested for treatment of other malignancies and chronic inflammatory diseases such as rheumatoid arthritis.

“Ruxolitinib is also tested for the treatment of other malignancies as well as chronic inflammatory diseases such as rheumatoid arthritis (Williams et al., 2008; Quintas-Cardama et al., 2011).”

• cites Williams et al., 2008; Quintas-Cardama et al., 2011Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

May combine two claims.

Stattic targets the STAT3 SH2 domain, blocking receptor association and dimerization.

“The STAT3 inhibitor Stattic, which is not approved for clinical applications, targets the STAT3 SH2 domain, thus blocking receptor association and dimerization.”

Classified as probably not a substantial claim. May combine two claims.

Levels of phosphorylated and total protein species were measured by quantitative immunoblotting with randomized sample loading and normalization to housekeeping proteins or recombinant calibrator proteins.

“The levels of phosphorylated and total protein species were measured by quantitative immunoblotting (Schilling et al., 2005a), including randomized sample loading and normalization to suitable housekeeping proteins or, in case proteins were enriched by immunoprecipitation, to recombinant calibrator proteins.”

• cites Schilling et al., 2005aNot matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

May combine two claims.

Because nuclear STAT3 dephosphorylation is so rapid that nuclear phosphorylated STAT3 exactly follows cytoplasmic phospho-STAT3 concentration, the model was reduced by one equation.

“Since nuclear STAT3 dephosphorylation is so rapid that the level of nuclear phosphorylated STAT3 exactly follows the cytoplasmic concentration of phospho-STAT3, the model was reduced by one equation.”

May combine two claims.

SOCS3 inhibits the signaling pathway by increasing degradation of the receptor complex and inhibiting phosphorylation of STAT3 by the fully activated receptor complex.

“SOCS3 inhibits the signaling pathway by increasing degradation of the receptor complex as well as inhibiting phosphorylation of STAT3 by the fully activated receptor complex (Starr et al., 1997; Babon et al., 2012; Kershaw et al., 2013).”

• cites Starr et al., 1997; Babon et al., 2012; Kershaw et al., 2013Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Probably not a substantial claim: may not pass S3 (load-bearing).

Hp and Hpx have previously been reported to be IL-6 responsive and STAT3-dependent.

“The APP genes Hp and Hpx were not significantly regulated in our microarray analysis (Figure 2C), but have previously been reported to be IL-6 responsive and STAT3-dependent (Alonzi et al., 2001).”

• cites Alonzi et al., 2001 sourceNot checked — no full text of the source

May combine two claims. The quote only partly states this claim.

The model was calibrated in two stages: an upstream core model (receptor, STAT3 pools, SOCS3) calibrated on wild type and inhibitor data, and a downstream APP model parameterized separately with upstream parameters fixed.

“To summarize, the model was calibrated in two stages. First the upstream model of IL-6 signaling was developed and calibrated. The upstream model also termed “core model” consists of the receptor level, the STAT3 pools and SOCS3 and is calibrated on both wild type as well as inhibitor data.”

• AssumptionThe authors state this as an assumption: None of the APP genes feed back into the system.

Classified as probably not a substantial claim. May combine two claims.

IL-6 has repeatedly been suggested to contribute to inflammatory or malignant diseases, and targeting this mediator needs careful evaluation to maintain beneficial regenerative functions.

“While IL-6 has repeatedly been suggested to contribute to inflammatory or malignant diseases, targeting this central mediator needs to be carefully evaluated to maintain its beneficial regenerative functions (Hunter and Jones, 2015).”

• cites Hunter and Jones, 2015 sourceNot checked — no full text of the source

Probably not a substantial claim: may not pass S3 (load-bearing).

CXCL10 is secreted by macrophages in an IL-6/STAT3-dependent manner.

“CXCL10 was described previously to be secreted by macrophages in an IL-6/STAT3-dependent manner”

• cites Xu et al., 2012, 2015Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

May combine two claims.

The JAK-STAT pathway is relevant for IL-6-induced APP expression, whereas MAPK activation is dispensable.

“we focused our model scope on the JAK-STAT pathway, which according to Dierssen et al. is relevant for IL-6-induced APP expression whereas MAPK activation is dispensable”

• cites Dierssen et al., 2008 sourceNot checked — no full text of the source

May combine two claims.

The maximal tolerable dose of Ruxolitinib in healthy volunteers is 100 mg once daily, already inducing severe side effects such as neutropenia.

“The maximal tolerable dose of Ruxolitinib in healthy volunteers was described to be 100 mg once daily, already inducing severe side effects as neutropenia (Shi et al., 2011).”

• cites Shi et al., 2011 sourceNot checked — no full text of the source

May combine two claims.

LPS-induced IL-6 induction is more rapid and more than two orders of magnitude higher than IL-22 induction.

“suggesting that the induction of IL-6 in response to LPS is more rapid and more than two orders of magnitude higher compared to IL-22”

May combine two claims.

The initial dose of 500 nM Ruxolitinib was selected based on dose response experiments and closely relates to the determined IC50.

“The initial dose of 500 nM Ruxolitinib was selected based on dose response experiments (Appendix Figures S70, S71) in primary mouse hepatocytes and closely relates to the determined IC50.”

May combine two claims.

Because IL-6 appears to be the main inducer of STAT3 activation in hepatocytes, inferring IL-6 concentrations from STAT3 phosphorylation in whole liver lysates provides a good estimate of IL-6 concentrations in the hepatocyte microenvironment.

“Because IL-6 appears to be the main inducer of STAT3 activation in hepatocytes (Cressman et al., 1996), the major hepatic cell type, this approach provides a good estimate of IL-6 concentrations in the hepatocytes' microenvironment.”

• cites Cressman et al., 1996 sourceNot checked — no full text of the source

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

The mathematical model is available to the community at the biomodels database and at www.data2dynamics.org.

“The mathematical model is available to the community at the biomodels database as well as on www.data2dynamics.org.”

May combine two claims.

Negligible accumulation of Ruxolitinib occurs after multiple doses, minimizing risk of potential side effects.

“Shi et al. found negligible accumulation of Ruxolitinib after multiple doses, thus minimizing the risk of potential side effects.”

• cites Shi et al., 2011 sourceNot checked — no full text of the source

Probably not a substantial claim: may not pass S3 (load-bearing).

PHx was performed based on the standardized procedure described by Mitchell and Willenbring (2008).

“PHx was performed based on the standardized procedure described by Mitchell and Willenbring (2008).”

• cites Mitchell and Willenbring (2008) sourceNot checked — no full text of the source

Probably not a substantial claim: may not pass S3 (load-bearing).

All model parameters were estimated directly from experimental data using Maximum Likelihood Estimation.

“All model parameters were estimated directly from the experimental data using Maximum Likelihood Estimation.”

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

For core model, 270 parameters (22 dynamic) were estimated on 2220 data points; for downstream, 471 additional parameters (29 dynamic) on 2288 data points.

“For the core model, 270 parameters (of which 22 dynamic parameters) were estimated on a total of 2220 data points. For the downstream components, we estimated 471 additional parameters (of which 29 dynamic parameters) on a total of 2,288 data points.”

Probably not a substantial claim: may not pass S3 (load-bearing).

The study generated an extensive amount of experimental data using different technologies to assess dynamics of signal transduction and target gene expression.

“For the presented study an extensive amount of experimental data was generated using different technologies ranging from quantitative immunoblotting, multiplexed bead-based arrays and quantitative mass spectrometry to qRT- PCR and microarray analysis in order to assess the dynamics of signal transduction and target gene expression.”

May combine two claims.

The mathematical model has high predictive power, confirmed by experimental validation of previously untested scenarios.

“We established a mathematical representation of the signaling network and could confirm its high predictive power by experimentally validating previously untested scenarios.”

Probably not a substantial claim: may not pass S3 (load-bearing).

Quality of cellular fractionation was checked by correct subcellular localization of marker proteins Sp1 (nuclear) and Eps15 (cytosolic).

“Quality of fractionation was checked by correct subcellular localization of marker proteins Sp1 (nuclear; Santa Cruz Biotechnology, #sc-59) and Eps15 (cytosolic; Santa Cruz Biotechnology, #sc-534).”

May combine two claims.

Ruxolitinib has rapid metabolism and a short half-life.

“thus counteracting its rapid metabolism (Shilling et al., 2010) resulting in its short half-life (Shi et al., 2011).”

• cites Shilling et al., 2010 sourceNot checked — no full text of the source
• cites Shi et al., 2011 sourceNot checked — no full text of the source

Probably not a substantial claim: may not pass S3 (load-bearing).

Ontology analysis used a model-based ontology analysis with Wiki Pathways and an enrichment threshold of probability of being regulated > 0.5.

“Ontology analysis of the three response lists was performed using a model-based ontology analysis (http://nar.oxfordjournals.org/content/early/2010/02/19/nar.gkq045.full) using Wiki Pathways and implementing an enrichment threshold using pathways with a probability of being regulated > 0.5.”

Probably not a substantial claim: may not pass S3 (load-bearing).

Selectively reducing Socs3 mRNA degradation rate would benefit from synergistic effects between SOCS3 and Ruxolitinib.

“One option would be to selectively reduce the Socs3 mRNA degradation rate to benefit from synergistic effects between the pathway's natural inhibitor SOCS3 and the drug Ruxolitinib.”

Probably not a substantial claim: may not pass S3 (load-bearing).

The mKate2-STAT3 knock-in reporter's expression mirrors endogenous STAT3 expression in different organs.

“Since the fluorescently labeled STAT3 was created as knock-in into the endogenous STAT3 locus, its expression should mirror the expression of STAT3 in different organs.”