SteatoSITE: an Integrated Gene-to-Outcome Data Commons for Precision Medicine Research in NAFLD

Nonalcoholic fatty liver disease (NAFLD) is the commonest cause of chronic liver disease worldwide and a growing healthcare burden. The pathobiology of NAFLD is complex, disease progression is variable and unpredictable, and there are no qualified prognostic biomarkers or licensed pharmacotherapies that can improve clinical outcomes; it represents an unmet precision medicine challenge. We established a retrospective multicentre national cohort of 940 patients, across the complete NAFLD spectrum, integrating quantitative digital pathology, hepatic RNA-sequencing and 5.67 million days of longitudinal electronic health record follow-up into a secure, searchable, open resource (SteatoSITE) to inform rational biomarker and drug development and facilitate personalised medicine approaches for NAFLD. A complementary web-based gene browser was also developed. Here, our initial analysis uncovers disease stage-specific gene expression signatures, pathogenic hepatic cell subpopulations and master regulator networks associated with disease progression in NAFLD. Additionally, we construct novel transcriptional risk prediction tools for the development of future hepatic decompensation events

Phenotypic Overlap between MMP-13 and the Plasminogen Activation System during Wound Healing in Mice

BACKGROUND: Proteolytic degradation of extracellular matrix is a crucial step in the healing of incisional skin wounds. Thus, healing of skin wounds is delayed by either plasminogen-deficiency or by treatment with the broad-spectrum metalloproteinase (MP) inhibitor Galardin alone, while the two perturbations combined completely prevent wound healing. Both urokinase-type plasminogen activator and several matrix metallo proteinases (MMPs), such as MMP-3, -9 and -13, are expressed in the leading-edge keratinocytes of skin wounds, which may account for this phenotypic overlap between these classes of proteases. METHODOLOGY: To further test that hypothesis we generated Mmp13;Plau and Mmp13;Plg double-deficient mice in a cross between Mmp13- and Plau-deficient mice as well as Mmp13- and Plg-deficient mice. These mice were examined for normal physiology in a large cohort study and in a well-characterized skin wound healing model, in which we made incisional 20 mm-long full-thickness skin wounds. PRINCIPAL FINDINGS: While mice that are deficient in Mmp13 have a mean healing time indistinguishable to wild-type mice, wound healing in both Plau- and Plg-deficient mice is significantly delayed. Histological analysis of healed wounds revealed a significant increase in keratin 10/14 immunoreactive layers of kerationcytes in the skin surface in Mmp13;Plau double-deficient mice. Furthermore, we observe, by immunohistological analysis, an aberrant angiogenic pattern during wound healing induced by Plau-deficiency, which has not previously been described. CONCLUSIONS: We demonstrate a phenotypic overlap, defined as an additional delay in wound healing in the double-deficient mice compared to the individual single-deficient mice, between MMP-13 and the plasminogen activation system in the process of wound healing, but not during gestation and in postnatal development. Thus, a dual targeting of uPA and MMP-13 might be a possible future strategy in designing therapies aimed at tissue repair or other pathological processes, such as cancer invasion, where proteolytic degradation is a hallmark

Genetic distribution of F2 offspring.

<p>The F2 offspring from interbreeding of double-heterozygous F1 breeding pairs (<i>Mmp13</i>;<i>Plau</i> and <i>Mmp13</i>;<i>Plg</i>) were genotyped at weaning. The numbers in brackets indicate the calculated incidence percentage.</p

Time course of skin wound healing in <i>Mmp13;Plau</i> and <i>Mmp13;Plg</i> double-deficient mice.

<p>(<b>A</b>+<b>C</b>) The percentage fraction of mice with complete re-epithelialization is plotted vs. time after incision of 20 mm long wounds. (<b>B</b>+<b>D</b>) The average wound length is plotted vs. time after incision. Wound healing in <i>Mmp13</i>-deficient mice is indistinguishable from that in wild-type mice, while wound healing in both <i>Plau</i>- and <i>Plg</i>-deficient mice is significantly delayed compared to wildtype wound healing (p = 0.002 and p<0.001 in a two-tailed <i>t</i>-test). However, <i>Mmp13;Plau</i> and <i>Mmp13;Plg</i> double-deficient mice have an additional significant delay in wound healing compared to either <i>Plau</i>- or <i>Plg</i>-deficient mice (p = 0.016 and p<0.001 in a two-tailed t-test), indicating a phenotypic overlap between MMP-13 and the PA system.</p

Survival, femur length and hepatic fibrin deposition in <i>Mmp13;Plau</i> double-deficient cohort mice.

<p>(<b>A</b>) Four genotype groups of siblings were selected for a survival cohort. (<b>B</b>) Femurs were removed from wild-type, <i>Mmp13</i>-deficient, <i>Plau</i>-deficient and <i>Mmp13;Plau</i> double-deficient mice at six months of age. Data are represented as scatter plots and mean values are depicted as horizontal lines. (<b>C–G</b>) Livers from mice were removed when mice were six months old, processed for immunohistochemistry and stained for fibrin. (<b>D–G</b>) Scale bar  = 0.2 mm. (<b>C</b>) The total area of liver cells positive for fibrin per mille of liver cells negative for fibrin was quantified. Bars represent the means ± SEM of each group. *p≤0.05; **p≤0.01.</p