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1.  Tcf3 promotes cell migration and wound repair through regulation of lipocalin 2 
Nature communications  2014;5:4088.
Cell migration is an integral part of re-epithelialization during skin wound healing, a complex process involving molecular controls that are still largely unknown. Here we identify a novel role for Tcf3, an essential transcription factor regulating embryonic and adult skin stem cell functions, as a key effector of epidermal wound repair. We show that Tcf3 is upregulated in skin wounds and that Tcf3 overexpression accelerates keratinocyte migration and skin wound healing. We also identify Stat3 as an upstream regulator of Tcf3. We show that the pro-migration effects of Tcf3 are non-cell autonomous and occur independently of its ability to interact with β-catenin. Finally, we identify lipocalin-2 as the key secreted factor downstream of Tcf3 that promotes cell migration in vitro and wound healing in vivo. Our findings provide new insights into the molecular controls of wound-associated cell migration and identify potential therapeutic targets for the treatment of defective wound repair.
doi:10.1038/ncomms5088
PMCID: PMC4052366  PMID: 24909826
Tcf3; Stat3; lipocalin 2; cell migration; wound healing; keratinocytes
2.  Detection of internal exon deletion with exon Del 
BMC Bioinformatics  2014;15(1):332.
Background
Exome sequencing allows researchers to study the human genome in unprecedented detail. Among the many types of variants detectable through exome sequencing, one of the most over looked types of mutation is internal deletion of exons. Internal exon deletions are the absence of consecutive exons in a gene. Such deletions have potentially significant biological meaning, and they are often too short to be considered copy number variation. Therefore, to the need for efficient detection of such deletions using exome sequencing data exists.
Results
We present ExonDel, a tool specially designed to detect homozygous exon deletions efficiently. We tested ExonDel on exome sequencing data generated from 16 breast cancer cell lines and identified both novel and known IEDs. Subsequently, we verified our findings using RNAseq and PCR technologies. Further comparisons with multiple sequencing-based CNV tools showed that ExonDel is capable of detecting unique IEDs not found by other CNV tools.
Conclusions
ExonDel is an efficient way to screen for novel and known IEDs using exome sequencing data. ExonDel and its source code can be downloaded freely at https://github.com/slzhao/ExonDel.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2105-15-332) contains supplementary material, which is available to authorized users.
doi:10.1186/1471-2105-15-332
PMCID: PMC4288651  PMID: 25322818
3.  Remission of Rheumatoid Arthritis in Clinical Practice: Application of the ACR/EULAR 2011 Remission Criteria 
Arthritis and rheumatism  2011;63(11):3204-3215.
Purpose
To describe use of the ACR/EULAR (AE) rheumatoid arthritis (RA) remission criteria in clinical practice.
Methods
We examined remission in the US Veterans Affairs RA (VARA) registry of 1,341 patients (91% men) with 9,700 visits and a community rheumatology practice (ARCK) of 1,168 patients (28% men) with 6,362 visits. We studied cross-sectional and cumulative probabilities, agreement among various remission criteria, and aspects of reliability using Boolean definitions and CDAI and SDAI methods proposed by AE.
Results
By AE definition for community practice (swollen and tender joints ≤1, patient global ≤1), cross-sectional remission was 7.5% (6.4, 8.7) for ARCK and 8.9% (7.9, 9.9) for VARA. Cumulative or remission at any observation was 18.0% (ARCK) and 24.4% (VARA) over a mean of 2.2 years. Addition of ESR or CRP to criteria reduced remission to 5.0-6.2%, and use of CDAI/SDAI increased proportions to 6.9-10.1%. 1.8%-4.6% of patients met remission criteria at ≥2 visits. Agreement between criteria definitions was good by Kappa and Jaccard measures. Among patients in remission, the probability of a remission lasting 2 years was 6.0%-14.1%. Among all patients the probability of a remission lasting 2 years was <3%. Remission and examination results varied substantially among physicians by multilevel analyses.
Conclusion
Cross-sectional remission occurs at 5.0%-10.1%, with cumulative remission 2-3 times greater. Long-term remissions are rare. Problems with reliability and agreement limit criteria usefulness in the individual patient. However, the criteria can be an effective method for measuring clinical status and treatment effect in groups of patients in the community.
doi:10.1002/art.30524
PMCID: PMC3202065  PMID: 21739423
Rheumatoid arthritis; Remission; Reliability
4.  Deletion of Porcn in Mice Leads to Multiple Developmental Defects and Models Human Focal Dermal Hypoplasia (Goltz Syndrome) 
PLoS ONE  2012;7(3):e32331.
Background
Focal Dermal Hypoplasia (FDH) is a genetic disorder characterized by developmental defects in skin, skeleton and ectodermal appendages. FDH is caused by dominant loss-of-function mutations in X-linked PORCN. PORCN orthologues in Drosophila and mice encode endoplasmic reticulum proteins required for secretion and function of Wnt proteins. Wnt proteins play important roles in embryo development, tissue homeostasis and stem cell maintenance. Since features of FDH overlap with those seen in mouse Wnt pathway mutants, FDH likely results from defective Wnt signaling but molecular mechanisms by which inactivation of PORCN affects Wnt signaling and manifestations of FDH remain to be elucidated.
Results
We introduced intronic loxP sites and a neomycin gene in the mouse Porcn locus for conditional inactivation. Porcn-ex3-7flox mice have no apparent developmental defects, but chimeric mice retaining the neomycin gene (Porcn-ex3-7Neo-flox) have limb, skin, and urogenital abnormalities. Conditional Porcn inactivation by EIIa-driven or Hprt-driven Cre recombinase results in increased early embryonic lethality. Mesenchyme-specific Prx-Cre-driven inactivation of Porcn produces FDH-like limb defects, while ectodermal Krt14-Cre-driven inactivation produces thin skin, alopecia, and abnormal dentition. Furthermore, cell-based assays confirm that human PORCN mutations reduce WNT3A secretion.
Conclusions
These data indicate that Porcn inactivation in the mouse produces a model for human FDH and that phenotypic features result from defective WNT signaling in ectodermal- and mesenchymal-derived structures.
doi:10.1371/journal.pone.0032331
PMCID: PMC3295752  PMID: 22412863
5.  Organ-specific carboxylesterase profiling identifies the small intestine and kidney as major contributors of activation of the anticancer prodrug CPT-11 
Biochemical pharmacology  2010;81(1):24-31.
The activation of the anticancer prodrug CPT-11, to its active metabolite SN-38, is primarily mediated by carboxylesterases (CE). In humans, three CEs have been identified, of which human liver CE (hCE1; CES1) and human intestinal CE (hiCE; CES2) demonstrate significant ability to hydrolyze the drug. However, while the kinetic parameters of CPT-11 hydrolysis have been measured, the actual contribution of each enzyme to activate the drug in biological samples has not been addressed. Hence, we have used a combination of specific CE inhibition and conventional chromatographic techniques to determine the amounts, and hydrolytic activity, of CEs present within human liver, kidney, intestinal and lung specimens. These studies confirm that hiCE demonstrates the most efficient kinetic parameters for CPT-11 activation, however, due to the high levels of hCE1 that are expressed in liver, the latter enzyme can contribute up to 50% of the total of drug hydrolysis in this tissue. Conversely, in human duodenum, jejunum, ileum and kidney, where hCE1 expression is very low, greater than 99% of the conversion of CPT-11 to SN-38 was mediated by hiCE. Furthermore, analysis of lung microsomal extracts indicated that CPT-11 activation was more proficient in samples obtained from smokers. Overall, our studies demonstrate that hCE1 plays a significant role in CPT-11 hydrolysis even though it is up to 100-fold less efficient at drug activation than hiCE, and that drug activation in the intestine and kidney are likely major contributors to SN-38 production in vivo.
doi:10.1016/j.bcp.2010.09.001
PMCID: PMC2991631  PMID: 20833148
Carboxylesterase; CPT-11; SN-38; drug activation
6.  The Lupus Family Registry and Repository 
Rheumatology (Oxford, England)  2010;50(1):47-59.
The Lupus Family Registry and Repository (LFRR) was established with the goal of assembling and distributing materials and data from families with one or more living members diagnosed with SLE, in order to address SLE genetics. In the present article, we describe the problems and solutions of the registry design and biometric data gathering; the protocols implemented to guarantee data quality and protection of participant privacy and consent; and the establishment of a local and international network of collaborators. At the same time, we illustrate how the LFRR has enabled progress in lupus genetics research, answering old scientific questions while laying out new challenges in the elucidation of the biologic mechanisms that underlie disease pathogenesis. Trained staff ascertain SLE cases, unaffected family members and population-based controls, proceeding in compliance with the relevant laws and standards; participant consent and privacy are central to the LFRR’s effort. Data, DNA, serum, plasma, peripheral blood and transformed B-cell lines are collected and stored, and subject to strict quality control and safety measures. Coded data and materials derived from the registry are available for approved scientific users. The LFRR has contributed to the discovery of most of the 37 genetic associations now known to contribute to lupus through 104 publications. The LFRR contains 2618 lupus cases from 1954 pedigrees that are being studied by 76 approved users and their collaborators. The registry includes difficult to obtain populations, such as multiplex pedigrees, minority patients and affected males, and constitutes the largest collection of lupus pedigrees in the world. The LFRR is a useful resource for the discovery and characterization of genetic associations in SLE.
doi:10.1093/rheumatology/keq302
PMCID: PMC3307518  PMID: 20864496
Systemic lupus erythematosus; Registry; Repository; Autoimmune diseases; Genetics; Heritability; Genome-wide association studies; Linkage analysis; Minorities; Women
7.  Development and Initial Validation of the Self-Assessed Lupus Damage Index Questionnaire (LDIQ) 
Arthritis care & research  2010;62(4):559-568.
Purpose
The SLICC Damage Index (SDI) is a validated instrument for assessing organ damage in systemic lupus erythematosus (SLE). Trained physicians must complete it, limiting utility where this is impossible.
Methods
We developed and pilot-tested a self-assessed organ damage instrument, the Lupus Damage Index Questionnaire (LDIQ), in 37 SLE subjects and 7 physicians. After refinement, 569 English-speaking SLE subjects and 14 rheumatologists from 11 international SLE clinics participated in validation. Subjects and physicians completed instruments separately. We calculated sensitivity, specificity, Spearman correlations and agreement, using the SDI as gold standard. 605 SLE participants in the community-based National Data Bank for Rheumatic Diseases (NDB) study completed the LDIQ and we assessed correlations with outcome and disability measures.
Results
Mean LDIQ score was 3.3 (0-16) and mean SDI score was 1.5 (0-9). LDIQ had a moderately high correlation with SDI (Spearman r=0.50, p<0.001). Specificities of individual LDIQ items were >80%, except for neuropathy. Sensitivities were variable and lowest for damage with <1% prevalence. Agreement between SDI and LDIQ was > 85% for all but neuropathy, reduced renal function, deforming arthritis and alopecia. In the NDB, LDIQ correlated well with comorbidity index (r=0.45), SF-36 physical component scale (0.43), Medical Research Council dyspnea scale (0.40), disability (0.37) and SLE Activity Questionnaire score (0.37).
Conclusions
The LDIQ’s metric properties are good compared to the SDI. It has construct validity and correlations with health assessments similar to the SDI. The LDIQ should allow expansion of SLE research. Its ultimate value will be determined in longitudinal studies.
doi:10.1002/acr.20193
PMCID: PMC3179258  PMID: 20391512
systemic lupus erythematosus; questionnaire; damage; SLICC damage index; validation; self-assessed
9.  Tcf3 and Tcf4 are essential for long-term homeostasis of skin epithelia 
Nature genetics  2009;41(10):1068-1075.
Single-layered embryonic skin either stratifies to form epidermis or responds to Wnt signaling (stabilized β-catenin) to form hair follicles. Postnatally, stem cells continue to differentially use Wnt signaling in long-term tissue homeostasis. We have discovered that embryonic progenitor cells and postnatal hair follicle stem cells coexpress Tcf3 and Tcf4, which can act as transcriptional activators or repressors. Using loss-of-function studies and transcriptional analyses, we uncovered consequences to the absence of Tcf3 and Tcf4 in skin that only partially overlap with those caused by β-catenin deficiency. We established roles for Tcf3 and Tcf4 in long-term maintenance and wound repair of both epidermis and hair follicles, suggesting that Tcf proteins have both Wnt-dependent and Wnt-independent roles in lineage determination.
doi:10.1038/ng.431
PMCID: PMC2792754  PMID: 19718027

Results 1-9 (9)