An Integrated Reconciliation Framework for Domain, Gene, and Species Level Evolution

Efficacy and safety of iguratimod in the treatment of rheumatic and autoimmune diseases: a meta-analysis and systematic review of 84 randomized controlled trials

Objective: To evaluate efficacy and safety of iguratimod (IGU) in the treatment of rheumatic and autoimmune diseases. Methods: Databases such as Pubmed, Embase, Sinomed were searched (as of July 2022) to collect randomized controlled trials (RCTs) of IGU in the treatment of rheumatic and autoimmune diseases. Two researchers independently screened the literature, extracted data, assessed the risk of bias of the included literature, and performed meta-analysis using RevMan 5.4 software. Results: A total of 84 RCTs and 4 types of rheumatic and autoimmune diseases [rheumatoid arthritis (RA), ankylosing spondylitis (AS), primary Sjögren's syndrome (PSS) and Autoimmune disease with interstitial pneumonia]. Forty-three RCTs reported RA and showed that IGU + MTX therapy can improve ACR20 (RR 1.45 [1.14, 1.84], p = 0.003), ACR50 (RR 1.80 [1.43, 2.26], p < 0.0000), ACR70 (RR 1.84 [1.27, 2.67], p = 0.001), DAS28 (WMD -1.11 [-1.69, -0.52], p = 0.0002), reduce ESR (WMD -11.05 [-14.58, -7.51], p < 0.00001), CRP (SMD -1.52 [-2.02, -1.02], p < 0.00001), RF (SMD -1.65 [-2.48, -0.82], p < 0.0001), and have a lower incidence of adverse events (RR 0.84 [0.78, 0.91], p < 0.00001) than the control group. Nine RCTs reported AS and showed that IGU can decrease the BASDAI score (SMD -1.62 [-2.20, -1.05], p < 0.00001), BASFI score (WMD -1.07 [-1.39, -0.75], p < 0.00001), VAS (WMD -2.01 [-2.83, -1.19], p < 0.00001), inflammation levels (decreasing ESR, CRP and TNF-α). Thirty-two RCTs reported PSS and showed that IGU can reduce the ESSPRI score (IGU + other therapy group: WMD -1.71 [-2.44, -0.98], p < 0.00001; IGU only group: WMD -2.10 [-2.40, -1.81], p < 0.00001) and ESSDAI score (IGU + other therapy group: WMD -1.62 [-2.30, -0.94], p < 0.00001; IGU only group: WMD -1.51 [-1.65, -1.37], p < 0.00001), inhibit the inflammation factors (reduce ESR, CRP and RF) and increase Schirmer's test score (IGU + other therapy group: WMD 2.18 [1.76, 2.59], p < 0.00001; IGU only group: WMD 1.55 [0.35, 2.75], p = 0.01); The incidence of adverse events in IGU group was also lower than that in control group (IGU only group: RR 0.66 [0.48, 0.98], p = 0.01). Three RCTs reported Autoimmune disease with interstitial pneumonia and showed that IGU may improve lung function. Conclusion: Based on current evidence, IGU may be a safe and effective therapy for RA, AS, PSS and autoimmune diseases with interstitial pneumonia. Systematic Review Registration: (CRD42021289489).

Phylogenetic inference of the emergence of sequence modules and protein-protein interactions in the ADAMTS-TSL family

Numerous computational methods based on sequences or structures have been developed for the characterization of protein function, but they are still unsatisfactory to deal with the multiple functions of multi-domain protein families. Here we propose an original approach based on 1) the detection of conserved sequence modules using partial local multiple alignment, 2) the phylogenetic inference of species/genes/modules/functions evolutionary histories, and 3) the identification of co-appearances of modules and functions. Applying our framework to the multidomain ADAMTS-TSL family including ADAMTS (A Disintegrin-like and Metalloproteinase with ThromboSpondin motif) and ADAMTS-like proteins over nine species including human, we identify 45 sequence module signatures that are associated with the occurrence of 278 Protein-Protein Interactions in ancestral genes. Some of these signatures are supported by published experimental data and the others provide new insights (e.g. ADAMTS-5). The module signatures of ADAMTS ancestors notably highlight the dual variability of the propeptide and ancillary regions suggesting the importance of these two regions in the specialization of ADAMTS during evolution. Our analyses further indicate convergent interactions of ADAMTS with COMP and CCN2 proteins. Overall, our study provides 186 sequence module signatures that discriminate distinct subgroups of ADAMTS and ADAMTSL and that may result from selective pressures on novel functions and phenotypes.

Deciphering Microbial Gene Family Evolution Using Duplication-Transfer-Loss Reconciliation and RANGER-DTL

Phylogenetic reconciliation has emerged as a principled, highly effective technique for investigating the origin, spread, and evolutionary history of microbial gene families. Proper application of phylogenetic reconciliation requires a clear understanding of potential pitfalls and sources of error, and knowledge of the most effective reconciliation-based tools and protocols to use to maximize accuracy. In this book chapter, we provide a brief overview of Duplication-Transfer-Loss (DTL) reconciliation, the standard reconciliation model used to study microbial gene families and provide a step-by-step computational protocol to maximize the accuracy of DTL reconciliation and minimize false-positive evolutionary inferences.

DoubleRecViz: a web-based tool for visualizing transcript-gene-species tree reconciliation

MOTIVATION

A phylogenetic tree reconciliation is a mapping of one phylogenetic tree onto another which represents the co-evolution of two sets of taxa (e.g. parasite-host co-evolution, gene-species co-evolution). The reconciliation framework was extended to allow modeling the co-evolution of three sets of taxa such as transcript-gene-species co-evolutions. Several web-based tools have been developed for the display and manipulation of phylogenetic trees and co-phylogenetic trees involving two trees, but there currently exists no tool for visualizing the joint reconciliation between three phylogenetic trees.

RESULTS

Here, we present DoubleRecViz, a web-based tool for visualizing double reconciliations between phylogenetic trees at three levels: transcript, gene and species. DoubleRecViz extends the RecPhyloXML model-developed for gene-species tree reconciliation-to represent joint transcript-gene and gene-species tree reconciliations. It is implemented using the Dash library, which is a toolbox that provides dynamic visualization functionalities for web data visualization in Python.

AVAILABILITY AND IMPLEMENTATION

DoubleRecViz is available through a web server at https://doublerecviz.cobius.usherbrooke.ca. The source code and information about installation procedures are also available at https://github.com/UdeS-CoBIUS/DoubleRecViz.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Improved inference of tandem domain duplications

MOTIVATION

Protein domain duplications are a major contributor to the functional diversification of protein families. These duplications can occur one at a time through single domain duplications, or as tandem duplications where several consecutive domains are duplicated together as part of a single evolutionary event. Existing methods for inferring domain-level evolutionary events are based on reconciling domain trees with gene trees. While some formulations consider multiple domain duplications, they do not explicitly model tandem duplications; this leads to inaccurate inference of which domains duplicated together over the course of evolution.

RESULTS

Here, we introduce a reconciliation-based framework that considers the relative positions of domains within extant sequences. We use this information to uncover tandem domain duplications within the evolutionary history of these genes. We devise an integer linear programming approach that solves our problem exactly, and a heuristic approach that works well in practice. We perform extensive simulation studies to demonstrate that our approaches can accurately uncover single and tandem domain duplications, and additionally test our approach on a well-studied orthogroup where lineage-specific domain expansions exhibit varying and complex domain duplication patterns.

AVAILABILITY AND IMPLEMENTATION

Code is available on github at https://github.com/Singh-Lab/TandemDuplications.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

SaGePhy: an improved phylogenetic simulation framework for gene and subgene evolution

SUMMARY

SaGePhy is a software package for improved phylogenetic simulation of gene and subgene evolution. SaGePhy can be used to generate species trees, gene trees and subgene or (protein) domain trees using a probabilistic birth-death process that allows for gene and subgene duplication, horizontal gene and subgene transfer and gene and subgene loss. SaGePhy implements a range of important features not found in other phylogenetic simulation frameworks/software. These include (i) simulation of subgene or domain level evolution inside one or more gene trees, (ii) simultaneous simulation of both additive and replacing horizontal gene/subgene transfers and (iii) probabilistic sampling of species tree and gene tree nodes, respectively, for gene- and domain-family birth. SaGePhy is open-source, platform independent and written in Java and Python.

AVAILABILITY AND IMPLEMENTATION

Executables, source code (open-source under the revised BSD license) and a detailed manual are freely available from http://compbio.engr.uconn.edu/software/sagephy/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.