scholarly journals Analysis of 272 genetic variants in the upgraded interactive FXI web database reveals new insights on FXI deficiency

TH Open ◽  
2021 ◽  
Author(s):  
Victoria Anne Harris ◽  
Weining Lin ◽  
Stephen J Perkins
Keyword(s):  
Genetic Variants ◽  
Solvent Accessibility ◽  
Coagulation Factor ◽  
Factor Ix ◽  
Type I ◽  
Web Database ◽  
Initial Development ◽  
Missense Variants ◽  
Web Resource ◽  
And Function

Coagulation Factor XI (FXI) is a plasma glycoprotein composed of four apple (Ap) domains and a serine protease (SP) domain. FXI circulates as a dimer and activates Factor IX (FIX), promoting thrombin production and preventing excess blood loss. Genetic variants that degrade FXI structure and function often lead to bleeding diatheses, commonly termed FXI deficiency. The first interactive FXI variant database underwent initial development in 2003 at https://www.factorxi.org. Here, based on a much improved FXI crystal structure, the upgraded FXI database contains information regarding 272 FXI variants (including 154 missense variants) found in 657 patients, this being a significant increase from the 183 variants identified in the 2009 update. Type I variants involve the simultaneous reduction of FXI coagulant activity (FXI:C) and FXI antigen levels (FXI:Ag), whereas Type II variants result in decreased FXI:C yet normal FXI:Ag. The database updates now highlight the predominance of Type I variants in FXI. Analysis in terms of a consensus Ap domain revealed the near-uniform distribution of 81 missense variants across the Ap domains. A further 66 missense variants were identified in the SP domain, showing that all regions of the FXI protein were important for function. The variants clarified the critical importance of changes in surface solvent accessibility, as well as those of cysteine residues and the dimer interface. Guidelines are provided below for clinicians who wish to use the database for diagnostic purposes. In conclusion, the updated database provides an easy-to-use web resource on FXI deficiency for clinicians.

scholarly journals Effects of codon optimization on coagulation factor IX translation and structure: Implications for protein and gene therapies

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Aikaterini Alexaki ◽  
Gaya K. Hettiarachchi ◽  
John C. Athey ◽  
Upendra K. Katneni ◽  
Vijaya Simhadri ◽  
...  
Keyword(s):  
Protein Expression ◽  
Codon Optimization ◽  
Critical Mass ◽  
Coagulation Factor ◽  
Factor Ix ◽  
Gene Therapies ◽  
Synonymous Codons ◽  
Coagulation Factor Ix ◽  
And Function ◽  
The Impact

Abstract Synonymous codons occur with different frequencies in different organisms, a phenomenon termed codon usage bias. Codon optimization, a common term for a variety of approaches used widely by the biopharmaceutical industry, involves synonymous substitutions to increase protein expression. It had long been presumed that synonymous variants, which, by definition, do not alter the primary amino acid sequence, have no effect on protein structure and function. However, a critical mass of reports suggests that synonymous codon variations may impact protein conformation. To investigate the impact of synonymous codons usage on protein expression and function, we designed an optimized coagulation factor IX (FIX) variant and used multiple methods to compare its properties to the wild-type FIX upon expression in HEK293T cells. We found that the two variants differ in their conformation, even when controlling for the difference in expression levels. Using ribosome profiling, we identified robust changes in the translational kinetics of the two variants and were able to identify a region in the gene that may have a role in altering the conformation of the protein. Our data have direct implications for codon optimization strategies, for production of recombinant proteins and gene therapies.

scholarly journals Regulation of the Tertiary Structure and Function of Coagulation Factor IX by Magnesium(II) Ions

1995 ◽  
Vol 270 (24) ◽  
pp. 14325-14331 ◽  
Author(s):  
Fujio Sekiya ◽  
Toshiko Yamashita ◽  
Hideko Atoda ◽  
Yutaka Komiyama ◽  
Takashi Morita
Keyword(s):  
Tertiary Structure ◽  
Coagulation Factor ◽  
Structure And Function ◽  
Factor Ix ◽  
Coagulation Factor Ix ◽  
And Function

scholarly journals Coagulation factor IX analysis in bioreactor cell culture supernatant predicts quality of the purified product

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Lucia F. Zacchi ◽  
Dinora Roche-Recinos ◽  
Cassandra L. Pegg ◽  
Toan K. Phung ◽  
Mark Napoli ◽  
...  
Keyword(s):  
Coagulation Factor ◽  
Operating Conditions ◽  
Factor Ix ◽  
Cell Culture Supernatant ◽  
Bioreactor Culture ◽  
Data Independent Acquisition ◽  
Host Cell Proteins ◽  
Coagulation Factor Ix ◽  
And Function

AbstractCoagulation factor IX (FIX) is a complex post-translationally modified human serum glycoprotein and high-value biopharmaceutical. The quality of recombinant FIX (rFIX), especially complete γ-carboxylation, is critical for rFIX clinical efficacy. Bioreactor operating conditions can impact rFIX production and post-translational modifications (PTMs). With the goal of optimizing rFIX production, we developed a suite of Data Independent Acquisition Mass Spectrometry (DIA-MS) proteomics methods and used these to investigate rFIX yield, γ-carboxylation, other PTMs, and host cell proteins during bioreactor culture and after purification. We detail the dynamics of site-specific PTM occupancy and structure on rFIX during production, which correlated with the efficiency of purification and the quality of the purified product. We identified new PTMs in rFIX near the GLA domain which could impact rFIX GLA-dependent purification and function. Our workflows are applicable to other biologics and expression systems, and should aid in the optimization and quality control of upstream and downstream bioprocesses.

scholarly journals Analysis of 180 genetic variants in a new interactive FX variant database reveals novel insights into FX deficiency

TH Open ◽  
2021 ◽  
Author(s):  
Victoria Anne Harris ◽  
Weining Lin ◽  
Stephen J Perkins
Keyword(s):  
Genetic Variants ◽  
Case Reports ◽  
Coagulation Factor ◽  
Coagulation Cascade ◽  
Type I ◽  
Type Ii ◽  
Factor X ◽  
Coagulation Proteins ◽  
Set Up ◽  
Variant Database

Coagulation Factor X (FX), often termed Stuart-Prower Factor, is a plasma glycoprotein composed of the γ-carboxyglutamic acid (Gla) domain, two epidermal growth factor domains (EGF-1, EGF-2) and the serine protease (SP) domain. FX plays a pivotal role in the coagulation cascade, activating thrombin to promote platelet plug formation and prevent excess blood loss. Genetic variants in FX disrupt coagulation and lead to FX or Stuart-Prower Factor deficiency. To better understand the relationship between FX deficiency and disease severity, an interactive FX variant database has been set up at https://www.factorx-db.org, based on earlier websites for the Factor XI and IX coagulation proteins. To date (April 2021), we report 427 case reports on FX deficiency corresponding to 180 distinct F10 genetic variants. Of these, 149 are point variants (of which 128 are missense), 22 are deletions, three are insertions and six are polymorphisms. FX variants are phenotypically classified as being Type I or Type II. Type I variants involve the simultaneous reduction of FX coagulant activity (FX:C) and FX antigen levels (FX:Ag), whereas Type II variants involve a reduction in FX:C with normal FX:Ag plasma levels. Both types of variants were distributed throughout the FXa protein structure. Analyses based on residue surface accessibilities showed the most damaging variants to occur at residues with low accessibilities. The interactive FX web database provides a novel easy-to-use resource for clinicians and scientists to improve the understanding of FX deficiency. Guidelines are provided for clinicians who wish to use the database for diagnostic purposes.

Von Willebrand disease and Weibel-Palade bodies

2010 ◽  
Vol 30 (03) ◽  
pp. 150-155 ◽  
Author(s):  
J. W. Wang ◽  
J. Eikenboom
Keyword(s):  
Platelet Adhesion ◽  
Coagulation Factor ◽  
Von Willebrand Disease ◽  
Inflammatory Factors ◽  
Limited Data ◽  
Storage Organelle ◽  
And Function ◽  
Von Willebrand ◽  
Willebrand Factor

SummaryVon Willebrand factor (VWF) is a pivotal haemostatic protein mediating platelet adhesion to injured endothelium and carrying coagulation factor VIII (FVIII) in the circulation to protect it from premature clearance. Apart from the roles in haemostasis, VWF drives the formation of the endothelial cell specific Weibel-Palade bodies (WPBs), which serve as a regulated storage of VWF and other thrombotic and inflammatory factors. Defects in VWF could lead to the bleeding disorder von Willebrand disease (VWD).Extensive studies have shown that several mutations identified in VWD patients cause an intracellular retention of VWF. However, the effects of such mutations on the formation and function of its storage organelle are largely unknown. This review gives an overview on the role of VWF in WPB biogenesis and summarizes the limited data on the WPBs formed by VWD-causing mutant VWF.

Type I Interferons promote maintenance and function of follicular T helper cells in vitro

2019 ◽  
Author(s):  
S Ehrlich ◽  
K Wild ◽  
M Smits ◽  
K Zoldan ◽  
M Hofmann ◽  
...  
Keyword(s):  
T Helper Cells ◽  
Type I Interferons ◽  
Type I ◽  
T Helper ◽  
Helper Cells ◽  
Follicular T Helper Cells ◽  
And Function

Collagen-the Ultrastructural Element of the Bone Matrix

2018 ◽  
Vol 69 (7) ◽  
pp. 1706-1709
Author(s):  
Nicoleta Dumitru ◽  
Andra Cocolos ◽  
Andra Caragheorgheopol ◽  
Constantin Dumitrache ◽  
Ovidiu Gabriel Bratu ◽  
...  
Keyword(s):  
Type I Collagen ◽  
Bone Microarchitecture ◽  
Complex Structure ◽  
Bone Matrix ◽  
Organic Matrix ◽  
Bone Diseases ◽  
Bone Collagen ◽  
Type I ◽  
New Therapeutic Approaches ◽  
And Function

There is an increased interest and more studies highlight the fact that bone strength depends not only on bone tissue quantity, but also on its quality, which is characterized by the geometry and shape of bones, trabecular bone microarchitecture, mineral content, organic matrix and bone turnover. Fibrillar type I collagen is the major organic component of bone matrix, providing form and a stable template for mineralization. The biomedical importance of collagen as a biomaterial for medical and cosmetic purposes and the improvement of the molecular, cellular biology and analytical technologies, led to increasing interest in establishing the structure of this protein and in setting of the relationships between sequence, structure, and function. Bone collagen crosslinking chemistry and its molecular packing structure are considered to be distinct features. This unique post-translational modifications provide to the fibrillar collagen matrices properties such as tensile strength and viscoelasticity. Understanding the complex structure of bone type I collagen as well as the dynamic nature of bone tissues will help to manage new therapeutic approaches to bone diseases.

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