bims-supasi 2022-07-03 papers

bims-supasi

Biomed News

on Sulfation pathways and signalling

Issue of 2022–07–03
seventeen papers selected by
Jonathan Wolf Mueller, University of Birmingham

Sulfated Glycoprotein Synthesis.
Hydrogel composed of type II collagen, chondroitin sulfate and hyaluronic acid for cartilage tissue engineering.
A quartz crystal microbalance method to quantify the size of hyaluronan and other glycosaminoglycans on surfaces.
HS3ST2 expression induces the cell autonomous aggregation of tau.
Cortisol and dehydroepiandrosterone sulfate in patients with schizophrenia spectrum disorders with respect to cognitive performance.
Effects of mucopolysaccharide polysulfate on tight junction barriers in human epidermal keratinocytes.
Glycocalyx heparan sulfate cleavage promotes endothelial cell angiopoietin-2 expression by impairing shear stress-related AMPK/FoxO1 signaling.
Anticoagulant and anti-inflammatory effects of a degraded sulfate glycosaminoglycan from swimming bladder.
The Role of Glucosamine and Chondroitin Sulfate in the Prevention of Colorectal Cancer: A Systematic Review.
Dehydroepiandrosterone sulfate levels predict weight gain in women with anorexia nervosa.
Divergent Associations Between Serum Androgens and Ovarian Reserve Markers Revealed in Patients With Polycystic Ovary Syndrome.
The extracellular matrix and perineuronal nets in memory.
HSMotifDiscover: identification of motifs in sequences composed of non-single-letter elements.
Serum total indoxyl sulfate levels and all-cause and cardiovascular mortality in maintenance hemodialysis patients: a prospective cohort study.
Nuclear magnetic resonance spectroscopy as an elegant tool for a complete quality control of crude heparin material.
The impact of warfarin on overall survival in cancer patients.
Crosstalk Between Iron and Sulfur Homeostasis Networks in Arabidopsis.

Methods Mol Biol. 2022 ;2530 1-17

Sulfated Glycoprotein Synthesis.

Tianlu Li, Peng Peng, Xuefei Huang.

  Chemical protein synthesis has achieved tremendous progress in the past decades. With the development of chemical ligation as powerful tools, the scope of synthetic protein is greatly expanded. Proteoglycans are a class of sulfated glycoproteins widely distributed on the cell surface and in the extracellular matrix, which are extensively engaged in cellular communication events. Consisting of protein backbone and glycosaminoglycan(s) side chain, proteoglycans are highly complex and heterogeneous in nature. Chemical synthesis provides facile and reliable approach to these molecules, with defined glycan structure and sulfation pattern. One remaining problem is that the acid-labile sulfates could hardly survive during the typical solid phase peptide synthesis (SPPS) process. In this chapter, strategic design of a "glycopeptide cassette" for the preparation of sulfated glycoprotein is described. In particular, we provide protocols for the chemical synthesis of ectodomain fragment (23-120) of sulfated glycoprotein syndecan-1.

Keywords:  Glycopeptide cassette; Heparan sulfates; Protein chemical ligation; Proteoglycan; Sulfated glycoprotein

DOI:  https://doi.org/10.1007/978-1-0716-2489-0_1
Biomed Mater Eng. 2022 May 30.

Hydrogel composed of type II collagen, chondroitin sulfate and hyaluronic acid for cartilage tissue engineering.

Yunong Ao, Wenbao Tang, Hongbo Tan, Jun Li, Fuyou Wang, Liu Yang.

   BACKGROUND: Cartilage tissue engineering is a promising way to repair cartilage defects. Different materials have been applied in the preparation of cartilage hydrogels, but all with various disadvantages.
OBJECTIVE: The aim of this study was to prepare cartilage hydrogel using type II collagen, chondroitin sulfate and hyaluronic acid, to explore their gelation effect and compressive strength, and to analyze the feasibility of their application in cartilage tissue engineering.
METHODS: Type II collagen (Col II), hyaluronic acid (HA) and chondroitin sulfate (CS) were mixed in a certain proportion to prepare gel scaffolds; changes in chemical groups were detected by Fourier transform infrared. After the hydrogel was prepared, its compressive strength was measured. Umbilical cord stem cells were co-cultured with hydrogel scaffolds to observe its cytocompatibility and analyze whether stem cells had cellular activity during co-culture; histological staining was applied to observe the hydrogel loaded with stem cells.
RESULTS: Cartilage hydrogels were successfully prepared with good compressive strength, and Fourier transform infrared analysis showed that Schiff base reaction occurred during the preparation process and tight chemical cross-linking was formed. The results of umbilical cord stem cell co-culture showed that the hydrogel had good cytocompatibility and the stem cells had good activity in the hydrogel.
CONCLUSIONS: Cartilage hydrogels with stable structures were successfully prepared and had good compressive strength. Hydrogel scaffold could provide a suitable living environment for umbilical cord stem cells, so that they maintain normal cell morphology and activity, and has a good application potential in cartilage tissue engineering.

Keywords:  Cartilage; hydrogel; scaffold; tissue engineering

DOI:  https://doi.org/10.3233/BME-221404
Sci Rep. 2022 Jun 29. 12(1): 10980

A quartz crystal microbalance method to quantify the size of hyaluronan and other glycosaminoglycans on surfaces.

Sumitra Srimasorn, Luke Souter, Dixy E Green, Lynda Djerbal, Ashleigh Goodenough, James A Duncan, Abigail R E Roberts, Xiaoli Zhang, Delphine Débarre, Paul L DeAngelis, Jessica C F Kwok, Ralf P Richter.

Hyaluronan (HA) is a major component of peri- and extra-cellular matrices and plays important roles in many biological processes such as cell adhesion, proliferation and migration. The abundance, size distribution and presentation of HA dictate its biological effects and are also useful indicators of pathologies and disease progression. Methods to assess the molecular mass of free-floating HA and other glycosaminoglycans (GAGs) are well established. In many biological and technological settings, however, GAGs are displayed on surfaces, and methods to obtain the size of surface-attached GAGs are lacking. Here, we present a method to size HA that is end-attached to surfaces. The method is based on the quartz crystal microbalance with dissipation monitoring (QCM-D) and exploits that the softness and thickness of films of grafted HA increase with HA size. These two quantities are sensitively reflected by the ratio of the dissipation shift (ΔD) and the negative frequency shift (- Δf) measured by QCM-D upon the formation of HA films. Using a series of size-defined HA preparations, ranging in size from ~ 2 kDa tetrasaccharides to ~ 1 MDa polysaccharides, we establish a monotonic yet non-linear standard curve of the ΔD/ - Δf ratio as a function of HA size, which reflects the distinct conformations adopted by grafted HA chains depending on their size and surface coverage. We demonstrate that the standard curve can be used to determine the mean size of HA, as well as other GAGs, such as chondroitin sulfate and heparan sulfate, of preparations of previously unknown size in the range from 1 to 500 kDa, with a resolution of better than 10%. For polydisperse samples, our analysis shows that the process of surface-grafting preferentially selects smaller GAG chains, and thus reduces the average size of GAGs that are immobilised on surfaces comparative to the original solution sample. Our results establish a quantitative method to size HA and other GAGs grafted on surfaces, and also highlight the importance of sizing GAGs directly on surfaces. The method should be useful for the development and quality control of GAG-based surface coatings in a wide range of research areas, from molecular interaction analysis to biomaterials coatings.

DOI: https://doi.org/10.1038/s41598-022-14948-7
Sci Rep. 2022 Jun 27. 12(1): 10850

HS3ST2 expression induces the cell autonomous aggregation of tau.

M B Huynh, N Rebergue, H Merrick, W Gomez-Henao, E Jospin, D S F Biard, D Papy-Garcia.

Heparan sulfates have long been known to intracellularly accumulate in Alzheimer's disease neurons, where they colocalize with neurofibrillary tangles made of abnormally phosphorylated and aggregated tau protein. However, the reasons and consequences of the heparan sulfates accumulation in the Alzheimer's cells are not yet well understood. Previously, we showed that the neural heparan sulfate 3-O-sulfotransferase HS3ST2 is critical for the abnormal phosphorylation of tau in Alzheimer's disease-related tauopathy. Using cell models of tauopathy we showed that intracellular 3-O-sulfatated heparan sulfates interact with tau inducing its abnormal phosphorylation. However, it is unknown whether HS3ST2 expression induces the intracellular aggregation of tau in cells. Here, by using replicative pEBV plasmids, we engineered HEK293 cells to stably express HS3ST2 together with human tau carrying or not the P301S mutation. We show that HS3ST2 gain of function induces the cell autonomous aggregation of tau not only in cells expressing tauP301S, but also in cells expressing the wild type tau. Our engineered cells mimicked both the HS intracellular accumulation observed in neurons of Alzheimer's disease and the tau aggregation characteristic of tauopathy development and evolution. These results give evidence that the neural HS3ST2 plays a critical role in the cell autonomous self-aggregation of tau.

DOI: https://doi.org/10.1038/s41598-022-13486-6
Compr Psychoneuroendocrinol. 2021 May;6 100041

Cortisol and dehydroepiandrosterone sulfate in patients with schizophrenia spectrum disorders with respect to cognitive performance.

Błażej Misiak, Patryk Piotrowski, Magdalena Chęć, Jerzy Samochowiec.

  Prolonged activation of the hypothalamic-pituitary-adrenal (HPA) axis associated with hypercortisolemia may lead to impairments of cognition in various populations. Dehydroepiandrosterone sulfate (DHEA-S) can protect the hippocampus from the detrimental effects of cortisol. However, this phenomenon has not been widely investigated in patients with schizophrenia spectrum disorders (SSD). Therefore, in this study, we aimed to assess the levels of cortisol, DHEA-S and cortisol/DHEA-S ratio in patients with SSD and healthy controls with respect to cognitive performance. Participants were 85 patients with SSD and 56 healthy controls, matched for age, sex and body-mass index. Cognitive performance was examined using the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS). The levels of hormones were measured in fasting serum samples. The levels of morning cortisol were significantly higher in patients with SSD compared to healthy controls, even after co-varying for potential confounding factors. There were no significant between-group differences in the levels of DHEA-S and cortisol/DHEA-S ratio. Higher levels of cortisol and greater cortisol/DHEA-S ratio were related to significantly lower RBANS scores of delayed memory in patients with SSD, but not in healthy controls after controlling for the effects of age, sex, BMI, the number of education years, cigarette smoking status and the dosage of antipsychotics. Our findings imply that elevated cortisol levels may contribute to impairments of memory processes in patients with SSD. However, longitudinal studies are needed to confirm causal associations.

Keywords:  Glucocorticoids; Psychosis; Psychotic disorder; Stress

DOI:  https://doi.org/10.1016/j.cpnec.2021.100041
Exp Dermatol. 2022 Jun 29.

Effects of mucopolysaccharide polysulfate on tight junction barriers in human epidermal keratinocytes.

Mika Fujikawa, Hiroko Sugimoto, Rie Tamura, Koki Fujikawa, Ami Yamagishi, Yuhki Ueda.

  Tight junctions (TJs) play important roles in epidermal barrier function and their dysfunction is involved in the pathogenesis of various skin diseases, including atopic dermatitis (AD). Mucopolysaccharide polysulfate (MPS) is the active ingredient of a moisturizing agent used to treat xerosis in patients with AD; however, its mechanism of action on TJ barrier function remains unclear. To elucidate the effects of MPS on TJs, adult human epidermal keratinocyte (HEKa) cells were exposed to MPS, subjected to western blotting and quantitative PCR analyses for the investigation of TJ-related factors. MPS treatment significantly increased the mRNA and protein expression of claudin-1 (CLDN1) and zonula occludens-1, and significantly increased transepithelial electrical resistance (TEER), which indicates TJ integrity. Conversely, the sulfated and non-sulfated glycosaminoglycans, chondroitin sulfate and hyaluronic acid, respectively, had little effect on TEER or the expression of mRNAs or TJ-related proteins. Interestingly, MPS treatment also inactivated the extracellular signal-regulated kinase signaling pathway, which is known to negatively regulate CLDN1 expression. Furthermore, MPS notably improved the reduction in CLDN1 expression and TEER caused by histamine, which is upregulated in the skin of patients with AD and is known to disrupt the TJ barrier function. Taken together, these findings demonstrate that treatment with the moisturizing agent, MPS, can repair TJ dysfunction and could therefore represent a new therapeutic option for treating patients with AD.

Keywords:  claudin-1; heparinoid; mucopolysaccharide polysulfate; skin barrier; tight junction

DOI:  https://doi.org/10.1111/exd.14637
JCI Insight. 2022 Jun 28. pii: e155010. [Epub ahead of print]

Glycocalyx heparan sulfate cleavage promotes endothelial cell angiopoietin-2 expression by impairing shear stress-related AMPK/FoxO1 signaling.

Robert P Richter, Amit R Ashtekar, Lei Zheng, Danielle Pretorius, Tripathi Kaushlendra, Ralph D Sanderson, Amit Gaggar, Jillian R Richter.

  Angiopoietin-2 (Ang-2) is a key mediator of vascular disease during sepsis, and elevated plasma levels of Ang-2 are associated with organ injury scores and poor clinical outcomes. We have previously observed that biomarkers of endothelial glycocalyx (EG) damage correlate with plasma Ang-2 levels, suggesting a potential mechanistic linkage between EG injury and Ang-2 expression during states of systemic inflammation. However, the cell signaling mechanisms regulating Ang-2 expression following EG damage are unknown. In the current study, we determined the temporal associations between plasma heparan sulfate (HS) levels as a marker of EG erosion and plasma Ang-2 levels in children with sepsis and in mouse models of sepsis. Secondly, we evaluated the role of shear stress-mediated 5'-adenosine monophosphate-activated protein kinase (AMPK) signaling in Ang-2 expression following enzymatic HS cleavage from the surface of human primary lung microvascular endothelial cells (HLMVEC). We found that plasma HS levels peak prior to plasma Ang-2 levels in children and mice with sepsis. Further, we discovered that impaired AMPK signaling contributes to increased Ang-2 expression following HS cleavage from flow conditioned HLMVECs, establishing a novel paradigm by which Ang-2 may be upregulated during sepsis.

Keywords:  Endothelial cells; Glycobiology; Proteases; Vascular Biology

DOI:  https://doi.org/10.1172/jci.insight.155010
Food Res Int. 2022 Jul;pii: S0963-9969(22)00501-4. [Epub ahead of print]157 111444

Anticoagulant and anti-inflammatory effects of a degraded sulfate glycosaminoglycan from swimming bladder.

Jing Chen, Siyi Zhou, Zhuo Wang, Shouchun Liu, Rui Li, Xuejing Jia, Jianping Chen, Xiaofei Liu, Bingbing Song, Saiyi Zhong.

  Low molecular weight sulfate glycosaminoglycan has attracted more attention recently for its great bioactivity. In the present study, a degraded sulfate glycosaminoglycan (named D-SBSG) was prepared from swimming bladder by enzymatic depolymerization, the structure characteristics of D-SBSG and its effects on blood coagulation and inflammation in vitro was investigated. HPGPC analysis showed that the molecular weight (Mw) of SBSG was 115.84 kDa, while the Mw of D-SBSG was 4.96 kDa. The bioactivities had arose dramatic differences, though its main molecule structure had little change after enzymatic degradation. Compared with heparin sodium, relatively milder anticoagulant activity in vitro, which were positively associated with molecular weight, were found in SBSG and D-SBSG. In contrast, the results of anti-inflammatory assays indicated that D-SBSG with the lower molecular weight possessed higher bioactivity than SBSG. Additionally, the D-SBSG inhibited the LPS-induced inflammatory in RAW264.7 macrophages by down-regulation of inflammatory mediators, both of NF-κB (including p65) and MAPK (including p38) signaling pathways to exert its anti-inflammatory function. These results indicated that enzymolysis is a viable strategy for degradation of sulfate glycosaminoglycan, and D-SBSG could be a promising ingredient for inflammation management.

Keywords:  Anti-inflammatory; Degradation; Hyaluronidase; Low molecular sulfate glycosaminoglycan; Swimming bladder

DOI:  https://doi.org/10.1016/j.foodres.2022.111444
Cureus. 2022 May;14(5): e25401

The Role of Glucosamine and Chondroitin Sulfate in the Prevention of Colorectal Cancer: A Systematic Review.

Asma A Khan, Vij Mannan, Muhammad Ahad Pervaiz, Aqsa Akram, Elina S Momin, Muhammad Sanusi, Tejasvi Kashyap, Abeer O Elshaikh.

  Currently, colorectal cancer is the third most common cancer in the world. Recently, glucosamine and chondroitin have gained popularity for their beneficial effects on cancer. They have already been recognized for their therapeutic role in osteoarthritis. This systematic review aims to analyze the relationship between the combined consumption of glucosamine and chondroitin and the prevention of colorectal cancer. Three databases: PubMed, Google Scholar, and Science Direct, were searched to collect relevant articles. After screening full-text articles, seven studies were included in the systematic review. The review found a supportive association between glucosamine and chondroitin and the decreased incidence of colorectal cancer. Through an anti-inflammatory effect on the cell signaling pathway, the supplementation caused a reduction in colorectal cancer occurrence. The dose, frequency of usage of the supplement, and weight of individuals, along with the use of non-steroidal anti-inflammatory drugs, also affected the efficacy. To further assess this relationship, it is necessary to conduct double-blind, randomized controls trials for the supplements in cancer prevention and further explore their safety and efficacy with different ethnicities, drugs, doses, and weight individuals.

Keywords:  chondroitin sulfate; colorectal cancer; dietary supplements; disability & cancer prevention; glucosamine; preventive practices

DOI:  https://doi.org/10.7759/cureus.25401
Int J Eat Disord. 2022 Jul 02.

Dehydroepiandrosterone sulfate levels predict weight gain in women with anorexia nervosa.

Allison Kimball, Caitlin Colling, Melanie S Haines, Erinne Meenaghan, Kamryn T Eddy, Madhusmita Misra, Karen K Miller.

   OBJECTIVE: Anorexia nervosa (AN) is a serious condition characterized by undernutrition, complicated by endocrine dysregulation, and with few predictors of recovery. Urinary free cortisol (UFC) is a predictor of weight gain, but 24-h urine samples are challenging to collect. We hypothesized that serum dehydroepiandrosterone sulfate (DHEAS), which like cortisol is regulated by adrenocorticotropic hormone (ACTH), would predict weight gain and increases in fat mass in women with AN.
METHODS: We prospectively studied 34 women with AN and atypical AN, mean age 27.4 ± 7.7 years (mean ± SD), who received placebo in a 6-month randomized trial. Baseline DHEAS and 24-h UFC were measured by liquid chromatography with tandem mass spectrometry. Body composition was assessed at baseline and 6 months by DXA and cross-sectional abdominal CT at L4.
RESULTS: Mean baseline DHEAS level was 173 ± 70 μg/dl (0.7 ± 0.3 times the mean normal range for age) and mean baseline UFC (n = 15) was 20 ± 18 μg/24 h (normal: 0-50 μg/24 h). Higher DHEAS levels predicted weight gain over 6 months (r = 0.61, p < .001). DHEAS levels also predicted increases in fat mass (r = 0.40, p = .03), appendicular lean mass (r = 0.38, p = .04), and abdominal adipose tissue (r = 0.60, p < .001). All associations remained significant after controlling for age, baseline BMI, OCP use, duration of AN, and SSRI/SNRI use. DHEAS levels correlated with UFC (r = 0.61, p = .02).
DISCUSSION: In women with AN, higher serum DHEAS predicts weight gain and increases in fat and muscle mass. Additional studies are needed to confirm these findings and further elucidate the association between DHEAS and weight gain.
PUBLIC SIGNIFICANCE: Anorexia nervosa is a severe psychiatric condition, and predictors of weight recovery are needed to improve prognostication and guide therapeutic decision making. While urinary cortisol is a predictor of weight gain, 24-h urine collections are challenging to obtain. Like cortisol, dehydroepiandrosterone sulfate (DHEAS) is a hormone produced by the adrenal glands. As a readily available blood test, DHEAS holds promise as more practical biomarker of weight gain in anorexia nervosa.

Keywords:  DHEAS; anorexia nervosa; cortisol; eating disorder

DOI:  https://doi.org/10.1002/eat.23767
Front Endocrinol (Lausanne). 2022 ;13 881740

Divergent Associations Between Serum Androgens and Ovarian Reserve Markers Revealed in Patients With Polycystic Ovary Syndrome.

Youran Li, Yanhong Zhai, Lin Li, Yifan Lu, Shaofei Su, Ying Liu, Zhengwen Xu, Mingwei Xin, Qiaoli Zhang, Zheng Cao.

   Background: The role of excess androgen in ovarian reserve remains unclear in patients with polycystic ovary syndrome (PCOS). Our study highlights the associations of serum androgen levels and ovarian reserve markers in PCOS and non-PCOS women.
Methods: Totally 584 menstrual abnormalities women of 20-45 years were retrospectively evaluated at the Beijing Obstetrics and Gynecology Hospital between January 2021 to October 2021. The enrolled patients were classified into two groups: the PCOS group (n=288) and the non-PCOS group (n=296) based on the Rotterdam consensus for PCOS diagnosis. The serum androgens, including testosterone (T), free testosterone (FT, calculated), bioavailable testosterone (Bio-T, calculated), androstenedione (A2), dihydrotestosterone (DHT), dehydroepiandrosterone (DHEA), and dehydroepiandrosterone sulfate (DHEAS) were assessed with an in-house developed liquid chromatography tandem mass spectrometry (LC-MS/MS) method. The associations between the serum androgens and the hormone markers commonly used for evaluating ovarian reserve function, such as anti-mullerian hormone (AMH) and the ratio of luteinizing hormone (LH)/follicle stimulating hormone (FSH) were explored.
Results: The serum T, FT, Bio-T, A2, DHT, DHEA, DHEAS, AMH and LH/FSH of the PCOS group were 51.7 ± 23.2 ng/dL/mL, 8.5 ± 5.0 pg/mL, 210.1 ± 127.7 pg/mL, 1.9 ± 0.8 ng/mL, 0.2 ± 0.1 ng/mL, 6.4 ± 4.2 ng/mL, 2431.0 ± 1030.7 ng/mL, 6.7 ± 3.8 ng/mL, and 1.8 ± 1.4 respectively, which were significantly higher than those in the non-PCOS group (p<0.05). In the group of PCOS patients, T and A2 levels were positively associated with AMH in both multivariate linear regression analysis and Pearson's correlation analysis. Similar but weaker associations were observed in the non-PCOS patients. In the PCOS patients with hyperandrogenemia (HA), the AMH level was significantly higher in the subjects with T increased than in the subjects with non-T androgen(s) increased (A2, DHT, DHEA or DHEAS).
Conclusions: The serum androgen levels are positively associated with ovarian reserve markers in both of the PCOS and the non-PCOS patients in our study. In the PCOS group, the highest AMH level was observed in the subjects with the T elevation subgroup, suggesting that T is more closely related with the increase of AMH when compared with other androgens investigated.

Keywords:  AMH; LC-MS/MS; PCOS; androgen; ovarian reserve

DOI:  https://doi.org/10.3389/fendo.2022.881740
Mol Psychiatry. 2022 Jun 27.

The extracellular matrix and perineuronal nets in memory.

James W Fawcett, Marianne Fyhn, Pavla Jendelova, Jessica C F Kwok, Jiri Ruzicka, Barbara A Sorg.

All components of the CNS are surrounded by a diffuse extracellular matrix (ECM) containing chondroitin sulphate proteoglycans (CSPGs), heparan sulphate proteoglycans (HSPGs), hyaluronan, various glycoproteins including tenascins and thrombospondin, and many other molecules that are secreted into the ECM and bind to ECM components. In addition, some neurons, particularly inhibitory GABAergic parvalbumin-positive (PV) interneurons, are surrounded by a more condensed cartilage-like ECM called perineuronal nets (PNNs). PNNs surround the soma and proximal dendrites as net-like structures that surround the synapses. Attention has focused on the role of PNNs in the control of plasticity, but it is now clear that PNNs also play an important part in the modulation of memory. In this review we summarize the role of the ECM, particularly the PNNs, in the control of various types of memory and their participation in memory pathology. PNNs are now being considered as a target for the treatment of impaired memory. There are many potential treatment targets in PNNs, mainly through modulation of the sulphation, binding, and production of the various CSPGs that they contain or through digestion of their sulphated glycosaminoglycans.

DOI: https://doi.org/10.1038/s41380-022-01634-3
Bioinformatics. 2022 Jun 30. pii: btac437. [Epub ahead of print]

HSMotifDiscover: identification of motifs in sequences composed of non-single-letter elements.

Vinod Kumar Singh, Rohan Misra, Steven C Almo, Ulrich G Steidl, Hannes E Bülow, Deyou Zheng.

SUMMARY: The functional sub-string(s) of a biopolymer sequence defines the specificity of its interaction with other biomolecules and is often referred to as motifs. Computational algorithms and software have been broadly developed for finding such motifs in sequences in which the individual elements are single characters, such as those in DNA and protein sequences. However, there are more complex scenarios where the motifs exist in non-single-letter contexts, for example, preferred patterns of chemical modifications on proteins, DNAs, RNAs, or polysaccharides. To search for those motifs, we describe a new method that converts the modified sequence elements to representative single-letter codes and then uses a modified Gibbs-sampling algorithm to define the position specific scoring matrix (PSSM) representing the motif(s). As a proof of principle, we describe the implementation and application of an R package for discovering heparan sulfate (HS) motifs in glycan sequences, which are important in regulating protein-protein interactions. This software can be valuable for analyzing high-throughput glycoprotein binding data using microarrays with HS oligosaccharides or other biological polymers.
AVAILABILITY AND IMPLEMENTATION: HSMotifDiscover is freely available as an open source R package released under an MIT license at https://github.com/bioinfoDZ/HSMotifDiscover and also available in the form of an app at https://hsmotifdiscover.shinyapps.io/HSMotifDiscover_ShinyApp/.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DOI: https://doi.org/10.1093/bioinformatics/btac437
BMC Nephrol. 2022 Jun 28. 23(1): 231

Serum total indoxyl sulfate levels and all-cause and cardiovascular mortality in maintenance hemodialysis patients: a prospective cohort study.

Qian Li, Shuang Zhang, Qi-Jun Wu, Jia Xiao, Zhi-Hong Wang, Xiang-Wei Mu, Yu Zhang, Xue-Na Wang, Lian-Lian You, Sheng-Nan Wang, Jia-Ni Song, Xiu-Nan Zhao, Zhen-Zhen Wang, Xin-Yi Yan, Yu-Xin Jin, Bo-Wen Jiang, Shu-Xin Liu.

   BACKGROUND: The association between serum total indoxyl sulfate (tIS), and cardiovascular disease (CVD) and all-cause mortality is a matter of debate. In the current study we sought to determine the association, if any, between serum tIS, and all-cause and CVD-associated mortality in patients on maintenance hemodialysis (MHD).
METHODS: A prospective cohort study was conducted involving 500 MHD patients at Dalian Municipal Central Hospital from 31 December 2014 to 31 December 2020. Serum tIS levels were measured at baseline and classified as high (≥44.16 ng/ml) or low (< 44.16 ng/ml) according to the "X-tile" program. Besides, the associations between continuous serum tIS and outcomes were also explored. Predictors were tested for colinearity using variance inflation factor analysis. Hazard ratios (HRs) and 95% confidence intervals (CIs) were calculated using Cox proportional hazards regression models. Restricted cubic spline model was performed to assess dose-response relationships between tIS concentration and all-cause and CVD mortality.
RESULTS: During a 58-month median follow-up period, 224 deaths (132 CVD deaths) were documented. After adjustment for potential confounders, the serum tIS level was positively associated with all-cause mortality (HR = 1.02, 95% = 1.01-1.03); however, we did not detect a significant association when tIS was a dichotomous variable. Compared with the MHD population with a serum tIS level < 44.16 ng/ml, the adjusted HR for CVD mortality among those with a serum tIS level ≥ 44.16 ng/ml was 1.76 (95% = 1.10-2.82). Furthermore, we also noted the same association when the serum tIS level was a continuous variable.
CONCLUSION: The serum tIS level was associated with higher risk of all-cause and CVD mortality among MHD patients. Further prospective large-scale studies are required to confirm this finding.

Keywords:  Cohort study; Hemodialysis; Indoxyl sulfate; Mortality

DOI:  https://doi.org/10.1186/s12882-022-02862-z
J Pharm Biomed Anal. 2022 Jun 27. pii: S0731-7085(22)00336-3. [Epub ahead of print]219 114915

Nuclear magnetic resonance spectroscopy as an elegant tool for a complete quality control of crude heparin material.

Yulia B Monakhova, Bernd W K Diehl.

  Nuclear magnetic resonance (NMR) spectrometric methods for the quantitative analysis of pure heparin in crude heparin is proposed. For quantification, a two-step routine was developed using a USP heparin reference sample for calibration and benzoic acid as an internal standard. The method was successfully validated for its accuracy, reproducibility, and precision. The methodology was used to analyze 20 authentic porcine heparinoid samples having heparin content between 4.25 w/w % and 64.4 w/w %. The characterization of crude heparin products was further extended to a simultaneous analysis of these common ions: sodium, calcium, acetate and chloride. A significant, linear dependence was found between anticoagulant activity and assayed heparin content for thirteen heparinoids samples, for which reference data were available. A Diffused-ordered NMR experiment (DOSY) can be used for qualitative analysis of specific glycosaminoglycans (GAGs) in heparinoid matrices and, potentially, for quantitative prediction of molecular weight of GAGs. NMR spectrometry therefore represents a unique analytical method suitable for the simultaneous quantitative control of organic and inorganic composition of crude heparin samples (especially heparin content) as well as an estimation of other physical and quality parameters (molecular weight, animal origin and activity).

Keywords:  Crude heparin; Heparin; Ions; NMR spectroscopy; USP

DOI:  https://doi.org/10.1016/j.jpba.2022.114915
Thromb Res. 2022 May;213(Suppl 1): S113-S119

The impact of warfarin on overall survival in cancer patients.

Thita Chiasakul, Jeffrey I Zwicker.

  Venous thromboembolism (VTE) is a common complication in patients with cancer. Warfarin has largely been replaced by low-molecular-weight heparin (LMWHs) and direct oral anticoagulants (DOACs) as the standard of care in cancer-associated VTE. The survival benefit of these anticoagulants over warfarin in the cancer population was not demonstrated in clinical trials, possibly due to insufficient sample size and limited follow-up duration. There are emerging population-based studies suggesting that warfarin may be associated with improved overall survival in cancers and may have a protective effect against certain types of cancers. Warfarin may exert its anti-neoplastic properties through both coagulation pathway -dependent and -independent mechanisms, the latter of which are mediated by inhibition of the Gas6-AXL signaling pathway. Further research should emphasize on identifying clinical and laboratory predictors of beneficial effects of warfarin. In this review article, we summarize and update the current evidence regarding the potential impact of warfarin on the overall survival of cancer patients and incidence of cancer, as well as review the potential mechanism of such effect and future perspectives.

Keywords:  Oral anticoagulants; cancer-associated thrombosis; low-molecular weight heparin; warfarin

DOI:  https://doi.org/10.1016/j.thromres.2021.11.004
Front Plant Sci. 2022 ;13 878418

Crosstalk Between Iron and Sulfur Homeostasis Networks in Arabidopsis.

Muhammad Sayyar Khan, Qiao Lu, Man Cui, Hala Rajab, Huilan Wu, Tuanyao Chai, Hong-Qing Ling.

  The widespread deficiency of iron (Fe) and sulfur (S) is becoming a global concern. The underlying mechanisms regulating Fe and S sensing and signaling have not been well understood. We investigated the crosstalk between Fe and S using mutants impaired in Fe homeostasis, sulfate assimilation, and glutathione (GSH) biosynthesis. We showed that chlorosis symptoms induced by Fe deficiency were not directly related to the endogenous GSH levels. We found dynamic crosstalk between Fe and S networks and more interestingly observed that the upregulated expression of IRT1 and FRO2 under S deficiency in Col-0 was missing in the cad2-1 mutant background, which suggests that under S deficiency, the expression of IRT1 and FRO2 was directly or indirectly dependent on GSH. Interestingly, the bottleneck in sulfite reduction led to a constitutively higher IRT1 expression in the sir1-1 mutant. While the high-affinity sulfate transporter (Sultr1;2) was upregulated under Fe deficiency in the roots, the low-affinity sulfate transporters (Sultr2;1, and Sultr2;2) were down-regulated in the shoots of Col-0 seedlings. Moreover, the expression analysis of some of the key players in the Fe-S cluster assembly revealed that the expression of the so-called Fe donor in mitochondria (AtFH) and S mobilizer of group II cysteine desulfurase in plastids (AtNFS2) were upregulated under Fe deficiency in Col-0. Our qPCR data and ChIP-qPCR experiments suggested that the expression of AtFH is likely under the transcriptional regulation of the central transcription factor FIT.

Keywords:  Arabidopsis; crosstalk; homeostasis; iron; sulfur

DOI:  https://doi.org/10.3389/fpls.2022.878418