Identification and analysis of miRNAs-lncRNAs-mRNAs modules involved in stem-elongation of deepwater rice (Oryza sativa L.)

Deepwater is an abiotic stress that limits rice cultivation worldwide due to recurrent floods. The miRNAs and lncRNAs are two non-coding RNAs emerging as major regulators of gene expressions under different abiotic stresses. However, the regulation of these two non-coding RNAs under deepwater stress in rice is still unexplored. In this study, small RNA-seq and RNA-seq from internode and node tissues were analyzed to predict deepwater stress responsive miRNAs and lncRNAs, respectively. Additionally, a competitive endogenous RNA (ceRNA) study revealed about 69 and 25 lncRNAs acting as endogenous target mimics (eTM) with the internode and node miRNAs, respectively. In ceRNA analyses, some of the key miRNAs such as miR1850.1, miR1848, and IN-nov-miR145 were upregulated while miR159e was downregulated, and their respective eTM lncRNAs and targets were found to have opposite expressions. Moreover, we have transiently expressed one module (IN-nov-miR145-Cc-TCONS_00011544-Os11g36430.3) in tobacco leaves. The integrated analysis has identified differentially expressed (DE) miRNAs, lncRNAs and their target genes, and the complex regulatory network, which might lead to stem elongation under deepwater stress. In this novel attempt to identify and characterize miRNAs and lncRNAs under deepwater stress in rice, we have provided, probably for the first time, a reference platform to study the interactions of these two non-coding RNAs with respective target genes through transient expression analyses.

POS0855 IMPAIRED PROMIS PHYSICAL FUNCTION IN IDIOPATHIC INFLAMMATORY MYOPATHY PATIENTS: RESULTS FROM THE MULTICENTER COVAD PATIENT REPORTED E-SURVEY

Background

Evaluation of physical function is fundamental in the management of idiopathic inflammatory myopathies (IIMs). Patient-Reported Outcome Measurement Information System (PROMIS) is a National Institute of Health initiative established in 2004 to develop patient-reported outcome measures (PROMs) with improved validity and efficacy. PROMIS Physical Function (PF) short forms have been validated for use in IIMs [1].

Objectives

To investigate the physical function status of IIM patients compared to those with non-IIM autoimmune diseases (AIDs) and healthy controls (HCs) utilizing PROMIS PF data obtained in the coronavirus disease-2019 (COVID-19) Vaccination in Autoimmune Diseases (COVAD) study, a large-scale, international self-reported e-survey assessing the safety of COVID-19 vaccines in AID patients [2].

Methods

The survey data regarding demographics, IIM and AID diagnosis, disease activity, and PROMIS PF short form-10a scores were extracted from the COVAD study database. The disease activity (active vs inactive) of each patient was assessed in 3 different ways: (1) physician’s assessment (active if there was an increased immunosuppression), (2) patient’s assessment (active vs inactive as per patient), and (3) current steroid use. These 3 definitions of disease activity were applied independently to each patient. PROMIS PF-10a scores were compared between each disease category (IIMs vs non-IIM AIDs vs HCs), stratified by disease activity based on the 3 definitions stated above, employing negative binominal regression model. Multivariable regression analysis adjusted for age, gender, and ethnicity was performed clustering countries, and the predicted PROMIS PF-10a score was calculated based on the regression result. Factors affecting PROMIS PF-10a scores other than disease activity were identified by another multivariable regression analysis in the patients with inactive disease (IIMs or non-IIM AIDs).

Results

1057 IIM patients, 3635 non-IIM AID patients, and 3981 HCs responded to the COVAD survey until August 2021. The median age of the respondents was 43 [IQR 30-56] years old, and 74.8% were female. Among IIM patients, dermatomyositis was the most prevalent diagnosis (34.8%), followed by inclusion body myositis (IBM) (23.6%), polymyositis (PM) (16.2%), anti-synthetase syndrome (11.8%), overlap myositis (7.9%), and immune-mediated necrotizing myopathy (IMNM) (4.6%). The predicted mean of PROMIS PF-10a scores was significantly lower in IIMs compared to non-IIM AIDs or HCs (36.3 [95% (CI) 35.5-37.1] vs 41.3 [95% CI 40.2-42.5] vs 46.2 [95% CI 45.8-46.6], P < 0.001), irrespective of disease activity or the definitions of disease activity used (physician’s assessment, patient’s assessment, or steroid use) (Figure 1). The largest difference between active IIMs and non-IIM AIDs was observed when the disease activity was defined by patient’s assessment (35.0 [95% CI 34.1-35.9] vs 40.1 [95% CI 38.7-41.5]). Considering the subgroups of IIMs, the scores were significantly lower in IBM in comparison with non-IBM IIMs (P < 0.001). The independent factors associated with low PROMIS PF-10a scores in the patients with inactive disease were older age, female gender, and the disease category being IBM, PM, or IMNM.

Conclusion

Physical function is significantly impaired in IIMs compared to non-IIM AIDs or HCs, even in patients with inactive disease. The elderly, women, and IBM groups are the worst affected, suggesting that developing targeted strategies to minimize functional disability in certain groups may improve patient reported physical function and disease outcomes.

References

[1]Saygin D, Oddis CV, Dzanko S, et al. Utility of patient-reported outcomes measurement information system (PROMIS) physical function form in inflammatory myopathy. Semin Arthritis Rheum. 2021; 51: 539-46.

[2]Sen P, Gupta L, Lilleker JB, et al. COVID-19 vaccination in autoimmune disease (COVAD) survey protocol. Rheumatol Int. 2022; 42: 23-9.

Acknowledgements

The authors thank all respondents for filling the questionnaire. The authors thank The Myositis Association, Myositis India, Myositis UK, the Myositis Global Network, Cure JM, Cure IBM, Sjögren’s India Foundation, EULAR PARE, and various other patient support groups and organizations for their invaluable contribution in the dissemination of this survey among patients which made the data collection possible. The authors also thank all members of the COVAD study group.

Disclosure of Interests

None declared

POS0899 HIGH FATIGUE SCORES IN PATIENTS WITH IDIOPATHIC INFLAMMATORY MYOPATHIES: A MULTIGROUP COMPARATIVE STUDY FROM THE COVAD E-SURVEY

Background

Idiopathic inflammatory myopathies (IIM) are a rare, multisystem, heterogeneous diseases, and contribute to high psychological burden. The patients’ perception of physical health, deteriorating independence and social and environmental relationships may not always be a direct function of disease activity. To face with these aspects, several worldwide specialized organization have recommended the use of patient reported outcome measures (PROMs) both in clinical trials and observational studies to highlight patient’s perception of the disease (1). Unfortunately, data on fatigue scores in IIM is limited.

Objectives

We compared fatigue VAS scores in patients with IIM, autoimmune diseases (AIDs) and healthy controls (HCs) and triangulated them with PROMIS physical function in a large international cohort made up of answers from the e-survey regarding the COVID-19 Vaccination in Autoimmune Diseases (COVAD) study.

Methods

Data of 16327 respondents was extracted from the COVAD database on August 31th 2021. VAS fatigue scores were compared between AID, HC and IIM using univariate followed by multivariate analysis after adjusting for baseline differences. We further performed a propensity score matched analysis on 1827 subjects after adjusting for age, gender and ethnicity. The Kruskal-Wallis test was used for continuous variables and chi-square test for categorical variables, and Bonferroni’s correction was applied for the post hoc analyses considering IIMs as a reference group.

Results

We analyzed answers from 6988 patients, with a mean age of 43.8 years (SD 16.2). The overall percentage of female was 72% and the population ethnicity was mainly composed of White (55.1%), followed by Asian (24.6%), and Hispanic (13.8%). The overall fatigue VAS was 3.6 mm (SD 2.7). IIMs VAS was 4.8 mm (SD 2.6), AIDs 4.5 mm (SD 2.6), and HC 2.8 mm (SD 2.6) (P <0,001). VAS fatigue scores of IIMs were comparable with AIDs (P 0.084), albeit significantly higher than the HCs (P <0,001). Notably, fatigue VAS was lower in IIMs than AIDs in two distinct subsets: inactive disease as defined by the patient’s perception and the “excellent” general health condition group, where IIMs had worse scores (P <0,05). Interestingly, fatigue VAS was comparable in active disease defined by physician assessment, patient perception, based on general functional status, or when defined by steroid dose being prescribed. Notably, after propensity matched analysis of patients adjusting for gender, age and ethnicity (1.827 answers, i.e. 609 subjects per group, P =1) the differences disappeared and IIMs and AIDs had comparable fatigue levels across all levels of disease activity, although the fatigue discrepancies with HCs were substantially confirmed.

After application of a multivariate linear regression analysis we found that lower fatigue VAS scores were related to HC (P <0,001), male gender (P <0,001), Asian and Hispanic ethnicities (P <0,001 and 0,003).

Conclusion

Our study confirms that there is a higher prevalence of fatigue in all the AIDs patients, with comparable VAS scores between IIMs and other AIDs. We can also read our data commenting that females and/or Caucasians patients suffer a higher impact of this manifestation of chronic autoimmune diseases upon their lives. This is why these subjects, to our judgement, should be carefully evaluated during outpatients visits and to whom we should spend some extra time to discuss health related issues and how to improve them.

References

[1]Regardt, M. et al. OMERACT 2018 Modified Patient-reported Outcome Domain Core Set in the Life Impact Area for Adult Idiopathic Inflammatory Myopathies. J. Rheumatol.46, 1351–1354 (2019).

Figure 1.

distribution of Fatigue VAS scores in the three population evaluated. IIM idiopathic inflammatory myositis; AID autoimmune diseases; HC healthy controls; * P < 0,05.

Disclosure of Interests

None declared

POS1260 COVID-19 VACCINATION-RELATED ADVERSE EVENTS AMONG AUTOIMMUNE DISEASE PATIENTS: RESULTS FROM THE COVID-19 VACCINATION IN AUTOIMMUNE DISEASES (COVAD) STUDY

Background

COVID-19 vaccines have been proven to be safe and effective in the healthy population at large. However, significant gaps remain in the evidence of their safety in patients with systemic autoimmune and inflammatory disorders (SAIDs). Patients and rheumatologists have expressed concerns regarding vaccination triggered allergic reactions, thrombogenic events, and other adverse events (ADEs) contributing to vaccine hesitancy (1)

Objectives

This study aimed to assess and compare short term COVID-19 vaccination associated ADEs in patients with SAIDs and healthy controls (HC) seven days post-vaccination, as well as between patients with SAIDs receiving different vaccines.

Methods

We developed an comprehensive, patient self-reporting electronic-survey to collect respondent demographics, SAID details, COVID-19 infection history, COVID-19 vaccination details, 7-day post vaccination adverse events and patient reported outcome measures using the PROMIS tool. After pilot testing, validation, translation into 18 languages on the online platform surveymonkey.com, and vetting by international experts, the survey was circulated in early 2021 by a multicenter study group of >110 collaborators in 94 countries. ADEs were categorized as injection site pain, minor ADEs, major ADEs, and hospitalizations. We analyzed data from the baseline survey for descriptive and intergroup comparative statistics based on data distribution and variable type (data as median, IQR).

Results

10900 respondents [42 (30-55) years, 74% females and 45% Caucasians] were analyzed. 5,867 patients (54%) with SAIDs were compared with 5033 HCs. All respondents included in the final analysis had received a single dose of the vaccine and 69% had received 2 primary doses. Pfizer (39.8%) was the most common vaccine received, followed by Oxford/AstraZeneca (13.4%), and Covishield (10.9%). Baseline demographics differed by an older SAID population (mean age 42 vs. 33 years) and a greater female predominance (M:F= 1:4.7 vs. 1:1.8) compared to HCs.

79% had minor and only 3% had major vaccine ADEs requiring urgent medical attention overall. In adjusted analysis, among minor ADEs, abdominal pain [multivariate OR 1.6 (1.14-2.3)], dizziness [multivariate OR 1.3 (1.2-1.5)], and headache [multivariate OR 1.67 (1.3-2.2)], were more frequent in SAIDs than HCs. Overall major ADEs [multivariate OR 1.9 (1.6-2.2)], and throat closure [multivariate OR 5.7 (2.9-11.3)] were more frequent in SAIDs though absolute risk was small (0-4%) and rates of hospitalization were similarly small in both groups, with a small absolute risk (0-4%). Specific minor ADEs frequencies were different among different vaccine types, however, major ADEs and hospitalizations overall were rare (0-4%) and comparable across vaccine types in patients with SAIDs (Figure 1).

Figure 1.

A. Post Vaccination ADEs in SAIDs compared to HCs. B. Proportions of post COVID-19 vaccination ADEs in SAIDs by vaccine type.

Conclusion

Vaccination against COVID-19 is relatively safe and tolerable in patients with SAIDs. Certain minor vaccine ADEs are more frequent in SAIDs than HCs in this study, though are not severe and do not require urgent medical attention. SAIDs were at a higher risk of major ADEs than HCs, though absolute risk was small, and did not lead to increased hospitalizations. There are small differences in minor ADEs between vaccine types in patients with SAIDs.

References

[1]Boekel L, Kummer LY, van Dam KPJ, Hooijberg F, van Kempen Z, Vogelzang EH, et al. Adverse events after first COVID-19 vaccination in patients with autoimmune diseases. Lancet Rheumatol. 2021 Aug;3(8):e542–5.

Acknowledgements

The authors thank all members of the COVAD study group for their invaluable role in the collection of data. The authors thank all respondents for filling the questionnaire. The authors thank The Myositis Association, Myositis India, Myositis UK, the Myositis Global Network, Cure JM, Cure IBM, Sjögren’s India Foundation, EULAR PARE, and various other patient support groups and organizations for their invaluable contribution in the dissemination of this survey among patients which made the data collection possible. The authors also thank all members of the COVAD study group.

Disclosure of Interests

Parikshit Sen: None declared, Naveen R: None declared, Arvind Nune: None declared, James B. Lilleker: None declared, Vishwesh Agarwal: None declared, Sinan Kardes: None declared, Minchul Kim: None declared, Jessica Day Grant/research support from: JD has received research funding from CSL Limited., Marcin Milchert: None declared, Tamer A Gheita: None declared, Babur Salim: None declared, Tsvetelina Velikova: None declared, Abraham Edgar Gracia-Ramos: None declared, Ioannis Parodis Speakers bureau: IP has received research funding and/or honoraria from Amgen, AstraZeneca, Aurinia Pharmaceuticals, Elli Lilly and Company, Gilead Sciences, GlaxoSmithKline, Janssen Pharmaceuticals, Novartis and F. Hoffmann-La Roche AG., Consultant of: IP has received research funding and/or honoraria from Amgen, AstraZeneca, Aurinia Pharmaceuticals, Elli Lilly and Company, Gilead Sciences, GlaxoSmithKline, Janssen Pharmaceuticals, Novartis and F. Hoffmann-La Roche AG., Grant/research support from: IP has received research funding and/or honoraria from Amgen, AstraZeneca, Aurinia Pharmaceuticals, Elli Lilly and Company, Gilead Sciences, GlaxoSmithKline, Janssen Pharmaceuticals, Novartis and F. Hoffmann-La Roche AG., Albert Selva-O’Callaghan: None declared, Elena Nikiphorou Speakers bureau: EN has received speaker honoraria/participated in advisory boards for Celltrion, Pfizer, Sanofi, Gilead, Galapagos, AbbVie, Lilly, Consultant of: EN has received speaker honoraria/participated in advisory boards for Celltrion, Pfizer, Sanofi, Gilead, Galapagos, AbbVie, Lilly, Grant/research support from: EN has received speaker honoraria/participated in advisory boards for Celltrion, Pfizer, Sanofi, Gilead, Galapagos, AbbVie, Lilly, and holds research grants from Pfizer and Lilly., Tulika Chatterjee: None declared, Ai Lyn Tan Speakers bureau: ALT has received honoraria for advisory boards and speaking for Abbvie, Gilead, Janssen, Lilly, Novartis, Pfizer, UCB., Consultant of: ALT has received honoraria for advisory boards and speaking for Abbvie, Gilead, Janssen, Lilly, Novartis, Pfizer, UCB., Grant/research support from: ALT has received honoraria for advisory boards and speaking for Abbvie, Gilead, Janssen, Lilly, Novartis, Pfizer, UCB., Lorenzo Cavagna: None declared, Miguel A Saavedra: None declared, Samuel Katsuyuki Shinjo: None declared, Nelly Ziade Speakers bureau: NZ has received speaker fees, advisory board fees and research grants from Pfizer, Roche, Abbvie, Eli Lilly, NewBridge, Sanofi-Aventis, Boehringer Ingelheim, Janssen, Pierre Fabre; none is related to this manuscript., Consultant of: NZ has received speaker fees, advisory board fees and research grants from Pfizer, Roche, Abbvie, Eli Lilly, NewBridge, Sanofi-Aventis, Boehringer Ingelheim, Janssen, Pierre Fabre; none is related to this manuscript., Grant/research support from: NZ has received speaker fees, advisory board fees and research grants from Pfizer, Roche, Abbvie, Eli Lilly, NewBridge, Sanofi-Aventis, Boehringer Ingelheim, Janssen, Pierre Fabre; none is related to this manuscript., Johannes Knitza: None declared, Masataka Kuwana: None declared, Oliver Distler Speakers bureau: OD has/had consultancy relationship with and/or has received research funding from or has served as a speaker for the following companies in the area of potential treatments for systemic sclerosis and its complications in the last three years: Abbvie, Acceleron, Alcimed, Amgen, AnaMar, Arxx, Baecon, Blade, Bayer, Boehringer Ingelheim, ChemomAb, Corbus, CSL Behring, Galapagos, Glenmark, GSK, Horizon (Curzion), Inventiva, iQvia, Kymera, Lupin, Medac, Medscape, Mitsubishi Tanabe, Novartis, Roche, Roivant, Sanofi, Serodapharm, Topadur and UCB. Patent issued “mir-29 for the treatment of systemic sclerosis” (US8247389, EP2331143)., Consultant of: OD has/had consultancy relationship with and/or has received research funding from or has served as a speaker for the following companies in the area of potential treatments for systemic sclerosis and its complications in the last three years: Abbvie, Acceleron, Alcimed, Amgen, AnaMar, Arxx, Baecon, Blade, Bayer, Boehringer Ingelheim, ChemomAb, Corbus, CSL Behring, Galapagos, Glenmark, GSK, Horizon (Curzion), Inventiva, iQvia, Kymera, Lupin, Medac, Medscape, Mitsubishi Tanabe, Novartis, Roche, Roivant, Sanofi, Serodapharm, Topadur and UCB. Patent issued “mir-29 for the treatment of systemic sclerosis” (US8247389, EP2331143)., Grant/research support from: OD has/had consultancy relationship with and/or has received research funding from or has served as a speaker for the following companies in the area of potential treatments for systemic sclerosis and its complications in the last three years: Abbvie, Acceleron, Alcimed, Amgen, AnaMar, Arxx, Baecon, Blade, Bayer, Boehringer Ingelheim, ChemomAb, Corbus, CSL Behring, Galapagos, Glenmark, GSK, Horizon (Curzion), Inventiva, iQvia, Kymera, Lupin, Medac, Medscape, Mitsubishi Tanabe, Novartis, Roche, Roivant, Sanofi, Serodapharm, Topadur and UCB. Patent issued “mir-29 for the treatment of systemic sclerosis” (US8247389, EP2331143)., Hector Chinoy Speakers bureau: HC has served as a speaker for UCB, Biogen., Consultant of: HC has received consulting fees from Novartis, Eli Lilly, Orphazyme, Astra Zeneca, Grant/research support from: HC has received grant support from Eli Lilly and UCB, Vikas Agarwal: None declared, Rohit Aggarwal Consultant of: RA has/had a consultancy relationship with and/or has received research funding from for the following companies-Bristol Myers-Squibb, Pfizer, Genentech, Octapharma, CSL Behring, Mallinckrodt, AstraZeneca, Corbus, Kezar, Kyverna, Janssen, Roivant, Boehringer Ingelheim, Argenx, Q32, Alexion, EMD Serono, Jubliant, Abbvie, Janssen, Alexion, Argenx, Q32, EMD-Serono, Boehringer Ingelheim, Roivant., Grant/research support from: RA has/had a consultancy relationship with and/or has received research funding from for the following companies-Bristol Myers-Squibb, Pfizer, Genentech, Octapharma, CSL Behring, Mallinckrodt, AstraZeneca, Corbus, Kezar, Kyverna, Janssen, Roivant, Boehringer Ingelheim, Argenx, Q32, Alexion, EMD Serono, Jubliant, Abbvie, Janssen, Alexion, Argenx, Q32, EMD-Serono, Boehringer Ingelheim, Roivant., Latika Gupta: None declared

POS0198 COVID-19 OUTCOMES IN PATIENTS WITH DERMATOMYOSITIS: A REGISTRY-BASED COHORT ANALYSIS

Background

Dermatomyositis (DM) patients have fewer risks of COVID-19 infection compared to the general population, however, certain subgroups with DM have worse outcomes. Men. African Americans, those with interstitial lung disease, exhibited higher risks of severe COVID-19. DMARD and glucocorticoid use was associated with frequent hospitalisations and severe sepsis.

Objectives

Rheumatic diseases (RDs) like DM, are previously known to be vulnerable towards various types of infections due to its aggressive activity mandating high dose immunosuppressive therapy. The severity of COVID-19 in RDs is limited in literature due to the heterogeneous nature of the condition. Therefore, specific details on mortality is essential to navigate any precautions required in the treatment.

Methods

Retrospective data of individuals with DM and COVID-19 and the general population with COVID-19 between January 2020 to August 2020 was retrieved from the TriNetX database. A one-to-one matched COVID-19 positive control was selected using propensity score (PS) matching. We assessed COVID-19 outcomes such as mortality, hospitalisation, ICU admission, severe COVID-19, mechanical ventilation (MV), acute kidney injury (AKI), venous thromboembolism (VTE), ischemic stroke, acute respiratory distress syndrome (ARDS), renal replacement therapy (RRT) and sepsis. Subgroup analyses included gender, race, ILD, cancer patients, disease-modifying rheumatic drugs (DMARDs) use, and glucocorticoids (GC) use (Figure 1).

Figure 1.

Overview of study

Results

We identified 5,574 DM patients with COVID-19, and 5,574 general population with COVID-19 (controls). DM with COVID-19 had a lower risk of mortality in comparison to controls [RR 0.76], hospitalisation [RR 0.8], severe COVID-19 [RR 0.76], AKI [RR 0.83], and sepsis [RR 0.73]. Males and African Americans were more likely to develop AKI [RR 1.35, 1.65], while African Americans had higher odds for severe COVID-19 [RR 1.62] and VTE [RR 1.54]. DM with ILD group also experienced higher odds for severe COVID-19 infection [RR 1.64], and VTE [RR 2.06] (Figure 1).

DM patients receiving DMARDs and glucocorticoids had higher odds for hospitalisation [RR 1.46, 2.12], and sepsis [RR 3.25] Subgroup analysis of neoplasms amongst DM patients with COVID-19 was inadequate for meaningful comparison (Figure 1).

Conclusion

DM patients are protected for certain aspects of COVID-19 disease, including severe COVID-19, hospitalization, and mortality. The African American race, male gender, ILD, DMARDS and glucocorticoid users, are associated with poor outcomes.

Disclosure of Interests

Latika Gupta: None declared, Haig Pakhchanian: None declared, Hiba Khan: None declared, Rahul Raiker: None declared, Maryam Abbasi: None declared, Charles DeYoung: None declared, Sinan Kardes Grant/research support from: SK has received congress travel, accommodation, and participation fee support (12th Anatolian Rheumatology Days) from Abbvie, Sakir Ahmed Speakers bureau: SA has received honorarium as speaker for Pfizer, Chengappa Kavadichanda: None declared, Parikshit Sen: None declared, Rohit Aggarwal Consultant of: RA has/had a consultancy relationship with and/or has received research funding from the following companies-Bristol Myers-Squibb, Pfizer, Genentech, Octapharma, CSL Behring, Mallinckrodt, AstraZeneca, Corbus, Kezar, and Abbvie, Janssen, Alexion, Argenx, Q32, EMD-Serono, Boehringer Ingelheim, Roivant., Grant/research support from: RA has/had a consultancy relationship with and/or has received research funding from the following companies-Bristol Myers-Squibb, Pfizer, Genentech, Octapharma, CSL Behring, Mallinckrodt, AstraZeneca, Corbus, Kezar, and Abbvie, Janssen, Alexion, Argenx, Q32, EMD-Serono, Boehringer Ingelheim, Roivant.

POS0201 COVID-19 SEVERITY AND VACCINE BREAKTHROUGH INFECTIONS IN IDIOPATHIC INFLAMMATORY MYOPATHIES, OTHER SYSTEMIC AUTOIMMUNE AND INFLAMMATORY DISEASES, AND HEALTHY INDIVIDUALS: RESULTS FROM THE COVID-19 VACCINATION IN AUTOIMMUNE DISEASES (COVAD) STUDY

Background

Significant gaps are present in the evidence of the spectrum and severity of COVID-19 infection in idiopathic inflammatory myopathies (IIM). IIM patients typically require immunosuppressive therapy, may have multiple disease sequelae, and frequent comorbidities, and thus may be more susceptible to severe COVID-19 infection and complications (1). The possibility of attenuated immunogenicity and reduced efficacy of COVID-19 vaccines due to concomitant immunosuppressive medication is a major concern in these patients, and there is little data available on COVID-19 vaccine breakthrough infections (BI) in IIM (2).

Objectives

This study aimed to compare disease spectrum and severity and COVID-19 BI in patients with IIM, other systemic autoimmune and inflammatory diseases (SAIDs) and healthy controls (HCs).

Methods

We developed an extensive self-reporting electronic-survey (COVAD survey) featuring 36 questions to collect respondent demographics, SAID details, COVID-19 infection history, COVID-19 vaccination details, 7-day post vaccination adverse events and patient reported outcome measures using the PROMIS tool. After pilot testing, validation, translation into 18 languages on the online platform surveymonkey.com, and vetting by international experts, the COVAD survey was circulated in early 2021 by a multicenter study group of >110 collaborators in 94 countries. BI was defined as COVID-19 infection occurring more than 2 weeks after receiving 1st or 2nd dose of a COVID-19 vaccine. We analyzed data from the baseline survey for descriptive and intergroup comparative statistics based on data distribution and variable type.

Results

10900 respondents [mean age 42 (30-55) years, 74% females and 45% Caucasians] were analyzed. 1,227 (11.2%) had IIM, 4,640 (42.6%) had other SAIDs, and 5,033 (46.2%) were HC. All respondents included in the final analysis had received a single dose of the vaccine and 69% had received 2 primary doses. Pfizer (39.8%) was the most common vaccine received, followed by Oxford/AstraZeneca (13.4%), and Covishield (10.9%). IIM patients were older, had a higher Caucasian representation and higher Pfizer uptake than other SAIDs, and HC. A higher proportion of IIM patients received immunosuppressants than other SAIDs.

IIMs were at a lower risk of symptomatic pre-vaccination COVID-19 infection compared to SAIDs [multivariate OR 0.6 (0.4-0.8)] and HCs [multivariate OR 0.39 (0.28-0.54)], yet at a higher risk of hospitalization due to COVID-19 compared to SAIDs [univariate OR 2.3 (1.2-3.5)] and HCs [multivariate OR 2.5 (1.1-5.8)]. BIs were very uncommon in IIM patients, with only 17 (1.4%) reporting BI. IIM patients were at a higher risk of contracting COVID-19 prior to vaccination than ≤2 weeks of vaccination [univariate OR 8 (4.1-15)] or BI [univariate OR 4.6 (2.7-8.0)]. BIs were equally severe compared to when they occurred prior to vaccination in IIMs, and were comparable between IIM, SAIDs, and HC (Figure 1), though BI disease duration was shorter in IIMs than SAIDs (7 vs 11 days, p 0.027). 13/17 IIM patients with BI were on immunosuppressants.

Conclusion

IIM patients experienced COVID-19 infection less frequently prior to vaccination but were at a higher risk of hospitalization and requirement for oxygen therapy compared with patients with HC. Breakthrough COVID-19 infections were rare (1.4%) in vaccinated IIM patients, and were similar to HC and SAIDs, except for shorter disease duration in IIM.

References

[1]Brito-Zerón P, Sisó-Almirall A, Flores-Chavez A, Retamozo S, Ramos-Casals M. SARS-CoV-2 infection in patients with systemic autoimmune diseases. Clin Exp Rheumatol. 2021 Jun;39(3):676–87.

[2]Wack S, Patton T, Ferris LK. COVID-19 vaccine safety and efficacy in patients with immune-mediated inflammatory disease: Review of available evidence. J Am Acad Dermatol. 2021 Nov;85(5):1274–84.

Acknowledgements

The authors thank all members of the COVAD study group for their invaluable role in the collection of data. The authors thank all respondents for filling the questionnaire. The authors thank The Myositis Association, Myositis India, Myositis UK, the Myositis Global Network, Cure JM, Cure IBM, Sjögren’s India Foundation, EULAR PARE, and various other patient support groups and organizations for their invaluable contribution in the dissemination of this survey among patients which made the data collection possible. The authors also thank all members of the COVAD study group.

Disclosure of Interests

Latika Gupta: None declared, Leonardo Santos Hoff: None declared, Naveen R: None declared, Parikshit Sen: None declared, Samuel Katsuyuki Shinjo: None declared, Jessica Day Grant/research support from: JD has received research funding from CSL Limited, James B. Lilleker: None declared, Vishwesh Agarwal: None declared, Sinan Kardes: None declared, Minchul Kim: None declared, Ashima Makol: None declared, Marcin Milchert: None declared, Tamer A Gheita: None declared, Babur Salim: None declared, Tsvetelina Velikova: None declared, Abraham Edgar Gracia-Ramos: None declared, Ioannis Parodis Speakers bureau: IP has received research funding and/or honoraria from Amgen, AstraZeneca, Aurinia Pharmaceuticals, Elli Lilly and Company, Gilead Sciences, GlaxoSmithKline, Janssen Pharmaceuticals, Novartis and F. Hoffmann-La Roche AG., Consultant of: IP has received research funding and/or honoraria from Amgen, AstraZeneca, Aurinia Pharmaceuticals, Elli Lilly and Company, Gilead Sciences, GlaxoSmithKline, Janssen Pharmaceuticals, Novartis and F. Hoffmann-La Roche AG., Grant/research support from: IP has received research funding and/or honoraria from Amgen, AstraZeneca, Aurinia Pharmaceuticals, Elli Lilly and Company, Gilead Sciences, GlaxoSmithKline, Janssen Pharmaceuticals, Novartis and F. Hoffmann-La Roche AG., Albert Selva-O’Callaghan: None declared, Elena Nikiphorou Speakers bureau: EN has received speaker honoraria/participated in advisory boards for Celltrion, Pfizer, Sanofi, Gilead, Galapagos, AbbVie, Lilly, Consultant of: EN has received speaker honoraria/participated in advisory boards for Celltrion, Pfizer, Sanofi, Gilead, Galapagos, AbbVie, Lilly, Grant/research support from: EN holds research grants from Pfizer and Lilly., Tulika Chatterjee: None declared, Ai Lyn Tan Speakers bureau: ALT has received honoraria for advisory boards and speaking for Abbvie, Gilead, Janssen, Lilly, Novartis, Pfizer, UCB., Consultant of: ALT has received honoraria for advisory boards and speaking for Abbvie, Gilead, Janssen, Lilly, Novartis, Pfizer, UCB., Arvind Nune: None declared, Lorenzo Cavagna: None declared, Miguel A Saavedra: None declared, Nelly Ziade Speakers bureau: NZ has received speaker fees, advisory board fees and research grants from Pfizer, Roche, Abbvie, Eli Lilly, NewBridge, Sanofi-Aventis, Boehringer Ingelheim, Janssen, Pierre Fabre; none is related to this manuscript, Consultant of: NZ has received speaker fees, advisory board fees and research grants from Pfizer, Roche, Abbvie, Eli Lilly, NewBridge, Sanofi-Aventis, Boehringer Ingelheim, Janssen, Pierre Fabre; none is related to this manuscript, Grant/research support from: NZ has received speaker fees, advisory board fees and research grants from Pfizer, Roche, Abbvie, Eli Lilly, NewBridge, Sanofi-Aventis, Boehringer Ingelheim, Janssen, Pierre Fabre; none is related to this manuscript, Johannes Knitza: None declared, Masataka Kuwana: None declared, Oliver Distler Speakers bureau: OD has/had consultancy relationship with and/or has received research funding from or has served as a speaker for the following companies in the area of potential treatments for systemic sclerosis and its complications in the last three years: Abbvie, Acceleron, Alcimed, Amgen, AnaMar, Arxx, Baecon, Blade, Bayer, Boehringer Ingelheim, ChemomAb, Corbus, CSL Behring, Galapagos, Glenmark, GSK, Horizon (Curzion), Inventiva, iQvia, Kymera, Lupin, Medac, Medscape, Mitsubishi Tanabe, Novartis, Roche, Roivant, Sanofi, Serodapharm, Topadur and UCB. Patent issued “mir-29 for the treatment of systemic sclerosis” (US8247389, EP2331143)., Consultant of: OD has/had consultancy relationship with and/or has received research funding from or has served as a speaker for the following companies in the area of potential treatments for systemic sclerosis and its complications in the last three years: Abbvie, Acceleron, Alcimed, Amgen, AnaMar, Arxx, Baecon, Blade, Bayer, Boehringer Ingelheim, ChemomAb, Corbus, CSL Behring, Galapagos, Glenmark, GSK, Horizon (Curzion), Inventiva, iQvia, Kymera, Lupin, Medac, Medscape, Mitsubishi Tanabe, Novartis, Roche, Roivant, Sanofi, Serodapharm, Topadur and UCB. Patent issued “mir-29 for the treatment of systemic sclerosis” (US8247389, EP2331143)., Grant/research support from: OD has/had consultancy relationship with and/or has received research funding from or has served as a speaker for the following companies in the area of potential treatments for systemic sclerosis and its complications in the last three years: Abbvie, Acceleron, Alcimed, Amgen, AnaMar, Arxx, Baecon, Blade, Bayer, Boehringer Ingelheim, ChemomAb, Corbus, CSL Behring, Galapagos, Glenmark, GSK, Horizon (Curzion), Inventiva, iQvia, Kymera, Lupin, Medac, Medscape, Mitsubishi Tanabe, Novartis, Roche, Roivant, Sanofi, Serodapharm, Topadur and UCB. Patent issued “mir-29 for the treatment of systemic sclerosis” (US8247389, EP2331143)., Hector Chinoy Speakers bureau: HC has been a speaker for UCB, Biogen., Consultant of: HC has received consulting fees from Novartis, Eli Lilly, Orphazyme, Astra Zeneca, Grant/research support from: HC has received grant support from Eli Lilly and UCB, Vikas Agarwal: None declared, Rohit Aggarwal Consultant of: RA has/had a consultancy relationship with and/or has received research funding from the following companies-Bristol Myers-Squibb, Pfizer, Genentech, Octapharma, CSL Behring, Mallinckrodt, AstraZeneca, Corbus, Kezar, and Abbvie, Janssen, Alexion, Argenx, Q32, EMD-Serono, Boehringer Ingelheim, Roivant., Grant/research support from: RA has/had a consultancy relationship with and/or has received research funding from the following companies-Bristol Myers-Squibb, Pfizer, Genentech, Octapharma, CSL Behring, Mallinckrodt, AstraZeneca, Corbus, Kezar, and Abbvie, Janssen, Alexion, Argenx, Q32, EMD-Serono, Boehringer Ingelheim, Roivant.

OP0161 TREATMENT PATTERNS OF IDIOPATHIC INFLAMMATORY MYOPATHIES: RESULTS FROM AN INTERNATIONAL COHORT OF OVER 1,400 PATIENTS

Background

Idiopathic inflammatory myopathies (IIM) are a group of heterogeneous autoimmune disorders with limited standardization of treatment protocols.

Objectives

To evaluate frequency and patterns of various treatments used for IIM based on disease subtype, world region, and organ involvement.

Methods

Cross-sectional data from the international CoVAD self-report e-survey1 was extracted on Sep 14th, 2021. Patient details included demographics, IIM subtypes (dermatomyositis (DM), polymyositis (PM), inclusion body myositis (IBM), antisynthetase syndrome (ASSD), necrotizing myositis (NM) and overlap myositis (OM)), clinical symptoms, disease duration and activity, and current treatments. Treatments were categorized in corticosteroids (CS), antimalarials, immunosuppressants (IS), intravenous immunoglobulins (IVIG), biologics, and others. Typical clinical symptoms (dyspnea, dysphagia) were used as surrogate for organ involvement. Factors associated with IS were analyzed using multivariable logistic regression, adjusting for IIM subtype, demographics, world region, disease activity, and prevalent clinical symptoms (>10%).

Results

In 1418 patients with IIM, median age was 61 years [IQR 49-70], 62.5% were females, median disease duration was 6 years [IQR 3-11], most common subset was DM (32.4%).

The most used treatments were IS (49.4%, including Methotrexate 19.6%, Mycophenolate Mofetil 18.2%, Azathioprine 8.8%, Cyclosporine 2.7%, Tacrolimus 2%, Leflunomide 1.6%, Sulfasalazine 1%, and Cyclophosphamide 0.6%), followed by CS (40.8%), antimalarials (13.8%) and IVIG (9.4%). Biologics were used in 4.3% of patients.

Treatment patterns differed significantly by IIM subtypes with a higher frequency of IS (77.7%) and CS (63.4%) use in ASSD; antimalarials (28.6%) and biologics (9.8%) use in OM and IVIG use in NM (24.6%) (Table 1). Also, treatment patterns were different in regions of the world (Figure 1), with a higher frequency of CS use in Europe (60.5%) and IS use in South America (77.2%). Antimalarials were most used in Asia (19.4%), while IVIG use was most common in Oceania (16.9%). Dyspnea was associated with higher use of IS (69.9%) and CS (65.8%) (p<0.001), whereas dysphagia was negatively associated with IS (39.7%) and CS (32.7%) likely due to a higher proportion in IBM patients reporting dysphagia.

Table 1.

Current Treatments for IIM, Stratified by Disease Subtypes

DermatomyositisPolymyositisInclusion Body MyositisAnti-synthetase syndromeNecrotizing myositisOverlap syndromeAll IIMp-valueNumber of patients459182348148572241418Immunosuppressants*269 (58.6)107 (58.8)39 (11.2)115 (77.7)40 (70.2)130 (58.0)700 (49.4)<0.001Corticosteroids208 (48.0)81 (46.8)32 (9.7)90 (63.4)32 (59.3)103 (50.0)546 (40.8)<0.001Antimalarials99 (21.6)7 (3.8)0 (0.0)25 (16.9)1 (1.8)64 (28.6)196 (13.8)<0.001Intravenous Immunoglobulins54 (11.8)16 (8.8)19 (5.5)10 (6.8)14 (24.6)20 (8.9)133 (9.4)<0.001Biologics**17 (3.7)7 (3.8)0 (0.0)13 (8.8)2 (3.5)22 (9.8)61 (4.3)<0.001Others***6 (1.3)0 (0.0)0 (0.0)1 (0.7)0 (0.0)5 (2,2)12 (0.8)0.098

*Methotrexate (278), Mycophenolate Mofetil (258), Azathioprine (125), Cyclosporine (38), Tacrolimus (28), Leflunomide (23), Sulfasalazine (14), Cyclophosphamide (9)

. **Rituximab (44), Abatacept (5), TNF inhibitors (4), Tocilizumab (3), Belimumab (3), Secukinumab (1)

. ***JAK(10) and PDE4 inhibitors (2)

Multivariable logistic regression analysis showed an association of IS with the IIM subtype (least used in IBM (OR 0.07 [95%CI 0.04-0.13] compared to DM), world region (most used in South America (OR 2.35 [1.12-4.91] compared to North America), active and worsening disease activity (OR 3.49 [1.76-6.91] compared to remission), and some clinical features (dyspnea, fatigue, and muscle weakness).

Conclusion

IIM treatment patterns differ significantly by disease subtypes, world regions and organ involvement, highlighting the need for unified international consensus-driven guidelines.

References

[1]Parikshit S. et al. Rheumatol Int. 2022 Jan;42(1):23–9.

Disclosure of Interests

None declared

Genome-wide association studies for agronomical traits in winter rice accessions of Assam

The 297 winter rice accessions of Assam, North East India were genotyped by sequencing (GBS). The 50,985 high-quality SNPs were filtered and assigned to 12 rice chromosomes. The population structure analysis revealed three major subgroups SG1, SG2, and SG3 consisting of 30, 8, and 143 accessions respectively. The remaining 116 accessions were grouped as admixture population. Phenotypic data were recorded on13 agronomical traits for genome-wide association studies (GWAS). The 60 significant marker-trait associations (MTAs) were identified for 11 agronomical traits, which explained 0 to 15% of phenotypic variance (PV). A QTL 'hot spot' was detected near the centromeric region on chromosome 6. The identified QTLs may be validated and utilized in 'genomics assisted breeding' for improvement of existing rice cultivars of Assam and North East India.

Alcohol functionality in the fatty acid backbone of sphingomyelin guides the inhibition of blood coagulation

Cell-surface sphingomyelin (SM) inhibits binary and ternary complex activity of blood coagulation by an unknown mechanism. Here we show the OH functionality of SM contributes in forming the close assembly through intermolecular H-bond and through Ca²⁺ chelation, which restricts the protein–lipid/protein–protein interactions and thus inhibits the coagulation procedure.

Cell-surface sphingomyelin (SM) inhibits binary and ternary complex activity of blood coagulation.

Utilization of absolute monocyte counts to predict cardiovascular events in people living with HIV

OBJECTIVES

Cardiovascular risk is increased in people living with HIV (PLWH). In HIV-uninfected populations, total absolute monocyte count (AMC) has been shown to be predictive of future cardiovascular events (CVEs). We sought to determine whether AMC predicts CVEs in PLWH independent of established and HIV-related cardiovascular risk factors.

METHODS

We identified all PLWH within the Partners HIV Cohort without factors that could confound the monocyte count. CVE was defined as fatal or non-fatal acute myocardial infarction or ischaemic stroke. Baseline-measured AMC was defined as the average of all outpatient AMC counts a year before and after the baseline date. Multivariable Cox proportional hazards models were used to assess the association of baseline AMC with CVEs.

RESULTS

Our cohort consisted of 1980 patients, with median follow-up of 10.9 years and 182 CVEs. Mean (± SD) age was 41.9 ± 9.3 years; 73.0% were male. Mean CD4 count was 506.3 ± 307.1 cells/µL, 48% had HIV viral load (VL) < 400 copies/mL, and 87% were on antiretroviral therapy. Mean AMC was 0.38 × 10³  ± 0.13 cells/µL. In multivariable modelling adjusted for traditional CV risk factors, CD4 cell count, and HIV VL, AMC quartile 2 (Q2) (HR = 1.01, P = 0.98), Q3 (HR = 1.07, P = 0.76), and Q4 (HR = 0.97, P = 0.89) were not significantly predictive of CVE compared with Q1.

DISCUSSION

Baseline AMC was not associated with long-term CVEs in PLWH. AMC obtained in routine clinical encounters does not appear to enhance CV risk stratification in PLWH.

Perioperative intravenous contrast administration and the incidence of acute kidney injury after major gastrointestinal surgery: prospective, multicentre cohort study

BACKGROUND

This study aimed to determine the impact of preoperative exposure to intravenous contrast for CT and the risk of developing postoperative acute kidney injury (AKI) in patients undergoing major gastrointestinal surgery.

METHODS

This prospective, multicentre cohort study included adults undergoing gastrointestinal resection, stoma reversal or liver resection. Both elective and emergency procedures were included. Preoperative exposure to intravenous contrast was defined as exposure to contrast administered for the purposes of CT up to 7 days before surgery. The primary endpoint was the rate of AKI within 7 days. Propensity score-matched models were adjusted for patient, disease and operative variables. In a sensitivity analysis, a propensity score-matched model explored the association between preoperative exposure to contrast and AKI in the first 48 h after surgery.

RESULTS

A total of 5378 patients were included across 173 centres. Overall, 1249 patients (23·2 per cent) received intravenous contrast. The overall rate of AKI within 7 days of surgery was 13·4 per cent (718 of 5378). In the propensity score-matched model, preoperative exposure to contrast was not associated with AKI within 7 days (odds ratio (OR) 0·95, 95 per cent c.i. 0·73 to 1·21; P = 0·669). The sensitivity analysis showed no association between preoperative contrast administration and AKI within 48 h after operation (OR 1·09, 0·84 to 1·41; P = 0·498).

CONCLUSION

There was no association between preoperative intravenous contrast administered for CT up to 7 days before surgery and postoperative AKI. Risk of contrast-induced nephropathy should not be used as a reason to avoid contrast-enhanced CT.

Genome-wide association studies using 50 K rice genic SNP chip unveil genetic architecture for anaerobic germination of deep-water rice population of Assam, India

North Eastern part of India such as Assam is inundated by flood every year where the farmers are forced to grow the traditional tall deep-water rice. Genetic improvement of this type of rice is slow because of insufficient knowledge about their genetic architecture and population structure. In the present investigation, the genetic diversity architecture of 94 deep-water rice genotypes of Assam and association mapping strategy was, for the first time, applied to determine the significant SNPs and genes for deep-water rice. These genotypes are known for their unique elongation ability under deep-water condition. The anaerobic germination (AG) related trait-associated genes identified here can provide affluent resources for rice breeding especially in flood-prone areas. We investigated the genome-wide association studies (GWAS) using 50 K rice genic SNP chip across 94 deep-water rice genotypes collected from different flood-prone districts/villages of Assam. Population structure and diversity analysis revealed that these genotypes were stratified into four sub-populations. Using GWAS approach, 20 significant genes were identified and found to be associated with AG-related traits. Of them, two most relevant genes (OsXDH1and SSXT) have been identified which explain phenotypic variability (R² > 20%) in the population. These genes were located in Chr 3 (LOC_Os03g31550) which encodes for enzyme xanthine dehydrogenase 1(OsXDH1) and in Chr 12 (LOC_Os12g31350) which encodes for SSXT family protein. Both of these genes were found to be associated with anaerobic response index (increase in the coleoptile length under water in anaerobic condition with respect to control), respectively. Interestingly, OsXDH1is involved in purine catabolism pathway and acts as a scavenger of reactive oxygen species in plants, whereas SSXT is GRF1-interacting factor 3. These two candidate genes associated with AG of deep-water rice have been found to be reported for the first time. Thus, this study provides a greater resource for breeders not only for improvement of deep-water rice, but also for AG tolerant variety useful for direct-seeded rice in flood-affected areas.

Kidney injury enhances renal G-CSF expression and modulates granulopoiesis and human neutrophil CD177 in vivo

Kidney injury significantly increases overall mortality. Neutrophilic granulocytes (neutrophils) are the most abundant human blood leukocytes. They are characterized by a high turnover rate, chiefly controlled by granulocyte colony stimulating factor (G‐CSF). The role of kidney injury and uremia in regulation of granulopoiesis has not been reported. Kidney transplantation, which inherently causes ischemia–reperfusion injury of the graft, elevated human neutrophil expression of the surface glycoprotein CD177. CD177 is among the most G‐CSF‐responsive neutrophil genes and reversibly increased on neutrophils of healthy donors who received recombinant G‐CSF. In kidney graft recipients, a transient rise in neutrophil CD177 correlated with renal tubular epithelial G‐CSF expression. In contrast, CD177 was unaltered in patients with chronic renal impairment and independent of renal replacement therapy. Under controlled conditions of experimental ischemia–reperfusion and unilateral ureteral obstruction injuries in mice, renal G‐CSF mRNA and protein expression significantly increased and systemic neutrophilia developed. Human renal tubular epithelial cell G‐CSF expression was promoted by hypoxia and proinflammatory cytokine interleukin 17A in vitro. Clinically, recipients of ABO blood group‐incompatible kidney grafts developed a larger rise in neutrophil CD177. Their grafts are characterized by complement C4d deposition on the renal endothelium, even in the absence of rejection. Indeed, complement activation, but not hypoxia, induced primary human endothelial cell G‐CSF expression. Our data demonstrate that kidney injury induces renal G‐CSF expression and modulates granulopoiesis. They delineate differential G‐CSF regulation in renal epithelium and endothelium. Altered granulopoiesis may contribute to the systemic impact of kidney injury.

Revealing shared differential co-expression profiles in rice infected by virus from reoviridae and sequiviridae group

Differential co-expression is a cutting-edge approach to analyze gene expression data and identify both shared and divergent expression patterns. The availability of high-throughput gene expression datasets and efficient computational approaches have unfolded the opportunity to a systems level understanding of functional genomics of different stresses with respect to plants. We performed the meta-analysis of the available microarray data for reoviridae and sequiviridae infection in rice with the aim to identify the shared gene co-expression profile. The microarray data were downloaded from ArrayExpress and analyzed through a modified Weighted Gene Co-expression Network Analysis (WGCNA) protocol. WGCNA clustered the genes based on the expression intensities across the samples followed by identification of modules, eigengenes, principal components, topology overlap, module membership and module preservation. The module preservation analysis identified 4 modules; salmon (638 genes), midnightblue (584 genes), lightcyan (686 genes) and red (562 genes), which are highly preserved in both the cases. The networks in case of reoviridae infection showed neatly packed clusters whereas, in sequiviridae, the clusters were loosely connected which is due to the differences in the correlation values. We also identified 83 common transcription factors targeting the hub genes from all the identified modules. This study provides a coherent view of the comparative aspect of the expression of common genes involved in different virus infections which may aid in the identification of novel targets and development of new intervention strategy against the virus.

Gold Nanoparticle-Based Detection of Low Molecular Weight AGEs from In Vitro Glycated Haemoglobin A0 Samples

Protein glycation is a major biochemical event that takes place in the plasma of diabetic patients due to increased sugar levels. Extensive glycation leads to the formation of advanced glycation end products (AGEs) that is well known for having detrimental effects on diabetic patients. In the current work, we have glycated the physiologically important protein Haemoglobin A0 in vitro to study AGE formation and activity by using them as a template for gold nanoparticle (GNPs) synthesis. It was found that the surface plasmon resonance of synthesised GNPs showed high correlation with the extent of glycation. On fractionation, the glycated Haemoglobin A0 segregated into two distinct population of products, one consisting of proteinaceous, cross-linked larger fragments of Haemoglobin A0 and a second population of non-proteinaceous low molecular weight AGEs. Only low molecular weight AGEs contributed to synthesis of GNPs upon using the fractions as a template, substantiating the principle of proposed GNP-based assay. Owing to its physiological importance, AGEs can be used as a diagnostic means for diabetes and its associated complications. In this study, we have employed the high reactivity of AGEs for the development of a GNP-based novel colorimetric sensor to enable their detection. Our proposed GNP-based sensing could have high clinical significance in detecting diabetes and its associated complexities.

Bruchid egg induced transcript dynamics in developing seeds of black gram (Vigna mungo)

Black gram (Vigna mungo) seeds are a rich source of digestible proteins, however, during storage these seeds are severely damaged by bruchids (Callosobruchus spp.), reducing seed quality and yield losses. Most of the cultivated genotypes of black gram are susceptible to bruchids, however, few tolerant genotypes have also been identified but the mechanism of tolerance is poorly understood. We employed Suppression Subtractive Hybridization (SSH) to identify specifically, but rarely expressed bruchid egg induced genes in black gram. In this study, Suppression Subtractive Hybridization (SSH) library was constructed to study the genes involved in defense response in black gram against bruchid infestation. An EST library of 277 clones was obtained for further analyses. Based on CAP3 assembly, 134 unigenes were computationally annotated using Blast2GOPRO software. In all, 20 defense related genes were subject to quantitative PCR analysis (qPCR) out of which 12 genes showed up-regulation in developing seeds of the pods oviposited by bruchids. Few major defense genes like defensin, pathogenesis related protein (PR), lipoxygenase (LOX) showed high expression levels in the oviposited population when compared with the non-oviposited plants. This is the first report on defense related gene transcript dynamics during the bruchid-black gram interaction using SSH library. This library would be useful to clone defense related gene(s) such as defensin as represented in our library for crop improvement.

An Insight Into Structure, Function, and Expression Analysis of 3-Hydroxy-3-Methylglutaryl-CoA Reductase of Cymbopogon winterianus

Citronella (Cymbopogon winterianus) is one of the richest sources of high-value isoprenoid aromatic compounds used as flavour, fragrance, and therapeutic elements. These isoprenoid compounds are synthesized by 2 independent pathways: mevalonate pathway and 2-C-methyl-d-erythritol-4-phosphate pathway. Evidence suggests that 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) is a rate-controlling enzyme for the synthesis of variety of isoprenoids. This study reports the isolation, characterization, and tissue-specific expression analysis of HMGR from citronella. The modelled HMGR is a class I type of HMGR enzyme with 3-domain architecture. The active site comprises a cofactor (nicotinamide adenine dinucleotide phosphate) and the substrate-binding motifs. The real-time and quantitative reverse transcription-polymerase chain reaction results revealed equal expression level in both leaf sheath and root tissue. The results from our study shall be a valuable resource for future molecular intervention to alter the metabolic flux towards improvement of key active ingredient in this important medicinal plant.

Intrinsic coincident linear polarimetry using stacked organic photovoltaics

Polarimetry has widespread applications within atmospheric sensing, telecommunications, biomedical imaging, and target detection. Several existing methods of imaging polarimetry trade off the sensor's spatial resolution for polarimetric resolution, and often have some form of spatial registration error. To mitigate these issues, we have developed a system using oriented polymer-based organic photovoltaics (OPVs) that can preferentially absorb linearly polarized light. Additionally, the OPV cells can be made semitransparent, enabling multiple detectors to be cascaded along the same optical axis. Since each device performs a partial polarization measurement of the same incident beam, high temporal resolution is maintained with the potential for inherent spatial registration. In this paper, a Mueller matrix model of the stacked OPV design is provided. Based on this model, a calibration technique is developed and presented. This calibration technique and model are validated with experimental data, taken with a cascaded three cell OPV Stokes polarimeter, capable of measuring incident linear polarization states. Our results indicate polarization measurement error of 1.2% RMS and an average absolute radiometric accuracy of 2.2% for the demonstrated polarimeter.

Next-generation sequencing confirms the implication of SLC24A1 in autosomal-recessive congenital stationary night blindness

Congenital stationary night blindness (CSNB) is a clinically and genetically heterogeneous retinal disorder which represents rod photoreceptor dysfunction or signal transmission defect from photoreceptors to adjacent bipolar cells. Patients displaying photoreceptor dysfunction show a Riggs-electroretinogram (ERG) while patients with a signal transmission defect show a Schubert-Bornschein ERG. The latter group is subdivided into complete or incomplete (ic) CSNB. Only few CSNB cases with Riggs-ERG and only one family with a disease-causing variant in SLC24A1 have been reported. Whole-exome sequencing (WES) in a previously diagnosed icCSNB patient identified a homozygous nonsense variant in SLC24A1. Indeed, re-investigation of the clinical data corrected the diagnosis to Riggs-form of CSNB. Targeted next-generation sequencing (NGS) identified compound heterozygous deletions and a homozygous missense variant in SLC24A1 in two other patients, respectively. ERG abnormalities varied in these three cases but all patients had normal visual acuity, no myopia or nystagmus, unlike in Schubert-Bornschein-type of CSNB. This confirms that SLC24A1 defects lead to CSNB and outlines phenotype/genotype correlations in CSNB subtypes. In case of unclear clinical characteristics, NGS techniques are helpful to clarify the diagnosis.

A rare case of a myofibroma presenting on the tongue

Myofibromas are benign neoplasms of myofibroblastic origin, rarely encountered in the oral cavity. Limited awareness of the clinical features of these lesions risks misdiagnosis of more sinister pathology. The objective of this report is to highlight the potential diversity of oral lesions by describing an uncommon presentation of a myofibroma. The case reveals the diagnostic difficulties encountered, along with postoperative complications, which exemplify the remarkable healing capacity of the oral cavity.

Molecular recognition of avirulence protein (avrxa5) by eukaryotic transcription factor xa5 of rice (Oryza sativa L.): insights from molecular dynamics simulations

The avirulence gene avrxa5 of bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) recognized by the resistant rice lines having corresponding resistance (xa5) gene in a gene-for-gene manner. We used a combinatorial approach involving protein-protein docking, molecular dynamics (MD) simulations and binding free energy calculations to gain novel insights into the gene-for-gene mechanism that governs the direct interaction of R-Avr protein. From the best three binding poses predicted by molecular docking, MD simulations were performed to explore the dynamic binding mechanism of xa5 and avrxa5. Molecular Mechanics/Poisson Boltzmann Surface Area (MM/PBSA) techniques were employed to calculate the binding free energy and to uncover the thriving force behind the molecular recognition of avrxa5 by eukaryotic transcription factor xa5. Binding free energy analysis revealed van der Waals term as the most constructive component that favors the xa5 and avrxa5 interaction. In addition, hydrogen bonds (H-bonds) and essential electrostatic interactions analysis highlighted amino acid residues Lys54/Asp870, Lys56/Ala868, Lys56/Ala866, Lys56/Glu871, Ile59/His862, Gly61/Phe858, His62/Arg841, His62/Leu856, Ser101/Ala872 and Ser105/Asp870 plays pivotal role for the energetically stability of the R-Avr complex. Insights gained from the present study are expected to unveil the molecular mechanisms that define the transcriptional activator mediated transcriptome modification in host plants.

Rediscovering medicinal plants' potential with OMICS: microsatellite survey in expressed sequence tags of eleven traditional plants with potent antidiabetic properties

Herbal medicines and traditionally used medicinal plants present an untapped potential for novel molecular target discovery using systems science and OMICS biotechnology driven strategies. Since up to 40% of the world's poor people have no access to government health services, traditional and folk medicines are often the only therapeutics available to them. In this vein, North East (NE) India is recognized for its rich bioresources. As part of the Indo-Burma hotspot, it is regarded as an epicenter of biodiversity for several plants having myriad traditional uses, including medicinal use. However, the improvement of these valuable bioresources through molecular breeding strategies, for example, using genic microsatellites or Simple Sequence Repeats (SSRs) or Expressed Sequence Tags (ESTs)-derived SSRs has not been fully utilized in large scale to date. In this study, we identified a total of 47,700 microsatellites from 109,609 ESTs of 11 medicinal plants (pineapple, papaya, noyontara, bitter orange, bermuda brass, ratalu, barbados nut, mango, mulberry, lotus, and guduchi) having proven antidiabetic properties. A total of 58,159 primer pairs were designed for the non-redundant 8060 SSR-positive ESTs and putative functions were assigned to 4483 unique contigs. Among the identified microsatellites, excluding mononucleotide repeats, di-/trinucleotides are predominant, among which repeat motifs of AG/CT and AAG/CTT were most abundant. Similarity search of SSR containing ESTs and antidiabetic gene sequences revealed 11 microsatellites linked to antidiabetic genes in five plants. GO term enrichment analysis revealed a total of 80 enriched GO terms widely distributed in 53 biological processes, 17 molecular functions, and 10 cellular components associated with the 11 markers. The present study therefore provides concrete insights into the frequency and distribution of SSRs in important medicinal resources. The microsatellite markers reported here markedly add to the genetic stock for cross transferability in these plants and the literature on biomarkers and novel drug discovery for common chronic diseases such as diabetes.

Mutation spectrum in BBS genes guided by homozygosity mapping in an Indian cohort

Bardet-Biedl syndrome (BBS), a ciliopathy disorder with pleiotropic effect manifests primarily as retinal degeneration along with renal insufficiency, polydactyly and obesity. In this study, we have performed homozygosity mapping using NspI 250K affymetrix gene chip followed by mutation screening of the candidate genes located in the homozygous blocks. These regions are prioritized based on the block length and candidature of the genes in BBS and other ciliopathies. Gene alterations in known BBS (22) and other ciliopathy genes such as ALMS1 (2) were seen in 24 of 30 families (80%). Mutations in BBS3 gene, inclusive of a novel recurrent mutation (p.I91T) accounted for 18% of the identified variations. Disease associated polymorphisms p.S70N (BBS2), rs1545 and rs1547 (BBS6) were also observed. This is the first study in Indian BBS patients and homozygosity mapping has proved to be an effective tool in prioritizing the candidate genes in consanguineous pedigrees. The study reveals a different mutation profile in the ciliopathy genes in Indian population and implication of novel loci/genes in 20% of the study group.

Computational identification and characterization of conserved miRNAs and their target genes in garlic (Allium sativum L.) expressed sequence tags

The endogenous small non-coding functional microRNAs (miRNAs) are short in size, range from ~21 to 24 nucleotides in length, play a pivotal role in gene expression in plants and animals by silencing genes either by destructing or blocking of translation of homologous mRNA. Although various high-throughput, time consuming and expensive techniques like forward genetics and direct cloning are employed to detect miRNAs in plants but comparative genomics complemented with novel bioinformatic tools pave the way for efficient and cost-effective identification of miRNAs through homologous sequence search with previously known miRNAs. In this study, an attempt was made to identify and characterize conserved miRNAs in garlic expressed sequence tags (ESTs) through computational means. For identification of novel miRNAs in garlic, a total 3227 known mature miRNAs of plant kingdom Viridiplantae were searched for homology against 21,637 EST sequences resulting in identification of 6 potential miRNA candidates belonging to 6 different miRNA families. The psRNATarget server predicted 33 potential target genes and their probable functions for the six identified miRNA families in garlic. Most of the garlic miRNA target genes seem to encode transcription factors as well as genes involved in stress response, metabolism, plant growth and development. The results from the present study will shed more light on the understanding of molecular mechanisms of miRNA in garlic which may aid in the development of novel and precise techniques to understand some post-transcriptional gene silencing mechanism in response to stress tolerance.

Insights into the structure-function relationship of disease resistance protein HCTR in maize (Zea mays L.): a computational structural biology approach

The disease resistance gene Hm1 of maize encodes a NADPH-dependent reductase enzyme, HC-toxin reductase (HCTR) that detoxifies the HC toxin secreted by the race specific fungus Cochliobolus carbonum race 1. HCTR enzyme shares 29.6% sequence identity with dihydroflavonol reductase (DFR) of grape, a key enzyme involved in flavonoid biosynthesis. Here we report the comparative modelling, molecular dynamics simulation and docking studies to explain the structure-function relationship and the mode of cofactor (NADPH) binding in HCTR enzyme at the molecular level. The nucleotide binding domain of modelled HCTR adopts a classic Rossmann fold and possesses a consensus glycine rich GxGxxG motif. Molecular simulation studies suggested that HCTR model retained stability throughout the simulation in aqueous solution. HCTR model showed considerable structural identities with the cofactor binding site of DFR, but significant difference in the catalytic site might be the reason of functional divergence between these families of proteins. Similarly electrostatic surface potential analysis of both HCTR and DFR revealed profound variations in the charge distribution over the substrate binding site, which can be correlated with the sequence variability and may suggest distinct substrate-binding patterns and differences in the catalytic mechanism. Docking results indicated Phe19, Gly21, Arg40, Thr90, Gly208, Arg218, Glu221 and Thr222 are important residues for cofactor (NADPH) binding through strong hydrogen bonding and electrostatic interactions. Alanine scanning and analysis of docking energies of mutant proteins suggested that Phe19, and Arg40 are two critical residues for the cofactor binding. The result from the present study is expected to pave the way for exploration of similar genes in other economically important crop varieties.

Polarization sensitive optical low-coherence reflectometry for blood glucose monitoring in human subjects

A device based on polarization sensitive optical low-coherence reflectometry is developed to monitor blood glucose levels in human subjects. The device was initially tested with tissue phantom. The measurements with human subjects for various glucose concentration levels are found to be linearly dependent on the ellipticity obtainable from the home-made phase-sensitive optical low-coherence reflectometry device. The linearity obtained between glucose concentration and ellipticity are explained with theoretical calculations using Mie theory. A comparison of results with standard clinical methods establishes the utility of the present device for non-invasive glucose monitoring.

Molecular phylogeny, homology modeling, and molecular dynamics simulation of race-specific bacterial blight disease resistance protein (xa5) of rice: a comparative agriproteomics approach

Rice (Oryza sativa L.), a model plant belonging to the family Poaceae, is a staple food for a majority of the people worldwide. Grown in the tropical and subtropical regions of the world, this important cereal crop is under constant and serious threat from both biotic and abiotic stresses. Among the biotic threats, Xanthomonas oryzae pv. oryzae, causing the damaging bacterial blight disease in rice, is a prominent pathogen. The xa5 gene in the host plant rice confers race-specific resistance to this pathogen. This recessive gene belongs to the Xa gene family of rice and encodes a gamma subunit of transcription factor IIA (TFIIAγ). In view of the importance of this gene in conferring resistance to the devastating disease, we reconstructed the phylogenetic relationship of this gene, developed a three-dimensional protein model, followed by long-term molecular dynamics simulation studies to gain a better understanding of the evolution, structure, and function of xa5. The modeled structure was found to fit well with the small subunit of TFIIA from human, suggesting that it may also act as a small subunit of TFIIA in rice. The model had a stable conformation in response to the atomic flexibility and interaction, when subjected to MD simulation at 20 nano second in aqueous solution. Further structural analysis of xa5 indicated that the protein retained its basic transcription factor function, suggesting that it might govern a novel pathway responsible for bacterial blight resistance. Future molecular docking studies of xa5 underway with its corresponding avirulence gene is expected to shed more direct light into plant-pathogen interactions at the molecular level and thus pave the way for richer agriproteomic insights.

In silico identification and characterization of conserved miRNAs and their target genes in sweet potato (Ipomoea batatas L.) expressed sequence tags (ESTs)

The endogenous small non-coding micro RNAs (miRNAs), which are typically ~21-24 nt nucleotides, play a crucial role in regulating the intrinsic normal growth of cells and development of the plants as well as in maintaining the integrity of genomes. These small non-coding RNAs function as the universal specificity factors in post-transcriptional gene silencing. Discovering miRNAs, identifying their targets, and further inferring miRNA functions is a routine process to understand normal biological processes of miRNAs and their roles in the development of plants. Comparative genomics based approach using expressed sequence tags (EST) and genome survey sequences (GSS) offer a cost-effective platform for identification and characterization of miRNAs and their target genes in plants. Despite the fact that sweet potato (Ipomoea batatas L.) is an important staple food source for poor small farmers throughout the world, the role of miRNA in various developmental processes remains largely unknown. In this paper, we report the computational identification of miRNAs and their target genes in sweet potato from their ESTs. Using comparative genomics-based approach, 8 potential miRNA candidates belonging to miR168, miR2911, and miR156 families were identified from 23 406 ESTs in sweet potato. A total of 42 target genes were predicted and their probable functions were illustrated. Most of the newly identified miRNAs target transcription factors as well as genes involved in plant growth and development, signal transduction, metabolism, defense, and stress response. The identification of miRNAs and their targets is expected to accelerate the pace of miRNA discovery, leading to an improved understanding of the role of miRNA in development and physiology of sweet potato, as well as stress response.

Construction of cDNA library and preliminary analysis of expressed sequence tags from tea plant [Camellia sinensis (L) O. Kuntze]

Tea is the most popular non-alcoholic and healthy beverage across the world. The understanding of the genetic organization and molecular biology of tea plant, which is very poorly understood at present, is required for quantum increase in productivity and efficient use of germplasm for either cultivation or breeding program. Single-pass sequencing of randomly selected cDNA clones is the most widely accepted technique for gene identification and cloning. In the present study, a good quality cDNA library was constructed and preliminary analysis of ESTs was carried out. The titers of unamplified and amplified libraries were 1.4 × 10(6)pfu/ml and 5.27 × 10(8)pfu/ml respectively. A total of 210 cDNA clones from the constructed cDNA library were sequenced and analyzed. A total of 84 high quality Expressed Sequence Tags (ESTs) were generated, among which 71 ESTs had significant homology with sequences in NCBI non-redundant protein database by BLAST X analysis. About 80% ESTs had poly (A) tail at 3' end indicating that the cDNAs were full length. The database-matched ESTs were classified into putative cellular roles, viz. energy-related category (corresponding to 20% of total BLAST X matched ESTs), Transcription (14.2%), protein synthesis (14.2%) cell growth and division (8.6%), cell structure (5.7%), signal transduction (5.7%), transporters (2.9%), disease and defenses (2.9%), secondary metabolism (2.9%) and gene regulation (2.9%). This study provides an overview of the mRNA expression profile and first hand information of gene sequence expressed in tender leaves and apical buds of tea plant.

Arsenic(III) sorption on nanostructured cerium incorporated manganese oxide (NCMO): a physical insight into the mechanistic pathway

Arsenic(III) sorption was investigated with nanostructured cerium incorporated manganese oxide (NCMO). The pH between 6.0 and 8.0 was optimized for the arsenic(III) sorption. Kinetics and equilibrium data (pH=7.0±0.2, T=303±1.6 K, and I=0.01 M) of arsenic(III) sorption by NCMO described, respectively, the pseudo-second order and the Freundlich isotherm equations well. The sorption process was somewhat complicated in nature and divided into two different segments, initially very fast sorption followed by slow intraparticle diffusion process. Sorption reaction of arsenic(III) on NCMO was endothermic (ΔH°=+13.46 kJ mol(-1)) and spontaneous (ΔG°=-24.75 to -30.15 kJ mol(-1) at T=283-323 K), which took place with increasing entropy (ΔS°=+0.14 kJ mol(-1)K(-1)) at solid-liquid interface. Energy of arsenic(III) sorption estimated by analyzing the equilibrium data using the D-R isotherm model was 15.4 kJ mol(-1), indicating the ion-exchange type mechanism. Raman, FT-IR, pH effect, desorption, etc. studies indicated that arsenic(III) was oxidized to arsenic(V) during the sorption process.

Mining for SSRs and FDMs from expressed sequence tags of Camellia sinensis

Simple Sequence Repeats (SSRs) developed from Expressed Sequence Tags (ESTs), known as EST-SSRs are most widely used and potentially valuable source of gene based markers for their high levels of crosstaxon portability, rapid and less expensive development. The EST sequence information in the publicly available databases is increasing in a faster rate. The emerging computational approach provides a better alternative process of development of SSR markers from the ESTs than the conventional methods. In the present study, 12,851 EST sequences of Camellia sinensis, downloaded from National Center for Biotechnology Information (NCBI) were mined for the development of Microsatellites. 6148 (4779 singletons and 1369 contigs) non redundant EST sequences were found after preprocessing and assembly of these sequences using various computational tools. Out of total 3822.68 kb sequence examined, 1636 (26.61%) EST sequences containing 2371 SSRs were detected with a density of 1 SSR/1.61 kb leading to development of 245 primer pairs. These mined EST-SSR markers will help further in the study of variability, mapping, evolutionary relationship in Camellia sinensis. In addition, these developed SSRs can also be applied for various studies across species.

An approach to delineate primers for a group of poorly conserved sequences incorporating the common motif region

Glutathione synthetase (gshB) has previously been reported to confer tolerance to acidic soil condition in Rhizobium species. Cloning the gene coding for this enzyme necessitates the designing of proper primer sets which in turn depends on the identification of high quality sequence similarity in multiple global alignments. In this experiment, a group of homologous gene sequences related to gshB gene (accession no: gi-86355669:327589-328536) of Rhizobium etli CFN 42, were extracted from NCBI nucleotide sequence databases using BLASTN and were analyzed for designing degenerate primers. However, the T-coffee multiple global alignment results did not show any block of conserved region for the above sequence set to design the primers. Therefore, we attempted to identify the location of common motif region based on multiple local alignments employing the MEME algorithm supported with MAST and Primer3. The results revealed some common motif regions that enabled us to design the primer sets for related gshB gene sequences. The result will be validated in wet lab.

ESMP: A high-throughput computational pipeline for mining SSR markers from ESTs

With the advent of high-throughput sequencing technology, sequences from many genomes are being deposited to public databases at a brisk rate. Open access to large amount of expressed sequence tag (EST) data in the public databases has provided a powerful platform for simple sequence repeat (SSR) development in species where sequence information is not available. SSRs are markers of choice for their high reproducibility, abundant polymorphism and high inter-specific transferability. The mining of SSRs from ESTs requires different high-throughput computational tools that need to be executed individually which are computationally intensive and time consuming. To reduce the time lag and to streamline the cumbersome process of SSR mining from ESTs, we have developed a user-friendly, web-based EST-SSR pipeline "EST-SSR-MARKER PIPELINE (ESMP)". This pipeline integrates EST pre-processing, clustering, assembly and subsequently mining of SSRs from assembled EST sequences. The mining of SSRs from ESTs provides valuable information on the abundance of SSRs in ESTs and will facilitate the development of markers for genetic analysis and related applications such as marker-assisted breeding.

AVAILABILITY

The database is available for free at http://bioinfo.aau.ac.in/ESMP.

Towards an efficient computational mining approach to identify EST-SSR markers

Microsatellites are the markers of choice due to their high abundance reproducibility, degree of polymorphism and co-dominant nature. These are mainly used for studying the genetic variability in different species and Marker assisted selection. Expressed Sequence Tags (ESTs) serve as the main resource for Simple Sequence Repeats (SSRs). The computational approach for detecting SSRs and developing SSR markers from EST-SSRs is preferred over the conventional methods as it reduces time and cost to a great extent. The available EST sequence databases, various web interfaces and standalone tools provide the platform for an easy analysis of the EST sequences leading to the development of potential EST-SSR Markers. This paper is an overview of in silico approach to develop SSR Markers from the EST sequence using some of the most efficient tools that are available freely for academic purpose.

Patients' perception of health services for sexually transmitted infections in Singapore

INTRODUCTION

The Department of Sexually Transmitted Infections (STI) Control (DSC) Clinic is the only public STI clinic in Singapore. This study aimed to determine patients' perception of the clinic as well as the factors that may influence their choice of DSC Clinic over other medical facilities. The concerns of certain risk groups were also assessed.

METHODS

Self-administered anonymous questionnaires were offered to Singaporeans and Permanent Residents over 18 years of age who were seeking treatment at the DSC Clinic. 1,000 responses were collected over a period of four weeks in May 2009.

RESULTS

More than two-thirds of the patients had a positive experience at the DSC Clinic and would recommend the clinic to their family and friends. Positive attributes included competence of staff and the convenience of a one-stop treatment facility. The patients' visits to the DSC Clinic also prompted them to engage in safer sexual practices. Stigma was surprisingly not an issue among more than three-quarters of the patients. Confidentiality of medical records was a major concern, with more than half of the patients unwilling to share their records with other healthcare providers, employers or insurance companies. The majority of patients would like to see the provision of clinics catering to special groups such as young people, women as well as men-who-have-sex-with-men.

CONCLUSION

The majority of patients were satisfied with the health services provided at the DSC Clinic. Confidentiality in consultation was of prime importance to patients.

Tumour-like presentations of anogenital herpes simplex in HIV-positive patients

Genital and perianal ulcers seen in patients with HIV are commonly due to herpes simplex virus (HSV) infection. While it is well known that the characteristic presentation of HSV is a vesicular rash or crops of erosions, the clinical presentation of genital HSV infection in HIV is varied and can assume vegetative, hypertrophic, condyloma-like, nodular, ulcerative and tumour-like nodules or plaques. These unusual presentations often lead to a delayed diagnosis. We describe five immunocompromised HIV-positive patients with CD4 counts ranging from 114 to 326 cells/μL with unusual presentations of anogenital herpes.

Plasminogen activator inhibitor-1 inhibits factor VIIa bound to tissue factor

BACKGROUND AND OBJECTIVE

A growing body of experimental evidence supports broad inhibitory and regulatory activity of plasminogen activator inhibitor 1 (PAI-1). The present study was designed to investigate whether PAI-1 inhibits factor (F) VIIa complexed with tissue factor (TF), a well-known procoagulant risk factor.

METHODS AND RESULTS

The ability of PAI-1 to inhibit FVIIa-TF activity was evaluated in both clotting and factor X (FX) activation assays. PAI-1 and its complex with vitronectin inhibit: (i) clotting activity of FVIIa-TF (PAI-1(IC50) , 817 and 125 nm, respectively); (ii) FVIIa-TF-mediated FX activation (PAI-1(IC50) , 260 and 50 nm, respectively); and (iii) FVIIa bound to TF expressed on the surface of stimulated endothelial cells (PAI-1(IC50) , 260 and 120 nm, respectively). The association rate constant (k(a)) for PAI-1 inhibition of FVIIa-TF was determined using a chromogenic assay. K(a) for PAI-1 inhibition of FVIIa bound to relipidated TF is 3.3-fold higher than that for FVIIa bound to soluble TF (k(a) = 0.09 ± 0.01 and 0.027 ± 0.03 μm(-1) min(-1), respectively). Vitronectin increases k(a) for both soluble and relipidated TF by 3.5- and 30-fold, respectively (to 0.094 ± 0.020 and 2.7 ± 0.2 μm(-1) min(-1)). However, only a 3.5- to 5.0-fold increase in the acylated FVIIa was observed on SDS PAGE in the presence of vitronectin for both relipidated and soluble TF, indicating fast formation of PAI-1/vitronectin/FVIIa/relipidated TF non-covalent complex.

CONCLUSIONS

Our results demonstrate potential anticoagulant activity of PAI-1 in the presence of vitronectin, which could contribute to regulation of hemostasis under pathological conditions such as severe sepsis, acute lung injury and pleural injury, where PAI-1 and TF are overexpressed.