Expression of IFN-Gamma is significantly reduced during severity of covid-19 infection in hospitalized patients

Cytokines play an important role in SARS-CoV-2 infection progression and severity. A number of inflammatory cytokines have been directly associated with disease severity including IL-6 (interleukin-6), IL-10, TNF-α (tumor necrosis factor alpha), IFN-γ (interferon-gamma). Here, in this study, the aim was to better understand the interplay between host immune response mediated by cytokines and severity of SARS-CoV-2 infection by assessing cytokine expression. Therefore, we measured expression levels of a total of 12 genes (IFNA-1, IFN-γ, IL-1α, IL-1β, IL-4, IL-6, IL-7, IL-10, IL-11, IL-13, IL-15, and IL-27) encoding inflammatory, anti-inflammatory and regulatory cytokines using QRT-PCR in hospitalized patients with severe infection compared to mildly infected. IFN-γ was identified as a potent marker of disease severity as indicated previously. Moreover, levels of IL-7 were also found to be partially reduced in patients compared to the healthy controls and linked negatively to disease severity. Identification of these cytokines may be helpful in not only understanding disease pathogenesis but also in better management of the patients after covid infection.

Knowledge, Attitudes and Perceptions towards COVID-19 Vaccinations: A Cross-Sectional Survey in Pakistan

Background and Objectives: Several vaccines have been approved for the prevention of the coronavirus disease, discovered on 31 December in Wuhan, China. Pakistan procured vaccines from various countries. However, the lack of knowledge and reluctance of the general population to embrace the use of the vaccines are considered to be the major determinant of the slow vaccination rate. Hence, it is necessary to evaluate the willingness of the general population about their perception of the COVID-19 vaccination. Materials and Methods: A cross sectional survey based on a self-structured questionnaire comprising 18 questions was conducted (from 21 April-21 June) on 400 Pakistani participants to evaluate their knowledge, attitude, and perception towards the COVID-19 vaccination. Chi-square independent t-test and one-way Anova including a multiple step wise linear regression were used to draw conclusions about the results. p < 0.05 was considered significant. Results: A total of 400 participants responded in the knowledge, attitude, and perception (KAP) survey of which 46.5% were female and 53.5% were male. The mean age of participants was 36.08 years. This survey showed a poor knowledge (50.5%), a fair attitude (75.1%) and a poor perception (58.1%) towards the COVID-19 vaccination. Higher mean knowledge and attitude scores were reported in the age group 21-40, females, and unmarried urban citizens. Regression analysis showed that age, education, residence, and employment status influenced the knowledge and perception score to a considerable extent. Conclusions: The findings reflect an inadequate knowledge and perception on the one hand, but a better attitude towards the COVID-19 vaccination. This knowledge attitude and perception (KAP) survey will help in better understanding the opinion of the general population towards vaccination, and will be useful for policy makers and health care authorities aiming to increase the vaccination rate.

Study of HLA class II loci reveals DQB1*03:03:02 as a risk factor for asthma in a Pakistani population

Asthma, a chronic inflammatory disorder of the lungs and airways, typically results from a combination of multiple environmental and genetic factors. Human leucocyte antigen (HLA) region on chromosome 6p21 encodes the most highly polymorphic loci in the human genome, encoding genes with central roles in the immune function where HLA loci are strongly associated with various immune-mediated diseases such as autoimmunity, allergies and infection. The alleles of HLA class II genes such as DRB1 and DQB1 are the key genetic markers in the development of asthma and have been extensively studied in different ethnicities of the world population. However, the genetic screening of HLA class II alleles and haplotypes in Pakistani asthmatics has not been studied so far. The aim of the present study was to screen the HLA class II DRB1 and DQB1 alleles in asthma cases and controls in a Pakistani population. Seven hundred and two healthy controls and asthma patients were genotyped for HLA class II by sequence-specific polymerase chain reaction assays. The HLA-DRB1 and HLA-DQB1 allele and haplotype frequencies were calculated, and their risk or protective association with asthma was determined. Two-locus haplotypes of DRB1 and DQB1 alleles were imputed using Arlequin version 3.1 software. The signals of association with asthma were stronger at the DQB1 locus as compared to DRB1. HLA DQB1*03:03:02 (odds ratio [OR] = 2.42, 95% confidence interval [CI] = 1.34-4.25) was significantly associated with an increased risk of asthma, as was the haplotype comprised allele DRB1*07:01-DQB1*03:03:02 (OR = 2.40, 95% CI = 1.25-4.62). In contrast, DQB1*06 (OR = 0.39, 95% CI = 0.22-0.70) and DQB1*06:02 (OR = 0.27, 95% CI = 0.10-0.71) emerged as protective alleles for asthma. Our data concludes that the HLA DQB1*03:03:02 allele was a risk allele for asthma, whereas two DQB1 alleles, DQB1*06 and DQB1*06:02, were associated with asthma protection. Our findings highlight a prominent role for HLA-DQB1 alleles in asthma pathogenesis in studied Pakistani cases. More studies, especially with a larger study cohort are needed to confirm the utility of HLA DQB1*03:03:02 as a predictive marker.

Association of CYP2C19*2 and *17 genetic variants with hypertension in Pakistani population

Purpose: To investigate the association of *2 and *17 single nucleotide polymorphisms (SNPs) of CYP2C19 gene with hypertension in Pakistani population. Methods: The study was conducted on 527 hypertensive patients and 530 unrelated healthy controls from selected regions of Pakistan. DNA was extracted from leukocytes and all patients and controls were genotyped for two SNPs (rs4244285 and rs12248560) of CYP2C19 gene by allele specific polymerase chain reaction (AS-PCR). Results: Multi-allelic polymorphism in CYP2C19 identified four distinct phenotypes known as ultra-rapid metabolizer (UM), extensive metabolizer (EM), intermediate metabolizer (IM) and poor metabolizer (PM) in hypertensive patients and controls. For CYP2C19*2 polymorphisms, overall wild type and mutant allele frequency were 75 and 25 % in hypertensive patients, and 64.2 and 35.8 % in controls. For CYP2C19*17 polymorphisms, the overall wild type and mutant allele frequency were 66.6 and 33.4 % in hypertensive patients and 75.6 % and 24.4 % in controls. Significant difference in allele frequencies for CYP2C19*2 and *17 was demonstrated between hypertensive and non-hypertensive subjects. Conclusion: To the best of our knowledge, this is the first report on CYP2C19 frequencies in hypertensive Pakistani patients. The finds should help clinicians to determine a suitable optimal dosage of some drugs in order to reduce side effects.

Ectopic pregnancy management by V-NOTES technique

Ectopic pregnancy is a frequent and life-threatening risk of childbearing. Its management represents a mainstay of emergency gynecological surgery, and laparoscopy is the surgical gold standard technique. The technique of transvaginal natural orifice transluminal endoscopic surgery (V-NOTES) for the management of ectopic pregnancy is presented herein. The procedure is illustrated by an instructive video article that standardizes the essential steps to make the technique ergonomic and easy to perform (step-by-step explanations). This surgical technique allows to consider vaginal salpingectomy using a combined cœlio-vaginal approach. After a posterior colpotomy, an Alexis retractor was inserted in the pouch of Douglas followed by the placement of a dedicated platform on which three trocars were fixed. Pneumoperitoneum was then achieved. Once the diagnosis of ruptured tubal ectopic pregnancy was established, a salpingectomy was performed. As a minimally invasive approach, this procedure has high patient acceptance and seems to improve favorable clinical outcomes.

Direct-acting antiviral agents in the treatment of chronic hepatitis C-Real-life experience from clinical practices in Pakistan

This study aims to evaluate the clinical effectiveness in terms of sustained virological response (SVR), predictors of SVR and safety of available second-generation generic direct-acting antivirals in Pakistani chronic hepatitis C patients. This is a retrospective study conducted in multiple centers of Pakistan from January 2015 to January 2019. The samples include patients infected with chronic hepatitis C virus, regardless of virus genotype, cirrhosis, or prior treatment. A total of 993 patients were included in the present study, with the majority receiving sofosbuvir with daclatasvir (95%), sofosbuvir with daclatasvir and ribavirin (4%), and sofosbuvir with ribavirin (1%). There were 96% cases of chronic hepatitis, 3% cases compensated cirrhosis, and 1% cases of decompensated cirrhosis. Genotype 3 (99.6%) was the most common genotype. Overall SVR after 12 weeks was 98% for all treatment regimens. High SVR12 was observed with sofosbuvir in combination with daclatasvir (98.5%), then sofosbuvir in combination with daclatasvir and ribavirin (90.2%) and sofosbuvir in combination with ribavirin (75%). SVR rates were high in chronic hepatitis C patients (98.2%) as compared with cirrhotic patients (92.1%) and it was high in treatment-naive (98.8%) then interferon experienced patients (90.1%). In multivariate binary logistic regression analysis, patients' education status, treatment strategy, viral load, and alanine aminotransferase had a statistically significant association with SVR at 12 weeks. No major adverse events occurred which required treatment discontinuation. Generic oral direct acting antiviralss (sofosbuvir with daclatasvir) achieved higher SVR12 rates and were well tolerated in this large real-world cohort of genotype 3 infected patients.

Easy way to perform salpingectomy by transvaginal natural orifice transluminal endoscopic surgery (vNOTES) (with video)

The transvaginal natural orifice transluminal endoscopic surgery (vNOTES) is a new minimally invasive and emerging technique. Feasibility and safety profiles of peritoneal access via transvaginal routes have been demonstrated especially for the adnexal surgery. In order to be reproducible and replicable with a standardized procedure, we propose the step-by-step video description of the vNOTES salpingectomy. The advantages of the vNOTES (low postoperative pain, faster postoperative recovery, scarless surgery) could lead to a promising alternative to conventional laparoscopic salpingectomy/adnexectomy.

[Cystocele repair by a light tension-free vaginal mesh: results after 6 years of follow-up]

INTRODUCTION

The objective of this study was to evaluate the long-term anatomical and functional efficacy, but also the safety of tension-free vaginal mesh in cystocele repair.

METHODS

This retrospective and monocentric study included 90 women who underwent a prolapse repair between June 2006 and November 2008. A light-weight polypropylene vaginal mesh (22g/m2, Novasilk COLOPLAST®) was used without any fixation. Females were followed at 1 month, 1 year, 3 years and 6 years. Only long-term results are presented in this study. The anatomical result was assessed by the POP-Q classification and the functional results by standardized symptoms (PFDI-20), sexuality (PISQ-12) and quality of life (PFIQ-7) questionnaires.

RESULTS

6 years after surgery, the follow-up rate was 74%. Anatomically, the prolapse recurrence rate (Ba≥0) was 17% (n=8). Functionally, the overall patient satisfaction rate was 89%. Quality of life and symptoms scores (4,11±8.45 vs. 17.5±14.4 and 35.8±15.9 vs 94±23.4 respectively) were significantly improved (p<0.001). Concerning the prevalence of the complication, the retraction and exposition rate was 1.7% (n=1) and a re-intervention rate was 6.7% (n=4). The rate of de novo dyspareunia was 1.7% (n=1).

CONCLUSION

In this short retrospective series of vaginal mesh interposition for cystocele repair, the prevalence of medium-term patient satisfaction was high.

REPORT - CYP2D6*4 null allele frequency in sixteen Pakistani ethnic groups

CYP2D6 belongs to a family of Cytochrome P450 and is involved in metabolism of a number of commonly prescribed drugs. This study was designed to identify *4 allelic frequency of CYP2D6 in Pakistani population. The ethno-geographic variations in the CYP2D6 alleles are responsible for varied expression of this enzyme and thus influence the metabolic rate and efficacy of prescribed drugs. In total, 976 volunteers belonging to 16 different ethnic groups of Pakistan were screened for CYP2D6*4 polymorphism. The *4 allele was detected in all the ethnic groups with varied frequency ranging from 3.73%-13.64% and an overall average of 7.22% in different ethnic groups of the population. Maximum frequency was detected in northern Pakistani population including Meo (13.64%), Punjabi (11.96%) and Pathan (10.42%). Low frequency (<4%) of*4 polymorphism was observed in Kalash and Makrani groups, whereas an intermediate frequency (5-9%) was observed in all the other ethnic groups. The data indicates that despite ethnic diversity poor metabolizers in Pakistani population are expected to carry CYP2D6*4 allele at a relatively higher frequency than most other Asian populations. (Word count = 186).

Characterisation of immunogenotypes of diffuse large B-cell lymphoma

INTRODUCTION

Diffuse large B-cell lymphoma (DLBCL) is the most common aggressive type of non-Hodgkin lymphoma with variable clinical outcomes. The immunogenotypic features of this heterogeneous disease in Malaysia were not well characterized.

MATERIALS & METHODS

In total 141 local series of DLBCL cases from UKM Medical Centre were retrospectively studied.

RESULTS

Of these cases, we classified our patients into two subtypes: 32.7% (37/113) GCB and non-GCB 67.3% (76/113) by Hans algorithm and the results showed strong agreement with the results by Choi algorithm (κ = 0.828, P<0.001). Survival analysis indicated significant difference in between GCB and non-GCB subtypes (P=0.01), elevated serum LDH (P=0.016), age more than 60-year-old (P=0.021) and the presence of B symptoms (P=0.04). We observed 12% DLBCL cases were CD5 positive and 81.8% of them died of the disease (P=0.076). Analysis on the dual expression of MYC/BCL2 revealed that there is no significant difference in DE and non-DE groups (P=0.916). FISH study reported there were 9.22% (13/141) rearranged cases observed in our population at which highest frequency of BCL6 gene rearrangement (76.9%), followed by MYC (15.4%) and BCL2 (7.7%); no BCL10 and MALT-1 gene rearrangement found regardless of using TMAs or whole tissue samples. More cases of MYC protein overexpression observed compared to MYC translocation.

CONCLUSION

Relatively lower frequency of GCB tumours and low gene rearrangement rates were observed in Malaysian population. A national study is therefore warranted to know better the immunogenotypic characteristics of DLBCL in Malaysia and their implications on the survival.

MTHFR polymorphisms as risk for male infertility in Pakistan and its comparison with socioeconomic status in the world

Aim: 5,10-MTHFR-single nucleotide polymorphisms are important for normal functioning of the enzyme that plays a key role in DNA synthesis, folate metabolism and methylation reactions. Methodology & results: Male infertility association of C665T and A1298C polymorphisms was explored, this topic is still debatable. Infertile men (232) and controls (114) were genotyped and statistically analyzed. Comparison of patients (6180) and controls (5744) of Caucasian populations was performed by meta-analysis. Pooled results showed A1298C minor allele and homozygous genotype to be of a significantly higher frequency in the low-income group. Increase in per capita income has shown an increasing trend in the minor allele frequency in various world populations, potentially due to dietry-folate compensation. Conclusion: A1298C seems more relevant marker than C665T for infertility association in Caucasian populations and may be addressed by improving dietary folate.

Single nucleotide polymorphisms in asthma candidate genes TBXA2R, ADAM33 FCER1B and ORMDL3 in Pakistani asthmatics a case control study

BACKGROUND

Genetic variations in different loci and genes are important in asthma pathogenesis. There is much importance of various immunological pathways in the IgE secretion regulation. Alterations in any main part of these pathways can increase the risk of asthma development. Polymorphisms in these genetic markers can effect certain pathways which predict the asthma susceptibility. In the present study, SNPs directly or indirectly affecting the immunological process pathways are selected.

METHODS

This study was conducted to determine association of 16 SNPs in 10 candidate genes with asthma in Pakistani population in 333 asthmatic cases and 220 healthy controls. Genotyping was performed using the Sequenom Mass ARRAY iPLEX platform (14 SNPs) and TaqMan assay (2 SNPs).

RESULTS

The minor allele at two of the SNPs showed association with protection from asthma, rs1131882 in TBXA2R gene (OR 0.73, 95% CI 0.52-1.01, P = 0.05) and rs2280091 in the ADAM33 gene (OR 0.69, 95% CI 0.50-0.97, P = 0.03). For FCER1B gene, rs2583476 the asthmatic male gender had higher TT genotype counts as compared to controls (OR = 1.86, 95% CI = 1.09-3.17, p = 0.01). In rs11650680 of ORMDL3 gene the CT genotype is more prevalent in female asthma cases in comparison with female controls (OR = 1.99, 95% CI = 1.02-3.89, p = 0.03).

CONCLUSIONS

This data suggests that variations at TBXA2R and ADAM33 genes are found to be associated with asthma susceptibility in Pakistan. FCER1B gene is associated with male and ORMDL3 in female asthmatics. These genetic markers can be important source of asthma risk in Pakistani population.

An angiotensin I-converting enzyme insertion/deletion polymorphism is associated with Pakistani asthmatic cases and controls

Asthma is a chronic disease due to inflammation of the airways of lungs that is clinically characterized by variable symptoms including wheezing, coughing and shortness of breath. Angiotensin I-converting enzyme (ACE) plays a major role in fibrous tissue formation and is highly expressed in lungs. The main aim of this research work was to study the role of ACE insertion/deletion (I/D) polymorphism, rs4646994, in asthma in Pakistani patients. A total of 854 subjects, including 333 asthma patients and 521 ethnically matched controls, were studied. The ACE (I/D) polymorphism was genotyped using polymerase chain reaction (PCR). Chi-square, Fisher's exact and Hardy-Weinberg equilibrium tests were used to compare groups. Homozygous insertion genotype II (p less than 0.0001, OR=3.38) and insertion allele (I) was significantly more frequent in Pakistani asthmatics than in healthy controls (p=0.0007, OR=1.40). The ID genotype (p less than 0.0001, OR=0.43) and the deletion allele (D) were associated with protection of disease in Pakistani patients (p=0.0007, OR=0.71). These data suggest the involvement of ACE I/D polymorphism in asthma risk in the Pakistani population. This marker may be an important indication in the molecular mechanism of asthma and can become a useful tool in risk assessment and help in designing strategy to combat disease.

Development of an ovine model for training in vaginal surgery for pelvic organ prolapse

INTRODUCTION AND HYPOTHESIS

This aim of this study was to evaluate the feasibility and usefulness of an ovine model for training in vaginal surgery.

METHODS

Four senior urogynaecological surgeons and five residents attended five sessions of vaginal surgery for pelvic organ prolapse (POP) in five old multiparous female sheep. Urogynaecological examinations were performed and measurements similar to the POP-Q classification in humans were obtained. Standard POP surgical procedures with and without mesh were performed. A pelvic CT scan was done on one animal and the structures were compared with the pelvic structures in a woman. After the feasibility of vaginal surgery had been established in three cadavers, surgery was performed in two living animals under general anaesthesia and was followed by laparoscopy to explore the internal pelvic anatomy.

RESULTS

We found anatomic similarities in the vaginal and pelvic structures between sheep and women. After caudal traction on the cervix, all five sheep had significant POP of stage 3 or 4. We proved the feasibility of all types of vaginal surgery in this animal model: traditional anterior and posterior repair, apex fixation and anterior wall repair with mesh. The video shows the internal pelvic anatomy and different vaginal procedures.

CONCLUSION

This study showed that training in vaginal surgery for POP is feasible and useful in an animal model, the ewe, that has vaginal and pelvic structures very similar to those in women.

Abstract P3-14-12: Oncologic outcomes of immediate breast reconstruction after neoadjuvant chemotherapy in breast cancer patients: A matched case control study

Introduction: Although the indication for total mastectomy (TM) with immediate breast reconstruction (IBR) has been expanded, IBR after neoadjuvant chemotherapy (NACT) is still controversy. We assumed that TM with IBR after NACT is feasible surgical treatment in breast cancer patients. Methods: A retrospective review of breast cancer patients who underwent TM with IBR after NACT between 2008 and 2015 at a single center was conducted. These cases were matched by 1:5 to patients who underwent mastectomy alone after NACT. Matching variables included age, clinical T and N staging before NACT, response to NACT, and pathologic staging after NACT. Pathological stage was followed by seventh American Joint Committee on Cancer (AJCC) classification. Results: Overall, 31 patients were identified in the TM with IBR group (Study group) and 85 patients (Control group) were matched. In the study group, 13 (41.9%) patients underwent nipple-sparing mastectomy (NSM) and 18 (58.1%) underwent skin-sparing mastectomy (SSM). Median follow-up duration was 29.2 (7-31) and 38.8 (11-85) months for the study and control group, respectively. Median age was 37.0 (26-57) and 40.0 (24-56) years for the study and control group, respectively. The clinicopathologic characteristics of both groups are summarized in Table1. Disease-free survival (p=0.520), local recurrence-free survival (p=0.610), distant metastasis-free survival (p=0.795), and over survival (p=0.971) did not differ significantly between two groups. Conclusion: TM with IBR after NACT is feasible surgical treatment option in breast cancer patients.

Clinicopathologic characteristicsVariablesControl group (n=85)Study group (n=31)p-valueAge, years (matching variables)  0.890≤3515 (17.7)9 (29.0) 36-5061 (71.8)21 (67.7) 51≥9 (10.6)1 (3.2) BMI, m2/kg  0.13025≤62 (72.9)28 (90.3) 26-3018 (21.2)2 (6.5) 30&gt;5 (5.9)1 (3.2) Histology  0.326Ductal carcinoma in situ2 (2.4)3 (9.7) Invasive ductal carcinoma74 (87.1)28 (90.3) Invasive lobular carcinoma2 (2.4)0 (0) Others7 (8.2)0 (0) Multiplicity  0.063yes19 (22.6)12 (40.0) no65 (77.4)18 (60.0) Lymphovascular invasion  0.161yes33 (39.3)17 (54.8) no51 (60.7)14 (45.2) Nuclear grade  0.317Low10 (11.9)1 (3.3) Intermediate27 (32.1)14 (46.7) High47 (56.0)15 (24.2) Pathologic T stage (matching variable)  0.154T17 (8.2)6 (19.4) T229 (34.1)15 (48.4) T331 (36.5)4 (12.9) T418 (21.2)6 (19.4) Pathologic N stage (matching variable)  0.494N036 (42.4)13 (41.9) N123 (27.1)13 (41.9) N216 (18.8)4 (12.9) N310 (11.8)1 (3.2) Estrogen receptor  0.608positive49 (57.7)15 (48.4) negative36 (42.4)16 (51.6) Progesterone receptor  0.291positive40 (47.1)10 (32.3) negative45 (52.9)21 (67.7) HER2 status  0.345amplification29 (34.1)10 (32.3) not amplification56 (65.9)21 (67.7) Clinical T-stage (matching variable)  0.897cT12 (2.4)1 (3.2) cT231 (36.5)12 (38.7) cT346 (54.1)16 (51.6) cT46 (7.1)2 (6.5) Clinical N stage (matching variable)  0.947cN03 (3.5)1 (3.2) cN120 (23.5)10 (32.3) cN236 (42.4)10 (32.3) cN326 (30.6)10 (32.3) Response (matching variable)  1.000Partial response64 (75.3)27 (29.7) Stable disease21 (24.7)4 (12.9) 

Citation Format: Ryu JM, Lee JE, Kim SW, Yu J, Rayzah M, Lee SK, Mansoor A, Bae SY, Park S, Paik H-J, Kim I, Bang SI, Jeon BJ, Mun G-H, Pyon J-K. Oncologic outcomes of immediate breast reconstruction after neoadjuvant chemotherapy in breast cancer patients: A matched case control study [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P3-14-12.

A homozygous FITM2 mutation causes a deafness-dystonia syndrome with motor regression and signs of ichthyosis and sensory neuropathy

A consanguineous family from Pakistan was ascertained to have a novel deafness-dystonia syndrome with motor regression, ichthyosis-like features and signs of sensory neuropathy. By applying a combined strategy of linkage analysis and whole-exome sequencing in the presented family, a homozygous nonsense mutation, c.4G>T (p.Glu2*), in FITM2 was identified. FITM2 and its paralog FITM1 constitute an evolutionary conserved protein family involved in partitioning of triglycerides into cellular lipid droplets. Despite the role of FITM2 in neutral lipid storage and metabolism, no indications for lipodystrophy were observed in the affected individuals. In order to obtain independent evidence for the involvement of FITM2 in the human pathology, downregulation of the single Fitm ortholog, CG10671, in Drosophila melanogaster was pursued using RNA interference. Characteristics of the syndrome, including progressive locomotor impairment, hearing loss and disturbed sensory functions, were recapitulated in Drosophila, which supports the causative nature of the FITM2 mutation. Mutation-based genetic counseling can now be provided to the family and insight is obtained into the potential impact of genetic variation in FITM2.

Editors' choice: Loss of FITM2 function in humans causes syndromic hearing loss without any signs of a lipodystrophy, although FITM2 is known to function in lipid droplet synthesis and metabolism.

Can IFNL3 polymorphisms predict response to interferon/ribavirin treatment in hepatitis C patients with genotype 3?

Favourable genotypes of IFNL3 polymorphism CC for rs12979860 and TT for rs8099917 are strongly associated with the interferon/ribavirin treatment outcome in hepatitis C virus (HCV) patients with genotypes 1 and 4. Contrarily, conflicting results have been reported for patients with HCV genotypes 2 and 3. Therefore, we sought to investigate the association between IFNL3 with sustained virological response (SVR) after treatment to ascertain the predictive value of IFNL3 single-nucleotide polymorphisms (SNPs) in HCV patients with genotype 3. For this purpose, we genotyped five IFNL3 SNPs, rs12980275, rs12979860, rs9109886, rs8099917 and rs7248668, in HCV patients with genotype 3 and assessed its association with SVR, individually and in haplotype. Interestingly, we report that the IFNL3 SNPs we genotyped have shown no association with SVR following treatment, either individually or in haplotype, indicating that genotyping IFNL3 SNPs have limited predictive value in HCV patients with genotype 3. Therefore, we propose that IFNL3 genotyping can be excluded from a patient's pre-treatment workup for subsequent treatment choice. This will greatly reduce the economic burden for HCV patients with genotype 3 in resource-limited regions, especially South Asia where genotype 3 is predominant.

Association of Tumor Necrosis Factor Alpha 308 G/A Polymorphism with Asthma in Pakistani Population

Asthma is a chronic inflammatory and remodeling disorder of the airways, in which many cells, cellular elements, and cytokines play important roles. The role of tumor necrosis factor-α (TNF-α) in asthma is unclear in Pakistani population. The aim of this study was to assess the relationship between TNF-α-308 polymorphism and asthma. Polymorphism of TNF-α (G-308-A locus; rs 1800629) in 329 asthmatic patients and 151 healthy controls was evaluated. DNA was prepared from blood samples of cases and controls. Samples were genotyped for TNF-α 308 G/A polymorphism. There was no significant difference in the frequency of GG (OR 1.049 with 95% CI 0.68-1.63) and GA (OR 0.987 with 95% CI 0.64-1.53) genotypes of TNF-α-308. The AA genotype was absent in cases and only one AA genotype was observed in the controls. The genetic polymorphism of TNF-α does not seem to be associated with asthma in Pakistani population.

Molecular diagnosis of Fragile X syndrome in subjects with intellectual disability of unknown origin: implications of its prevalence in regional Pakistan

Fragile-X syndrome (FXS) is the most common form of inherited intellectual disability (ID) and affects 0.7–3.0% of intellectually compromised population of unknown etiology worldwide. It is mostly caused by repeat expansion mutations in the FMR1 at chromosome Xq27.3. The present study aimed to develop molecular diagnostic tools for a better detection of FXS, to assess implementation of diagnostic protocols in a developing country and to estimate the prevalence of FXS in a cohort of intellectually disabled subjects from Pakistan. From a large pool of individuals with below normal IQ range, 395 subjects with intellectual disability of unknown etiology belonging to different regions of the country were recruited. Conventional-PCR, modified-PCR and Southern blot analysis methods were employed for the detection of CGG repeat polymorphisms in the FMR1 gene. Initial screening with conventional-PCR identified 13 suspected patients. Subsequent investigations through modified PCR and Southern blot analyses confirmed the presence of the FMR1 mutation, suggesting a prevalence of 3.5% and 2.8% (mean 3.3%) among the male and female ID patients, respectively. These diagnostic methods were further customized with the in-house conditions to offer robust screening of referral patients/families for diagnostics and genetic counseling. Prescreening and early diagnosis are crucial for designing a prudent strategy for the management of subjects with ID. Outcome of the study recommends health practitioners for implementation of molecular based FXS diagnosis in routine clinical practice to give a better care for patients similar to the ones included in the study.

A novel splice-site mutation in ALS2 establishes the diagnosis of juvenile amyotrophic lateral sclerosis in a family with early onset anarthria and generalized dystonias

The diagnosis of childhood neurological disorders remains challenging given the overlapping clinical presentation across subgroups and heterogeneous presentation within subgroups. To determine the underlying genetic cause of a severe neurological disorder in a large consanguineous Pakistani family presenting with severe scoliosis, anarthria and progressive neuromuscular degeneration, we performed genome-wide homozygosity mapping accompanied by whole-exome sequencing in two affected first cousins and their unaffected parents to find the causative mutation. We identified a novel homozygous splice-site mutation (c.3512+1G>A) in the ALS2 gene (NM_020919.3) encoding alsin that segregated with the disease in this family. Homozygous loss-of-function mutations in ALS2 are known to cause juvenile-onset amyotrophic lateral sclerosis (ALS), one of the many neurological conditions having overlapping symptoms with many neurological phenotypes. RT-PCR validation revealed that the mutation resulted in exon-skipping as well as the use of an alternative donor splice, both of which are predicted to cause loss-of-function of the resulting proteins. By examining 216 known neurological disease genes in our exome sequencing data, we also identified 9 other rare nonsynonymous mutations in these genes, some of which lie in highly conserved regions. Sequencing of a single proband might have led to mis-identification of some of these as the causative variant. Our findings established a firm diagnosis of juvenile ALS in this family, thus demonstrating the use of whole exome sequencing combined with linkage analysis in families as a powerful tool for establishing a quick and precise genetic diagnosis of complex neurological phenotypes.

A canonical splice site mutation in GIPC3 causes sensorineural hearing loss in a large Pakistani family

With homozygosity mapping we have identified two large homozygous regions on chromosome 3q13.11-q13.31 and chromosome 19p13.3-q31.32 in a large Pakistani family suffering from autosomal recessive nonsyndromic hearing impairment (arNSHI). The region on chromosome 19 overlaps with the previously described deafness loci DFNB15, DFNB72 and DFNB95. Mutations in GIPC3 have been shown to underlie the nonsyndromic hearing impairment linked to these loci. Sequence analysis of all exons and exon-intron boundaries of GIPC3 revealed a homozygous canonical splice site mutation, c.226-1G>T, in GIPC3. This is the first mutation described in GIPC3 that affects splicing. The c.226-1G>T mutation is located in the acceptor splice site of intron 1 and is predicted to affect the normal splicing of exon 2. With a minigene assay it was shown to result in the use of an alternative acceptor site in exon 2, resulting in a frameshift and a premature stop codon. This study expands the mutational spectrum of GIPC3 in arNSHI.

Genotype CC of rs12979860 is providing protection against infection rather than assisting in treatment response for HCV genotype 3a infection

Recent discovery of single-nucleotide polymorphisms located in the upstream region of interleukin-28B (IL28B) has shown association with interferon (IFN) treatment response especially in hepatitis C virus (HCV) genotype 1-infected patients. Pakistan, being the country with second highest prevalence of HCV with predominantly 3a genotype infection, bears a significant disease burden. The present study was conducted to evaluate the effect of rs12979860 genotypes on treatment response in HCV-3a-infected patients. This study shows that the CC genotype is providing protection against infection to HCV. But once infected, the CC genotype patients show viral persistence following IFN therapy. The TT genotype is assisting the 3a patients in viral clearance after IFN treatment. To our knowledge, this is the first study showing rs12979860 genotype association with IFN response in Pakistani HCV-3a-infected patients.

Genetic spectrum of autosomal recessive non-syndromic hearing loss in Pakistani families

The frequency of inherited bilateral autosomal recessive non-syndromic hearing loss (ARNSHL) in Pakistan is 1.6/1000 individuals. More than 50% of the families carry mutations in GJB2 while mutations in MYO15A account for about 5% of recessive deafness. In the present study a cohort of 30 ARNSHL families was initially screened for mutations in GJB2 and MYO15A. Homozygosity mapping was performed by employing whole genome single nucleotide polymorphism (SNP) genotyping in the families that did not carry mutations in GJB2 or MYO15A. Mutation analysis was performed for the known ARNSHL genes present in the homozygous regions to determine the causative mutations. This allowed the identification of a causative mutation in all the 30 families including 9 novel mutations, which were identified in 9 different families (GJB2 (c.598G>A, p.Gly200Arg); MYO15A (c.9948G>A, p.Gln3316Gln; c.3866+1G>A; c.8767C>T, p.Arg2923* and c.8222T>C, p.Phe2741Ser), TMC1 (c.362+18A>G), BSND (c.97G>C, p.Val33Leu), TMPRSS3 (c.726C>G, p.Cys242Trp) and MSRB3 (c.20T>G, p.Leu7Arg)). Furthermore, 12 recurrent mutations were detected in 21 other families. The 21 identified mutations included 10 (48%) missense changes, 4 (19%) nonsense mutations, 3 (14%) intronic mutations, 2 (9%) splice site mutations and 2 (9%) frameshift mutations. GJB2 accounted for 53% of the families, while mutations in MYO15A were the second most frequent (13%) cause of ARNSHL in these 30 families. The identification of novel as well as recurrent mutations in the present study increases the spectrum of mutations in known deafness genes which could lead to the identification of novel founder mutations and population specific mutated deafness genes causative of ARNSHL. These results provide detailed genetic information that has potential diagnostic implication in the establishment of cost-efficient allele-specific analysis of frequently occurring variants in combination with other reported mutations in Pakistani populations.

Study of PKRBD in HCV genotype 3a infected patients in response to interferon therapy in Pakistani population

Background

Hepatitis C virus (HCV) is a major cause of liver cirrhosis and hepatocellular carcinoma and infects about 3% world population. Response to interferon therapy depends upon the genotype of the virus and factors associated with the host. Despite a good response to interferon therapy, a considerable number of genotype 3a infected patients remains unalleviated.

Results

In total forty-nine patients including twenty-five non-responders (non-SVR) and twenty-four responders (SVR) were recruited. Patients were tested for viral status at different intervals and the isolated RNA was sequenced for the NS5A region in both groups. The comparison of PKRBD of HCV between the SVR and non-SVR patients did not confirm any significant difference in the number of mutations. However, when the sequence downstream to the PKRBD of NS5A was compared, two important statistically significant mutations were observed; at positions 2309 (Ala to Ser) and 2326 (Gly to Ala). These mutations were then analysed for tertiary protein structure and important structural changes were observed. Statistically significant difference was also observed when age groups of patients were compared; younger patients showed better response than the older ones.

Conclusions

The region between PKRBD and IRRDR may be important for prediction of response to IFN therapy for genotype 3a. ISDR and PKRBD have not shown any involvement in treatment response. Further functional analyses of these findings can help in understanding the involvement of the NS5A region in interferon treatment of HCV-3a infected patients.

Reovirus as a successful ex vivo purging modality for multiple myeloma

Autologous stem cell rescue (ASCT) following high-dose myeloablative chemotherapy is considered to be a therapeutic option for many multiple myeloma (MM) patients; however relapse post ASCT presents a major challenge. The oncolytic potential of reovirus has been previously demonstrated and is currently undergoing phase I monotherapy clinical trials for MM and phase II/III clinical trials for solid tumors. Here we tested the hypothesis that reovirus can successfully purge MM in a murine model that partially recapitulates human MM. RPMI 8226, MM1S, H929 and U266 human myeloma cell lines were exposed to reovirus and oncolysis was assessed. Apheresis product admixed with MM cells was purged with live reovirus (LV) or dead virus (DV) and purging efficacy was monitored via flow cytometry, reverse transcribed-PCR (RT-PCR) and disease relapse in non obese diabetic/severe combined immune deficient (NOD/SCID) mice. Significant LV purging was seen with MM1S, H929 and U266 and the complete ex vivo purging achieved with RPMI 8226 was confirmed by flow cytometry, RT-PCR and absence of disease relapse in vivo. Mice that received LV-purged autografts exhibited 100% survival in comparison to mice that received DV-purged controls. Reovirus's unique ability to kill MM while sparing hematopoietic stem cells places it as an attractive purging agent for MM during ASCT.

Association of HLA-DRB1 and -DQB1alleles and haplotypes with rheumatoid arthritis in a Pakistani population

Introduction

Rheumatoid arthritis is an autoimmune disease with poorly understood pathophysiology. Genetic components of disease etiology, especially human leukocyte antigen (HLA) associations, are well known. Ethnic differences account for a number of variations in disease association with the HLA locus and there seem to be differences in various studies regarding its genetic predisposition. This study was aimed at determining the contribution of DRB1 and DQB1 components of HLA class II in rheumatoid arthritis in a Pakistani cohort.

Method

For this study, 110 patients and 120 healthy controls from the same geographical area and matched ethnicity were enrolled. Blood DNA was isolated from all the subjects and HLA alleles were typed following allele specific amplification. Subsequently, haplotypes were generated and allelic and haplotype distribution frequencies were compared among the patients and controls using χ² and Arlequin software. The data obtained by this analysis were also compared with other reported associations found in the Pakistani population by meta-analysis.

Results

HLA allelic status was determined among the patients and controls from the same geographical area to account for differences in ethnicity and environmental factors. Significant associations were found for alleles as well as haplotypes among the patients of rheumatoid arthritis. DRB1*10, DQB1*05 and DQB1*602 were found to be associated with disease susceptibility, whereas DRB1*11 and DQB1*02 had protective effect against the disease. Similarly, haplotype DRB1*10-DQB1*05 was associated disease risk, whereas DRB1*07-DQB1*02 and DRB1*11-DQB1*0301 had a protective effect.

Conclusion

There is a significant DRB1and DQB1 allele and haplotype association with rheumatoid arthritis susceptibility and protection.

[Prospective evaluation of an intravaginal electrical stimulation in the treatment of women with pure genuine stress urinary incontinence]

OBJECTIVES

To study the objective and subjective effectiveness of transvaginal electrical stimulation for treatment of female pure genuine stress incontinence.

PATIENTS AND METHODS

This was a multicenter prospective trial including 207 patients with genuine stress incontinence who used the stimulator for 10 weeks. Similar pre-treatment and post-treatment assessments included both validated symptom severity index and health-related quality of life.

RESULTS

Objective evaluation showed a significant improvement in 65.7% of subjects with stress incontinence. All domains of quality of life improved significantly after treatment (P=0.0001) and rate of satisfactory was 84.7%. There were no statistical differences between the two stimulators.

DISCUSSION AND CONCLUSION

Pelvic floor electrical stimulation seems to be effective in treating female genuine stress incontinence and could be considered first-line therapy.

Occult HCV or delayed viral clearance from lymphocytes of Chronic HCV genotype 3 patients after interferon therapy

Background

A recently discovered occult HCV entity reported by various investigators seems to be highly controversial. Especially, the clinical significance of these findings remains uncertain. For optimal outcome of antiviral therapy, investigation of occult HCV needs a broad-based probe in order to investigate the results of viral therapy and its host/viral interaction. The current study was aimed at determining the prevalence of occult HCV in peripheral blood lymphocytes of predominantly genotype 3 HCV-infected patients after completion of antiviral therapy and to investigate long term outcomes in the presence or absence of PBMC positivity.

Method

A total of 151 chronic, antiHCV and serum RNA-positive patients were enrolled in the study. Patients with a complete virological response at the end of treatment were screened for the presence of viral RNA in their PBMCs and were followed for up to one year for the presence of serum and PBMC viral genomic RNA.

Results

Out of 151 patients, 104 (70%) responded to the prescribed interferon treatment and showed viral-clearance from serum. These were screened for the presence of genomic RNA in their PBMCs. Sixteen samples were PBMC-positive for viral RNA at the end of treatment (EOT). All these patients had also cleared the virus from peripheral blood cells after the 6-12 month follow-up study.

Conclusion

True occult hepatitis C virus does not exist in our cohort. Residual viremia at the EOT stage merely reflects a difference in viral kinetics in various compartments that remains a target of immune response even after the end of antiviral therapy and is eventually cleared out at the sustained viral response (SVR).

Characterization of Y-chromosomal short tandem repeat markers in Pakistani populations

The Y chromosome microsatellite markers have been extensively used for population genetic studies and in individual identification and paternity testing in forensic medicine. In the present study, we report the data of five male-specific, polymorphic microsatellites in 740 unrelated male individuals from 12 different ethnic groups of Pakistan. The overall diversities of these individual loci in Pakistan ranged from 0.236 to 0.799. The total haplotypes identified were 152, and of these, 70 different haplotypes were present in only single individuals. Two haplotypes were found more frequently, 9_8_17_11_24 (13.5%) and 9_8_17_11_25 (8.6%), showing population-specific clustering in the Mohanna and the Brahui, respectively. An overall haplotype diversity of 0.965 in Pakistan suggested a high power of discrimination for these loci. Few populations, particularly the Mohanna and the Balti, showed lower haplotype diversity values for these loci (0.662 and 0.758, respectively). This set of microsatellite loci reported in the study can be used for population genetics and forensic medicine analysis. This study also demonstrates the importance of studying haplotype distribution pattern in population genetics.

Patient HLA-DRB1* and -DQB1* allele and haplotype association with hepatitis C virus persistence and clearance

Hepatitis C virus (HCV) infection is prevalent throughout the world and interferon (IFN)-based treatments are currently the only therapeutic option. However, depending upon variations in their human leukocyte antigen (HLA), some patients do not respond well to IFN therapy. The current study evaluated the HLA allele and haplotype distribution of 204 HCV-seropositive individuals from Islamabad, Pakistan, who were receiving standard IFN therapy. In this cohort, 150 patients (74%) showed a sustained virological response to IFN therapy, whereas 54 (26%) did not. In addition to the HCV patients, 102 unrelated healthy volunteers were used as controls. DNA was isolated from the blood of the patients and controls for HLA-DRB1 and HLA-DQB1 allele typing, whilst plasma was used for HCV detection and genotyping. HLA-DRB1*04 was found to impart a significant protective advantage [Bonferroni-corrected P value (pc)=0.047] against HCV infection. In patients on IFN therapy, HLA-DRB1*11 and -DQB1*0301 (pc=0.044) were found to be associated with viral clearance. In contrast, HLA-DRB1*07 (pc=0.008) individually or in combination with HLA-DQB1*02 was found to be associated with viral persistence. These associations of HLA with HCV persistence or clearance will be beneficial in deciding the therapeutic regimen for Pakistani patients infected with HCV genotype 3a.

Patient HLA-DRB1* and -DQB1* allele and haplotype association with hepatitis C virus persistence and clearance

Hepatitis C virus (HCV) infection is prevalent throughout the world and interferon (IFN)-based treatments are currently the only therapeutic option. However, depending upon variations in their human leukocyte antigen (HLA), some patients do not respond well to IFN therapy. The current study evaluated the HLA allele and haplotype distribution of 204 HCV-seropositive individuals from Islamabad, Pakistan, who were receiving standard IFN therapy. In this cohort, 150 patients (74%) showed a sustained virological response to IFN therapy, whereas 54 (26%) did not. In addition to the HCV patients, 102 unrelated healthy volunteers were used as controls. DNA was isolated from the blood of the patients and controls for HLA-DRB1 and HLA-DQB1 allele typing, whilst plasma was used for HCV detection and genotyping. HLA-DRB1*04 was found to impart a significant protective advantage [Bonferroni-corrected P value (pc)=0.047] against HCV infection. In patients on IFN therapy, HLA-DRB1*11 and -DQB1*0301 (pc=0.044) were found to be associated with viral clearance. In contrast, HLA-DRB1*07 (pc=0.008) individually or in combination with HLA-DQB1*02 was found to be associated with viral persistence. These associations of HLA with HCV persistence or clearance will be beneficial in deciding the therapeutic regimen for Pakistani patients infected with HCV genotype 3a.

[Health-related quality of life in women operated on by surgical anti-incontinence procedures: comparison of three techniques]

OBJECTIVES

To assess the health-related quality of life (Contilife) after three surgical anti-incontinence procedures (Tension-Free Vaginal Tape [TVT], Transobturator Vaginal Tape [TOT], and Transobturator Vaginal Tape [TVT-O]).

PATIENTS AND METHODS

We performed a prospective analysis of 90 women (30 TVT, 30 TOT, 30 TVT-0) with genuine stress incontinence pre- and postoperatively at 18 months. The objective cure rate was determined by clinical and urodynamic examination and the subjective cure rate by the Contilife questionnaire.

RESULTS

Prior to surgery, patients complained more of effort activities, followed by global well-being. Postoperatively, all domains improved significantly without statistical difference between the three groups and 90% of the patients would advise the intervention to one of their friends.

DISCUSSION AND CONCLUSION

Surgical outcomes vary greatly depending on the methodology of the study. Health-related quality of life seems paramount to decide time of surgery and to evaluate postoperatory results. We have chosen the Contilife questionnaire because of its scientific and clinical validity, reliability, responsiveness and linguistic validation. These results confirm that TVT/TOT/TVT-O procedures are a safe and effective surgical method and that they significantly improved health-related quality of life.

[Unusual perineal pain in postpartum period: contribution of perineal ultrasound]

We report two cases of persistent [correction of persistant] perineal pain in postpartum period due to transfixation of the anus with a suture and the contribution of perineal ultrasound in the diagnosis of unusual perineal pain.