Publications by authors named "Kalpana Luthra"

112 Publications

Differential expression of insulin receptor substrate-1(IRS-1) in visceral and subcutaneous adipose depots of morbidly obese subjects undergoing bariatric surgery in a tertiary care center in north India; SNP analysis and correlation with metabolic profile.

Diabetes Metab Syndr 2021 May 5;15(3):981-986. Epub 2021 May 5.

Department of Biochemistry, All India Institute of Medical Sciences, Delhi, India. Electronic address:

Background: /aim: Abdominal obesity and associated metabolic consequences are a burgeoning problem in Asian Indians and studying their genetic predisposition is important. This study is aimed at assessing variations in Insulin receptor substrate-1 (IRS-1), its expression at regional fat-depots (visceral and subcutaneous) in morbidly obese patients, and correlation with genotype-phenotype traits.

Methods: Gene expression of IRS-1 in paired adipose tissue from 35 morbidly obese subjects (BMI) > 40 kg/m) with co-morbidities and 15 controls (BMI<25 kg/m), undergoing bariatric/elective abdominal surgery, respectively was determined by quantitative real time PCR. Genotyping of IRS-1Gly972Arg (n = 436) (rs 1801278) was performed by PCR-RFLP. Metabolic parameters were assessed. Full length sequencing of IRS-1 was performed to identify known/novel variations.

Results: A marked reduction in IRS-1 expression was observed in visceral as compared to subcutaneous adipose tissue of morbidly obese subjects (p = 0.02). Homozygous variant of IRS-1 Gly972Arg was absent and there was no association with obesity or insulin resistance. A salient finding of this study was identification of two new variants in IRS-1 gene, representing G > A (codon 1102) encoding Glu > Lys and a deletion of (A) at codon 658 in morbidly obese subjects with insulin resistance.

Conclusions: Observation of a substantially lower expression of IRS-1 for first time in visceral adipose tissue of morbidly obese subjects is suggestive of predictive role of IRS-1 expression in insulin responsiveness of visceral adipose tissue. New variants in IRS-1, a non-synonymous mutation and a deletion should be evaluated further for their role in development of obesity and/orT2DM.
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http://dx.doi.org/10.1016/j.dsx.2021.04.014DOI Listing
May 2021

Measurement of Serum EGFR mRNA Expression is a Reliable Predictor of Treatment Response and Survival Outcomes in Non- Small Cell Lung Cancer.

Asian Pac J Cancer Prev 2020 Nov 1;21(11):3153-3163. Epub 2020 Nov 1.

Department of Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences, New Delhi, India.

Background: EGFR over-expression plays a key role in the development and progression of lung cancer. However, its status as a prognostic biomarker for survival outcomes is unclear.

Objectives: To evaluate the prognostic utility of serum EGFR mRNA expression in Non-Small cell lung cancer (NSCLC) for treatment response and survival.

Methods: EGFR mRNA levels were determined in serum using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). Based on ROC curve, a cut off value of 16.0-fold increase was selected to categorize patients into low EGFR (≤ 16.0) and high EGFR (> 16.0) groups.

Results: A total of 350 subjects were included (78.3% males), with mean (± SD) age of 57.1 (± 11.2) years, and including 247 (70.6%) adenocarcinoma (ADC). Majority (73.1%) had metastatic (stage IV) disease. Patients had higher pre-treatment serum EGFR mRNA levels than controls [median fold-increase (min, max), 16.2 (1.9, 66.7). Serum EGFR mRNA levels significantly reduced in those who achieved objective response and disease control. Significantly longer OS and PFS was observed in subjects having baseline EGFR mRNA expression ≤ 16.0 fold- increase compared to those with > 16.0 fold- increase [median (95% CI) OS: 25.0 (14.9, NR) versus 7.7 (6.3, 8.9) months; HR (95% CI) 2.9 (2.3, 4.0), p < 0.001; and PFS: 9.9 (7.1, 11.5) versus 6.0 (4.1, 7.5) months; HR (95% CI) 1.8 (1.3, 2.4), p < 0.001].

Conclusion: Serum EGFR mRNA expression is a useful parameter for predicting treatment response and survival outcomes in NSCLC.
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http://dx.doi.org/10.31557/APJCP.2020.21.11.3153DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8033130PMC
November 2020

Spectrum of uncommon and compound epidermal growth factor receptor mutations in non-small-cell lung carcinomas with treatment response and outcome analysis: A study from India.

Lung Cancer 2020 11 13;149:53-60. Epub 2020 Sep 13.

Department of Pathology, All India Institute of Medical Sciences, New Delhi, India. Electronic address:

Introduction: Mutations in the tyrosine kinase domain of the epidermal growth factor receptor gene (EGFR) are key driver alterations in lung adenocarcinomas (ADCAs). Exon 19 deletions (exon19del) and exon 21 L858R (L858R) mutations account for 70-90 % of all such alterations and predict sensitivity to EGFR tyrosine kinase inhibitors (TKIs). However, the predictive value of uncommon and compound EGFR mutations for TKIs has not been clearly established.

Objective: To assess the spectrum of EGFR mutations in non-small-cell lung carcinoma (NSCLC), and to compare the treatment responses and outcomes among single common, single uncommon, and compound mutations.

Method: The study was of combined retrospective (January 2010-December 2015) and prospective (January 2016-February 2020) design spanning 10 years. Tumor samples from TKI-naive NSCLC patients were tested for EGFR mutations by a qPCR-based method. Objective response rates (ORRs) and survival outcomes were analyzed.

Result: In total, 1227 tumor samples were tested. EGFR mutations were detected in 391 samples (31.8 %), and included 79.5 % (311/391) single common (exon19del/L858R), 6.6 % (26/391) single uncommon (non-exon19del/L858R), and 13.8 % (54/391) compound mutations. Exon 20 T790M mutations were most prevalent among uncommon/compound mutations (40/391, 10.2 %). Overall, patients with single uncommon/compound mutations responded poorly to both EGFRTKI (47 % ORR) and chemotherapy (43 % ORR), with significantly shorter time to progression (median 7 months) compared to those with exon19del/L858R mutations (median 14.7 months). Patients with baseline T790M mutations (single/compound) were least responsive to EGFR TKIs (11 % ORR) and chemotherapy (27 % ORR) and showed the shortest progression-free survival compared to other uncommon and compound mutations.

Conclusion: Approximately one fifth of EGFR-mutant patients harbor uncommon and compound mutations. Unlike those with exon19del/L858R, these patients-particularly those with baseline T790M mutations-show significantly inferior response rates to treatment (EGFR TKI or chemotherapy) and early disease progression.
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http://dx.doi.org/10.1016/j.lungcan.2020.07.038DOI Listing
November 2020

Effect of combination antiretroviral therapy on human immunodeficiency virus 1 specific antibody responses in subtype-C infected children.

J Gen Virol 2020 12 11;101(12):1289-1299. Epub 2020 Sep 11.

Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India.

Protective antibody responses to human immunodeficiency virus (HIV)-1 infection evolve only in a fraction of infected individuals by developing broadly neutralizing antibodies (bnAbs) and/or effector functions such as antibody-dependent cellular cytotoxicity (ADCC). HIV-1 chronically infected adults and children on combination antiretroviral therapy (cART) showed a reduction in ADCC activity and improvement in HIV-1 specific neutralizing antibody (nAb) responses. Early initiation of cART in infected adults is found to be beneficial in reducing the viral load and delaying disease progression. Herein, we longitudinally evaluated the effect of cART on HIV-1 specific plasma ADCC and nAb responses in a cohort of 20 perinatally HIV-1 subtype-C infected infants and children ≤2 years of age, pre-cART and up to 1 year post-cART initiation. Significant reductions in HIV-1 specific plasma ADCC responses to subtype-C and subtype-B viruses and improvement in HIV-1 neutralization were observed in HIV-1 infected children 1 year post-cART initiation. A positive correlation between reduction in viral load and the loss of ADCC response was observed. This study provides information aiding the understanding of the effects of early initiation of cART on antibody effector functions and viral neutralization in HIV-1 infected children, which needs to be further evaluated in large cohorts of HIV-1 infected children on cART to plan future intervention strategies.
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http://dx.doi.org/10.1099/jgv.0.001480DOI Listing
December 2020

Broadly neutralizing plasma antibodies effective against autologous circulating viruses in infants with multivariant HIV-1 infection.

Nat Commun 2020 09 2;11(1):4409. Epub 2020 Sep 2.

Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029, India.

Broadly neutralizing antibodies (bnAbs) develop in a subset of HIV-1 infected individuals over 2-3 years of infection. Infected infants develop plasma bnAbs frequently and as early as 1-year post-infection suggesting factors governing bnAb induction in infants are distinct from adults. Understanding viral characteristics in infected infants with early bnAb responses will provide key information about antigenic triggers driving B cell maturation pathways towards induction of bnAbs. Herein, we evaluate the presence of plasma bnAbs in a cohort of 51 HIV-1 clade-C infected infants and identify viral factors associated with early bnAb responses. Plasma bnAbs targeting V2-apex on the env are predominant in infant elite and broad neutralizers. Circulating viral variants in infant elite neutralizers are susceptible to V2-apex bnAbs. In infant elite neutralizers, multivariant infection is associated with plasma bnAbs targeting diverse autologous viruses. Our data provides information supportive of polyvalent vaccination approaches capable of inducing V2-apex bnAbs against HIV-1.
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http://dx.doi.org/10.1038/s41467-020-18225-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7468291PMC
September 2020

Assessing the serum chymase level as an early predictor of dengue severity.

J Med Virol 2021 06 8;93(6):3330-3337. Epub 2020 Oct 8.

Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India.

We conducted a prospective, observational study to assess the serum chymase level, a mast cell derived protease, as a predictor of dengue severity. NS1-positive non-severe dengue patients of age ≥14 years with duration of fever ≤4 days were included in the study. At the time of admission, the serum sample was taken for chymase estimation. Patients were followed up to four days after they became afebrile to find out the final diagnosis. Total of 338 non-severe dengue patients were recruited (mean age: 29.15 years; male: 66%). On follow-up, 26 patients (7.8%) developed severe dengue. Only chymase level (adjusted odds ratio [aOR]: 1.787; 95% confidence interval [CI]: 1.309-2.440) and platelet count at admission (aOR: 0.981; 95% CI: 0.968-0.993) were able to predict the severity after adjustment for all variables. But, for prediction of severe dengue, the area under receiver's operating curve of chymase was 0.835 (95% CI: 0.765-0.905), which was significantly higher than that of the platelet count at admission (0.760, 95% CI: 0.650-0.870) (p < .001). Patients who developed severe dengue in due course of illness had significantly higher serum chymase level at admission as compared with the rest of the patients. Similar findings were noted across all age-groups. At an optimum cut-off value of 1.35 ng/ml, chymase had a positive likelihood ratio (LR) of 3.5 and a negative LR of 0.15, for predicting severe dengue. This study demonstrated the potential ability of serum chymase levels at admission, as a biomarker for prediction of severe dengue in due course of illness.
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http://dx.doi.org/10.1002/jmv.26468DOI Listing
June 2021

A Rare Mutation in an Infant-Derived HIV-1 Envelope Glycoprotein Alters Interprotomer Stability and Susceptibility to Broadly Neutralizing Antibodies Targeting the Trimer Apex.

J Virol 2020 09 15;94(19). Epub 2020 Sep 15.

Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India

The envelope glycoprotein (Env) of human immunodeficiency virus type 1 (HIV-1) is the sole target of broadly neutralizing antibodies (bnAbs). Several mechanisms, such as the acquisition of mutations, variability of the loop length, and alterations in the glycan pattern, are employed by the virus to shield neutralizing epitopes on Env to sustain survival and infectivity within the host. The identification of mutations that lead to viral evasion of the host immune response is essential for the optimization and engineering of Env-based trimeric immunogens. Here, we report a rare leucine-to-phenylalanine escape mutation (L184F) at the base of hypervariable loop 2 (population frequency of 0.0045%) in a 9-month-old perinatally HIV-1-infected infant broad neutralizer. The L184F mutation altered the trimer conformation by modulating intramolecular interactions stabilizing the trimer apex and led to viral escape from autologous plasma bnAbs and known N160 glycan-targeted bnAbs. The L184F amino acid change led to the acquisition of a relatively open trimeric conformation, often associated with tier 1 HIV-1 isolates and increased susceptibility to neutralization by polyclonal plasma antibodies of weak neutralizers. While there was no impact of the L184F mutation on free virus transmission, a reduction in cell-to-cell transmission was observed. In conclusion, we report a naturally selected viral mutation, L184F, that influenced a change in the conformation of the Env trimer apex as a mechanism of escape from contemporaneous plasma V2 apex-targeted nAbs. Further studies should be undertaken to define viral mutations acquired during natural infection, to escape selection pressure exerted by bnAbs, to inform vaccine design and bnAb-based therapeutic strategies. The design of HIV-1 envelope-based immunogens capable of eliciting broadly neutralizing antibodies (bnAbs) is currently under active research. Some of the most potent bnAbs target the quaternary epitope at the V2 apex of the HIV-1 Env trimer. By studying naturally circulating viruses from a perinatally HIV-1-infected infant with plasma neutralizing antibodies targeted to the V2 apex, we identified a rare leucine-to-phenylalanine substitution, in two out of six functional viral clones, that destabilized the trimer apex. This single-amino-acid alteration impaired the interprotomeric interactions that stabilize the trimer apex, resulting in an open trimer conformation and escape from broadly neutralizing autologous plasma antibodies and known V2 apex-directed bnAbs, thereby favoring viral evasion of the early bnAb response of the infected host. Defining the mechanisms by which naturally occurring viral mutations influence the sensitivity of HIV-1 to bnAbs will provide information for the development of vaccines and bnAbs as anti-HIV-1 reagents.
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http://dx.doi.org/10.1128/JVI.00814-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7495384PMC
September 2020

Trehalose limits opportunistic mycobacterial survival during HIV co-infection by reversing HIV-mediated autophagy block.

Autophagy 2021 02 20;17(2):476-495. Epub 2020 Feb 20.

Cellular Immunology Group, International Center for Genetic Engineering and Biotechnology, New Delhi, India.

Opportunistic bacterial infections amongst HIV-infected individuals contribute significantly to HIV-associated mortality. The role of HIV-mediated modulation of innate mechanisms like autophagy in promoting opportunistic infections, however, remains obscure. Here we show, HIV reactivation in or infection of macrophages inhibits autophagy and helps the survival of pathogenic and nonpathogenic non-tuberculous mycobacterial strains (NTMs). The HIV-mediated impairment of xenophagy flux facilitated bacterial survival. Activation of autophagy by trehalose could induce xenophagy flux and kill intracellular or NTMs either during single or co-infections. Trehalose, we delineate, activates PIKFYVE leading to TFEB nuclear translocation in MCOLN1-dependent manner to induce autophagy. Remarkably, trehalose significantly reduced HIV-p24 levels in -infected PBMCs or PBMCs from treatment-naive HIV patients and also controlled mycobacterial survival within -infected animals. To conclude, we report leveraging of HIV-mediated perturbed host innate-immunity by opportunistic bacterial pathogens and show an attractive therapeutic strategy for HIV and associated co-morbidities. AIDS: acquired immune deficiency syndrome; AMPK: AMP-activated protein kinase; ATG5: autophagy related 5; BafA1: bafilomycin A; CFU: colony forming unit; CTSD: cathepsin D; CD63: CD63 molecule; EGFP: enhanced green fluorescent protein; FRET: Förster resonance energy transfer; GABARAP: gamma-aminobutyric acid receptor-associated protein; GAPDH: glyceraldehyde 3-phosphate dehydrogenase; GLUT: glucose transporter; HIV: human immunodeficiency virus; hMDMs: human monocyte derived macrophages; IL2: interleukin 2; LAMP1: lysosomal-associated membrane protein 1; LC3B-II: lipidated microtubule-associated proteins 1A/1B light chain 3B; Mtb: ; MTOR: mechanistic target of rapamycin; mRFP: monomeric red fluorescent protein; M6PR: mannose-6-phosphate receptor; NAC: N- acetyl- L -cysteine; NTM's: non-tuberculous mycobacteria; PBMC: Peripheral Blood Mononuclear cells; PIKFYVE: phosphoinositide kinase; FYVE-Type Zinc Finger; PHA: phytohemagglutinin; PMA: phorbol 12-myristate 13-acetate; PtdIns(3,5)P2: Phosphatidylinositol 3,5-bisphosphate; ; ROS: reactive oxygen species; SQSTM1: sequestosome1; TFEB: transcription factor EB; MCOLN1/TRPML1: mucolipin 1; PIP4P1/TMEM55B: Human trans-membrane Protein 55B; UVRAG: UV Radiation Resistance Associate; VPS35: vacuolar protein sorting associated protein 35; WDR45: WD repeat domain 45; YCAM: Yellow Chameleon.
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http://dx.doi.org/10.1080/15548627.2020.1725374DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7610453PMC
February 2021

Association of Fok1 VDR polymorphism with Vitamin D and its associated molecules in pulmonary tuberculosis patients and their household contacts.

Sci Rep 2019 10 24;9(1):15251. Epub 2019 Oct 24.

Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029, India.

Status of Fok I VDR polymorphism along with vitamin D, Vitamin D receptor (VDR), and cathelicidin levels in Tuberculosis (TB) patients compared to household contacts and implication of these findings in susceptibility to TB is not known. 150 active TB patients, 150 household contacts and 150 healthy controls were recruited from North Indian population. Fok1 VDR polymorphism was studied by polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP).VDR mRNA and protein levels were studied using quantitative real time PCR (q rt PCR) and enzyme linked immunosorbent assay (ELISA) respectively. Cathelicidin and Vitamin D levels were measured using ELISA and chemiluminescence immunoassay (CLIA) respectively. Significant association was found between Fok1 polymorphism and susceptibility to TB (P < 0.0005). VDR mRNA, VDR protein and vitamin D levels were significantly lower in active TB group when compared to household contacts and healthy controls (P < 0.0001, 0.0001 and 0.0005 respectively). Cathelicidin levels were higher in active TB patients compared to other groups (P < 0.0001). Expression of VDR and cathelicidin was significantly higher among 'FF' genotypes of VDR (more active form of VDR) compared to 'ff' genotype (less active form of VDR). 'f' allele was associated with increased susceptibility to TB. Higher frequency of 'F' allele, increased VDR expression along with increased vitamin D levels in household contacts compared to active TB group might be responsible for protection against active TB.
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http://dx.doi.org/10.1038/s41598-019-51803-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6813333PMC
October 2019

Altered Expression of Complement Regulatory Proteins CD35, CD46, CD55, and CD59 on Leukocyte Subsets in Individuals Suffering From Coronary Artery Disease.

Front Immunol 2019 29;10:2072. Epub 2019 Aug 29.

Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India.

Studies conducted in animal models have suggested that membrane complement regulatory proteins play an important role in the pathophysiology of coronary artery disease (CAD). In this study, a total of 100 individuals, with stable CAD and 100 healthy controls, both groups predominantly male, were recruited. We evaluated the plasma levels of complement regulatory proteins (Cregs) CD35, CD46, CD55, and CD59 and their surface expression on granulocytes, lymphocytes, and monocytes by flow cytometry. The mRNA expression of these Cregs in total leukocytes was determined by quantitative PCR. The soluble forms of Cregs, C3c, Mannose binding protein-associated serine protease 2 (MASP-2), Platelet activating factor-acetyl hydrolase (PAF-AH), and inflammatory cytokines were quantified by ELISA. High plasma levels of C3c, indicative of complement activation, in addition to significantly low levels of Cregs, were observed in CAD patients. A significantly lower expression of CD46 and CD55 on the surface of lymphocytes, monocytes, and granulocytes and higher surface expression of CD35 and CD59 on granulocytes ( < 0.0001) was seen in CAD patients as compared to healthy donors. The high expression of CD59 on granulocytes positively correlated with the severity of disease and may serve as a potential marker of disease progression in CAD.
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http://dx.doi.org/10.3389/fimmu.2019.02072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6727527PMC
September 2020

Status of VEGF in preeclampsia and its effect on endoplasmic reticulum stress in placental trophoblast cells.

Eur J Obstet Gynecol Reprod Biol X 2019 Oct 21;4:100070. Epub 2019 Jun 21.

Department of Anatomy, All India Institute of Medical Sciences (AIIMS), New Delhi, 110029, India.

Objective: To explore the role of VEGF in attenuating endoplasmic reticulum stress in placental trophoblast cells.

Study Design: Study was divided into following parts: 1. Serum Analysis of GRP78 and VEGF using sandwich ELISA. 2. Expression of VEGF and GRP78 in placentae by immunohistochemistry (IHC). 3. experiments. Status of ER stress markers (GRP78, eIF2α, XBP1, ATF6 and CHOP) was assessed at various time points (8 h, 14 h, 24 h) when trophoblast cells were treated with varying concentration(s) of VEGF and also by adding recombinant VEGF at protein (Immunofluorescence, Western blot) and transcript levels (qRT-PCR).

Results: Increased GRP78 and decreased VEGF protein levels in sera and placentae of preeclamptic pregnant women and reduced expression of various ER stress markers at both transcript and protein levels was observed in trophoblast cells when they were exposed to recombinant VEGF thereby indicating positive role of VEGF in alleviating ER stress.

Conclusions: Reduced expression of ER stress markers in trophoblast cells against increased VEGF highlighted a new window to explore prospective drugs that can be designed to modulate the activities of various ER stress sensors in order to alleviate ER stress in pregnant women with preeclampsia.
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http://dx.doi.org/10.1016/j.eurox.2019.100070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6728727PMC
October 2019

Status of vitamin D and the associated host factors in pulmonary tuberculosis patients and their household contacts: A cross sectional study.

J Steroid Biochem Mol Biol 2019 10 27;193:105419. Epub 2019 Jun 27.

Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029, India. Electronic address:

Innate immunity plays an important role in pathophysiology of tuberculosis which is influenced by various host factors. One such factor is vitamin D which, along with its associated molecule, can alter the host defense against Mycobacterium Tuberculosis (M.Tb.) via altered production of cathelicidin and nitric oxide, both having bactericidal effect. Therefore, assessment of vitamin D and its associated molecules in tuberculosis patients and household contacts as compared to healthy controls were done and the implication of these findings in susceptibility to tuberculosis (TB) was studied. 80 active TB patients, 75 household contacts and 70 healthy controls were included. Vitamin D receptor (VDR), vitamin D binding protein (VDBP) and inducible nitric oxide synthase (iNOS) mRNA levels were studied using quantitative PCR. Serum VDR, cathelicidin, and iNOS levels were measured using ELISA. Vitamin D and NO levels were measured in serum using chemiluminescence based immunoassay and greiss reaction based colorimetry kit respectively. Decreased serum levels of vitamin D were observed in active TB patients as compared to healthy controls (p < 0.001). VDR and iNOS mRNA levels were found to be significantly lower in active TB patients compared to household contacts and healthy controls (p < 0.0001 and 0.005 respectively). VDBP mRNA expression was found to be lower in active TB group as compared to household contacts and healthy controls however the difference was not found to be significant (p > 0.21). Although, mRNA expression of VDR, VDR protein and iNOS along with vitamin D levels were significantly (p < 0.05) higher in household contacts compared to active TB group. However, levels of iNOS, NO and cathelicidin were found to be higher in TB patients as compared to household contacts and healthy controls (p < 0.01, 0.05 and 0.01 respectively). Higher levels of Vitamin D along with VDR and iNOS expression in household contacts as compared to active TB patients suggest vitamin D might have a protective role against TB plausibly decreasing disease susceptibility. Low vitamin D levels in active TB patients warrants further studies to determine the role of vitamin D supplementation in prevention and treatment of TB.
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http://dx.doi.org/10.1016/j.jsbmb.2019.105419DOI Listing
October 2019

Viral Characteristics Associated with Maintenance of Elite Neutralizing Activity in Chronically HIV-1 Clade C-Infected Monozygotic Pediatric Twins.

J Virol 2019 09 13;93(17). Epub 2019 Aug 13.

Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India

Broad and potent neutralizing antibodies (bnAbs) with multiple epitope specificities evolve in HIV-1-infected children. Herein, we studied two antiretroviral-naive chronically HIV-1 clade C-infected monozygotic pediatric twins, AIIMS_329 and AIIMS_330, with potent plasma bnAbs. Elite plasma neutralizing activity was observed since the initial sampling at 78 months of age in AIIMS_330 and persisted throughout, while in AIIMS_329 it was seen at 90 months of age, after which the potency decreased over time. We evaluated potential viral characteristics associated with the varied immune profiles by generating single genome-amplified pseudoviruses. The AIIMS_329 viruses generated from the 90-month time point were neutralization sensitive to bnAbs and contemporaneous plasma antibodies, while viruses from the 112-month and 117-month time points were resistant to most bnAbs and contemporaneous plasma. AIIMS_329 viruses developed resistance to plasma neutralizing antibodies (nAbs) plausibly by N160 glycan loss and V1 and V4 loop lengthening. The viruses generated from AIIMS_330 (at 90 and 117 months) showed varied susceptibility to bnAbs and autologous contemporaneous plasma antibodies, while the viruses of the 112-month time point, at which the plasma nAb specificities mapped to the V2 glycan, V3 glycan, and CD4 binding site (CD4bs), were resistant to contemporaneous plasma antibodies as well as to most bnAbs. Chimeric viruses were constructed from 90-month-time-point PG9-sensitive AIIMS_329 and AIIMS_330 viruses with swapped V1V2 regions of their respective evolved viruses (at 112 and 117 months), which led to higher resistance to neutralization by PG9 and autologous plasma antibodies. We observed the evolution of a viral pool in the AIIMS_330 donor comprising plasma antibody neutralization-sensitive or -resistant diverse autologous viruses that may have contributed to the development and maintenance of elite neutralizing activity. Herein, we report the longitudinal development of bnAbs in a pair of chronically HIV-1 clade C-infected monozygotic pediatric twins, AIIMS_329 and AIIMS_330, who acquired the infection by vertical transmission. The plasma from both donors, sharing a similar genetic makeup and infecting virus, showed the evolvement of bnAbs targeting common epitopes in the V2 and V3 regions of the envelope, suggesting that bnAb development in these twins may perhaps be determined by specific sequences in the shared virus that can guide the development of immunogens aimed at eliciting V2 and V3 bNAbs. Characterization of the neutralization-sensitive and -resistant viruses coevolving with bNAbs in the contemporaneous AIIMS_330 plasma provides information toward understanding the viral alterations that may have contributed to the development of resistance to bnAbs. Further longitudinal studies in more monozygotic and dizygotic twin pairs will help in delineating the role of host and viral factors that may contribute to the development of bnAbs.
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http://dx.doi.org/10.1128/JVI.00654-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6694815PMC
September 2019

Phage display antibody libraries: A robust approach for generation of recombinant human monoclonal antibodies.

Int J Biol Macromol 2019 Aug 3;135:907-918. Epub 2019 Jun 3.

Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India. Electronic address:

Monoclonal antibodies (mAbs) and their derivatives have achieved remarkable success as medicine, targeting both diagnostic and therapeutic applications associated with communicable and non-communicable diseases. In the last 3 to 4 decades, tremendous success has been manifested in the field of cancer therapy, autoimmune diseases, cardiovascular and infectious diseases. MAbs are the fastest growing class of biopharmaceuticals, with more than 25 derivatives are in clinical use and 7 of these have been isolated through phage display technology. Phage display technology has gained impetus in the field of medical and health sciences, as a large repertoire of diverse recombinant antibodies, targeting various antigens have been generated in a short span of time. A prominent number of phage display derived antibodies are already approved for therapy and significant numbers are currently in clinical trials. In this review we have discussed the various strategies employed for generation of monoclonal antibodies; their advantages, limitations and potential therapeutic applications. We also discuss the potential of phage display antibody libraries in isolation of monoclonal antibodies.
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http://dx.doi.org/10.1016/j.ijbiomac.2019.06.006DOI Listing
August 2019

Epidermal growth factor receptor (EGFR), KRAS, and BRAF mutations in lung adenocarcinomas: A study from India.

Curr Probl Cancer 2019 10 17;43(5):391-401. Epub 2018 Dec 17.

Department of Pathology, All India Institute of Medical Sciences, New Delhi, India. Electronic address:

Mitogen-Activated Protein (MAP) Kinase pathway involves several oncogenic genes which can serve as potential targets for therapy. Therefore, aim of the present study is to analyze mutations in the MAP Kinase pathway in pulmonary adenocarcinoma (ADCA) of Indian patients along with clinico-pathologic correlation and determination of the survival status in patients receiving therapy. Blocks and slides of 125 pulmonary ADCA of last 5 years were retrieved. Histo-morphology and tumor content were determined. EGFR, KRAS, BRAF and MEK1 genes were analyzed using Sanger sequencing and Real-time polymerase chain reaction (PCR). Clinico-pathologic correlation and survival analysis were performed. Fifty-eight (46.4%) patients harbored genetic mutations of which 49 had single somatic mutations, 5 had multiple exonic and 4 showed coexisting EGFR and KRAS mutations. EGFR mutations were seen in 24.8%, KRAS in 19.2% and BRAF (non-V600E) in 2.4% cases. There was no difference in progression-free survival of wild- type/single mutations when compared with multiple/ coexisting mutations (P = 0.09). However, the P value may indicate borderline correlation. To conclude, EGFR and KRAS mutations may coexist in the same patient in lung ADCA. Multiple exonic mutations of KRAS gene formed substantial percentage of our cohort, requiring further exploration. Lung ADCA harbouring BRAF mutations are commonly non-V600E. Testing of all major genetic driver mutations of lung ADCA irrespective of histology and other demographic characteristics is necessary.
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http://dx.doi.org/10.1016/j.currproblcancer.2018.12.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6579716PMC
October 2019

An HIV-1 Broadly Neutralizing Antibody from a Clade C-Infected Pediatric Elite Neutralizer Potently Neutralizes the Contemporaneous and Autologous Evolving Viruses.

J Virol 2019 02 5;93(4). Epub 2019 Feb 5.

Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India

Broadly neutralizing antibodies (bNAbs) have demonstrated protective effects against HIV-1 in primate studies and recent human clinical trials. Elite neutralizers are potential candidates for isolation of HIV-1 bNAbs. The coexistence of bNAbs such as BG18 with neutralization-susceptible autologous viruses in an HIV-1-infected adult elite controller has been suggested to control viremia. Disease progression is faster in HIV-1-infected children than in adults. Plasma bNAbs with multiple epitope specificities are developed in HIV-1 chronically infected children with more potency and breadth than in adults. Therefore, we evaluated the specificity of plasma neutralizing antibodies of an antiretroviral-naive HIV-1 clade C chronically infected pediatric elite neutralizer, AIIMS_330. The plasma antibodies showed broad and potent HIV-1 neutralizing activity with >87% (29/33) breadth, a median inhibitory dilution (ID) value of 1,246, and presence of N160 and N332 supersite-dependent HIV-1 bNAbs. The sorting of BG505.SOSIP.664.C2 T332N gp140 HIV-1 antigen-specific single B cells of AIIMS_330 resulted in the isolation of an HIV-1 N332 supersite-dependent bNAb, AIIMS-P01. The AIIMS-P01 neutralized 67% of HIV-1 cross-clade viruses, exhibited substantial indels despite limited somatic hypermutations, interacted with native-like HIV-1 trimer as observed in negative stain electron microscopy, and demonstrated high binding affinity. In addition, AIIMS-P01 neutralized the coexisting and evolving autologous viruses, suggesting the coexistence of vulnerable autologous viruses and HIV-1 bNAbs in the AIIMS_330 pediatric elite neutralizer. Such pediatric elite neutralizers can serve as potential candidates for isolation of novel HIV-1 pediatric bNAbs and for understanding the coevolution of virus and host immune response. More than 50% of the HIV-1 infections globally are caused by clade C viruses. To date, there is no effective vaccine to prevent HIV-1 infection. Based on the structural information of the currently available HIV-1 bNAbs, attempts are under way to design immunogens that can elicit correlates of protection upon vaccination. Here, we report the isolation and characterization of an HIV-1 N332 supersite-dependent bNAb, AIIMS-P01, from a clade C chronically infected pediatric elite neutralizer. The N332 supersite is an important epitope and is one of the current HIV-1 vaccine targets. AIIMS-P01 potently neutralized the contemporaneous and autologous evolving viruses and exhibited substantial indels despite low somatic hypermutations. Taken together with the information on infant bNAbs, further isolation and characterization of bNAbs contributing to the plasma breadth in HIV-1 chronically infected children may help provide a better understanding of their role in controlling HIV-1 infection.
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http://dx.doi.org/10.1128/JVI.01495-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364018PMC
February 2019

Isolation and Characterization of Cross-Neutralizing Human Anti-V3 Single-Chain Variable Fragments (scFvs) Against HIV-1 from an Antigen Preselected Phage Library.

Appl Biochem Biotechnol 2019 Mar 28;187(3):1011-1027. Epub 2018 Aug 28.

Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India.

Recently conducted human phase- I trials showed protective effect of anti-HIV-1 broadly neutralizing antibodies (bnAbs). The V3 region of the HIV-1 envelope is highly conserved as it is the co-receptor binding site, and is highly immunogenic. Recombinant single-chain antibody fragments (scFvs) can serve as potential tools for construction of chimeric/bispecific antibodies that can target different epitopes on the HIV-1 envelope. Previously, we have constructed a V3 specific human scFv phage recombinant library by a combinational approach of Epstein-Barr virus (EBV) transformation and antigen (V3) preselection, using peripheral blood mononuclear cells (PBMCs), from a subtype C HIV-1 infected antiretroviral naive donor. In the present study, by biopanning this recombinant scFv phage library with V3B (subtype B) and V3C (subtype C) peptides, we identified unique cross reactive anti-V3 scFv monoclonals. These scFvs demonstrated cross-neutralizing activity when tested against subtype A, subtype B, and subtype C viruses. Further, molecular modeling of the anti-V3 scFvs with V3C and V3B peptides predicted their sites of interaction with the scFvs, providing insights for future immunogen design studies. A large collection of such monoclonal antibody fragments with diverse epitope specificities can be useful immunotherapeutic reagents along with antiretroviral drugs to prevent HIV-1 infection and disease progression.
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http://dx.doi.org/10.1007/s12010-018-2862-8DOI Listing
March 2019

Expression of complement receptor 3 (CR3) and regulatory protein CD46 on dendritic cells of antiretroviral naïve and treated HIV-1 infected individuals: Correlation with immune activation status.

Mol Immunol 2018 04;96:83-87

Department of Biochemistry, All India Institute of Medical Science, New Delhi, 110029, India.

During infection and budding, human immunodeficiency virus-1 (HIV-1) acquires regulators of Complement Activation (RCAs) along with the host cell membrane on the viral envelope. Activation of host complement system results in opsonization of virus by complement fragments, however the virus evades complement mediated lysis (CoML) by virtue of the RCAs on the viral envelope. The RCAs on HIV-1 envelope process complement protein C3 into various fragments that promote viral entry and infection of cells through different complement receptors. Complement opsonized HIV-1 has been shown in vitro to infect dendritic cells (DCs) in a CR3 dependent manner, although the role of CR3 and CD46 in natural HIV-1 infection is not clear. Surface expression of CR3 and CD46 on DC subsets of 30 antiretroviral naïve, 31 treated (cART) HIV-1 infected individuals and 30 seronegative controls was measured by flow cytometry and plasma levels of cytokines and complement activity (C3c levels) were quantitated by sandwich ELISA. Significantly lower surface expression of CR3 and CD46 was observed on DC subsets in naïve and treated HIV-1 infected individuals compared to controls. Significantly higher complement activation and plasma levels of IL-4, IL-8, IL-10 and IFN-γ were observed in treatment naïve HIV-1 infected individuals than controls. Significantly lower plasma levels of IL-4, IL-6, IL-8 and IL-10 were observed in treated vs. naïve HIV-1 infected individuals. Our findings suggest that alterations in expression of CR3 and CD46 on DCs along with complement activity could be factors that influence viral persistence and HIV-1 disease progression and need to be further evaluated.
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http://dx.doi.org/10.1016/j.molimm.2018.02.011DOI Listing
April 2018

Challenges in integrating component level technology and system level information from Ayurveda: Insights from NMR phytometabolomics and anti-HIV potential of select Ayurvedic medicinal plants.

J Ayurveda Integr Med 2019 Apr - Jun;10(2):94-101. Epub 2018 Jan 3.

Department of Ocular Pharmacology and Pharmacy, All India Institute of Medical Sciences, New Delhi, India.

Background: Information from Ayurveda meeting the analytical challenges of modern technology is an area of immense relevance. Apart from the cerebral task of bringing together two different viewpoints, the question at the pragmatic level remains 'who benefits whom'.

Objective: The aim is to highlight the challenges in integration of information (Ayurvedic) and technology using test examples of Nuclear Magnetic Resonance (NMR) metabolomics and anti-HIV-1 potential of select Ayurvedic medicinal plants. The other value added objective is implications and relevance of such work for Ayurveda.

Materials And Methods: Six medicinal plants (Azadirachta indica, Tinospora cordifolia, Swertia chirata, Terminalia bellerica, Zingiber officinale and Symplocos racemosa) were studied using high resolution proton NMR spectroscopy based metabolomics and also evaluated for anti-HIV-1 activity on three pseudoviruses (ZM53 M.PB12, ZM109F.PB4, RHPA 4259.7).

Results: Of the six plants, T. bellerica and Z. officinale showed minimum cell cytotoxicity and maximum anti-HIV-1 potential. T. bellerica was effective against all the three HIV-1 pseudoviruses. Untargeted NMR profiling and multivariate analyses demonstrated that the six plants, all of which had different Ayurvedic pharmacological properties, showed maximum differences in the aromatic region of the spectra.

Conclusion: The work adds onto the list of potential plants for anti-HIV-1 drug molecules. At the same time, it has drawn attention to the different perspectives of Ayurveda and Western medicine underscoring the inherent limitations of conceptual bilinguism between the two systems, especially in the context of medicinal plants. The study has also highlighted the potential of NMR metabolomics in study of plant extracts as used in Ayurveda.
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http://dx.doi.org/10.1016/j.jaim.2017.06.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6598850PMC
January 2018

Alterations in B Cell Compartment Correlate with Poor Neutralization Response and Disease Progression in HIV-1 Infected Children.

Front Immunol 2017 1;8:1697. Epub 2017 Dec 1.

Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India.

Several B cell defects are reported in HIV-1 infected individuals including variation in B cell subsets, polyclonal B cell activation and exhaustion, with broadly neutralizing antibodies elicited in less than 10-20% of the infected population. HIV-1 disease progression is faster in children than adults. B Lymphocyte Stimulator (BLyS), expressed on dendritic cells (DCs), is a key regulator of B cell homeostasis. Understanding how DCs influence B cell phenotype and functionality (viral neutralization), thereby HIV-1 disease outcome in infected children, is important to develop interventional strategies for restoration of B cell function. In this study, a total of 38 vertically transmitted HIV-1 infected antiretroviral therapy (ART) naïve children and 25 seronegative controls were recruited. Based on the CD4 counts and years post-infection, infected children were categorized as long-term non-progressors (LTNPs) ( = 20) and progressors ( = 18). Eight of these progressors were followed up at 6-12 months post-ART. Percentages (%) of DCs, B cell subsets, and expression of BLyS on DCs were analyzed by flow-cytometry. Plasma levels of B cell growth factors were measured by ELISA and viral neutralization activity was determined using TZM-bl assay. Lower (%) of myeloid DCs (mDCs), plasmacytoid DCs, and high expression of BLyS on mDCs were observed in HIV-1 infected progressors than seronegative controls. Progressors showed lower % of naive B cells, resting memory B cells and higher % of mature activated, tissue-like memory B cells as compared to seronegative controls. Higher plasma levels of IL-4, IL-6, IL-10, and IgA were observed in progressors vs. seronegative controls. Plasma levels of IgG were high in progressors and in LTNPs than seronegative controls, suggesting persistence of hypergammaglobulinemia at all stages of disease. High plasma levels of BLyS in progressors positively correlated with poor viral neutralizing activity. Interestingly on follow up, treatment naïve progressors, post-ART showed increase in resting memory B cells along with reduction in plasma BLyS levels that correlated with improvement in viral neutralization. This is the first study to demonstrate that reduction in plasma BLyS levels correlates with restoration of B cell function, in terms of viral neutralization in HIV-1-infected children.
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http://dx.doi.org/10.3389/fimmu.2017.01697DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5717014PMC
December 2017

CD4-Binding Site Directed Cross-Neutralizing scFv Monoclonals from HIV-1 Subtype C Infected Indian Children.

Front Immunol 2017 15;8:1568. Epub 2017 Nov 15.

Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India.

Progression of human immunodeficiency virus type-1 (HIV-1) infection in children is faster than adults. HIV-1 subtype C is responsible for more than 50% of the infections globally and more than 90% infections in India. To date, there is no effective vaccine against HIV-1. Recent animal studies and human Phase I trials showed promising results of the protective effect of anti-HIV-1 broadly neutralizing antibodies (bnAbs). Interaction between CD4 binding site (CD4bs) on the HIV-1 envelope glycoprotein and CD4 receptor on the host immune cells is the primary event leading to HIV-1 infection. The CD4bs is a highly conserved region, comprised of a conformational epitope, and is a potential target of bnAbs such as VRC01 that is presently under human clinical trials. Recombinant scFvs can access masked epitopes due to their small size and have shown the potential to inhibit viral replication and neutralize a broad range of viruses. Pediatric viruses are resistant to many of the existing bnAbs isolated from adults. Therefore, in this study, pooled peripheral blood mononuclear cells from 9 chronically HIV-1 subtype C infected pediatric cross-neutralizers whose plasma antibodies exhibited potent and cross-neutralizing activity were used to construct a human anti-HIV-1 scFv phage library of 9 × 10 individual clones. Plasma mapping using CD4bs-specific probes identified the presence of CD4bs directed antibodies in 4 of these children. By extensive biopanning of the library with CD4bs-specific antigen RSC3 core protein, we identified two cross-neutralizing scFv monoclonals 2B10 and 2E4 demonstrating a neutralizing breadth and GMT of 77%, 17.9 µg/ml and 32%, 51.2 µg/ml, respectively, against a panel of 49 tier 1, 2 and 3 viruses. Both scFvs competed with anti-CD4bs bnAb VRC01 confirming their CD4bs epitope specificity. The 2B10 scFv was effective in neutralizing the 7 subtype C and subtype A pediatric viruses tested. Somatic hypermutations in the VH gene of scFvs (10.1-11.1%) is comparable with that of the adult antibodies. These cross-neutralizing CD4bs-directed scFvs can serve as potential reagents for passive immunotherapy. A combination of cross-neutralizing scFvs of diverse specificities with antiretroviral drugs may be effective in suppressing viremia at an early stage of HIV-1 infection and prevent disease progression.
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http://dx.doi.org/10.3389/fimmu.2017.01568DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5694743PMC
November 2017

Evolution of cross-neutralizing antibodies and mapping epitope specificity in plasma of chronic HIV-1-infected antiretroviral therapy-naïve children from India.

J Gen Virol 2017 Jul 12;98(7):1879-1891. Epub 2017 Jul 12.

Department of Biochemistry, All India Institute of Medical Sciences, New Delhi 110029, India.

Delineating the factors leading to the development of broadly neutralizing antibodies (bnAbs) during natural HIV-1 infection and dissecting their epitope specificities generates useful information for vaccine design. This is the first longitudinal study to assess the plasma-neutralizing antibody response and neutralizing determinants in HIV-1-infected children from India. We enrolled 26 and followed up 20 antiretroviral therapy (ART)-naïve, asymptomatic, chronic HIV-1-infected children. Five (19.2 %) baseline and 10 (50 %) follow-up plasma samples neutralized ≥50 % of subtypes A, B and C tier 2 viruses at an ID50 titre ≥150. A modest improvement in neutralization breadth and potency was observed with time. At baseline, subtype C-specific neutralization predominated (P=0.026); interestingly, follow-up samples exhibited cross-neutralizing activity. Epitope mapping revealed V3C reactive antibodies with significantly increased Max50 binding titres in follow-up samples from five infected children; patient #4's plasma antibodies exhibited V3-directed neutralization. A salient observation was the presence of CD4 binding site (CD4bs)-specific NAbs in patient #18 that improved with time (1.76-fold). The RSC3 wild-type (RSC3WT) protein-depleted plasma eluate of patient #18 demonstrated a more than 50% ID50 decrease in neutralization capacity against five HIV-1 pseudoviruses. Further, the presence of CD4bs-neutralizing determinants in patient #18's plasma was confirmed by the neutralizing activity demonstrated by the CD4bs-directed IgG fraction purified from this plasma, and competition with sCD4 against JRFLgp120, identifying this paediatric donor as a potential candidate for the isolation of CD4bs-directed bnAbs. Overall, we observed a relative increase in plasma-neutralizing activity with time in HIV-1-infected children, which suggests that the bnAbs evolve.
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http://dx.doi.org/10.1099/jgv.0.000824DOI Listing
July 2017

Impact of chemotherapy on symptom profile, oxidant-antioxidant balance and nutritional status in non-small cell Lung Cancer.

Lung India 2017 Jul-Aug;34(4):336-340

Department of Pulmonary Medicine and Sleep Disorders, AIIMS, New Delhi, India.

Background: Lung cancer is associated with an oxidant-antioxidant imbalance that is implicated in tumor progression. However, the association of this imbalance on disease burden and treatment response is unclear. The effect of chemotherapy on oxidative stress, antioxidant status, and nutritional profile in patients with advanced nonsmall cell lung cancer (NSCLC) was prospectively evaluated.

Subjects And Methods: Patients with confirmed cytological/histological diagnosis of NSCLC were recruited. Performance status was determined using the Eastern Cooperative Oncology Group grading and the Karnofsky Performance Scale. Skin fold anthropometry was done for nutritional assessment. All patients received chemotherapy with intravenous carboplatin and paclitaxel at three-weekly intervals. Response was assessed after four cycles by repeat imaging. Plasma levels of total antioxidant status (TAS), malondialdehyde (MDA), and glutathione peroxidase (GPx) levels were estimated using commercially available kits, and the change was correlated with clinical outcome, response to chemotherapy, performance status, and nutritional profile.

Results: Thirty-five cases were studied (92% males), with a mean (SD) age of 56.2 (9.3) years. Following treatment, majority of patients demonstrated stable disease (n = 15 [42%]), followed by partial response (29%), progressive disease (22%), and complete remission (6%). Significant improvement occurred in respiratory symptoms. Body fat declined while subscapular skinfold thickness and 6-min walk distance increased. Spirometric values and performance status remained unchanged. GPx levels declined significantly while no notable change was observed in MDA and TAS levels.

Conclusions: Chemotherapy for NSCLC improves symptoms, nutritional status, and exercise capacity but worsens the antioxidant status.
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http://dx.doi.org/10.4103/0970-2113.209230DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5504890PMC
July 2017

Detection of Promoter DNA Methylation of APC, DAPK, and GSTP1 Genes in tissue Biopsy and Matched Serum of Advanced-Stage Lung Cancer Patients.

Cancer Invest 2017 Jul 19;35(6):423-430. Epub 2017 May 19.

a Department of Pulmonary Medicine and Sleep Disorders , All India Institute of Medical Science , New Delhi , India.

Promoter DNA hypermethylation of APC, DAPK, and GSTP1 genes was evaluated in biopsy and matched serum of 160 lung cancer patients and 70 controls. In biopsy, 83.1, 83.1, and 78.1% of lung cancer patients and 72.9, 70, and 70% of controls, while in serum, 52.5, 30.6, and 65.6% of lung cancer patients and 14.3, 18.6, and 30% of controls were positive for APC, DAPK, and GSTP1 hypermethylation respectively. We couldn't find any significant role of DNA hypermethylation in lung cancer. However, long follow-up of methylation positive controls will be required to confirm its role for the prediction of lung cancer.
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http://dx.doi.org/10.1080/07357907.2017.1309547DOI Listing
July 2017

Cross-neutralizing anti-HIV-1 human single chain variable fragments(scFvs) against CD4 binding site and N332 glycan identified from a recombinant phage library.

Sci Rep 2017 03 23;7:45163. Epub 2017 Mar 23.

Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India.

More than 50% of HIV-1 infection globally is caused by subtype_C viruses. Majority of the broadly neutralizing antibodies (bnAbs) targeting HIV-1 have been isolated from non-subtype_C infected donors. Mapping the epitope specificities of bnAbs provides useful information for vaccine design. Recombinant antibody technology enables generation of a large repertoire of monoclonals with diverse specificities. We constructed a phage recombinant single chain variable fragment (scFv) library with a diversity of 7.8 × 10 clones, using a novel strategy of pooling peripheral blood mononuclear cells (PBMCs) of six select HIV-1 chronically infected Indian donors whose plasma antibodies exhibited potent cross neutralization efficiency. The library was panned and screened by phage ELISA using trimeric recombinant proteins to identify viral envelope specific clones. Three scFv monoclonals D11, C11 and 1F6 selected from the library cross neutralized subtypes A, B and C viruses at concentrations ranging from 0.09 μg/mL to 100 μg/mL. The D11 and 1F6 scFvs competed with mAbs b12 and VRC01 demonstrating CD4bs specificity, while C11 demonstrated N332 specificity. This is the first study to identify cross neutralizing scFv monoclonals with CD4bs and N332 glycan specificities from India. Cross neutralizing anti-HIV-1 human scFv monoclonals can be potential candidates for passive immunotherapy and for guiding immunogen design.
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http://dx.doi.org/10.1038/srep45163DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5362912PMC
March 2017

Evaluation of plasma leptin, tumor necrosis factor-α, and prealbumin as prognostic biomarkers during clinical recovery from acute exacerbations of chronic obstructive pulmonary disease.

Lung India 2017 Jan-Feb;34(1):3-8

Department of Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences, New Delhi, India.

Background: Inflammatory and nutritional biomarkers have an important bearing on outcomes of acute exacerbations of chronic obstructive pulmonary disease (AECOPD), but the temporal profile of these compounds during an acute episode is unclear.

Patients And Methods: Plasma leptin, prealbumin, and tumor necrosis factor-alpha (TNF-α) were estimated at baseline and before hospital discharge in patients with AECOPD.

Results: A total of 82 patients were evaluated (66 males; mean (standard deviation) age, 61.6 (10.1) years. Of these, 74 subjects (90.2%) were current or former smokers, with median (range) pack-years of 15 (0-96), duration of COPD of 8 years (range, 2-25 years) and duration of current symptoms being 5 days (range, 1-30 days). Majority (41.5%) had type I (severe) exacerbation. During the current episode, 46 patients (58.9%) required mechanical ventilation for a median of 6 days (range, 1-34). The median duration of hospital stay was 13 days, (range, 1-110). At discharge, significant reduction was observed in dyspnea, total leukocyte count, erythrocyte sedimentation rate (ESR), partial pressure of carbon dioxide, hemoglobin, urea, creatinine, potassium, aspartate transferase, and TNF-α levels compared to baseline, whereas arterial pH, PO, serum albumin, prealbumin, and leptin significantly improved. No difference was seen in leptin, prealbumin, and TNF-α between patients with mild/moderate and severe exacerbation, or between patients who required or did not require mechanical ventilation. Change in leptin correlated with body mass index and change in ESR; no associations were observed between leptin, prealbumin, and TNF-α with other clinico-laboratory variables.

Conclusion: Plasma levels of novel inflammatory and nutritional biomarkers, i.e., leptin, TNF-α, and prealbumin are altered in AECOPD episodes and lag behind other parameters during recovery. These biomarkers are not reliable predictors of clinical outcomes in these patients.
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http://dx.doi.org/10.4103/0970-2113.197101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5234195PMC
February 2017

Variability in proteinase-antiproteinase balance, nutritional status, and quality of life in stable chronic obstructive pulmonary disease due to tobacco and nontobacco etiology.

Lung India 2016 Nov-Dec;33(6):605-610

Department of Pulmonary Medicine and Sleep Disorders, All Institute of Medical Sciences, New Delhi, India.

Context: Although the role of proteinase/antiproteinase imbalance in chronic obstructive pulmonary disease (COPD) due to tobacco is well established, information in COPD due to nontobacco etiology is sparse.

Aims: To assess the variability in metalloproteinase activity in COPD related to tobacco and nontobacco causes.

Settings And Design: This is a hospital-based, prospective, observational study.

Subjects And Methods: Serum matrix metalloproteinase-9 (MMP-9) and tissue inhibitor of metalloproteinases-1 (TIMP-1) were estimated in 200 subjects divided equally into four groups, i.e. COPD in tobacco smokers, COPD in nonsmokers but with exposure to biomass-related indoor air pollution, smokers without COPD, and nonsmoking healthy controls. Anthropometric skinfold measurements, quality of life (QOL) using St. George Respiratory Questionnaire, and exercise capacity using the 6-min walk test (6-MWT) were carried out. Groups were compared using analysis of variance and Kruskal-Wallis plus Mann-Whitney U-test to assess differences between groups. The Chi-square and Fisher's exact tests were used to evaluate associations among categorical variables. Spearman's rank correlation was calculated to assess the correlation between data.

Results: Patients with COPD due to either tobacco or nontobacco etiology were older, more malnourished, had worse QOL, and poorer exercise capacity compared to non-COPD subjects. Triceps, subscapular, and suprailiac skinfold thicknesses were less in smokers with COPD than biomass-related COPD. MMP-9 and TIMP-1 levels were similar across all groups. TIMP-1 significantly correlated with 6-MWT among all groups.

Conclusions: The protease-antiprotease balance in COPD is similar irrespective of the presence or absence of tobacco exposure but is related to poor exercise capacity.
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http://dx.doi.org/10.4103/0970-2113.192859DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5112816PMC
November 2016

Waist-to-Height Ratio Compared to Standard Obesity Measures as Predictor of Cardiometabolic Risk Factors in Asian Indians in North India.

Metab Syndr Relat Disord 2016 12 14;14(10):492-499. Epub 2016 Oct 14.

7 Biostatistics, All India Institute of Medical Sciences , New Delhi, India .

Objective: The aim of this study was to compare the discriminatory ability of body mass index (BMI), waist circumference (WC), waist-to-hip ratio (WHR), and waist-to-height ratio (WHtR) in identifying the presence of cardiometabolic risk factors in Asian Indians.

Methods: This cross-sectional study involved 509 subjects (278 males and 231 females) aged 20-60 years from New Delhi, India. Measurements included complete clinical examination, blood pressure, weight, height, WC, BMI, WHR and WHtR, fasting blood glucose, lipid profile, and fasting insulin levels. Receiver operating characteristic curve analyses were performed to compare predictive validity of various adiposity measures against the cardiometabolic risk factors (dyslipidemia, hyperinsulinemia, impaired fasting glucose, hypertension, and metabolic syndrome). The odds ratio for the presence of individual cardiometabolic risk factors in the presence of overweight, abdominal obesity, and high WHtR were calculated using logistic regression analysis.

Results: WC had the highest area under ROC for all other cardiometabolic risk factors except hyperinsulinemia in males and for dyslipidemia, metabolic syndrome and presence of at least one cardiometabolic risk factor in females. For metabolic syndrome, WC, followed by WHtR, was observed to be the better predictor than other measures of adiposity, and WHtR appeared to be the best predictor for hypertension in both genders, particularly in women.

Conclusions: In the northern Asian Indian population with high prevalence of cardiometabolic risk factors, a combination of WC and WHtR appeared to be having better clinical utility than BMI and WHR in identifying individuals with cardiometabolic risk factors.
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http://dx.doi.org/10.1089/met.2016.0041DOI Listing
December 2016

Neutralization resistant HIV-1 primary isolates from antiretroviral naïve chronically infected children in India.

Virology 2016 12 17;499:105-113. Epub 2016 Sep 17.

Department of Biochemistry, All India Institute of Medical Sciences, New Delhi 110029, India. Electronic address:

Anti-HIV-1 broadly neutralizing antibodies (bnAbs) have been extensively tested against pesudoviruses of diverse strains. We generated and characterized HIV-1 primary isolates from antiretroviral naïve infected Indian children, and determined their susceptibility to known NAbs. All the 8 isolates belonged to subtype-C and were R5 tropic. Majority of these viruses were resistant to neutralization by NAbs, suggesting that the bnAbs, known to efficiently neutralize pseudoviruses (adult and pediatric) of different strains, are less effective against pediatric primary isolates. Interestingly, AIIMS_329 isolate displayed high susceptibility to neutralization by PG9 and PG16bnAbs, with IC titer of 1.3 and 0.97μg/ml, suggesting exposure of this epitope on this virus. All isolates except AIIMS_506 were neutralized by contemporaneous plasma antibodies. Our findings suggest that primary isolates, due to close resemblance to viruses in natural infection, should be used to evaluate NAbs as effective vaccine candidates in both children and adults.
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http://dx.doi.org/10.1016/j.virol.2016.09.011DOI Listing
December 2016

IL-8 Alterations in HIV-1 Infected Children With Disease Progression.

Medicine (Baltimore) 2016 May;95(21):e3734

From the Department of Biochemistry (ANP, HA, SSP, MAM, KL), Department of Pediatrics (RS, RL, SKK), Department of Microbiology (BKD), Department of Pediatrics Surgery (MS), Department of Biostatistics (RMP), All India Institute of Medical Sciences (RMP), and Department of Biochemistry, Jamia Hamdard University, New Delhi, India (ANP, SA).

Disease progression in HIV-1 infected children is faster than in adults. Less than 5% of the infected children maintain stable CD4 counts beyond 7 years of infection and are termed long-term nonprogressors (LTNPs). Delineating the host immune response in antiretroviral naïve (ART) and treated HIV-1 infected children at different disease stages will help in understanding the immunopathogenesis of the disease.A total of 79 asymptomatic, perinatally HIV-1 infected children (50 ART naïve and 29 ART treated) and 8 seronegative donors were recruited in this study. T- and B-cell activation PCR arrays were performed from the cDNA, using total RNA extracted from the peripheral blood mononuclear cells (PBMCs) of 14 HIV-1 infected children at different stages of the disease. The differentially expressed genes were identified. Quantitative RT-PCR was performed for the (interleukin-8) IL-8 gene and its transcriptional mediators, that is, SHP2, GRB2, and IL-8R (IL-8 receptor/CXCR1). Plasma levels of IL-8 were measured by flow cytometry.Gene array data revealed a higher expression of IL-8 in the ART naïve HIV-1 infected progressors and in ART nonresponders than LTNPs and ART responders, respectively. Quantitative RT-PCR analysis demonstrated a significant higher expression of IL-8 (P < 0.001), its receptor CXCR1 (P = 0.03) and the upstream signaling molecule SHP2 (P = 0.04) in the progressors versus LTNPs. Plasma levels of IL-8 were significantly higher in progressors versus LTNPs (P < 0.001), and ART nonresponders versus ART responders (P < 0.001). A significant negative correlation of plasma levels of IL-8 with CD4 counts (cells/μL) was observed in HIV-1 infected ART naïve subjects (r = -0.488; P < 0.001), while the IL-8 levels positively correlated with viral load in the ART treated children (r = 0.5494; P < 0.001). ART naïve progressors on follow up demonstrated a significant reduction in the mRNA expression (P = 0.05) and plasma levels of IL-8 (P = 0.05) post 6 months of ART initiation suggesting the beneficial role of ART therapy in reducing inflammation in infected children.Our data suggest that IL-8 may serve as a potential prognostic marker in adjunct with CD4 counts to monitor disease progression in the HIV-1 infected children and the efficacy of ART.
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http://dx.doi.org/10.1097/MD.0000000000003734DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4902358PMC
May 2016