Selection of Recent Key References 

Arunachalam Ramaiah, Soumya Nayak, Srabanti Rakshit, Abigail L. Manson, Thomas Abeel, Sivakumar Shanmugam , Pravat Nalini Sahoo , Anto Jesuraj Uday Kumar John, Jagadish Chandrabose Sundaramurthi, Sujatha Narayanan, George D’Souza, Paul von Hoegen, Tom H. M. Ottenhoff, Soumya Swaminathan, Ashlee M. Earl and Annapurna Vyakarnam. Evidence for highly variable, region-specific patterns of T-Cell epitope mutations accumulating in Mycobacterium tuberculosis strains. Front. Immunol. 2019, 10:195.

Ahmed A, Adiga V, Nayak S, Uday Kumar JAJ, Dhar C, Sahoo PN, Sundararaj BK, Souza GD, Vyakarnam A. Circulating HLA-DR+CD4+ effector memory T cells resistant to CCR5 and PD-L1 mediated suppression compromise regulatory T cell function in tuberculosis. PLoS Pathog. 2018; 14(9): e1007289.

Alampalli SV, Thomson MM, Sampathkumar R, Sivaraman K, U K J AJ, Dhar C, DSouza G, Berry N, Vyakarnam A. Deep sequencing of near full-length HIV-1 genomes from plasma identifies circulating subtype C and infrequent occurrence of AC recombinant form in Southern India. PLoS One. 2017; 12(12): e0188603.

Rakshit S, Adiga V, Nayak S, Sahoo PN, Sharma PK, van Meijgaarden KE, Uk J AJ, Dhar C, Souza GD, Finak G, De Rosa SC, Ottenhoff THM, Vyakarnam A. Circulating Mycobacterium tuberculosis DosR latency antigen-specific, polyfunctional, regulatory IL10+ Th17 CD4 T-cells differentiate latent from active tuberculosis. Sci. Rep. 2017; 7(1): 11948.

Sambarey A, Devaprasad A, Mohan A, Ahmed A, Nayak S, Swaminathan S, D’Souza G, Jesuraj A, Dhar C, Babu S, Vyakarnam A, Chandra N. Unbiased identification of blood-based biomarkers for pulmonary uberculosis by modeling and mining molecular interaction networks. EBioMedicine. 2017;15: 112-126.
Theme 1 
HIV-TB co-infection: mechanisms that drive reactivation of Mycobacterium tuberculosis in HIV infection. Ahmed A, Rakshit S, Vyakarnam A. Oral Dis. 2016 Apr;22Suppl 1:53-60. 

Evolutionary patterns of T cell epitopes in Mycobacterium tuberculosis strains isolated in India.  Arunachalam Ramaiah, Soumya Nayak, SrabantiRakshit, Abigail McGuire, Sivakumar Shanmugam, Jagadish Chandra  Bose, Sujatha Narayanan, Ashlee EarL, Soumya Swaminathan, Annapurna VyakarnamAbstract published: 17th International Congress on Infectious Diseases. Location/Date: March 2-5, 2016; Hyderabad, India Meeting Chief Organizer: Ramanan Laximnarayan, India & Jonathan Cohen, UK. Winner of Young Investigator Award for Best Abstract. 

Comparative analysis of the host mediated antigen-specific responses in Indian cohorts with latent, pulmonary and extra- pulmonary TB. SrabantiRakshit, Bharath K. Sundararaj, Prabha N. Sahoo, Tom H. Ottenhoff, Kirsta E. van Meijgaarden, George D’Souza, Annapurna Vyakarnam. Abstract published: 17th International Congress on Infectious Diseases. Location/Date: March 2-5, 2016; Hyderabad, India Meeting Chief Organizer: RamananLaximnarayan, India & Jonathan Cohen, UK. 

Impact of Type I IFN dysregulation in M. tuberculosis infection on T cell responses Asma Ahmed, SowmyaNaik, SubashBabu, George D’Souza and Annapurna Vyakarnam. Abstract published: 17th International Congress on Infectious Diseases. Location/Date: March 2-5, 2016; Hyderabad, India Meeting Chief Organizer: RamananLaximnarayan, India & Jonathan Cohen, UK. 

Elevated effector cell sensitivity to Treg-cell suppression that is not associated with reduced Th17-cell expression distinguishes HIV+ asymptomatic subjects from progressors. Thorborn GS, Pomeroy L, Ishohanni H, Peters BS, Vyakarnam A. Eur J Immunol. 2012 Jan;42(1):138-46. 

Increased sensitivity of CD4+ T-effector cells to CD4+CD25+ Treg suppression compensates for reduced Treg number in asymptomatic HIV-1 infection. Thorborn G, Pomeroy L, Isohanni H, Perry M, Peters B, Vyakarnam A. PLoS One. 2010 Feb 17;5(2):e9254. 

CD4 responses to conserved HIV-1 T helper epitopes show both negative and positive associations with virus load in chronically infected subjects. Boaz MJ, Waters A, Murad S, Easterbrook PJ, D’Sousa E, van Wheeley C, Vyakarnam A. ClinExpImmunol. 2003 Dec;134(3):454-63. 

Evidence for Gag p24-specific CD4 T cells with reduced susceptibility to R5 HIV-1 infection in a UK cohort of HIV-exposed-seronegative subjects. Eyeson J, King D, Boaz MJ, Sefia E, Tomkins S, Waters A, Easterbrook PJ, Vyakarnam A. AIDS. 2003 Nov 7;17(16):2299-311. 

Comparison between HIV- and CMV-specific T cell responses in long-term HIV infected donors. Papagno L, Appay V, Sutton J, Rostron T, Gillespie GM, Ogg GS, King A, Makadzanhge AT, Waters A, Balotta C, Vyakarnam A, Easterbrook PJ, Rowland-Jones SL. ClinExpImmunol. 2002 Dec;130(3):509-17.39 citations

Presence of HIV-1 Gag-specific IFN-gamma+IL-2+ and CD28+IL-2+ CD4 T cell responses is associated with nonprogression in HIV-1 infection. Boaz MJ, Waters A, Murad S, Easterbrook PJ, Vyakarnam A. J Immunol. 2002 Dec 1;169(11):6376-85.185 citations.

Theme 2 

A comparative phase 1 clinical trial to identify anti-infective mechanisms of vitamin D in people with HIV infection. Lachmann R, Bevan MA, Kim S, Patel N, Hawrylowicz C, Vyakarnam A, Peters BS. AIDS. 2015 Jun 19;29(10):1127-35. 
Theme 3 
Expression of two WFDC1/ps20 isoforms in prostate stromal cells induces paracrine apoptosis through regulation of PTGS2/COX-2. Hickman OJ, Smith RA, Dasgupta P, Rao SN, Nayak S, Sreenivasan S, Vyakarnam A, Galustian C. Br J Cancer. 2016 May 24;114(11):1235-42. 

WFDC1 is a key modulator of inflammatory and wound repair responses. Ressler SJ, Dang TD, Wu SM, Tse DY, Gilbert BE, Vyakarnam A, Yang F, Schauer IG, Barron DA, Rowley DR. Am J Pathol. 2014 Nov;184(11):2951-64. 

Whey acidic proteins (WAPs): novel modulators of innate immunity to HIV infection. Reading JL, Meyers AF, Vyakarnam A. CurrOpin HIV AIDS. 2012 Mar;7(2):172-9. doi: 10.1097/COH.0b013e32835005d9. Review. 

WFDC1 expression identifies memory CD4 T-lymphocytes rendered vulnerable to cell-cell HIV-1 transfer by promoting intercellular adhesive junctions. Alvarez RA, Thorborn G, Reading JL, Reddy SK, Vyakarnam A. Retrovirology. 2011 May 5;8:29. doi: 10.1186/1742-4690-8-29. 

Innate immunity against HIV: a priority target for HIV prevention research. Borrow P, Shattock RJ, Vyakarnam A; EUROPRISE Working Group. Retrovirology. 2010 Oct 11;7:84. doi: 10.1186/1742-4690-7-84. Review.33 citations 

Novel innate immune functions of the whey acidic protein family. Bingle CD, Vyakarnam A. Trends Immunol. 2008 Sep;29(9):444-53. 61 citations 

WFDC1/ps20 is a novel innate immunomodulatory signature protein of human immunodeficiency virus (HIV)-permissive CD4+ CD45RO+ memory T cells that promotes infection by upregulating CD54 integrin expression and is elevated in HIV type 1 infection. Alvarez R, Reading J, King DF, Hayes M, Easterbrook P, Farzaneh F, Ressler S, Yang F, Rowley D, Vyakarnam A. J Virol. 2008 Jan;82(1):471-86.