Research group - Ujjwal Neogi

My research group aims to study the mechanism of natural control of viral replication using HIV-1 positive Elite Controllers (EC) as a model, focusing more on mechanistic studies identified from integrated high-throughput multi-omics data.

EC is group of HIV-1 positive individuals who control viral replication and restrained progression to immunodeficiency, without any antiretroviral therapy for a longer duration of time. We will systemically perform the novel high-throughput transcriptomics, proteomics, microbiome and metabolomics data with the aim of identifying the mechanistic insights of the novel biomarkers of natural immune control.  Finally, we want to map the cellular pathways related to cell surface receptor signaling, immune checkpoint and death receptor signaling pathway that are significantly modulated in HIV-1 immune control and it’s cross-talk with the HIV-1 viruses. Systemic understanding the unique gene and proteome profiling and immunological characteristics of EC will predict a frame of reference for what may be required in clinical intervention strategies to induce immune control of HIV-1. Thus, these studies aim to generate immense knowledge that can be translated to the future development of functional HIV-cure including therapeutic vaccine strategies. My group closely work with Prof. Anders Sonnerborg’s group and with Dr. Piotr Nowak on the translational aspect of the project.

Research Group Leader

Ujjwal Neogi, Senior Researcher

I obtained my doctoral degree from Department of Medicine Huddinge, Karolinska Institutet (KI) in 2013. My research expertise is in virology, molecular biology, high-throughput sequencing and translational research. My research focuses on bedside to bench and back approach using well defined clinical material and ex vivo immunological assays amalgamating the translational research to understand the host and viral factors associated with disease progression and control in HIV-1. I intend to use high-throughput multi-omics integrated trans-omics approach to find out the mechanism of natural immune control of HIV-1 replication followed by deep insight in the individual pathways. My research interest also includes evaluation of the gut-microbiome metabolome axis and it’s role in disease progression and treatment efficacy.

Group members

Maike Sperk, PhD Student

I completed my master degree in Molecular Medicine from Tuebingen University, Germany (January 2018). In my master thesis, I focused on proteomics as well as cell biology and I will pursue these fields in a deeper way during my Ph.D. In particular, in my doctoral studies, I aim to perform immuno-proteomics research to map the intracellular pathways that are significantly modulated in HIV-1 immune control in Elite Controllers. I use high throughput techniques such as mass spectrometry, proximity extension assay, FACS, confocal microscopy, etc. My primary interests are death receptor signaling and stimulatory immune checkpoint molecules, and their roles in HIV-1 disease progression.

Anoop T Ambikan, PhD Student

I got my Master’s Degree in Bioinformatics from Amrita School of Biotechnology, India in 2012 and had more than two years experience as Bioinformatics Programmer, at SciGenome Pvt Ltd.  My doctoral studies aim at dealing with bioinformatics analysis of various kinds of "omics data" like transcriptome, proteome, microbiome and metabolome data related to HIV research. I am working to develop a simplified and efficient pipeline to integrate multi-omics data to draw a clinically relevant inference with reduced manual effort

Duncan T Njenda, PhD Student

Joint Karolinska Institutet- Stellenbosch University Double Degree program.

I obtained my master degree in Medical Virology, Stellenbosch University, South Africa. My expertise is in virology and molecular biology. My Ph.D. program is to identify resistance mechanisms against protease inhibitors in South African HIV-1C patients’ high throughput system biology approach. I aim to integrate molecular biology, biochemistry, virology and structural biology to understand the resistance mechanisms. 

Naveen Reddy Muppani, Visiting Researcher

I received a Ph.D. at Karolinska Institutet in 2013, and worked as a postdoc at Wright State University, USA 2014-2016. I held a researcher position at the Uppsala University during 2017-2018. I have expertise in transcription factors mediated regulation of gene and microRNA expressions governing cell life and death.

Currently, I am developing multiplexed assays for simultaneous detection of proteins and nucleic acids in situ and in solution that are exhibiting increased sensitivity and specificity. My aim is to develop multiplexed methods which employ routinely available laboratory instruments and establish them at limited recourse laboratory settings.

Anxiong Long, Visiting researcher

I obtained my MD in Clinical Laboratory Medicine from Medicine Institute of Nanchang University, China. My research involved was to explore and identify novel biomarkers to predict or diagnose pre-eclampsia using ultra-performance liquid chromatography-tandem mass spectrometry. I hold a patent on the application of arachidonic acid metabolites in the preparation of pre-eclampsia test kit (ZL201410539268). At present I obtained China Scholarship Council Fellowship, Govt. of China to perform Ph.D. study at Karolinska Institutet with Dr. Ujjwal Neogi as the main supervisor. My Ph.D. research project is to understand the microbiome-metabolome cross-talk in HIV-1 disease progression and treatment response. I am performing the microbiome analysis with shotgun sequencing and metabolomics using LC-MS/MS.

Ashok Manickam, Guest Researcher

I am a Ph.D. research scholar at National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India. My research focus is to understand the molecular mechanism of the ability of transmitted/founder (TF) HIV-1 virus which is capable of establishing infections while the majority of the viruses compromising the infectiousness for survival, if not, for other reasons. I joined Dr. Neogi’s group as a Guest researcher after obtaining the HIV Research Trust Scholarship, UK. My interest is to carry out state-of-the-art experiments to understand host-virus interaction at the cellular and molecular level which helps to identify unique features of TF viruses that help them to establish infection successfully. 

Associated members

Postdoc

Robert Van Domselaar

Organizational unit: Division of Infection and Dermatology
E-mail: robert.van.domselaar.1@ki.se

Graduate Student

Wang Zhang

Organizational unit: Division of Clinical Microbiology
E-mail: wang.zhang@ki.se

Associated

Kamlendra Singh

Organizational unit: Division of Clinical Microbiology
E-mail: kamlendra.singh@ki.se

Techniques

High throughput sequencing, transcriptomics, proteomics, RNAscope, Microfluidics, miRNA profiling

Collaborations

Dr. Luke Elisabeth Hanna, National Institute for Research in Tuberculosis, India

Prof. Andrew D Badley, Mayo Clinic, US

Prof. Susan Engelbrecht and Dr. Graeme Jacobs, Stellenbosch University, South Africa

Asso. Prof. Aman Russom, KTH Royal Institute of Technology, Sweden

Prof. Stefan Sarafianos, Emory University, US

Prof. Thomas Klimkait, University of Basel, Switzerland

Prof. Ulf Landgren, Uppsala University, Sweden

Funding

Swedish Research Council-Establishment Grant (2017-01330)

Harald and Greta Jeansson Foundation (JS2016-0185)

Karolinska Institutet Doctoral Student Funding (KID2015-154)

Karolinska Institutet Research Foundation Grants special grant for Young Scientist

Swedish Physicians against AIDS Foundation (Fob20170004/Fob2015-009)

Jonas Söderquist’s Stipendium for Experimental Virology and Immunology Research-2016 (Award)

US National Institute of Health (R01 GM118012-01) (Site-PI)

Swedish Research Council (2015-05914/2017- 05848) (Co-I)

Stockholm County Council, ALF-Project Funding Medicine (Ref#20160074) (Co-I)

Selected publications

Transcriptomics and Targeted Proteomics Analysis to Gain Insights Into the Immune-control Mechanisms of HIV-1 Infected Elite Controllers.
Zhang W, Ambikan A, Sperk M, van Domselaar R, Nowak P, Noyan K, et al
EBioMedicine 2018 Jan;27():40-50

Phenotypic co-receptor tropism and Maraviroc sensitivity in HIV-1 subtype C from East Africa.
Siddik A, Haas A, Rahman M, Aralaguppe S, Amogne W, Bader J, et al
Sci Rep 2018 Feb;8(1):2363

Plasma soluble factor following two decades prolonged suppressive antiretroviral therapy in HIV-1-positive males: A cross-sectional study.
Sperk M, Zhang W, Nowak P, Neogi U
Medicine (Baltimore) 2018 Feb;97(5):e9759

Virological failure in patients with HIV-1 subtype C receiving antiretroviral therapy: an analysis of a prospective national cohort in Sweden.
Häggblom A, Svedhem V, Singh K, Sönnerborg A, Neogi U
Lancet HIV 2016 Apr;3(4):e166-74

Genomics