Multi-omics Research Team

The aim of my research team is through translational research integrating multi-omics techniques and clinical data to understand the disease control mechanism in a 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 (Elite controllers). 

In a systemic approach, we apply the molecular data-first approach (using genomics, transcriptomics, proteomics, and metabolomics) classifies persistent genetic variants or expression patterns to reduce host influenced heterogeneity followed by the phenotypic profiling, virological and immunological characterizations of the disease control mechanisms. This understanding of the unique gene expression 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 and the future development of functional HIV-cure.

Apart from this my research interests also include phenotypic drug sensitivity assay, viral fitness and spread of the HIV-1 epidemic in low- and middle-income countries.

Research Team Leader

Assistant professor

Ujjwal Neogi

Organizational unit: Division of Clinical Microbiology
E-mail: ujjwal.neogi@ki.se

Team members

Duncan T Njenda, PhD Student (Supervisor)

I am PhD student in 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 PhD 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. 

Wang Zhang, PhD Student, (Supervisor at KI)

KI-KTH PhD Programme in medical technology

I am PhD student in KI-KTH joint doctoral programme in medical technology, an interdisciplinary program for development of technology and application in medicine. I did master degree in Laboratory Medicine followed by thesis in Microfluidics from Shenzhen Institute of Advanced Technology, Chinese Academy of Science. I am interested in interdisciplinary research on the development and validation of new technologies for biological research and identify novel biomarkers for natural immune control. Current projects included the use of microfluidic devices for high-throughput single cell analysis, proteomics and transcriptomics. I am recipient of China Scholarship Council.

Maike Sperk, Master Thesis Student, University of Tuebingen, Germany (Supervisor)

I am a Master student of Molecular Medicine at University of Tuebingen, Germany. I joined Prof Sönnerborgs group and Dr. Neogi’s team in March 2017 for finalizing my studies with a research project for my Master’s thesis. There, I focus on plasma and cell proteomics of different groups of HIV infected individuals (elite controllers, viral progressors and patients on antiretroviral therapy) using high throughput techniques like proximity ligation assay, antibody array, FACS etc. I am particularly interested in the death receptor pathways and regulation of immune checkpoints in HIV infection and investigate them in cell culture experiments. 

Anoop T Ambikan, Research Assistant (Bioinformatics)

I got my Master’s Degree in Bioinformatics from Amrita School of Biotechnology, India in 2012. I have more than two years experience as Bioinformatics Programmer, at SciGenome Pvt ltd with advanced level skill in programming with interpreted language Perl and statistical software R. I am well versed with open-source bioinformatics tools for NGS analyzing like de-novo whole genome and transcriptome analysis, reference based analysis and microbiome analysis including the commercial NGS data analysis software CLC genomics workbench. In my present research group I am dealing with bioinformatics analysis of various kinds of "omics data" viz, 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 relevent inference with reduced manual effort.

Robert van Domselaar, PostDoc (co-supervisor)

I am a cellular and molecular biologist from University Medical Center Utrecht and Utrecht University, The Netherlands, where I received my PhD degree within the fields of immunology and virology. My PhD project focused on how cytotoxic lymphocytes can control cytomegalovirus infections. In February 2017, I started as a postdoc in the group of Prof Sönnerborg and Dr Ujjwal Neogi. Here, I am studying the immunological anti-HIV-1 mechanisms by which a small subgroup of HIV-1-infected individuals, called Elite Controllers, can control their infection without receiving antiretroviral therapy.

Sara Svensson Akusjärvi, PhD Student (Co-supervisor)

I have an MSc in Molecular Medicine from Uppsala University, focusing on cellular mechanisms underlying disease states. During my master thesis, I worked with drug induced effects and cellular aberrations in in vitro model, aiming towards personal therapy for Glioblastoma Multiforme with Satish Kitambi at Karolinska Institutet. My main expertise lies on utilizing molecular techniques to study cellular systems and therapy induced responses. In the doctoral program, I am going to understand and characterize the latent HIV reservoir by using high throughput technologies like RNAscope, single cell sequencing along with basic research techniques.

Ashok Manickam, Guest Researcher

PhD Student, National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India

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 molecular mechanism of the ability of transmitted/founder (TF) HIV-1 virus which are 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 team 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 successfully establish infection. 

Techniques

High throughput sequencing, transcriptomics, proteomics, RNAscope, Microfludics, miRNA profiling, integrated system biology

Collaborations

Stefan Sarafianos, University of Missouri

Andrew Bradley, Mayo Clinic

Susan Engelbrecht, Stellenbosch University

Luke Elisabeth Hanna, NIRT, Chennai

Team photo