Soham Gupta

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About me

The focus of my research is to expand our understanding of the interplay between viruses and host immune system using an integrative approach. I completed my Ph.D. studies on translational genomics of HIV-1 subtypes circulating in India (HIV-1CIN) at St. John’s Medical College, Rajiv Gandhi University of Health Sciences, India, in 2014. Post Ph.D. in 2015 I joined Prof. Maria Masucci’s group at Department of Cell and Molecular Biology, Karolinska Institutet as a postdoctoral researcher studying the role of herpesvirus encoded cysteine protease on evasion of host innate immune response. In 2019 I was appointed Assistant Professor at Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet.

Research

My research is aimed at understanding the mechanism of immune regulation during viral infections. The focus of my research is on emerging and re-emerging viruses like Coronaviruses, Zika virus, CCHFV etc. and latent viruses like herpesviruses and HIV-1 and expand our understanding of the interplay between these viruses and host immune system using an integrative approach combining multi-omics with immunology, molecular, cell-biological and biochemical assays.

Articles

Article: GENOME BIOLOGY. 2023;24(1):237

Dual spatially resolved transcriptomics for human host-pathogen colocalization studies in FFPE tissue sections.

Sounart H; Lázár E; Masarapu Y; Wu J; Várkonyi T; Glasz T; Kiss A; Borgström E; Hill A; Rezene S; Gupta S; Jurek A; Niesnerová A; Druid H; Bergmann O; Giacomello S
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2023;120(37):e2304722120

Systems-level temporal immune-metabolic profile in Crimean-Congo hemorrhagic fever virus infection.

Ambikan AT; Elaldi N; Svensson-Akusjärvi S; Bagci B; Pektas AN; Hewson R; Bagci G; Arasli M; Appelberg S; Mardinoglu A; Sood V; Végvári Á; Benfeitas R; Gupta S; Cetin I; Mirazimi A; Neogi U
Article: CELL SYSTEMS. 2022;13(8):665-681.e4

Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity.

Ambikan AT; Yang H; Krishnan S; Svensson Akusjärvi S; Gupta S; Lourda M; Sperk M; Arif M; Zhang C; Nordqvist H; Ponnan SM; Sönnerborg A; Treutiger CJ; O'Mahony L; Mardinoglu A; Benfeitas R; Neogi U
Article: ELIFE. 2022;11:e76071

Multi-omics insights into host-viral response and pathogenesis in Crimean-Congo hemorrhagic fever viruses for novel therapeutic target.

Neogi U; Elaldi N; Appelberg S; Ambikan A; Kennedy E; Dowall S; Bagci BK; Gupta S; Rodriguez JE; Svensson-Akusjärvi S; Monteil V; Vegvari A; Benfeitas R; Banerjea A; Weber F; Hewson R; Mirazimi A
Article: COMMUNICATIONS BIOLOGY. 2022;5(1):357

Peripheral blood CD4+CCR6+ compartment differentiates HIV-1 infected or seropositive elite controllers from long-term successfully treated individuals.

Svensson Akusjärvi S; Krishnan S; Jütte BB; Ambikan AT; Gupta S; Rodriguez JE; Végvári Á; Sperk M; Nowak P; Vesterbacka J; Svensson JP; Sönnerborg A; Neogi U
Article: VIROLOGY. 2022;569:13-28

Azadirachta indica A. Juss bark extract and its Nimbin isomers restrict β-coronaviral infection and replication.

Sarkar L; Oko L; Gupta S; Bubak AN; Das B; Gupta P; Safiriyu AA; Singhal C; Neogi U; Bloom D; Banerjee A; Mahalingam R; Cohrs RJ; Koval M; Shindler KS; Pal D; Nagel M; Sarma JD
Article: ISCIENCE. 2022;25(1):103607

Integrative proteo-transcriptomic and immunophenotyping signatures of HIV-1 elite control phenotype: A cross-talk between glycolysis and HIF signaling.

Akusjärvi SS; Ambikan AT; Krishnan S; Gupta S; Sperk M; Végvári Á; Mikaeloff F; Healy K; Vesterbacka J; Nowak P; Sönnerborg A; Neogi U
Article: COMMUNICATIONS BIOLOGY. 2022;5(1):27

Trans cohort metabolic reprogramming towards glutaminolysis in long-term successfully treated HIV-infection.

Mikaeloff F; Svensson Akusjärvi S; Ikomey GM; Krishnan S; Sperk M; Gupta S; Magdaleno GDV; Escós A; Lyonga E; Okomo MC; Tagne CT; Babu H; Lorson CL; Végvári Á; Banerjea AC; Kele J; Hanna LE; Singh K; de Magalhães JP; Benfeitas R; Neogi U
Article: FRONTIERS IN IMMUNOLOGY. 2022;13:1002823

ZC3H11A loss of function enhances NF-κB signaling through defective IκBα protein expression.

Darweesh M; Younis S; Hajikhezri Z; Ali A; Jin C; Punga T; Gupta S; Essand M; Andersson L; Akusjärvi G
Article: AUTOPHAGY. 2021;17(11):3461-3474

The Epstein-Barr virus deubiquitinase BPLF1 targets SQSTM1/p62 to inhibit selective autophagy.

Ylä-Anttila P; Gupta S; Masucci MG
Article: PLOS PATHOGENS. 2021;17(9):e1009954

The Epstein-Barr virus deubiquitinating enzyme BPLF1 regulates the activity of topoisomerase II during productive infection.

Li J; Nagy N; Liu J; Gupta S; Frisan T; Hennig T; Cameron DP; Baranello L; Masucci MG
Article: ISCIENCE. 2021;24(5):102420

Cell-type-resolved quantitative proteomics map of interferon response against SARS-CoV-2.

Saccon E; Chen X; Mikaeloff F; Rodriguez JE; Szekely L; Vinhas BS; Krishnan S; Byrareddy SN; Frisan T; Végvári Á; Mirazimi A; Neogi U; Gupta S
Article: CELL DEATH DISCOVERY. 2021;7(1):114

Type-I interferon signatures in SARS-CoV-2 infected Huh7 cells.

Chen X; Saccon E; Appelberg KS; Mikaeloff F; Rodriguez JE; Vinhas BS; Frisan T; Végvári Á; Mirazimi A; Neogi U; Gupta S
Article: HELIYON. 2021;7(5):e07134

Pulmonary stromal expansion and intra-alveolar coagulation are primary causes of COVID-19 death.

Szekely L; Bozoky B; Bendek M; Ostad M; Lavignasse P; Haag L; Wu J; Jing X; Gupta S; Saccon E; Sönnerborg A; Cao Y; Björnstedt M; Szakos A
Article: BMC INFECTIOUS DISEASES. 2021;21(1):214

Increased acquired protease inhibitor drug resistance mutations in minor HIV-1 quasispecies from infected patients suspected of failing on national second-line therapy in South Africa.

Obasa AE; Ambikan AT; Gupta S; Neogi U; Jacobs GB
Article: MOLECULAR & CELLULAR PROTEOMICS. 2021;20:100159

Metabolic Perturbation Associated With COVID-19 Disease Severity and SARS-CoV-2 Replication.

Krishnan S; Nordqvist H; Ambikan AT; Gupta S; Sperk M; Svensson-Akusjärvi S; Mikaeloff F; Benfeitas R; Saccon E; Ponnan SM; Rodriguez JE; Nikouyan N; Odeh A; Ahlén G; Asghar M; Sällberg M; Vesterbacka J; Nowak P; Végvári Á; Sönnerborg A; Treutiger CJ; Neogi U
Article: EMERGING MICROBES & INFECTIONS. 2020;9(1):1748-1760

Dysregulation in Akt/mTOR/HIF-1 signaling identified by proteo-transcriptomics of SARS-CoV-2 infected cells.

Appelberg S; Gupta S; Svensson Akusjärvi S; Ambikan AT; Mikaeloff F; Saccon E; Végvári Á; Benfeitas R; Sperk M; Ståhlberg M; Krishnan S; Singh K; Penninger JM; Mirazimi A; Neogi U
Article: FRONTIERS IN IMMUNOLOGY. 2020;11:437

Interaction With 14-3-3 Correlates With Inactivation of the RIG-I Signalosome by Herpesvirus Ubiquitin Deconjugases.

Gupta S; Ylä-Anttila P; Sandalova T; Achour A; Masucci MG
Article: COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL. 2020;18:3734-3744

In silico and in vitro studies reveal complement system drives coagulation cascade in SARS-CoV-2 pathogenesis.

Tiwari R; Mishra AR; Mikaeloff F; Gupta S; Mirazimi A; Byrareddy SN; Neogi U; Nayak D
Article: PLOS PATHOGENS. 2019;15(11):e1008146

14-3-3 scaffold proteins mediate the inactivation of trim25 and inhibition of the type I interferon response by herpesvirus deconjugases.

Gupta S; Ylä-Anttila P; Sandalova T; Sun R; Achour A; Masucci MG
Article: PLOS PATHOGENS. 2018;14(1):e1006852

Herpesvirus deconjugases inhibit the IFN response by promoting TRIM25 autoubiquitination and functional inactivation of the RIG-I signalosome.

Gupta S; Ylä-Anttila P; Callegari S; Tsai M-H; Delecluse H-J; Masucci MG
Article: BMJ OPEN. 2016;6(1):e008795

Can HIV reverse transcriptase activity assay be a low-cost alternative for viral load monitoring in resource-limited settings?

Gupta S; Palchaudhuri R; Neogi U; Srinivasa H; Ashorn P; De Costa A; Källander C; Shet A
Article: TRANSACTIONS OF THE ROYAL SOCIETY OF TROPICAL MEDICINE AND HYGIENE. 2015;109(12):769-774

Prevalence of virulence factors and phylogenetic characterization of uropathogenic Escherichia coli causing urinary tract infection in patients with and without diabetes mellitus.

Harwalkar A; Gupta S; Rao A; Srinivasa H
Article: INTERVIROLOGY. 2015;58(1):1-5

Performance of genotypic tools for prediction of tropism in HIV-1 subtype C V3 loop sequences.

Gupta S; Neogi U; Srinivasa H; Shet A
Article: BMJ-BRITISH MEDICAL JOURNAL. 2014;349:g5978

Effect of mobile telephone reminders on treatment outcome in HIV: evidence from a randomised controlled trial in India.

Shet A; De Costa A; Kumarasamy N; Rodrigues R; Rewari BB; Ashorn P; Eriksson B; Diwan V; HIVIND Study Team
Article: JOURNAL OF INFECTION AND PUBLIC HEALTH. 2014;7(5):413-419

Lower prevalence of hlyD, papC and cnf-1 genes in ciprofloxacin-resistant uropathogenic Escherichia coli than their susceptible counterparts isolated from southern India.

Harwalkar A; Gupta S; Rao A; Srinivasa H
Article: GERMS. 2014;4(3):70-72

Daptomycin resistance in methicillin-resistant Staphylococcus aureus: a report from Southern India.

Vamsimohan A; Gupta S; Muralidharan S
Article: JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES. 2014;65(4):397-404

HIV-1 coreceptor tropism in India: increasing proportion of X4-tropism in subtype C strains over two decades.

Gupta S; Neogi U; Srinivasa H; Banerjea AC; Shet A
Article: ANTIVIRAL THERAPY. 2014;19(8):813-818

Limited evolution but increasing trends of primary non-nucleoside reverse transcriptase inhibitor resistance mutations in therapy-naive HIV-1-infected individuals in India.

Neogi U; Gupta S; Palchaudhuri R; Rao SD; Shastri S; Diwan V; Laishram RS; De Costa A; Shet A
Article: INTERNATIONAL JOURNAL OF BIOMATERIALS. 2014;2014:383756-6

In Vitro Evaluation of the Antimicrobial Efficacy of Four Endodontic Biomaterials against Enterococcus faecalis, Candida albicans, and Staphylococcus aureus.

Nirupama DN; Nainan MT; Ramaswamy R; Muralidharan S; Usha HHL; Sharma R; Gupta S
Article: JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY. 2013;68(9):2003-2006

High concordance of genotypic coreceptor prediction in plasma-viral RNA and proviral DNA of HIV-1 subtype C: implications for use of whole blood DNA in resource-limited settings.

Gupta S; Neogi U; Srinivasa H; Shet A
Article: JOURNAL OF INFECTION AND PUBLIC HEALTH. 2013;6(2):108-114

The detection of ESBL-producing Escherichia coli in patients with symptomatic urinary tract infections using different diffusion methods in a rural setting.

Harwalkar A; Sataraddi J; Gupta S; Yoganand R; Rao A; Srinivasa H
Journal article: CLINICAL MICROBIOLOGY NEWSLETTER. 2013;35(3):25-26

Candida tropicalis Recovered from a Bone Marrow Aspirate in a Diabetic Patient

Aruna C; Savio J; Gupta S; Muralidharan S
Article: INTERNATIONAL JOURNAL OF MICROBIOLOGY RESEARCH. 2012;136(6):956-962

Dried blood spot HIV-1 RNA quantification: a useful tool for viral load monitoring among HIV-infected individuals in India.

Neogi U; Gupta S; Rodridges R; Sahoo PN; Rao SD; Rewari BB; Shastri S; Costa AD; Shet A
Article: AIDS RESEARCH AND HUMAN RETROVIRUSES. 2012;28(9):1152-1156

Genetic characterization of HIV type 1 Tat exon 1 from a southern Indian clinical cohort: identification of unique epidemiological signature residues.

Neogi U; Gupta S; Sahoo PN; Shet A; Rao SD; Ranga U; Prasad VR
Article: TROPICAL DOCTOR. 2012;42(1):35-37

Multi-drug-resistant tuberculosis: the experience of an urban tertiary care hospital in South India using automated BACTEC 460 TB.

Mishra B; Rockey SM; Gupta S; Srinivasa H; Muralidharan S
Article: PLOS ONE. 2012;7(6):e39819

Molecular epidemiology of HIV-1 subtypes in India: origin and evolutionary history of the predominant subtype C.

Neogi U; Bontell I; Shet A; De Costa A; Gupta S; Diwan V; Laishram RS; Wanchu A; Ranga U; Banerjea AC; Sönnerborg A
Article: INDIAN JOURNAL OF PEDIATRICS. 2011;78(12):1495-1497

Prevalence of respiratory syncytial virus infection among hospitalized children presenting with acute lower respiratory tract infections.

Gupta S; Shamsundar R; Shet A; Chawan R; Srinivasa H
Article: JOURNAL OF INFECTION AND PUBLIC HEALTH. 2011;4(3):140-144

Diabetes mellitus and HIV as co-morbidities in tuberculosis patients of rural south India.

Gupta S; Shenoy VP; Bairy I; Srinivasa H; Mukhopadhyay C
Article: INDIAN JOURNAL OF PATHOLOGY AND MICROBIOLOGY. 2011;54(3):569-571

In vitro production of biofilm in a flow cell system in a strain of Pseudomonas aeruginosa and Staphylococcus aureus and determination of efficiency of ciprofloxacin against them.

Gupta S; Agarwal S; Sahoo DR; Muralidharan S
Article: REVISTA DA SOCIEDADE BRASILEIRA DE MEDICINA TROPICAL. 2011;44(3):309-312

Community prevalence of methicillin and vancomycin resistant Staphylococcus aureus in and around Bangalore, southern India.

Goud R; Gupta S; Neogi U; Agarwal D; Naidu K; Chalannavar R; Subhaschandra G
Article: CLINICAL LABORATORY. 2011;57(9-10):767-769

Misidentification of a commensal inactive Escherichia coli as Shigella sonnei by an automated system in a critically ill patient.

Gupta S; Aruna C; Muralidharan S
Article: TROPICAL MEDICINE & INTERNATIONAL HEALTH. 2011;16(1):74-78

Role of risk factors and socio-economic status in pulmonary tuberculosis: a search for the root cause in patients in a tertiary care hospital, South India.

Gupta S; Shenoy VP; Mukhopadhyay C; Bairy I; Muralidharan S
Article: NEPHROLOGY. 2011;16(1):63-67

Epidemiology of culture isolates from peritoneal dialysis peritonitis patients in southern India using an automated blood culture system to culture peritoneal dialysate.

Gupta S; Muralidharan S; Gokulnath; Srinivasa H
Article: INDIAN JOURNAL OF MEDICAL SCIENCES. 2010;64(12):553-556

Ceftriaxone resistant Shigella flexneri, an emerging problem.

Gupta S; Mishra B; Muralidharan S; Srinivasa H
Article: AIDS RESEARCH AND HUMAN RETROVIRUSES. 2010;26(10):1097-1101

Naturally occurring polymorphisms and primary drug resistance profile among antiretroviral-naive individuals in Bangalore, India.

Neogi U; Prarthana BS; Gupta S; D'souza G; De Costa A; Kuttiatt VS; Arumugam K; Shet A
Article: JORNAL BRASILEIRO DE PNEUMOLOGIA. 2010;36(5):612-616

Comparison among three cold staining methods in the primary diagnosis of tuberculosis: a pilot study.

Gupta S; Shenoy VP; Bairy I; Muralidharan S
Journal article: ASIAN PACIFIC JOURNAL OF TROPICAL MEDICINE. 2010;3(4):328-329

Diagnostic efficacy of Ziehl-Neelsen method against fluorescent microscopy in detection of acid fast bacilli

Gupta S; Shenoy VP; Bairy I; Muralidharan S
Article: SOUTHEAST ASIAN JOURNAL OF TROPICAL MEDICINE AND PUBLIC HEALTH. 2009;40(4):765-769

Comparative evaluation of two cold staining methods with the Ziehl-Neelsen method for the diagnosis of tuberculosis.

Gupta S; Prasad V; Bairy I; Muralidharan S
Article: JOURNAL OF INFECTION IN DEVELOPING COUNTRIES. 2009;3(2):83-87

PCR for M. tuberculosis in tissue samples.

Chawla K; Gupta S; Mukhopadhyay C; Rao PS; Bhat SS
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Editorial comment: FRONTIERS IN IMMUNOLOGY. 2023;14:1148296

Editorial: Ubiquitin and ubiquitin-like modifications in viral infection and innate immunity.

Sparrer KMJ; Bergeron É; Gupta S
Review: JOURNAL OF PROTEOME RESEARCH. 2020;19(11):4259-4274

Utility of Proteomics in Emerging and Re-Emerging Infectious Diseases Caused by RNA Viruses.

Sperk M; van Domselaar R; Rodriguez JE; Mikaeloff F; Sá Vinhas B; Saccon E; Sönnerborg A; Singh K; Gupta S; Végvári Á; Neogi U
Editorial comment: ECLINICALMEDICINE. 2020;18:100251

Following the path: Increasing trends of HIV-1 drug resistance in China.

Gupta S; Neogi U
Editorial comment: MICROBIAL CELL. 2018;5(5):259-261

A novel mechanism for regulation of the type I IFN response by herpesvirus deconjugases.

Gupta S; Ylä-Anttila P; Masucci MG
Letter: CLINICAL LABORATORY. 2013;59(7-8):929-931

Rapid detection of respiratory syncytial virus (RSV) in children with acute lower respiratory tract infections: a pilot evaluation of an immuno-chromatographic rapid antigen detection method.

Gupta S; Shamsundar R; Shet A; Srinivasa H
Letter: JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY. 2012;67(5):1293-1295

In vitro activity of tigecycline against multidrug-resistant Gram-negative blood culture isolates from critically ill patients.

Gupta S; Aruna C; Nagaraj S; Dias M; Muralidharan S

Grants

ISG15 at the interface of innate immune response and metabolic pathways during respiratory viral infections

Swedish Research Council

1 January 2022 - 31 December 2025

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