Biology subjects

Jagtap, S.

Publications and source records attributed to Jagtap, S..

5 recordsLinked to original sources

bioRxiv2026

Increased CD33 levels tune activation and function of iinduced human microglial cells through inhibition of the TREM2 pathway

The microglial CD33 gene is overexpressed in the brains of individuals with Alzheimers disease, and multiple CD33 genetic variants are directly linked to disease risk. Here, we investigate CD33 function in induced human microglial cells by increasing or decreasing CD33 levels with AAV6-mediated gene transfer and with CD33-targeting siRNA, respectively. Phagocytosis of oligomeric amyloid beta into live microglia was doubled by reducing CD33 levels, with concomitant increases in secreted TREM2 and in TREM2 activation as assayed by phosphorylation of downstream SYK. Increasing CD33 had opposing effects on microglial activity, decreasing amyloid beta uptake by approximately half, reducing LPS-induced increases in IL-10, and decreasing the efficacy of a TREM2-activating antibody. Experiments combining siRNA and AAV6 demonstrated a linear relationship between CD33 protein and amyloid beta uptake. Results show that CD33 largely governs multiple microglial functions associated with Alzheimers disease and affects both pharmacological and physiological activation of TREM2.

neuroscience↗

bioRxiv2024

Combined inhibition of SHP2 overcomes adaptive resistance to type 1 BRAF inhibitors in BRAF V600E-driven high-grade glioma

BRAF-mutant gliomas can be therapeutically targeted with BRAF mutant-selective inhibitors, yet responses are often transient due to short-term adaptive or long-term treatment-emergent resistance. We hypothesized that vertical inhibition of multiple signaling nodes could improve the durability of BRAF inhibition and prevent or overcome adaptive resistance. Using human tissue samples, we identified frequent RAS pathway reactivation in gliomas resistant to BRAF inhibitors, suggesting a common escape mechanism. Using patient-derived cell lines, we observed that upregulation of RAS activity was an adaptive response to BRAFi and that knockdown of SHP2, a central regulator of RAS activity, resulted in enhanced sensitivity to BRAF or MEK inhibition. Moreover, combined small molecule inhibition with SHP2 and BRAF or MEK inhibitors increased the depth and durability of ERK pathway inhibition, as well as prevented paradoxical upregulation of RAS activity. RNA sequencing analysis revealed deeper suppression of ERK transcriptional output with combined therapy, along with decreased reactivation of EGFR. Combined SHP2/BRAF small molecule inhibitors prevented growth and induced cell death in some cell line models. In cell lines with treatment-emergent resistance, moreover, combined SHP2 and BRAF inhibition overcame resistance to BRAF inhibitor monotherapy. In vivo orthotopic and patient-derived xenograft models confirmed enhanced tumor growth inhibition with combined therapy. Together, our findings demonstrate the critical role of RAS/ERK signaling reactivation in driving resistance to BRAF inhibition in glioma, and demonstrate the potential utility for adding SHP2 inhibitors to overcome resistance in BRAF V600E mutant glioma. SignificanceThe addition of a SHP2i to BRAFi in BRAF-V600E glioma cells prevents tumor growth and can overcome resistance to BRAFi in preclinical models in vitro and in vivo.

cancer biology↗

bioRxiv2024

DNA density is a better indicator of a nuclear bleb than lamin B loss

Nuclear blebs are herniations of the nucleus that occur in diseased nuclei that cause nuclear rupture leading to cellular dysfunction. Chromatin and lamins are two of the major structural components of the nucleus that maintain its shape and function, but their relative roles in nuclear blebbing remain elusive. Lamin B is reported to be lost in blebs by qualitative data while quantitative studies reveal a spectrum of lamin B levels in nuclear blebs dependent on perturbation and cell type. Chromatin has been reported to be decreased or de-compacted in nuclear blebs, but again the data are not conclusive. To determine the composition of nuclear blebs, we compared the immunofluorescence intensity of lamin B and DNA in the main nucleus body and nuclear bleb across cell types and perturbations. Lamin B nuclear bleb levels varied drastically across MEF wild type and chromatin or lamins perturbations, HCT116 lamin B1-GFP imaging, and human disease model cells of progeria and prostate cancer. However, DNA concentration was consistently decreased to about half that of the main nucleus body across all measured conditions. Using Partial Wave Spectroscopic (PWS) microscopy to measure chromatin density in the nuclear bleb vs body we find similar results that DNA is consistently less dense in nuclear blebs. Thus, our data spanning many different cell types and perturbations supports that decreased DNA is a better marker of a nuclear bleb than lamin B levels that vary widely.

cell biology↗

bioRxiv2023

Enhanced inflammatory signaling driven by metabolic switch in Aicardi-Goutieres syndrome

Aicardi-Goutieres syndrome (AGS) is a genetic type I interferon (IFN)-mediated disease characterised by neurological involvement with onset in childhood. Chronic inflammation in response to uncontrolled type I IFN production is, among other things, associated with IP-10 secretion. We analysed, at the single-cell transcriptomic levels, peripheral blood samples from patients bearing AGS-causing mutations in SAMHD1, RNASEH2B or ADAR1 genes. Using machine-learning approaches and differential gene expression we identified a drastic loss of transcription factor hypoxia induced factor 1 (HIF-1) expression and activity associated with features of a metabolic switch and mitochondrial stress in monocytes/dendritic cells. Chemical stabilization of HIF-1, with a synthetic drug in an in vitro model of AGS, allowed us to reverse the energy metabolic switch, attenuate mitochondrial stress and markedly reduce IP-10 production. We therefore propose that energy metabolic switch contributes to exacerbated chronic inflammation in AGS, and that targeting this pathway might represent a promising therapeutic approach.

immunology↗

bioRxiv2022

Evolutionary dynamics of dengue virus in India

More than a hundred thousand dengue cases are diagnosed in India annually, and about half of the countrys population carries dengue virus-specific antibodies. Dengue propagates and adapts to the selection pressures imposed by a multitude of factors that can lead to the emergence of new variants. Yet, there has been no systematic analysis of the evolution of the dengue virus in the country. Here, we present a comprehensive analysis of all DENV gene sequences collected between 1956 and 2018 from India. We examine the spatio-temporal dynamics of India-specific genotypes, their evolutionary relationship with global and local dengue virus strains, interserotype dynamics and their divergence from the vaccine strains. Our analysis highlights the co-circulation of all DENV serotypes in India with cyclical outbreaks every 3-4 years. Since 2000, genotype III of DENV1, cosmopolitan genotype of DENV2, genotype III of DENV3 and genotype I of DENV4 have been dominating across the country. Substitution rates are comparable across the serotypes, suggesting a lack of serotype-specific evolutionary divergence. Yet, the envelope (E) protein displays strong signatures of evolution under immune selection. Apart from drifting away from its ancestors and other contemporary serotypes in general, we find evidence for recurring interserotype drift towards each other, suggesting selection via cross-reactive antibody-dependent enhancement. We identify the emergence of the highly divergent DENV4-Id lineage in South India, which has acquired half of all E gene mutations in the antigenic sites. Moreover, the DENV4-Id is drifting towards DENV1 and DENV3 clades, suggesting the role of cross-reactive antibodies in its evolution. Due to the regional restriction of the Indian genotypes and immunity-driven virus evolution in the country, [~]50% of all E gene differences with the current vaccines are focused on the antigenic sites. Our study shows how high incidence and pre-existing population immunity are shaping dengue virus evolution in India. Author summaryDengue is a mosquito-borne disease with four closely related serotypes of the virus (DENV1-4). Further, cross-reacting dengue antibodies from a previous infecting dengue serotype can protect or enhance infection from other serotypes. This can force the emergence of new dengue variants that find ways to escape the immune action or take advantage of it. In endemic countries like India, high rates of previous dengue infection can drive the evolution of dengue serotypes in complex ways. We compare all published dengue virus sequences to understand how new variants of dengue are emerging in India. Dengue cases and corresponding viruses display triennial surges. Further, the dengue envelope protein for each serotype shows recurring divergence and reversal towards its ancestral strain over a three-year window. Such fluctuations are also correlated among the dengue serotypes in India and could arise from the changing levels of cross-reactive antibodies. This, combined with the regional exchange of the virus among Asia-Pacific countries, has led to the emergence of India-specific DENV lineages, including a new DENV4 (Id) variant. This has also contributed to significant variations in the epitope regions of the current dengue viruses in India compared to the vaccines with implications for their efficacy.

evolutionary biology↗