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Papers by Debanjan Goswami

Research paper thumbnail of ISDN2012_0286: Postsynaptic complexin controls AMPA receptor exocytosis during long term potentiation

International Journal of Developmental Neuroscience, Dec 1, 2012

Research paper thumbnail of Supplementary Figure S4 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers

Research paper thumbnail of Supplementary Data from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers

DMEM or in (BxPC-3, Capan-1, SU.86.86, PK-1) RPMI supplemented with 10% FBS. We have used either ... more DMEM or in (BxPC-3, Capan-1, SU.86.86, PK-1) RPMI supplemented with 10% FBS. We have used either DMEM (D6429-Sigma) or RPMI (R8758-Sigma) supplemented with 10% FBS (F4135-Sigma) for culturing the cell lines. HPNE-hTERT cells were cultured in base medium following the instructions from ATCC. In short, the base medium for this cell line is: 75% DMEM without glucose (Sigma Cat #D-5030 with additional 2 mM L-glutamine and 1.5 g/L sodium bicarbonate) and 25% Medium M3 Base (INCELL Corp. Cat #M300F-500). To make the complete growth medium, we added the following components to the base medium: fetal bovine serum 5% (final conc.), 10 g/ml human recombinant EGF (#PHG0311L, Gibco), 5.5 mM D-glucose (1g/L), and 750 g/ml puromycin (Gibco). NRF2 overexpressing stable cell lines were generated by using Capan-1 and BxPC-3 cell lines. Before generating stable cell lines, cells were authenticated via short tandem repeat analysis with resulting allelic profiles matching those found in online databases. Cells were then seeded into six-well plates and incubated overnight at a density that yielded 60-70% confluency at the time of transduction. Media was removed from the cultures and replaced with one milliliter of media containing 8 µg/mL hexadimethrine bromide (Sigma-Aldrich, St. Louis, MO). One

Research paper thumbnail of Leveraging Topological Events in Tracking Graphs for Understanding Particle Diffusion

Computer Graphics Forum, 2021

Figure 1: Single particle tracking (SPT) of fluorescently labeled proteins (bright spots in the l... more Figure 1: Single particle tracking (SPT) of fluorescently labeled proteins (bright spots in the left image) is traditionally used to derive distribution of Mean Square Displacement (MSD) for all observed features (gray) as a measure of their diffusion. However, due to experimental limitations, it is impossible to distinguish single particles from clusters in the image leading to broad distributions of MSD and no direct link between cluster size and diffusion. Analyzing the merge and split events in the corresponding tracking graph (middle) determines, for the first time, estimates of the number of particles in each cluster leading to conditional MSD distributions (colored). These results confirm the prior hypothesis that observed changes in MSD are due to clustering, and that smaller clusters diffuse faster than bigger clusters.

Research paper thumbnail of Machine Learning-Driven Multiscale Modeling: Bridging the Scales with a Next-Generation Simulation Infrastructure

Journal of Chemical Theory and Computation

Research paper thumbnail of Supplementary Figure S5 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers

Cell cycle analysis of PDAC cells upon NRF2 activation

Research paper thumbnail of Supplementary Table S1 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers

Clinical characteristics of NRF2 expression in pancreatic cancer patients

Research paper thumbnail of Supplementary Table S2 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers

Research paper thumbnail of Supplementary Figure S1 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers

NRF2-mediated pathway is upregulated in KRAS mutant PDAC

Research paper thumbnail of Supplementary Figure S7 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers

Glutamine starvation regulates cell growth and assembly of stress granules

Research paper thumbnail of Supplementary Figure S8 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers

Effects of glutamine deprivation on cell viability and NRF2 expression

Research paper thumbnail of Data from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers

Pancreatic cancer is a disease with limited therapeutic options. Resistance to chemotherapies pos... more Pancreatic cancer is a disease with limited therapeutic options. Resistance to chemotherapies poses a significant clinical challenge for patients with pancreatic cancer and contributes to a high rate of recurrence. Oncogenic KRAS, a critical driver of pancreatic cancer, promotes metabolic reprogramming and upregulates NRF2, a master regulator of the antioxidant network. Here, we show that NRF2 contributed to chemoresistance and was associated with a poor prognosis in patients with pancreatic cancer. NRF2 activation metabolically rewired and elevated pathways involved in glutamine metabolism. This curbed chemoresistance in KRAS-mutant pancreatic cancers. In addition, manipulating glutamine metabolism restrained the assembly of stress granules, an indicator of chemoresistance. Glutaminase inhibitors sensitized chemoresistant pancreatic cancer cells to gemcitabine, thereby improving the effectiveness of chemotherapy. This therapeutic approach holds promise as a novel therapy for patien...

Research paper thumbnail of Supplementary Figure S2 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers

Isotype control for NRF2 in IHC and survival measure for NRF2

Research paper thumbnail of Supplementary Figure S6 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers

Role of metabolic pathways imparting gemcitabine resistance in pancreatic cancer

Research paper thumbnail of Supplementary Figure S3 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers

Knockdown and over-expression of NRF2 in PDAC cells

Research paper thumbnail of Supplementary Table S3 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers

Metabolic Pathway Enrichment in PDAC Patients Treated with Gemcitabine (Data Pooled from TCGA)

Research paper thumbnail of Lifetime of actin-dependent protein nanoclusters

Research paper thumbnail of Long-term potentiation requires unique postsynaptic SNARE fusion machinery

Clinical microbiology, Nov 9, 2015

Research paper thumbnail of Abstract A47: Targeting glutaminolysis potentiates the efficacy of chemotherapy in RAS-driven pancreatic cancers

Molecular Cancer Research

Pancreatic cancer is an extremely aggressive and deadly malignancy. Despite a detailed understand... more Pancreatic cancer is an extremely aggressive and deadly malignancy. Despite a detailed understanding of pancreatic ductal adenocarcinoma (PDAC)’s biology, the outcome of the current therapeutic regimen remains grim. Chemotherapeutic treatment is one of the first-line systemic treatments for PDAC. However, creating resistance against chemotherapy remains a major challenge. Oncogenic K-Ras mutation is one of the most common events responsible for the initiation and progression of PDAC. K-Ras mutation also promotes the activation of a transcription factor called NRF2 that is crucial for tumor development and pancreatic cancer proliferation. Our study detects differential basal levels of NRF2 in a panel of PDAC cell lines. We hypothesized that this phenomenon might reflect a greater intrinsic capacity of PDAC cells to become resistant to chemotherapy. We then demonstrated that upregulation of NRF2 creates resistance against chemotherapy in PDAC cells. Consequently, NRF2 activation rewir...

Research paper thumbnail of Abstract IA07: KRAS4b’s unique diffusion behavior is defined by plasma membrane and effector interactions

Molecular Cancer Research, 2020

RAS proteins are GTP-dependent switches that control and regulate signaling pathways involved in ... more RAS proteins are GTP-dependent switches that control and regulate signaling pathways involved in cell fate and are frequently mutated in cancer. RAS association with the plasma membrane, or with certain endomembrane compartments, is a required step for its activity. Why precisely this is so remains an open question. One possibility is that RAS is merely required for recruitment of RAF and other effectors to the membrane where it can associate with key regulatory molecules that lead to signaling activation. However, four isoforms exist in humans (HRAS, NRAS, and two splice variants, KRAS4b and KRAS4a) and their differences lie within 22 amino acids in the C-terminal hypervariable region (HVR, aa 167-189). These differences in the domain responsible for membrane association result in the recruitment and organization of RAS into distinct membrane nanodomains, and it is thought that this results in differential signaling behavior from RAS isoforms. Isoform-specific RAS nanodomains are t...

Research paper thumbnail of ISDN2012_0286: Postsynaptic complexin controls AMPA receptor exocytosis during long term potentiation

International Journal of Developmental Neuroscience, Dec 1, 2012

Research paper thumbnail of Supplementary Figure S4 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers

Research paper thumbnail of Supplementary Data from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers

DMEM or in (BxPC-3, Capan-1, SU.86.86, PK-1) RPMI supplemented with 10% FBS. We have used either ... more DMEM or in (BxPC-3, Capan-1, SU.86.86, PK-1) RPMI supplemented with 10% FBS. We have used either DMEM (D6429-Sigma) or RPMI (R8758-Sigma) supplemented with 10% FBS (F4135-Sigma) for culturing the cell lines. HPNE-hTERT cells were cultured in base medium following the instructions from ATCC. In short, the base medium for this cell line is: 75% DMEM without glucose (Sigma Cat #D-5030 with additional 2 mM L-glutamine and 1.5 g/L sodium bicarbonate) and 25% Medium M3 Base (INCELL Corp. Cat #M300F-500). To make the complete growth medium, we added the following components to the base medium: fetal bovine serum 5% (final conc.), 10 g/ml human recombinant EGF (#PHG0311L, Gibco), 5.5 mM D-glucose (1g/L), and 750 g/ml puromycin (Gibco). NRF2 overexpressing stable cell lines were generated by using Capan-1 and BxPC-3 cell lines. Before generating stable cell lines, cells were authenticated via short tandem repeat analysis with resulting allelic profiles matching those found in online databases. Cells were then seeded into six-well plates and incubated overnight at a density that yielded 60-70% confluency at the time of transduction. Media was removed from the cultures and replaced with one milliliter of media containing 8 µg/mL hexadimethrine bromide (Sigma-Aldrich, St. Louis, MO). One

Research paper thumbnail of Leveraging Topological Events in Tracking Graphs for Understanding Particle Diffusion

Computer Graphics Forum, 2021

Figure 1: Single particle tracking (SPT) of fluorescently labeled proteins (bright spots in the l... more Figure 1: Single particle tracking (SPT) of fluorescently labeled proteins (bright spots in the left image) is traditionally used to derive distribution of Mean Square Displacement (MSD) for all observed features (gray) as a measure of their diffusion. However, due to experimental limitations, it is impossible to distinguish single particles from clusters in the image leading to broad distributions of MSD and no direct link between cluster size and diffusion. Analyzing the merge and split events in the corresponding tracking graph (middle) determines, for the first time, estimates of the number of particles in each cluster leading to conditional MSD distributions (colored). These results confirm the prior hypothesis that observed changes in MSD are due to clustering, and that smaller clusters diffuse faster than bigger clusters.

Research paper thumbnail of Machine Learning-Driven Multiscale Modeling: Bridging the Scales with a Next-Generation Simulation Infrastructure

Journal of Chemical Theory and Computation

Research paper thumbnail of Supplementary Figure S5 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers

Cell cycle analysis of PDAC cells upon NRF2 activation

Research paper thumbnail of Supplementary Table S1 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers

Clinical characteristics of NRF2 expression in pancreatic cancer patients

Research paper thumbnail of Supplementary Table S2 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers

Research paper thumbnail of Supplementary Figure S1 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers

NRF2-mediated pathway is upregulated in KRAS mutant PDAC

Research paper thumbnail of Supplementary Figure S7 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers

Glutamine starvation regulates cell growth and assembly of stress granules

Research paper thumbnail of Supplementary Figure S8 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers

Effects of glutamine deprivation on cell viability and NRF2 expression

Research paper thumbnail of Data from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers

Pancreatic cancer is a disease with limited therapeutic options. Resistance to chemotherapies pos... more Pancreatic cancer is a disease with limited therapeutic options. Resistance to chemotherapies poses a significant clinical challenge for patients with pancreatic cancer and contributes to a high rate of recurrence. Oncogenic KRAS, a critical driver of pancreatic cancer, promotes metabolic reprogramming and upregulates NRF2, a master regulator of the antioxidant network. Here, we show that NRF2 contributed to chemoresistance and was associated with a poor prognosis in patients with pancreatic cancer. NRF2 activation metabolically rewired and elevated pathways involved in glutamine metabolism. This curbed chemoresistance in KRAS-mutant pancreatic cancers. In addition, manipulating glutamine metabolism restrained the assembly of stress granules, an indicator of chemoresistance. Glutaminase inhibitors sensitized chemoresistant pancreatic cancer cells to gemcitabine, thereby improving the effectiveness of chemotherapy. This therapeutic approach holds promise as a novel therapy for patien...

Research paper thumbnail of Supplementary Figure S2 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers

Isotype control for NRF2 in IHC and survival measure for NRF2

Research paper thumbnail of Supplementary Figure S6 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers

Role of metabolic pathways imparting gemcitabine resistance in pancreatic cancer

Research paper thumbnail of Supplementary Figure S3 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers

Knockdown and over-expression of NRF2 in PDAC cells

Research paper thumbnail of Supplementary Table S3 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers

Metabolic Pathway Enrichment in PDAC Patients Treated with Gemcitabine (Data Pooled from TCGA)

Research paper thumbnail of Lifetime of actin-dependent protein nanoclusters

Research paper thumbnail of Long-term potentiation requires unique postsynaptic SNARE fusion machinery

Clinical microbiology, Nov 9, 2015

Research paper thumbnail of Abstract A47: Targeting glutaminolysis potentiates the efficacy of chemotherapy in RAS-driven pancreatic cancers

Molecular Cancer Research

Pancreatic cancer is an extremely aggressive and deadly malignancy. Despite a detailed understand... more Pancreatic cancer is an extremely aggressive and deadly malignancy. Despite a detailed understanding of pancreatic ductal adenocarcinoma (PDAC)’s biology, the outcome of the current therapeutic regimen remains grim. Chemotherapeutic treatment is one of the first-line systemic treatments for PDAC. However, creating resistance against chemotherapy remains a major challenge. Oncogenic K-Ras mutation is one of the most common events responsible for the initiation and progression of PDAC. K-Ras mutation also promotes the activation of a transcription factor called NRF2 that is crucial for tumor development and pancreatic cancer proliferation. Our study detects differential basal levels of NRF2 in a panel of PDAC cell lines. We hypothesized that this phenomenon might reflect a greater intrinsic capacity of PDAC cells to become resistant to chemotherapy. We then demonstrated that upregulation of NRF2 creates resistance against chemotherapy in PDAC cells. Consequently, NRF2 activation rewir...

Research paper thumbnail of Abstract IA07: KRAS4b’s unique diffusion behavior is defined by plasma membrane and effector interactions

Molecular Cancer Research, 2020

RAS proteins are GTP-dependent switches that control and regulate signaling pathways involved in ... more RAS proteins are GTP-dependent switches that control and regulate signaling pathways involved in cell fate and are frequently mutated in cancer. RAS association with the plasma membrane, or with certain endomembrane compartments, is a required step for its activity. Why precisely this is so remains an open question. One possibility is that RAS is merely required for recruitment of RAF and other effectors to the membrane where it can associate with key regulatory molecules that lead to signaling activation. However, four isoforms exist in humans (HRAS, NRAS, and two splice variants, KRAS4b and KRAS4a) and their differences lie within 22 amino acids in the C-terminal hypervariable region (HVR, aa 167-189). These differences in the domain responsible for membrane association result in the recruitment and organization of RAS into distinct membrane nanodomains, and it is thought that this results in differential signaling behavior from RAS isoforms. Isoform-specific RAS nanodomains are t...