Jerry Melchor - Academia.edu (original) (raw)

Papers by Jerry Melchor

Research paper thumbnail of Tables S1-S8 from The Evolutionary Origins of Recurrent Pancreatic Cancer

Research paper thumbnail of Supplementary Figure S3 from Targeting eIF4A-Dependent Translation of KRAS Signaling Molecules

Research paper thumbnail of Supplementary Table 2 from Targeting eIF4A-Dependent Translation of KRAS Signaling Molecules

Research paper thumbnail of Supplementary Figure S2 from Targeting eIF4A-Dependent Translation of KRAS Signaling Molecules

Research paper thumbnail of Video V2 from PanIN Neuroendocrine Cells Promote Tumorigenesis via Neuronal Cross-talk

Bright field and fluorescent live imaging of NK1-Rlow (red) and NK1-Rhi/GFP (yellow) cells plated... more Bright field and fluorescent live imaging of NK1-Rlow (red) and NK1-Rhi/GFP (yellow) cells plated together in organoid culture.

Research paper thumbnail of Supplemental Figure Legends from PanIN Neuroendocrine Cells Promote Tumorigenesis via Neuronal Cross-talk

Contains the figure legends for supplemental Figures S1-S8, Table S1 and Videos V1 and V2.

Research paper thumbnail of Targeting eIF4A-Dependent Translation of KRAS Signaling Molecules

Cancer Research, 2021

Pancreatic adenocarcinoma (PDAC) epitomizes a deadly cancer driven by abnormal KRAS signaling. He... more Pancreatic adenocarcinoma (PDAC) epitomizes a deadly cancer driven by abnormal KRAS signaling. Here, we show that the eIF4A RNA helicase is required for translation of key KRAS signaling molecules and that pharmacological inhibition of eIF4A has single-agent activity against murine and human PDAC models at safe dose levels. EIF4A was uniquely required for the translation of mRNAs with long and highly structured 5′ untranslated regions, including those with multiple G-quadruplex elements. Computational analyses identified these features in mRNAs encoding KRAS and key downstream molecules. Transcriptome-scale ribosome footprinting accurately identified eIF4A-dependent mRNAs in PDAC, including critical KRAS signaling molecules such as PI3K, RALA, RAC2, MET, MYC, and YAP1. These findings contrast with a recent study that relied on an older method, polysome fractionation, and implicated redox-related genes as eIF4A clients. Together, our findings highlight the power of ribosome footprint...

Research paper thumbnail of Unbiased in vivo preclinical evaluation of anticancer drugs identifies effective therapy for the treatment of pancreatic adenocarcinoma

Proceedings of the National Academy of Sciences, 2020

Significance The clinical management of pancreatic cancer has not seen significant improvement in... more Significance The clinical management of pancreatic cancer has not seen significant improvement in decades, in part because prediction of tumor drug sensitivity using in vitro assays has proven notoriously inaccurate in this disease. We performed a large-scale, unbiased in vivo screen of 57 different single agent and combination targeted therapies in an in vivo orthotopic mouse model. In this ambitious effort, we identified previously unsuspected synergy between HSP90 inhibition and MEK inhibition as effective combination therapy in this disease. The results underscore the utility of unbiased, in vivo drug screens in the identification of effective cancer therapies for evaluation in subsequent clinical trials.

Research paper thumbnail of Pancreatic cancer prognosis is predicted by a novel ATAC-array technology for assessing chromatin accessibility

We investigated tumor-cell-intrinsic chromatin accessibility patterns of pancreatic ductal adenoc... more We investigated tumor-cell-intrinsic chromatin accessibility patterns of pancreatic ductal adenocarcinoma (PDAC) by ATAC-seq on EpCAM+ PDAC malignant epithelial cells, sorted from 54 freshly resected human tumors, and discovered a signature of 1092 chromatin loci displaying differential accessibility between patients with disease free survival (DFS) < 1 year and patients with DFS > 1 year. Analyzing transcription factor (TF) binding motifs within these loci, we identified two TFs (ZKSCAN1 and HNF1b) displaying differential nuclear localization between patients with short vs. long DFS. We further developed a novel chromatin accessibility microarray methodology termed ATAC-Array, an easy-to-use platform obviating the time and cost of next generation sequencing. Applying this novel methodology to the original ATAC-seq libraries as well as independent libraries generated from patient-derived organoids, we validated ATAC-array technology in both the original ATAC-Seq cohort as well...

Research paper thumbnail of A unifying paradigm for transcriptional heterogeneity and squamous features in pancreatic ductal adenocarcinoma

Research paper thumbnail of Evolutionary Origins of Recurrent Pancreatic Cancer

Surgery is the only curative option for Stage I/II pancreatic cancer, nonetheless most patients w... more Surgery is the only curative option for Stage I/II pancreatic cancer, nonetheless most patients will recur after surgery and die of their disease. To identify novel opportunities for management of recurrent pancreatic cancer we performed whole exome or targeted sequencing of 10 resected primary cancers and matched intrapancreatic recurrences or distant metastases. We identified that adjuvant or first-line platinum therapy corresponds to an increased mutational burden of recurrent disease. Recurrent disease is enriched for mutations that activate Mapk/Erk and PI3K/AKT signaling and develops from a monophyletic or polyphyletic origin. Treatment induced genetic bottlenecks lead to a modified genetic landscape and subclonal heterogeneity for driver gene alterations in part due to intermetastatic seeding. In one patient what was believed to be recurrent disease was an independent (second) primary tumor. These findings advocate for combination therapies with immunotherapy and routine post...

Research paper thumbnail of The Tissue Plasminogen Activator-Plasminogen Proteolytic Cascade Accelerates Amyloid-β (Aβ) Degradation and Inhibits Aβ-Induced Neurodegeneration

The Journal of Neuroscience, 2003

Accumulation of the amyloid-β (Aβ) peptide depends on both its generation and clearance. To bette... more Accumulation of the amyloid-β (Aβ) peptide depends on both its generation and clearance. To better define clearance pathways, we have evaluated the role of the tissue plasminogen activator (tPA)-plasmin system in Aβ degradationin vivo. In two different mouse models of Alzheimer's disease, chronically elevated Aβ peptide in the brain correlates with the upregulation of plasminogen activator inhibitor-1 (PAI-1) and inhibition of the tPA-plasmin system. In addition, Aβ injected into the hippocampus of mice lacking either tPA or plasminogen persists, inducing PAI-1 expression and causing activation of microglial cells and neuronal damage. Conversely, Aβ injected into wild-type mice is rapidly cleared and does not cause neuronal degeneration. Thus, the tPA-plasmin proteolytic cascade aids in the clearance of Aβ, and reduced activity of this system may contribute to the progression of Alzheimer's disease.

Research paper thumbnail of PanIN neuroendocrine cells promote tumorigenesis via neuronal crosstalk

Cancer research, Jan 19, 2017

Nerves are a notable feature of the tumor microenvironment in some epithelial tumors, but their r... more Nerves are a notable feature of the tumor microenvironment in some epithelial tumors, but their role in the malignant progression of pancreatic ductal adenocarcinoma (PDAC) is uncertain. Here we identify dense innervation in the microenvironment of precancerous pancreatic lesions, known as pancreatic intraepithelial neoplasms (PanIN), and describe a unique subpopulation of neuroendocrine PanIN cells that express the neuropeptide substance P (SP) receptor Neurokinin 1-R (NK1-R). Using organoid culture, we demonstrated that sensory neurons promoted the proliferation of PanIN organoids via SP-NK1-R signaling and Stat3 activation. Nerve-responsive neuroendocrine cells exerted trophic influences and potentiated global PanIN organoid growth. Sensory denervation of a genetically engineered mouse model of PDAC led to loss of Stat3 activation, a decrease in the neoplastic neuroendocrine cell population, and impaired PanIN progression to tumor. Overall, our data provide evidence that nerves o...

Research paper thumbnail of 133 Sensory Denervation Decreases PanIN Progression in a Mouse Model of Pancreatic Cancer

Gastroenterology, 2015

BACKGROUND: Reciprocal molecular signaling between pancreatic ductal adenocarcinoma (PDAC) and ne... more BACKGROUND: Reciprocal molecular signaling between pancreatic ductal adenocarcinoma (PDAC) and nerves may promote perineural invasion (PNI) and tumor growth. The identity and function of sensory neuropeptides in the tumor microenvironment are unknown. We hypothesized that sensory neurons play an important role in tumor progression and that substance P (SP) is a candidate neuropeptide for mediating this effect. AIMS:1) to characterize SP receptor (NK1R) expression in PanIN epithelium 2) to determine NK1R expression in human PDAC cell lines 3) to study effects of sensory denervation on pancreatic intraepithelial neoplasia (PanIN) initiation and progression in the KPC ( Pdx1-Cre; LSL-Kras; LSLTrp53) mouse model. METHODS: KPC mice were injected with the sensory neurotoxin resiniferatoxin (RTX; Sigma) or control solution on postnatal day 7. Pancreata from 8and 12-week-old mice were fixed and subject to HE Santa Cruz). Images were taken with a Nikon Camera or Zeiss LSM 510 Meta microscope. PanINs were graded as early (grade 1) or advanced (grades 2 and 3). PanIN burden was calculated by the percentage of total surface area occupied in 5 random views per HE p = 0.02). All analyzed human PDAC cell lines expressed the NK1R. In vivo studies revealed axons in close proximity to PanIN epithelium (Fig.1). RTX-treated mice had a 50% decrease in pancreatic sensory axonal density when compared to control mice at 8 and 12 weeks (p < 0.05). RTX-treated mice had a significant reduction in advanced PanINs compared to control mice at both 8 weeks (0.05% versus 0.9%; p < 0.05) and 12 weeks (0.3% versus 8%; p < 0.05). CONCLUSIONS: The NK1R is expressed in distinct cells within the PanIN epithelium and the percentage of NK1R+ cells increases with PanIN grade. Human PDAC cell lines express the NK1R. Sensory denervation is associated with a significant reduction in progression from early to advanced PanIN in the KPC model. Sensory nerves are likely an important part of the PanIN microenvironment and may affect tumorigenesis via the NK1R. This study provides new insight into the pathogenesis and potential therapeutic targets in PDAC.

Research paper thumbnail of Analysis of tau post-translational modifications in rTg4510 mice, a model of tau pathology

Molecular Neurodegeneration, 2015

Research paper thumbnail of Tissue plasminogen activator in central nervous system physiology and pathology

Thrombosis and Haemostasis, 2005

SummaryAlthough conventionally associated with fibrin clot degradation, recent work has uncovered... more SummaryAlthough conventionally associated with fibrin clot degradation, recent work has uncovered new functions for the tissue plasminogen activator (tPA)/plasminogen cascade in central nervous system physiology and pathology. This extracellular proteolytic cascade has been shown to have roles in learning and memory, stress, neuronal degeneration, addiction and Alzheimer’s disease. The current review considers the different ways tPA functions in the brain.

Research paper thumbnail of Ethanol-withdrawal seizures are controlled by tissue plasminogen activator via modulation of NR2B-containing NMDA receptors

Proceedings of the National Academy of Sciences, 2005

Chronic ethanol abuse causes up-regulation of NMDA receptors, which underlies seizures and brain ... more Chronic ethanol abuse causes up-regulation of NMDA receptors, which underlies seizures and brain damage upon ethanol withdrawal (EW). Here we show that tissue-plasminogen activator (tPA), a protease implicated in neuronal plasticity and seizures, is induced in the limbic system by chronic ethanol consumption, temporally coinciding with up-regulation of NMDA receptors. tPA interacts with NR2B-containing NMDA receptors and is required for up-regulation of the NR2B subunit in response to ethanol. As a consequence, tPA-deficient mice have reduced NR2B, extracellular signal-regulated kinase 1/2 phosphorylation, and seizures after EW. tPA-mediated facilitation of EW seizures is abolished by NR2B-specific NMDA antagonist ifenprodil. These results indicate that tPA mediates the development of physical dependence on ethanol by regulating NR2B-containing NMDA receptors.

Research paper thumbnail of P2-018 Investigating the role of the tissue plasminogen activator/plasmin system in Alzheimer's disease

Neurobiology of Aging, 2004

Research paper thumbnail of Tissue plasminogen activator in the amygdala is critical for stress-induced anxiety-like behavior

Nature Neuroscience, 2003

Research paper thumbnail of Modulation of Sympathetic Activity by Tissue Plasminogen Activator Is Independent of Plasminogen and Urokinase

Journal of Pharmacology and Experimental Therapeutics, 2007

Research paper thumbnail of Tables S1-S8 from The Evolutionary Origins of Recurrent Pancreatic Cancer

Research paper thumbnail of Supplementary Figure S3 from Targeting eIF4A-Dependent Translation of KRAS Signaling Molecules

Research paper thumbnail of Supplementary Table 2 from Targeting eIF4A-Dependent Translation of KRAS Signaling Molecules

Research paper thumbnail of Supplementary Figure S2 from Targeting eIF4A-Dependent Translation of KRAS Signaling Molecules

Research paper thumbnail of Video V2 from PanIN Neuroendocrine Cells Promote Tumorigenesis via Neuronal Cross-talk

Bright field and fluorescent live imaging of NK1-Rlow (red) and NK1-Rhi/GFP (yellow) cells plated... more Bright field and fluorescent live imaging of NK1-Rlow (red) and NK1-Rhi/GFP (yellow) cells plated together in organoid culture.

Research paper thumbnail of Supplemental Figure Legends from PanIN Neuroendocrine Cells Promote Tumorigenesis via Neuronal Cross-talk

Contains the figure legends for supplemental Figures S1-S8, Table S1 and Videos V1 and V2.

Research paper thumbnail of Targeting eIF4A-Dependent Translation of KRAS Signaling Molecules

Cancer Research, 2021

Pancreatic adenocarcinoma (PDAC) epitomizes a deadly cancer driven by abnormal KRAS signaling. He... more Pancreatic adenocarcinoma (PDAC) epitomizes a deadly cancer driven by abnormal KRAS signaling. Here, we show that the eIF4A RNA helicase is required for translation of key KRAS signaling molecules and that pharmacological inhibition of eIF4A has single-agent activity against murine and human PDAC models at safe dose levels. EIF4A was uniquely required for the translation of mRNAs with long and highly structured 5′ untranslated regions, including those with multiple G-quadruplex elements. Computational analyses identified these features in mRNAs encoding KRAS and key downstream molecules. Transcriptome-scale ribosome footprinting accurately identified eIF4A-dependent mRNAs in PDAC, including critical KRAS signaling molecules such as PI3K, RALA, RAC2, MET, MYC, and YAP1. These findings contrast with a recent study that relied on an older method, polysome fractionation, and implicated redox-related genes as eIF4A clients. Together, our findings highlight the power of ribosome footprint...

Research paper thumbnail of Unbiased in vivo preclinical evaluation of anticancer drugs identifies effective therapy for the treatment of pancreatic adenocarcinoma

Proceedings of the National Academy of Sciences, 2020

Significance The clinical management of pancreatic cancer has not seen significant improvement in... more Significance The clinical management of pancreatic cancer has not seen significant improvement in decades, in part because prediction of tumor drug sensitivity using in vitro assays has proven notoriously inaccurate in this disease. We performed a large-scale, unbiased in vivo screen of 57 different single agent and combination targeted therapies in an in vivo orthotopic mouse model. In this ambitious effort, we identified previously unsuspected synergy between HSP90 inhibition and MEK inhibition as effective combination therapy in this disease. The results underscore the utility of unbiased, in vivo drug screens in the identification of effective cancer therapies for evaluation in subsequent clinical trials.

Research paper thumbnail of Pancreatic cancer prognosis is predicted by a novel ATAC-array technology for assessing chromatin accessibility

We investigated tumor-cell-intrinsic chromatin accessibility patterns of pancreatic ductal adenoc... more We investigated tumor-cell-intrinsic chromatin accessibility patterns of pancreatic ductal adenocarcinoma (PDAC) by ATAC-seq on EpCAM+ PDAC malignant epithelial cells, sorted from 54 freshly resected human tumors, and discovered a signature of 1092 chromatin loci displaying differential accessibility between patients with disease free survival (DFS) < 1 year and patients with DFS > 1 year. Analyzing transcription factor (TF) binding motifs within these loci, we identified two TFs (ZKSCAN1 and HNF1b) displaying differential nuclear localization between patients with short vs. long DFS. We further developed a novel chromatin accessibility microarray methodology termed ATAC-Array, an easy-to-use platform obviating the time and cost of next generation sequencing. Applying this novel methodology to the original ATAC-seq libraries as well as independent libraries generated from patient-derived organoids, we validated ATAC-array technology in both the original ATAC-Seq cohort as well...

Research paper thumbnail of A unifying paradigm for transcriptional heterogeneity and squamous features in pancreatic ductal adenocarcinoma

Research paper thumbnail of Evolutionary Origins of Recurrent Pancreatic Cancer

Surgery is the only curative option for Stage I/II pancreatic cancer, nonetheless most patients w... more Surgery is the only curative option for Stage I/II pancreatic cancer, nonetheless most patients will recur after surgery and die of their disease. To identify novel opportunities for management of recurrent pancreatic cancer we performed whole exome or targeted sequencing of 10 resected primary cancers and matched intrapancreatic recurrences or distant metastases. We identified that adjuvant or first-line platinum therapy corresponds to an increased mutational burden of recurrent disease. Recurrent disease is enriched for mutations that activate Mapk/Erk and PI3K/AKT signaling and develops from a monophyletic or polyphyletic origin. Treatment induced genetic bottlenecks lead to a modified genetic landscape and subclonal heterogeneity for driver gene alterations in part due to intermetastatic seeding. In one patient what was believed to be recurrent disease was an independent (second) primary tumor. These findings advocate for combination therapies with immunotherapy and routine post...

Research paper thumbnail of The Tissue Plasminogen Activator-Plasminogen Proteolytic Cascade Accelerates Amyloid-β (Aβ) Degradation and Inhibits Aβ-Induced Neurodegeneration

The Journal of Neuroscience, 2003

Accumulation of the amyloid-β (Aβ) peptide depends on both its generation and clearance. To bette... more Accumulation of the amyloid-β (Aβ) peptide depends on both its generation and clearance. To better define clearance pathways, we have evaluated the role of the tissue plasminogen activator (tPA)-plasmin system in Aβ degradationin vivo. In two different mouse models of Alzheimer's disease, chronically elevated Aβ peptide in the brain correlates with the upregulation of plasminogen activator inhibitor-1 (PAI-1) and inhibition of the tPA-plasmin system. In addition, Aβ injected into the hippocampus of mice lacking either tPA or plasminogen persists, inducing PAI-1 expression and causing activation of microglial cells and neuronal damage. Conversely, Aβ injected into wild-type mice is rapidly cleared and does not cause neuronal degeneration. Thus, the tPA-plasmin proteolytic cascade aids in the clearance of Aβ, and reduced activity of this system may contribute to the progression of Alzheimer's disease.

Research paper thumbnail of PanIN neuroendocrine cells promote tumorigenesis via neuronal crosstalk

Cancer research, Jan 19, 2017

Nerves are a notable feature of the tumor microenvironment in some epithelial tumors, but their r... more Nerves are a notable feature of the tumor microenvironment in some epithelial tumors, but their role in the malignant progression of pancreatic ductal adenocarcinoma (PDAC) is uncertain. Here we identify dense innervation in the microenvironment of precancerous pancreatic lesions, known as pancreatic intraepithelial neoplasms (PanIN), and describe a unique subpopulation of neuroendocrine PanIN cells that express the neuropeptide substance P (SP) receptor Neurokinin 1-R (NK1-R). Using organoid culture, we demonstrated that sensory neurons promoted the proliferation of PanIN organoids via SP-NK1-R signaling and Stat3 activation. Nerve-responsive neuroendocrine cells exerted trophic influences and potentiated global PanIN organoid growth. Sensory denervation of a genetically engineered mouse model of PDAC led to loss of Stat3 activation, a decrease in the neoplastic neuroendocrine cell population, and impaired PanIN progression to tumor. Overall, our data provide evidence that nerves o...

Research paper thumbnail of 133 Sensory Denervation Decreases PanIN Progression in a Mouse Model of Pancreatic Cancer

Gastroenterology, 2015

BACKGROUND: Reciprocal molecular signaling between pancreatic ductal adenocarcinoma (PDAC) and ne... more BACKGROUND: Reciprocal molecular signaling between pancreatic ductal adenocarcinoma (PDAC) and nerves may promote perineural invasion (PNI) and tumor growth. The identity and function of sensory neuropeptides in the tumor microenvironment are unknown. We hypothesized that sensory neurons play an important role in tumor progression and that substance P (SP) is a candidate neuropeptide for mediating this effect. AIMS:1) to characterize SP receptor (NK1R) expression in PanIN epithelium 2) to determine NK1R expression in human PDAC cell lines 3) to study effects of sensory denervation on pancreatic intraepithelial neoplasia (PanIN) initiation and progression in the KPC ( Pdx1-Cre; LSL-Kras; LSLTrp53) mouse model. METHODS: KPC mice were injected with the sensory neurotoxin resiniferatoxin (RTX; Sigma) or control solution on postnatal day 7. Pancreata from 8and 12-week-old mice were fixed and subject to HE Santa Cruz). Images were taken with a Nikon Camera or Zeiss LSM 510 Meta microscope. PanINs were graded as early (grade 1) or advanced (grades 2 and 3). PanIN burden was calculated by the percentage of total surface area occupied in 5 random views per HE p = 0.02). All analyzed human PDAC cell lines expressed the NK1R. In vivo studies revealed axons in close proximity to PanIN epithelium (Fig.1). RTX-treated mice had a 50% decrease in pancreatic sensory axonal density when compared to control mice at 8 and 12 weeks (p < 0.05). RTX-treated mice had a significant reduction in advanced PanINs compared to control mice at both 8 weeks (0.05% versus 0.9%; p < 0.05) and 12 weeks (0.3% versus 8%; p < 0.05). CONCLUSIONS: The NK1R is expressed in distinct cells within the PanIN epithelium and the percentage of NK1R+ cells increases with PanIN grade. Human PDAC cell lines express the NK1R. Sensory denervation is associated with a significant reduction in progression from early to advanced PanIN in the KPC model. Sensory nerves are likely an important part of the PanIN microenvironment and may affect tumorigenesis via the NK1R. This study provides new insight into the pathogenesis and potential therapeutic targets in PDAC.

Research paper thumbnail of Analysis of tau post-translational modifications in rTg4510 mice, a model of tau pathology

Molecular Neurodegeneration, 2015

Research paper thumbnail of Tissue plasminogen activator in central nervous system physiology and pathology

Thrombosis and Haemostasis, 2005

SummaryAlthough conventionally associated with fibrin clot degradation, recent work has uncovered... more SummaryAlthough conventionally associated with fibrin clot degradation, recent work has uncovered new functions for the tissue plasminogen activator (tPA)/plasminogen cascade in central nervous system physiology and pathology. This extracellular proteolytic cascade has been shown to have roles in learning and memory, stress, neuronal degeneration, addiction and Alzheimer’s disease. The current review considers the different ways tPA functions in the brain.

Research paper thumbnail of Ethanol-withdrawal seizures are controlled by tissue plasminogen activator via modulation of NR2B-containing NMDA receptors

Proceedings of the National Academy of Sciences, 2005

Chronic ethanol abuse causes up-regulation of NMDA receptors, which underlies seizures and brain ... more Chronic ethanol abuse causes up-regulation of NMDA receptors, which underlies seizures and brain damage upon ethanol withdrawal (EW). Here we show that tissue-plasminogen activator (tPA), a protease implicated in neuronal plasticity and seizures, is induced in the limbic system by chronic ethanol consumption, temporally coinciding with up-regulation of NMDA receptors. tPA interacts with NR2B-containing NMDA receptors and is required for up-regulation of the NR2B subunit in response to ethanol. As a consequence, tPA-deficient mice have reduced NR2B, extracellular signal-regulated kinase 1/2 phosphorylation, and seizures after EW. tPA-mediated facilitation of EW seizures is abolished by NR2B-specific NMDA antagonist ifenprodil. These results indicate that tPA mediates the development of physical dependence on ethanol by regulating NR2B-containing NMDA receptors.

Research paper thumbnail of P2-018 Investigating the role of the tissue plasminogen activator/plasmin system in Alzheimer's disease

Neurobiology of Aging, 2004

Research paper thumbnail of Tissue plasminogen activator in the amygdala is critical for stress-induced anxiety-like behavior

Nature Neuroscience, 2003

Research paper thumbnail of Modulation of Sympathetic Activity by Tissue Plasminogen Activator Is Independent of Plasminogen and Urokinase

Journal of Pharmacology and Experimental Therapeutics, 2007