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1.
Cell ; 184(25): 6119-6137.e26, 2021 12 09.
Article in English | MEDLINE | ID: mdl-34890551

ABSTRACT

Prognostically relevant RNA expression states exist in pancreatic ductal adenocarcinoma (PDAC), but our understanding of their drivers, stability, and relationship to therapeutic response is limited. To examine these attributes systematically, we profiled metastatic biopsies and matched organoid models at single-cell resolution. In vivo, we identify a new intermediate PDAC transcriptional cell state and uncover distinct site- and state-specific tumor microenvironments (TMEs). Benchmarking models against this reference map, we reveal strong culture-specific biases in cancer cell transcriptional state representation driven by altered TME signals. We restore expression state heterogeneity by adding back in vivo-relevant factors and show plasticity in culture models. Further, we prove that non-genetic modulation of cell state can strongly influence drug responses, uncovering state-specific vulnerabilities. This work provides a broadly applicable framework for aligning cell states across in vivo and ex vivo settings, identifying drivers of transcriptional plasticity and manipulating cell state to target associated vulnerabilities.


Subject(s)
Biomarkers, Tumor/metabolism , Carcinoma, Pancreatic Ductal/metabolism , Pancreatic Neoplasms/metabolism , Tumor Microenvironment , Adult , Aged , Cell Line, Tumor , Female , Gene Expression Regulation, Neoplastic , Humans , Male , Middle Aged , Single-Cell Analysis
2.
Cell ; 184(26): 6262-6280.e26, 2021 12 22.
Article in English | MEDLINE | ID: mdl-34910928

ABSTRACT

Colorectal cancers (CRCs) arise from precursor polyps whose cellular origins, molecular heterogeneity, and immunogenic potential may reveal diagnostic and therapeutic insights when analyzed at high resolution. We present a single-cell transcriptomic and imaging atlas of the two most common human colorectal polyps, conventional adenomas and serrated polyps, and their resulting CRC counterparts. Integrative analysis of 128 datasets from 62 participants reveals adenomas arise from WNT-driven expansion of stem cells, while serrated polyps derive from differentiated cells through gastric metaplasia. Metaplasia-associated damage is coupled to a cytotoxic immune microenvironment preceding hypermutation, driven partly by antigen-presentation differences associated with tumor cell-differentiation status. Microsatellite unstable CRCs contain distinct non-metaplastic regions where tumor cells acquire stem cell properties and cytotoxic immune cells are depleted. Our multi-omic atlas provides insights into malignant progression of colorectal polyps and their microenvironment, serving as a framework for precision surveillance and prevention of CRC.


Subject(s)
Colonic Polyps/pathology , Colorectal Neoplasms/pathology , Tumor Microenvironment , Adaptive Immunity , Adenoma/genetics , Adenoma/pathology , Adult , Aged , Animals , Carcinogenesis/genetics , Carcinogenesis/pathology , Cell Death , Cell Differentiation , Colonic Polyps/genetics , Colonic Polyps/immunology , Colorectal Neoplasms/genetics , Colorectal Neoplasms/immunology , Disease Progression , Female , Gene Expression Regulation, Neoplastic , Gene Regulatory Networks , Genetic Heterogeneity , Humans , Male , Mice , Middle Aged , Mutation/genetics , Neoplastic Stem Cells/metabolism , Neoplastic Stem Cells/pathology , RNA-Seq , Reproducibility of Results , Single-Cell Analysis , Tumor Microenvironment/immunology
3.
Cell ; 182(6): 1606-1622.e23, 2020 09 17.
Article in English | MEDLINE | ID: mdl-32888429

ABSTRACT

The enteric nervous system (ENS) coordinates diverse functions in the intestine but has eluded comprehensive molecular characterization because of the rarity and diversity of cells. Here we develop two methods to profile the ENS of adult mice and humans at single-cell resolution: RAISIN RNA-seq for profiling intact nuclei with ribosome-bound mRNA and MIRACL-seq for label-free enrichment of rare cell types by droplet-based profiling. The 1,187,535 nuclei in our mouse atlas include 5,068 neurons from the ileum and colon, revealing extraordinary neuron diversity. We highlight circadian expression changes in enteric neurons, show that disease-related genes are dysregulated with aging, and identify differences between the ileum and proximal/distal colon. In humans, we profile 436,202 nuclei, recovering 1,445 neurons, and identify conserved and species-specific transcriptional programs and putative neuro-epithelial, neuro-stromal, and neuro-immune interactions. The human ENS expresses risk genes for neuropathic, inflammatory, and extra-intestinal diseases, suggesting neuronal contributions to disease.


Subject(s)
Enteric Nervous System/cytology , Enteric Nervous System/metabolism , Gene Expression Regulation, Developmental/genetics , Neurons/metabolism , Nissl Bodies/metabolism , RNA, Messenger/metabolism , Single-Cell Analysis/methods , Aging/genetics , Aging/metabolism , Animals , Circadian Clocks/genetics , Colon/cytology , Colon/metabolism , Endoplasmic Reticulum, Rough/genetics , Endoplasmic Reticulum, Rough/metabolism , Endoplasmic Reticulum, Rough/ultrastructure , Epithelial Cells/metabolism , Female , Genetic Predisposition to Disease/genetics , Humans , Ileum/cytology , Ileum/metabolism , Inflammation/genetics , Inflammation/metabolism , Intestinal Diseases/genetics , Intestinal Diseases/metabolism , Male , Mice , Mice, Inbred C57BL , Mice, Transgenic , Microscopy, Electron, Transmission , Nervous System Diseases/genetics , Nervous System Diseases/metabolism , Neuroglia/cytology , Neuroglia/metabolism , Neurons/cytology , Nissl Bodies/genetics , Nissl Bodies/ultrastructure , RNA, Messenger/genetics , RNA-Seq , Ribosomes/metabolism , Ribosomes/ultrastructure , Stromal Cells/metabolism
4.
Nature ; 629(8013): 919-926, 2024 May.
Article in English | MEDLINE | ID: mdl-38589574

ABSTRACT

RAS oncogenes (collectively NRAS, HRAS and especially KRAS) are among the most frequently mutated genes in cancer, with common driver mutations occurring at codons 12, 13 and 611. Small molecule inhibitors of the KRAS(G12C) oncoprotein have demonstrated clinical efficacy in patients with multiple cancer types and have led to regulatory approvals for the treatment of non-small cell lung cancer2,3. Nevertheless, KRASG12C mutations account for only around 15% of KRAS-mutated cancers4,5, and there are no approved KRAS inhibitors for the majority of patients with tumours containing other common KRAS mutations. Here we describe RMC-7977, a reversible, tri-complex RAS inhibitor with broad-spectrum activity for the active state of both mutant and wild-type KRAS, NRAS and HRAS variants (a RAS(ON) multi-selective inhibitor). Preclinically, RMC-7977 demonstrated potent activity against RAS-addicted tumours carrying various RAS genotypes, particularly against cancer models with KRAS codon 12 mutations (KRASG12X). Treatment with RMC-7977 led to tumour regression and was well tolerated in diverse RAS-addicted preclinical cancer models. Additionally, RMC-7977 inhibited the growth of KRASG12C cancer models that are resistant to KRAS(G12C) inhibitors owing to restoration of RAS pathway signalling. Thus, RAS(ON) multi-selective inhibitors can target multiple oncogenic and wild-type RAS isoforms and have the potential to treat a wide range of RAS-addicted cancers with high unmet clinical need. A related RAS(ON) multi-selective inhibitor, RMC-6236, is currently under clinical evaluation in patients with KRAS-mutant solid tumours (ClinicalTrials.gov identifier: NCT05379985).


Subject(s)
Antineoplastic Agents , Mutation , Neoplasms , Oncogene Protein p21(ras) , Proto-Oncogene Proteins p21(ras) , Animals , Humans , Mice , Antineoplastic Agents/pharmacology , Antineoplastic Agents/therapeutic use , Cell Line, Tumor , Guanosine Triphosphate/metabolism , Mice, Inbred BALB C , Mice, Inbred C57BL , Neoplasms/drug therapy , Neoplasms/genetics , Neoplasms/pathology , Oncogene Protein p21(ras)/antagonists & inhibitors , Oncogene Protein p21(ras)/genetics , Proto-Oncogene Proteins p21(ras)/genetics , Proto-Oncogene Proteins p21(ras)/antagonists & inhibitors , Signal Transduction/drug effects , Xenograft Model Antitumor Assays
5.
Mol Cell ; 81(17): 3481-3495.e7, 2021 09 02.
Article in English | MEDLINE | ID: mdl-34358446

ABSTRACT

PRMT5 is an essential arginine methyltransferase and a therapeutic target in MTAP-null cancers. PRMT5 uses adaptor proteins for substrate recruitment through a previously undefined mechanism. Here, we identify an evolutionarily conserved peptide sequence shared among the three known substrate adaptors (CLNS1A, RIOK1, and COPR5) and show that it is necessary and sufficient for interaction with PRMT5. We demonstrate that PRMT5 uses modular adaptor proteins containing a common binding motif for substrate recruitment, comparable with other enzyme classes such as kinases and E3 ligases. We structurally resolve the interface with PRMT5 and show via genetic perturbation that it is required for methylation of adaptor-recruited substrates including the spliceosome, histones, and ribosomal complexes. Furthermore, disruption of this site affects Sm spliceosome activity, leading to intron retention. Genetic disruption of the PRMT5-substrate adaptor interface impairs growth of MTAP-null tumor cells and is thus a site for development of therapeutic inhibitors of PRMT5.


Subject(s)
Protein-Arginine N-Methyltransferases/metabolism , Protein-Arginine N-Methyltransferases/physiology , Animals , Cell Line, Tumor , Cytoplasm/metabolism , Female , HCT116 Cells , HEK293 Cells , Histones/metabolism , Humans , Intracellular Signaling Peptides and Proteins/metabolism , Ion Channels/metabolism , Male , Methylation , Mice , Mice, Nude , Nuclear Proteins/metabolism , Peptides/genetics , Protein Binding , Protein Processing, Post-Translational , Protein Serine-Threonine Kinases/metabolism , Protein-Arginine N-Methyltransferases/genetics , Spliceosomes/metabolism
6.
Nature ; 609(7926): 408-415, 2022 09.
Article in English | MEDLINE | ID: mdl-35831509

ABSTRACT

Receptor tyrosine kinase (RTK)-RAS signalling through the downstream mitogen-activated protein kinase (MAPK) cascade regulates cell proliferation and survival. The SHOC2-MRAS-PP1C holophosphatase complex functions as a key regulator of RTK-RAS signalling by removing an inhibitory phosphorylation event on the RAF family of proteins to potentiate MAPK signalling1. SHOC2 forms a ternary complex with MRAS and PP1C, and human germline gain-of-function mutations in this complex result in congenital RASopathy syndromes2-5. However, the structure and assembly of this complex are poorly understood. Here we use cryo-electron microscopy to resolve the structure of the SHOC2-MRAS-PP1C complex. We define the biophysical principles of holoenzyme interactions, elucidate the assembly order of the complex, and systematically interrogate the functional consequence of nearly all of the possible missense variants of SHOC2 through deep mutational scanning. We show that SHOC2 binds PP1C and MRAS through the concave surface of the leucine-rich repeat region and further engages PP1C through the N-terminal disordered region that contains a cryptic RVXF motif. Complex formation is initially mediated by interactions between SHOC2 and PP1C and is stabilized by the binding of GTP-loaded MRAS. These observations explain how mutant versions of SHOC2 in RASopathies and cancer stabilize the interactions of complex members to enhance holophosphatase activity. Together, this integrative structure-function model comprehensively defines key binding interactions within the SHOC2-MRAS-PP1C holophosphatase complex and will inform therapeutic development .


Subject(s)
Cryoelectron Microscopy , Intracellular Signaling Peptides and Proteins , Multiprotein Complexes , Protein Phosphatase 1 , ras Proteins , Amino Acid Motifs , Binding Sites , Guanosine Triphosphate/metabolism , Humans , Intracellular Signaling Peptides and Proteins/chemistry , Intracellular Signaling Peptides and Proteins/genetics , Intracellular Signaling Peptides and Proteins/metabolism , MAP Kinase Signaling System , Multiprotein Complexes/chemistry , Multiprotein Complexes/metabolism , Multiprotein Complexes/ultrastructure , Mutation, Missense , Phosphorylation , Protein Binding , Protein Phosphatase 1/chemistry , Protein Phosphatase 1/metabolism , Protein Phosphatase 1/ultrastructure , Protein Stability , raf Kinases , ras Proteins/chemistry , ras Proteins/metabolism , ras Proteins/ultrastructure
7.
Mol Cell ; 78(6): 1070-1085, 2020 06 18.
Article in English | MEDLINE | ID: mdl-32459988

ABSTRACT

Anti-cancer drugs targeting the DNA damage response (DDR) exploit genetic or functional defects in this pathway through synthetic lethal mechanisms. For example, defects in homologous recombination (HR) repair arise in cancer cells through inherited or acquired mutations in BRCA1, BRCA2, or other genes in the Fanconi anemia/BRCA pathway, and these tumors have been shown to be particularly sensitive to inhibitors of the base excision repair (BER) protein poly (ADP-ribose) polymerase (PARP). Recent work has identified additional genomic and functional assays of DNA repair that provide new predictive and pharmacodynamic biomarkers for these targeted therapies. Here, we examine the development of selective agents targeting DNA repair, including PARP inhibitors; inhibitors of the DNA damage kinases ataxia-telangiectasia and Rad3 related (ATR), CHK1, WEE1, and ataxia-telangiectasia mutated (ATM); and inhibitors of classical non-homologous end joining (cNHEJ) and alternative end joining (Alt EJ). We also review the biomarkers that guide the use of these agents and current clinical trials with these therapies.


Subject(s)
DNA Repair/drug effects , DNA Repair/physiology , Neoplasms/drug therapy , Animals , Antineoplastic Agents/therapeutic use , Biomarkers, Pharmacological , DNA Damage/drug effects , DNA End-Joining Repair/drug effects , DNA Repair/genetics , Genes, BRCA1/drug effects , Homologous Recombination , Humans , Poly(ADP-ribose) Polymerase Inhibitors/pharmacology , Poly(ADP-ribose) Polymerases/metabolism
8.
Gut ; 73(4): 639-648, 2024 Mar 07.
Article in English | MEDLINE | ID: mdl-38123998

ABSTRACT

OBJECTIVE: Pancreatic ductal adenocarcinoma (PDAC) is commonly diagnosed at an advanced stage. Liquid biopsy approaches may facilitate detection of early stage PDAC when curative treatments can be employed. DESIGN: To assess circulating marker discrimination in training, testing and validation patient cohorts (total n=426 patients), plasma markers were measured among PDAC cases and patients with chronic pancreatitis, colorectal cancer (CRC), and healthy controls. Using CA19-9 as an anchor marker, measurements were made of two protein markers (TIMP1, LRG1) and cell-free DNA (cfDNA) pancreas-specific methylation at 9 loci encompassing 61 CpG sites. RESULTS: Comparative methylome analysis identified nine loci that were differentially methylated in exocrine pancreas DNA. In the training set (n=124 patients), cfDNA methylation markers distinguished PDAC from healthy and CRC controls. In the testing set of 86 early stage PDAC and 86 matched healthy controls, CA19-9 had an area under the receiver operating characteristic curve (AUC) of 0.88 (95% CI 0.83 to 0.94), which was increased by adding TIMP1 (AUC 0.92; 95% CI 0.88 to 0.96; p=0.06), LRG1 (AUC 0.92; 95% CI 0.88 to 0.96; p=0.02) or exocrine pancreas-specific cfDNA methylation markers at nine loci (AUC 0.92; 95% CI 0.88 to 0.96; p=0.02). In the validation set of 40 early stage PDAC and 40 matched healthy controls, a combined panel including CA19-9, TIMP1 and a 9-loci cfDNA methylation panel had greater discrimination (AUC 0.86, 95% CI 0.77 to 0.95) than CA19-9 alone (AUC 0.82; 95% CI 0.72 to 0.92). CONCLUSION: A combined panel of circulating markers including proteins and methylated cfDNA increased discrimination compared with CA19-9 alone for early stage PDAC.


Subject(s)
Adenocarcinoma , Carcinoma, Pancreatic Ductal , Cell-Free Nucleic Acids , Pancreatic Neoplasms , Humans , CA-19-9 Antigen , Biomarkers, Tumor , Cell-Free Nucleic Acids/metabolism , Pancreatic Neoplasms/diagnosis , Pancreatic Neoplasms/genetics , Pancreatic Neoplasms/metabolism , Carcinoma, Pancreatic Ductal/diagnosis , Carcinoma, Pancreatic Ductal/genetics , Carcinoma, Pancreatic Ductal/pathology , Pancreas/pathology , Adenocarcinoma/diagnosis , Adenocarcinoma/genetics , Adenocarcinoma/pathology , DNA Methylation
9.
N Engl J Med ; 384(25): 2382-2393, 2021 06 24.
Article in English | MEDLINE | ID: mdl-34161704

ABSTRACT

BACKGROUND: Clinical trials of the KRAS inhibitors adagrasib and sotorasib have shown promising activity in cancers harboring KRAS glycine-to-cysteine amino acid substitutions at codon 12 (KRASG12C). The mechanisms of acquired resistance to these therapies are currently unknown. METHODS: Among patients with KRASG12C -mutant cancers treated with adagrasib monotherapy, we performed genomic and histologic analyses that compared pretreatment samples with those obtained after the development of resistance. Cell-based experiments were conducted to study mutations that confer resistance to KRASG12C inhibitors. RESULTS: A total of 38 patients were included in this study: 27 with non-small-cell lung cancer, 10 with colorectal cancer, and 1 with appendiceal cancer. Putative mechanisms of resistance to adagrasib were detected in 17 patients (45% of the cohort), of whom 7 (18% of the cohort) had multiple coincident mechanisms. Acquired KRAS alterations included G12D/R/V/W, G13D, Q61H, R68S, H95D/Q/R, Y96C, and high-level amplification of the KRASG12C allele. Acquired bypass mechanisms of resistance included MET amplification; activating mutations in NRAS, BRAF, MAP2K1, and RET; oncogenic fusions involving ALK, RET, BRAF, RAF1, and FGFR3; and loss-of-function mutations in NF1 and PTEN. In two of nine patients with lung adenocarcinoma for whom paired tissue-biopsy samples were available, histologic transformation to squamous-cell carcinoma was observed without identification of any other resistance mechanisms. Using an in vitro deep mutational scanning screen, we systematically defined the landscape of KRAS mutations that confer resistance to KRASG12C inhibitors. CONCLUSIONS: Diverse genomic and histologic mechanisms impart resistance to covalent KRASG12C inhibitors, and new therapeutic strategies are required to delay and overcome this drug resistance in patients with cancer. (Funded by Mirati Therapeutics and others; ClinicalTrials.gov number, NCT03785249.).


Subject(s)
Acetonitriles/therapeutic use , Carcinoma, Non-Small-Cell Lung/drug therapy , Colorectal Neoplasms/drug therapy , Drug Resistance, Neoplasm/genetics , Lung Neoplasms/drug therapy , Mutation , Piperazines/therapeutic use , Proto-Oncogene Proteins p21(ras)/genetics , Pyrimidines/therapeutic use , Appendiceal Neoplasms/drug therapy , Appendiceal Neoplasms/genetics , Carcinoma, Non-Small-Cell Lung/genetics , Colorectal Neoplasms/genetics , Humans , Lung Neoplasms/genetics , Protein Conformation , Proto-Oncogene Proteins p21(ras)/antagonists & inhibitors , Proto-Oncogene Proteins p21(ras)/ultrastructure , Pyridines/therapeutic use
10.
Gastroenterology ; 165(4): 874-890.e10, 2023 10.
Article in English | MEDLINE | ID: mdl-37263309

ABSTRACT

BACKGROUND & AIMS: Transforming growth factor-b (TGFb) plays pleiotropic roles in pancreatic cancer, including promoting metastasis, attenuating CD8 T-cell activation, and enhancing myofibroblast differentiation and deposition of extracellular matrix. However, single-agent TGFb inhibition has shown limited efficacy against pancreatic cancer in mice or humans. METHODS: We evaluated the TGFß-blocking antibody NIS793 in combination with gemcitabine/nanoparticle (albumin-bound)-paclitaxel or FOLFIRINOX (folinic acid [FOL], 5-fluorouracil [F], irinotecan [IRI] and oxaliplatin [OX]) in orthotopic pancreatic cancer models. Single-cell RNA sequencing and immunofluorescence were used to evaluate changes in tumor cell state and the tumor microenvironment. RESULTS: Blockade of TGFß with chemotherapy reduced tumor burden in poorly immunogenic pancreatic cancer, without affecting the metastatic rate of cancer cells. Efficacy of combination therapy was not dependent on CD8 T cells, because response to TGFß blockade was preserved in CD8-depleted or recombination activating gene 2 (RAG2-/-) mice. TGFß blockade decreased total α-smooth muscle actin-positive fibroblasts but had minimal effect on fibroblast heterogeneity. Bulk RNA sequencing on tumor cells sorted ex vivo revealed that tumor cells treated with TGFß blockade adopted a classical lineage consistent with enhanced chemosensitivity, and immunofluorescence for cleaved caspase 3 confirmed that TGFß blockade increased chemotherapy-induced cell death in vivo. CONCLUSIONS: TGFß regulates pancreatic cancer cell plasticity between classical and basal cell states. TGFß blockade in orthotropic models of pancreatic cancer enhances sensitivity to chemotherapy by promoting a classical malignant cell state. This study provides scientific rationale for evaluation of NIS793 with FOLFIRINOX or gemcitabine/nanoparticle (albumin-bound) paclitaxel chemotherapy backbone in the clinical setting and supports the concept of manipulating cancer cell plasticity to increase the efficacy of combination therapy regimens.


Subject(s)
Antineoplastic Agents , Pancreatic Neoplasms , Humans , Mice , Animals , Pancreatic Neoplasms/drug therapy , Pancreatic Neoplasms/genetics , Pancreatic Neoplasms/pathology , Antineoplastic Combined Chemotherapy Protocols/pharmacology , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Transforming Growth Factor beta/metabolism , Antineoplastic Agents/therapeutic use , Gemcitabine , Paclitaxel/pharmacology , Paclitaxel/therapeutic use , Albumins , Transforming Growth Factors/therapeutic use , Tumor Microenvironment , Pancreatic Neoplasms
11.
Oncologist ; 28(5): 425-432, 2023 05 08.
Article in English | MEDLINE | ID: mdl-36807743

ABSTRACT

BACKGROUND: In preclinical pancreatic ductal adenocarcinoma (PDAC) models, inhibition of hepatocyte growth factor (HGF) signaling using ficlatuzumab, a recombinant humanized anti-HGF antibody, and gemcitabine reduced tumor burden. METHODS: Patients with previously untreated metastatic PDAC enrolled in a phase Ib dose escalation study with 3 + 3 design of 2 dose cohorts of ficlatuzumab 10 and 20 mg/kg administered intravenously every other week with gemcitabine 1000 mg/m2 and albumin-bound paclitaxel 125 mg/m2 given 3 weeks on and 1 week off. This was followed by an expansion phase at the maximally tolerated dose of the combination. RESULTS: Twenty-six patients (sex, 12 male:14 female; median age, 68 years [range, 49-83 years]) were enrolled, 22 patients were evaluable. No dose-limiting toxicities were identified (N = 7 pts) and ficlatuzumab at 20 mg/kg was chosen as the maximum tolerated dose. Among the 21 patients treated at the MTD, best response by RECISTv1.1: 6 (29%) partial response, 12 (57%) stable disease, 1 (5%) progressive disease, and 2 (9%) not evaluable. Median progression-free survival and overall survival times were 11.0 months (95% CI, 7.6-11.4 months) and 16.2 months (95% CI, 9.1 months to not reached), respectively. Toxicities attributed to ficlatuzumab included hypoalbuminemia (grade 3, 16%; any grade, 52%) and edema (grade 3, 8%; any grade, 48%). Immunohistochemistry for c-Met pathway activation demonstrated higher tumor cell p-Met levels in patients who experienced response to therapy. CONCLUSION: In this phase Ib trial, ficlatuzumab, gemcitabine, and albumin-bound paclitaxel were associated with durable treatment responses and increased rates of hypoalbuminemia and edema.


Subject(s)
Hypoalbuminemia , Pancreatic Neoplasms , Humans , Male , Female , Aged , Gemcitabine , Albumin-Bound Paclitaxel , Hypoalbuminemia/chemically induced , Paclitaxel/adverse effects , Pancreatic Neoplasms/pathology , Albumins/adverse effects , Edema/etiology , Antineoplastic Combined Chemotherapy Protocols/adverse effects , Pancreatic Neoplasms
12.
Chembiochem ; 24(19): e202300141, 2023 10 04.
Article in English | MEDLINE | ID: mdl-37088717

ABSTRACT

Focal adhesion kinase (FAK) is an attractive drug target due to its overexpression in cancer. FAK functions as a non-receptor tyrosine kinase and scaffolding protein, coordinating several downstream signaling effectors and cellular processes. While drug discovery efforts have largely focused on targeting FAK kinase activity, FAK inhibitors have failed to show efficacy as single agents in clinical trials. Here, using structure-guided design, we report the development of a selective FAK inhibitor (BSJ-04-175) and degrader (BSJ-04-146) to evaluate the consequences and advantages of abolishing all FAK activity in cancer models. BSJ-04-146 achieves rapid and potent FAK degradation with high proteome-wide specificity in cancer cells and induces durable degradation in mice. Compared to kinase inhibition, targeted degradation of FAK exhibits pronounced improved activity on downstream signaling and cancer cell viability and migration. Together, BSJ-04-175 and BSJ-04-146 are valuable chemical tools to dissect the specific consequences of targeting FAK through small-molecule inhibition or degradation.


Subject(s)
Neoplasms , Proteolysis Targeting Chimera , Mice , Animals , Focal Adhesion Protein-Tyrosine Kinases/chemistry , Focal Adhesion Protein-Tyrosine Kinases/metabolism , Neoplasms/drug therapy , Signal Transduction , Phosphorylation , Protein Kinase Inhibitors/pharmacology , Protein Kinase Inhibitors/chemistry
13.
Nature ; 547(7664): 453-457, 2017 07 27.
Article in English | MEDLINE | ID: mdl-28678785

ABSTRACT

Plasticity of the cell state has been proposed to drive resistance to multiple classes of cancer therapies, thereby limiting their effectiveness. A high-mesenchymal cell state observed in human tumours and cancer cell lines has been associated with resistance to multiple treatment modalities across diverse cancer lineages, but the mechanistic underpinning for this state has remained incompletely understood. Here we molecularly characterize this therapy-resistant high-mesenchymal cell state in human cancer cell lines and organoids and show that it depends on a druggable lipid-peroxidase pathway that protects against ferroptosis, a non-apoptotic form of cell death induced by the build-up of toxic lipid peroxides. We show that this cell state is characterized by activity of enzymes that promote the synthesis of polyunsaturated lipids. These lipids are the substrates for lipid peroxidation by lipoxygenase enzymes. This lipid metabolism creates a dependency on pathways converging on the phospholipid glutathione peroxidase (GPX4), a selenocysteine-containing enzyme that dissipates lipid peroxides and thereby prevents the iron-mediated reactions of peroxides that induce ferroptotic cell death. Dependency on GPX4 was found to exist across diverse therapy-resistant states characterized by high expression of ZEB1, including epithelial-mesenchymal transition in epithelial-derived carcinomas, TGFß-mediated therapy-resistance in melanoma, treatment-induced neuroendocrine transdifferentiation in prostate cancer, and sarcomas, which are fixed in a mesenchymal state owing to their cells of origin. We identify vulnerability to ferroptic cell death induced by inhibition of a lipid peroxidase pathway as a feature of therapy-resistant cancer cells across diverse mesenchymal cell-state contexts.


Subject(s)
Glutathione Peroxidase/metabolism , Lipid Peroxidation/drug effects , Neoplasms/drug therapy , Neoplasms/enzymology , Cadherins/metabolism , Cell Death , Cell Line, Tumor , Cell Lineage , Cell Transdifferentiation , Drug Resistance, Neoplasm/genetics , Epithelial-Mesenchymal Transition , Humans , Iron/metabolism , Lipid Peroxides/metabolism , Male , Melanoma/drug therapy , Melanoma/enzymology , Melanoma/metabolism , Melanoma/pathology , Mesoderm/drug effects , Mesoderm/enzymology , Mesoderm/metabolism , Mesoderm/pathology , Neoplasms/genetics , Neoplasms/pathology , Phospholipid Hydroperoxide Glutathione Peroxidase , Prostatic Neoplasms/drug therapy , Prostatic Neoplasms/enzymology , Prostatic Neoplasms/metabolism , Prostatic Neoplasms/pathology , Proteomics , Proto-Oncogene Proteins B-raf/genetics , Reproducibility of Results , Zinc Finger E-box-Binding Homeobox 1/genetics
14.
Lancet Oncol ; 23(2): e62-e74, 2022 02.
Article in English | MEDLINE | ID: mdl-35114133

ABSTRACT

With increasing attention on the essential roles of the tumour microenvironment in recent years, the nervous system has emerged as a novel and crucial facilitator of cancer growth. In this Review, we describe the foundational, translational, and clinical advances illustrating how nerves contribute to tumour proliferation, stress adaptation, immunomodulation, metastasis, electrical hyperactivity and seizures, and neuropathic pain. Collectively, this expanding knowledge base reveals multiple therapeutic avenues for cancer neuroscience that warrant further exploration in clinical studies. We discuss the available clinical data, including ongoing trials investigating novel agents targeting the tumour-nerve axis, and the therapeutic potential for repurposing existing neuroactive drugs as an anti-cancer approach, particularly in combination with established treatment regimens. Lastly, we discuss the clinical challenges of these treatment strategies and highlight unanswered questions and future directions in the burgeoning field of cancer neuroscience.


Subject(s)
Neoplasms/drug therapy , Neurosciences , Cancer Pain/drug therapy , Clinical Trials as Topic , Drug Resistance, Neoplasm , Humans , Immune Checkpoint Inhibitors/therapeutic use , Neoplasms/etiology , Neoplasms/immunology , Neoplasms/pathology , Nervous System Physiological Phenomena/drug effects , Tumor Microenvironment
15.
Nat Chem Biol ; 16(6): 635-643, 2020 06.
Article in English | MEDLINE | ID: mdl-32251410

ABSTRACT

Doublecortin like kinase 1 (DCLK1) is an understudied kinase that is upregulated in a wide range of cancers, including pancreatic ductal adenocarcinoma (PDAC). However, little is known about its potential as a therapeutic target. We used chemoproteomic profiling and structure-based design to develop a selective, in vivo-compatible chemical probe of the DCLK1 kinase domain, DCLK1-IN-1. We demonstrate activity of DCLK1-IN-1 against clinically relevant patient-derived PDAC organoid models and use a combination of RNA-sequencing, proteomics and phosphoproteomics analysis to reveal that DCLK1 inhibition modulates proteins and pathways associated with cell motility in this context. DCLK1-IN-1 will serve as a versatile tool to investigate DCLK1 biology and establish its role in cancer.


Subject(s)
Carcinoma, Pancreatic Ductal/drug therapy , Intracellular Signaling Peptides and Proteins/antagonists & inhibitors , Pancreatic Neoplasms/drug therapy , Protein Kinase Inhibitors/chemistry , Protein Serine-Threonine Kinases/antagonists & inhibitors , Animals , Cell Line, Tumor , Cell Movement , Doublecortin Protein , Doublecortin-Like Kinases , Drug Screening Assays, Antitumor , Gene Expression Regulation , Humans , Intracellular Signaling Peptides and Proteins/metabolism , Male , Mice , Molecular Docking Simulation , Molecular Structure , Protein Kinase Inhibitors/pharmacokinetics , Proteomics , Rats , Structure-Activity Relationship , Zebrafish , Pancreatic Neoplasms
16.
Proc Natl Acad Sci U S A ; 114(17): E3434-E3443, 2017 04 25.
Article in English | MEDLINE | ID: mdl-28396387

ABSTRACT

Oncogenic PIK3CA mutations are found in a significant fraction of human cancers, but therapeutic inhibition of PI3K has only shown limited success in clinical trials. To understand how mutant PIK3CA contributes to cancer cell proliferation, we used genome scale loss-of-function screening in a large number of genomically annotated cancer cell lines. As expected, we found that PIK3CA mutant cancer cells require PIK3CA but also require the expression of the TCA cycle enzyme 2-oxoglutarate dehydrogenase (OGDH). To understand the relationship between oncogenic PIK3CA and OGDH function, we interrogated metabolic requirements and found an increased reliance on glucose metabolism to sustain PIK3CA mutant cell proliferation. Functional metabolic studies revealed that OGDH suppression increased levels of the metabolite 2-oxoglutarate (2OG). We found that this increase in 2OG levels, either by OGDH suppression or exogenous 2OG treatment, resulted in aspartate depletion that was specifically manifested as auxotrophy within PIK3CA mutant cells. Reduced levels of aspartate deregulated the malate-aspartate shuttle, which is important for cytoplasmic NAD+ regeneration that sustains rapid glucose breakdown through glycolysis. Consequently, because PIK3CA mutant cells exhibit a profound reliance on glucose metabolism, malate-aspartate shuttle deregulation leads to a specific proliferative block due to the inability to maintain NAD+/NADH homeostasis. Together these observations define a precise metabolic vulnerability imposed by a recurrently mutated oncogene.


Subject(s)
Class I Phosphatidylinositol 3-Kinases , Ketoglutarate Dehydrogenase Complex , Mutation , Neoplasm Proteins , Neoplasms , Animals , Cell Line, Tumor , Citric Acid Cycle/genetics , Class I Phosphatidylinositol 3-Kinases/genetics , Class I Phosphatidylinositol 3-Kinases/metabolism , Glycolysis/genetics , Humans , Ketoglutarate Dehydrogenase Complex/biosynthesis , Ketoglutarate Dehydrogenase Complex/genetics , Mice , Mice, Nude , Neoplasm Proteins/genetics , Neoplasm Proteins/metabolism , Neoplasms/enzymology , Neoplasms/genetics , Neoplasms/pathology
17.
Genet Med ; 21(1): 213-223, 2019 01.
Article in English | MEDLINE | ID: mdl-29961768

ABSTRACT

PURPOSE: Germline variants in double-strand DNA damage repair (dsDDR) genes (e.g., BRCA1/2) predispose to pancreatic adenocarcinoma (PDAC) and may predict sensitivity to platinum-based chemotherapy and poly(ADP) ribose polymerase (PARP) inhibitors. We sought to determine the prevalence and significance of germline cancer susceptibility gene variants in PDAC with paired somatic and survival analyses. METHODS: Using a customized next-generation sequencing panel, germline/somatic DNA was analyzed from 289 patients with resected PDAC ascertained without preselection for high-risk features (e.g., young age, personal/family history). All identified variants were assessed for pathogenicity. Outcomes were analyzed using multivariable-adjusted Cox proportional hazards regression. RESULTS: We found that 28/289 (9.7%; 95% confidence interval [CI] 6.5-13.7%) patients carried pathogenic/likely pathogenic germline variants, including 21 (7.3%) dsDDR gene variants (3 BRCA1, 4 BRCA2, 14 other dsDDR genes [ATM, BRIP1, CHEK2, NBN, PALB2, RAD50, RAD51C]), 3 Lynch syndrome, and 4 other genes (APC p.I1307K, CDKN2A, TP53). Somatic sequencing and immunohistochemistry identified second hits in the tumor in 12/27 (44.4%) patients with germline variants (1 failed sequencing). Compared with noncarriers, patients with germline dsDDR gene variants had superior overall survival (hazard ratio [HR] 0.54; 95% CI 0.30-0.99; P = 0.05). CONCLUSION: Nearly 10% of PDAC patients harbor germline variants, although the majority lack somatic second hits, the therapeutic significance of which warrants further study.


Subject(s)
Adenocarcinoma/genetics , Genetic Predisposition to Disease , Neoplasm Proteins/genetics , Pancreatic Neoplasms/genetics , Adenocarcinoma/epidemiology , Adenocarcinoma/pathology , Adenocarcinoma/surgery , Adult , Aged , DNA Breaks, Double-Stranded , Disease-Free Survival , Ethnicity/genetics , Female , Germ-Line Mutation/genetics , High-Throughput Nucleotide Sequencing , Humans , Male , Middle Aged , Pancreatic Neoplasms/epidemiology , Pancreatic Neoplasms/pathology , Pancreatic Neoplasms/surgery
19.
Am Soc Clin Oncol Educ Book ; 44(3): e438598, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38781541

ABSTRACT

Pancreatic ductal adenocarcinoma (PDA) is a challenging disease that presents at an advanced stage and results in many symptoms that negatively influence patients' quality of life and reduce their ability to receive effective treatment. Early implementation of expert multidisciplinary care with nutritional support, exercise, and palliative care for both early-stage and advanced disease promises to maintain or improve the patients' physical, social, and psychological well-being, decrease aggressive interventions at the end of life, and ultimately improve survival. Moreover, advances in treatment strategies in the neoadjuvant and metastatic setting combined with novel therapeutic agents targeting the key drivers of the disease are leading to improvements in the care of patients with pancreatic cancer. Here, we emphasize the multidisciplinary supportive and therapeutic care of patients with PDA, review current guidelines and new developments of neoadjuvant and perioperative treatments for localized disease, as well as the treatment standards and the evolving field of precision oncology and immunotherapies for advanced PDA.


Subject(s)
Pancreatic Neoplasms , Humans , Pancreatic Neoplasms/therapy , Combined Modality Therapy , Carcinoma, Pancreatic Ductal/therapy , Neoadjuvant Therapy/standards , Neoadjuvant Therapy/methods , Quality of Life , Patient Care Team , Palliative Care/methods
20.
Cancer Discov ; 14(5): 727-736, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38236605

ABSTRACT

KRASG12C inhibitors, like sotorasib and adagrasib, potently and selectively inhibit KRASG12C through a covalent interaction with the mutant cysteine, driving clinical efficacy in KRASG12C tumors. Because amino acid sequences of the three main RAS isoforms-KRAS, NRAS, and HRAS-are highly similar, we hypothesized that some KRASG12C inhibitors might also target NRASG12C and/or HRASG12C, which are less common but critical oncogenic driver mutations in some tumors. Although some inhibitors, like adagrasib, were highly selective for KRASG12C, others also potently inhibited NRASG12C and/or HRASG12C. Notably, sotorasib was five-fold more potent against NRASG12C compared with KRASG12C or HRASG12C. Structural and reciprocal mutagenesis studies suggested that differences in isoform-specific binding are mediated by a single amino acid: Histidine-95 in KRAS (Leucine-95 in NRAS). A patient with NRASG12C colorectal cancer treated with sotorasib and the anti-EGFR antibody panitumumab achieved a marked tumor response, demonstrating that sotorasib can be clinically effective in NRASG12C-mutated tumors. SIGNIFICANCE: These studies demonstrate that certain KRASG12C inhibitors effectively target all RASG12C mutations and that sotorasib specifically is a potent NRASG12C inhibitor capable of driving clinical responses. These findings have important implications for the treatment of patients with NRASG12C or HRASG12C cancers and could guide design of NRAS or HRAS inhibitors. See related commentary by Seale and Misale, p. 698. This article is featured in Selected Articles from This Issue, p. 695.


Subject(s)
Membrane Proteins , Proto-Oncogene Proteins p21(ras) , Pyridines , Humans , Membrane Proteins/genetics , Membrane Proteins/antagonists & inhibitors , Proto-Oncogene Proteins p21(ras)/genetics , Proto-Oncogene Proteins p21(ras)/antagonists & inhibitors , GTP Phosphohydrolases/genetics , Mutation , Cell Line, Tumor , Colorectal Neoplasms/drug therapy , Colorectal Neoplasms/genetics , Antineoplastic Agents/therapeutic use , Antineoplastic Agents/pharmacology , Pyrimidines/therapeutic use , Pyrimidines/pharmacology , Piperazines/pharmacology , Piperazines/therapeutic use
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