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1.
Cell ; 173(7): 1770-1782.e14, 2018 06 14.
Article in English | MEDLINE | ID: mdl-29906450

ABSTRACT

Using integrative genomic analysis of 360 metastatic castration-resistant prostate cancer (mCRPC) samples, we identified a novel subtype of prostate cancer typified by biallelic loss of CDK12 that is mutually exclusive with tumors driven by DNA repair deficiency, ETS fusions, and SPOP mutations. CDK12 loss is enriched in mCRPC relative to clinically localized disease and characterized by focal tandem duplications (FTDs) that lead to increased gene fusions and marked differential gene expression. FTDs associated with CDK12 loss result in highly recurrent gains at loci of genes involved in the cell cycle and DNA replication. CDK12 mutant cases are baseline diploid and do not exhibit DNA mutational signatures linked to defects in homologous recombination. CDK12 mutant cases are associated with elevated neoantigen burden ensuing from fusion-induced chimeric open reading frames and increased tumor T cell infiltration/clonal expansion. CDK12 inactivation thereby defines a distinct class of mCRPC that may benefit from immune checkpoint immunotherapy.


Subject(s)
Cyclin-Dependent Kinases/metabolism , Prostatic Neoplasms/pathology , Antibodies, Monoclonal/therapeutic use , Cell Line, Tumor , Chemokine CCL21/genetics , Chemokine CCL21/metabolism , Cyclin-Dependent Kinases/antagonists & inhibitors , Cyclin-Dependent Kinases/genetics , DNA Repair , Gene Expression Regulation, Neoplastic , Genomic Instability , Humans , Male , Mutation, Missense , Neoplasm Staging , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , Phenotype , Programmed Cell Death 1 Receptor/immunology , Prostate/diagnostic imaging , Prostatic Neoplasms/drug therapy , Prostatic Neoplasms/immunology , RNA Interference , RNA, Small Interfering/metabolism , Repressor Proteins/genetics , Repressor Proteins/metabolism , T-Lymphocytes/metabolism , T-Lymphocytes/pathology , Tomography, X-Ray Computed
2.
Cell ; 174(3): 758-769.e9, 2018 07 26.
Article in English | MEDLINE | ID: mdl-30033370

ABSTRACT

While mutations affecting protein-coding regions have been examined across many cancers, structural variants at the genome-wide level are still poorly defined. Through integrative deep whole-genome and -transcriptome analysis of 101 castration-resistant prostate cancer metastases (109X tumor/38X normal coverage), we identified structural variants altering critical regulators of tumorigenesis and progression not detectable by exome approaches. Notably, we observed amplification of an intergenic enhancer region 624 kb upstream of the androgen receptor (AR) in 81% of patients, correlating with increased AR expression. Tandem duplication hotspots also occur near MYC, in lncRNAs associated with post-translational MYC regulation. Classes of structural variations were linked to distinct DNA repair deficiencies, suggesting their etiology, including associations of CDK12 mutation with tandem duplications, TP53 inactivation with inverted rearrangements and chromothripsis, and BRCA2 inactivation with deletions. Together, these observations provide a comprehensive view of how structural variations affect critical regulators in metastatic prostate cancer.


Subject(s)
Genomic Structural Variation/genetics , Prostatic Neoplasms/genetics , Aged , Aged, 80 and over , BRCA2 Protein/metabolism , Cyclin-Dependent Kinases/metabolism , DNA Copy Number Variations , Exome , Gene Expression Profiling/methods , Genomics/methods , Humans , Male , Middle Aged , Mutation , Neoplasm Metastasis/genetics , Proto-Oncogene Proteins c-myc/genetics , Proto-Oncogene Proteins c-myc/metabolism , Receptors, Androgen/genetics , Receptors, Androgen/metabolism , Tandem Repeat Sequences/genetics , Tumor Suppressor Protein p53/metabolism , Whole Genome Sequencing/methods
4.
Nat Rev Mol Cell Biol ; 15(12): 786-801, 2014 Dec.
Article in English | MEDLINE | ID: mdl-25415508

ABSTRACT

The extracellular matrix (ECM) is a highly dynamic structure that is present in all tissues and continuously undergoes controlled remodelling. This process involves quantitative and qualitative changes in the ECM, mediated by specific enzymes that are responsible for ECM degradation, such as metalloproteinases. The ECM interacts with cells to regulate diverse functions, including proliferation, migration and differentiation. ECM remodelling is crucial for regulating the morphogenesis of the intestine and lungs, as well as of the mammary and submandibular glands. Dysregulation of ECM composition, structure, stiffness and abundance contributes to several pathological conditions, such as fibrosis and invasive cancer. A better understanding of how the ECM regulates organ structure and function and of how ECM remodelling affects disease progression will contribute to the development of new therapeutics.


Subject(s)
Extracellular Matrix/chemistry , Extracellular Matrix/metabolism , Morphogenesis , Neoplasms/pathology , Animals , Endopeptidases/metabolism , Epithelial Cells/chemistry , Epithelial Cells/metabolism , Extracellular Matrix/enzymology , Extracellular Matrix/pathology , Fibrosis/pathology , Humans
5.
Oncologist ; 2024 Jun 22.
Article in English | MEDLINE | ID: mdl-38908022

ABSTRACT

HER2, encoded by the ERBB2 gene, is an important druggable driver of human cancer gaining increasing importance as a therapeutic target in urothelial carcinoma (UC). The genomic underpinnings of HER2 overexpression in ERBB2 nonamplified UC are poorly defined. To address this knowledge gap, we investigated 172 UC tumors from patients treated at the University of California San Francisco, using immunohistochemistry and next-generation sequencing. We found that GATA3 and PPARG copy number gains individually predicted HER2 protein expression independently of ERBB2 amplification. To validate these findings, we interrogated the Memorial Sloan Kettering/The Cancer Genome Atlas (MSK/TCGA) dataset and found that GATA3 and PPARG copy number gains individually predicted ERBB2 mRNA expression independently of ERBB2 amplification. Our findings reveal a potential link between the luminal marker HER2 and the key transcription factors GATA3 and PPARG in UC and highlight the utility of examining GATA3 and PPARG copy number states to identify UC tumors that overexpress HER2 in the absence of ERBB2 amplification. In summary, we found that an increase in copy number of GATA3 and PPARG was independently associated with higher ERBB2 expression in patient samples of UC. This finding provides a potential explanation for HER2 overexpression in UC tumors without ERBB2 amplification and a way to identify these tumors for HER2-targeted therapies.

6.
Lancet Oncol ; 24(11): 1266-1276, 2023 Nov.
Article in English | MEDLINE | ID: mdl-37922930

ABSTRACT

BACKGROUND: Checkpoint inhibitors have been shown to have limited activity in patients with metastatic castration-resistant prostate cancer. We aimed to determine whether a single dose of lutetium-177 [177Lu]-prostate-specific membrane antigen (PSMA)-617 (177Lu-PSMA-617) followed by maintenance pembrolizumab was safe and could induce durable clinical benefit. METHODS: We did an open-label, dose-expansion, phase 1 study at the University of California, San Francisco (San Fransisco, CA, USA). Eligible patients were men aged 18 years or older with progressive metastatic castration-resistant prostate cancer who had an Eastern Cooperative Oncology Group performance status of 0 or 1, had progression on one or more androgen signalling inhibitors, and at least three PSMA-avid lesions on 68Ga-PSMA-11 positron emission tomography. In part A, patients were enrolled sequentially to one of three schedules in which a single dose of 177Lu-PSMA-617 (7·4 GBq) was given intravenously 28 days before (schedule 1), concomitant with (schedule 2), or 21 days after (schedule 3) the start of maintenance intravenous pembrolizumab (200 mg every 3 weeks). In part B, 25 patients were enrolled using the recommended phase 2 schedule. The primary endpoint in part A was determination of the recommended phase 2 schedule, and in part B, the objective response rate. The analysis set included all patients who received at least one dose of pembrolizumab or 177Lu-PSMA-617. This study is registered with ClinicalTrials.gov, NCT03805594. FINDINGS: Between Aug 8, 2019 and May 7, 2022, 43 male patients were enrolled (n=18 part A [six patients per schedule]; n=25 part B), with a median follow-up of 16·5 months (IQR 12·2-21·9). Schedule 1 was selected as the recommended phase 2 schedule for part B, on the basis of safety and feasibility of administration observed in part A. In part B, 14 (56%; 95% CI 35-76) of 25 patients had a confirmed objective response. Two (5%) of 43 patients had a treatment-related adverse event of grade 3 or worse (grade 3 arthritis in schedule 2, grade 3 pneumonitis in schedule 3). One serious adverse event (one death due to aspiration pneumonia) and no treatment-related deaths were observed. INTERPRETATION: A single priming dose of 177Lu-PSMA-617 followed by pembrolizumab maintenance was safe and had encouraging preliminary activity in patients with metastatic castration-resistant prostate cancer. FUNDING: Prostate Cancer Foundation, National Cancer Institute, Novartis Pharmaceuticals, and Merck.


Subject(s)
Prostatic Neoplasms, Castration-Resistant , Humans , Male , Heterocyclic Compounds, 1-Ring/therapeutic use , Prostate-Specific Antigen/therapeutic use , Prostatic Neoplasms, Castration-Resistant/drug therapy , Prostatic Neoplasms, Castration-Resistant/pathology , Treatment Outcome
7.
Chembiochem ; 24(15): e202300156, 2023 08 01.
Article in English | MEDLINE | ID: mdl-37170829

ABSTRACT

Bacterial acquisition of metabolites is largely facilitated by transporters with unique substrate scopes. The tripartite ATP-independent periplasmic (TRAP) transporters comprise a large family of bacterial proteins that facilitate the uptake of a variety of small molecules. It has been reported that some TRAP systems encode a fourth protein, the T component. The T-component, or TatT, is predicted to be a periplasmic-facing lipoprotein that enables the uptake of metabolites from the outer membrane. However, no substrates were revealed for any TatT and their functional role(s) remained enigmatic. We recently identified a homolog in Methylococcus capsulatus that binds to sterols, and herein, we report two additional homologs that demonstrate a preference for long-chain fatty acids. Our bioinformatics, quantitative analyses of protein-ligand interactions, and high-resolution crystal structures suggest that TatTs might facilitate the trafficking of hydrophobic or lipophilic substrates and represent a new class of bacterial lipid and fatty acid transporters.


Subject(s)
Bacteria , Membrane Transport Proteins , Membrane Transport Proteins/chemistry , Membrane Transport Proteins/metabolism , Bacteria/metabolism , Bacterial Proteins/metabolism , Biological Transport , Fatty Acids/metabolism
8.
Cancer ; 128(6): 1194-1205, 2022 Mar 15.
Article in English | MEDLINE | ID: mdl-34882781

ABSTRACT

BACKGROUND: Enfortumab vedotin (EV) is a novel antibody-drug conjugate approved for advanced urothelial cancer (aUC) refractory to prior therapy. In the Urothelial Cancer Network to Investigate Therapeutic Experiences (UNITE) study, the authors looked at the experience with EV in patient subsets of interest for which activity had not been well defined in clinical trials. METHODS: UNITE was a retrospective study of patients with aUC treated with recently approved agents. This initial analysis focused on patients treated with EV. Patient data were abstracted from chart reviews by investigators at each site. The observed response rate (ORR) was investigator-assessed for patients with at least 1 post-baseline scan or clear evidence of clinical progression. ORRs were compared across subsets of interest for patients treated with EV monotherapy. RESULTS: The initial UNITE analysis included 304 patients from 16 institutions; 260 of these patients were treated with EV monotherapy and included in the analyses. In the monotherapy cohort, the ORR was 52%, and it was >40% in all reported subsets of interest, including patients with comorbidities previously excluded from clinical trials (baseline renal impairment, diabetes, and neuropathy) and patients with fibroblast growth factor receptor 3 (FGFR3) alterations. Progression-free survival and overall survival were 6.8 and 14.4 months, respectively. Patients with a pure urothelial histology had a higher ORR than patients with a variant histology component (58% vs 42%; P = .06). CONCLUSIONS: In a large retrospective cohort, responses to EV monotherapy were consistent with data previously reported in clinical trials and were also observed in various patient subsets, including patients with variant histology, patients with FGFR3 alterations, and patients previously excluded from clinical trials with an estimated glomerular filtration rate < 30 mL/min and significant comorbidities. LAY SUMMARY: Enfortumab vedotin, approved by the Food and Drug Administration in 2019, is an important new drug for the treatment of patients with advanced bladder cancer. This study looks at the effectiveness of enfortumab vedotin as it has been used at multiple centers since approval, and focuses on important patient populations previously excluded from clinical trials. These populations include patients with decreased kidney function, diabetes, and important mutations. Enfortumab vedotin is effective for treating these patients. Previously reported clinical trial data have been replicated in this real-world setting, and support the use of this drug in broader patient populations.


Subject(s)
Carcinoma, Transitional Cell , Urinary Bladder Neoplasms , Urologic Neoplasms , Antibodies, Monoclonal , Carcinoma, Transitional Cell/drug therapy , Humans , Retrospective Studies , Urinary Bladder Neoplasms/chemically induced , Urinary Bladder Neoplasms/drug therapy , Urologic Neoplasms/drug therapy , Urologic Neoplasms/pathology
9.
Cancer ; 127(12): 1965-1973, 2021 06 15.
Article in English | MEDLINE | ID: mdl-33690902

ABSTRACT

BACKGROUND: DNA damage repair mutations (DDRm) are common in patients with metastatic castration-resistant prostate cancer (mCRPC). The optimal standard therapy for this population is not well described. METHODS: A multi-institutional, retrospective study of patients with mCRPC and DDRm was conducted. Patient data, including systemic therapies and responses, were collected. The decline in prostate-specific antigen ≥ 50% from baseline (PSA50) and overall survival (OS) from the treatment start were compared by mutation and treatment type. A multivariable Cox proportional hazards model for OS was created that controlled for DDRm, first-line treatment received for mCRPC, and clinical factors. RESULTS: The most common DDRm observed among 149 men with mCRPC were BRCA1/2 (44%), CDK12 (32%), and ATM (15%). The majority received first-line abiraterone (40%) or enzalutamide (30%). The PSA50 rate with first-line abiraterone was lower for CDK12 (52%) than BRCA1/2 (89%; P = .02). After first-line abiraterone or enzalutamide, the median OS was longest with second-line carboplatin-chemotherapy (38 months) in comparison with abiraterone or enzalutamide (33 months), docetaxel (17 months), or cabazitaxel (11 months; P = .02). PSA50 responses to carboplatin-based chemotherapy were higher for BRCA1/2 (79%) than ATM (14%; P = .02) or CDK12 (38%; P = .08). In a multivariable analysis, neither the specific DDRm type nor the first-line treatment was associated with improved OS. CONCLUSIONS: Responses to standard therapies were generally superior in patients with BRCA1/2 mutations and inferior in patients with ATM or CDK12 mutations. The DDRm type did not independently predict OS. After progression on first-line abiraterone or enzalutamide, carboplatin-based chemotherapy was associated with the longest OS. These findings may inform treatment discussions and clinical trial design and require prospective validation.


Subject(s)
Prostatic Neoplasms, Castration-Resistant , Ataxia Telangiectasia Mutated Proteins/genetics , BRCA1 Protein/genetics , Carboplatin/therapeutic use , Cyclin-Dependent Kinases/genetics , Docetaxel/therapeutic use , Humans , Male , Nitriles/therapeutic use , Prostatic Neoplasms, Castration-Resistant/drug therapy , Prostatic Neoplasms, Castration-Resistant/genetics , Prostatic Neoplasms, Castration-Resistant/pathology , Retrospective Studies , Treatment Outcome
10.
Proc Natl Acad Sci U S A ; 115(5): E992-E1001, 2018 01 30.
Article in English | MEDLINE | ID: mdl-29339479

ABSTRACT

Bone metastasis involves dynamic interplay between tumor cells and the local stromal environment. In bones, local hypoxia and activation of the hypoxia-inducible factor (HIF)-1α in osteoblasts are essential to maintain skeletal homeostasis. However, the role of osteoblast-specific HIF signaling in cancer metastasis is unknown. Here, we show that osteoprogenitor cells (OPCs) are located in hypoxic niches in the bone marrow and that activation of HIF signaling in these cells increases bone mass and favors breast cancer metastasis to bone locally. Remarkably, HIF signaling in osteoblast-lineage cells also promotes breast cancer growth and dissemination remotely, in the lungs and in other tissues distant from bones. Mechanistically, we found that activation of HIF signaling in OPCs increases blood levels of the chemokine C-X-C motif ligand 12 (CXCL12), which leads to a systemic increase of breast cancer cell proliferation and dissemination through direct activation of the CXCR4 receptor. Hence, our data reveal a previously unrecognized role of the hypoxic osteogenic niche in promoting tumorigenesis beyond the local bone microenvironment. They also support the concept that the skeleton is an important regulator of the systemic tumor environment.


Subject(s)
Hypoxia-Inducible Factor 1, alpha Subunit/genetics , Hypoxia-Inducible Factor 1, alpha Subunit/metabolism , Mammary Neoplasms, Experimental/genetics , Mammary Neoplasms, Experimental/metabolism , Osteoblasts/metabolism , Alleles , Amino Acid Motifs , Animals , Bone Neoplasms/secondary , Bone and Bones/metabolism , Cell Lineage , Chemokine CXCL12/blood , Disease Progression , Female , Green Fluorescent Proteins/metabolism , Hypoxia , Ligands , Mice , Mice, Transgenic , Neoplasm Metastasis , Osteoclasts/metabolism , Signal Transduction
11.
J Natl Compr Canc Netw ; 18(11): 1446-1452, 2020 11.
Article in English | MEDLINE | ID: mdl-33152701

ABSTRACT

Organ donors are systematically screened for infection, whereas screening for malignancy is less rigorous. The true incidence of donor-transmitted malignancies is unknown due to a lack of universal tumor testing in the posttransplant setting. Donor-transmitted malignancy may occur even when not suspected based on donor or recipient factors, including age and time to cancer diagnosis. We describe the detection of a gastrointestinal adenocarcinoma transmitted from a young donor to 4 transplant recipients. Multidimensional histopathologic and genomic profiling showed a CDH1 mutation and MET amplification, consistent with gastric origin. At the time of writing, one patient in this series remains alive and without evidence of cancer after prompt organ explant after cancer was reported in other recipients. Because identification of a donor-derived malignancy changes management, our recommendation is to routinely perform short tandem repeat testing (or a comparable assay) immediately upon diagnosis of cancer in any organ transplant recipient. Routine testing for a donor-origin cancer and centralized reporting of outcomes are necessary to establish a robust evidence base for the future development of clinical practice guidelines.


Subject(s)
Neoplasms , Organ Transplantation , Transplant Recipients , Humans , Incidence , Neoplasms/diagnosis , Neoplasms/genetics , Organ Transplantation/adverse effects , Tissue Donors
12.
Genes Dev ; 25(5): 471-84, 2011 Mar 01.
Article in English | MEDLINE | ID: mdl-21317240

ABSTRACT

Amplification of 8p11-12 in human breast cancers is associated with increased proliferation and tumor grade and reduced metastasis-free patient survival. We identified Zeppo1 (zinc finger elbow-related proline domain protein 1) (FLJ14299/ZNF703) within this amplicon as a regulator of cell adhesion, migration, and proliferation in mammary epithelial cells. Overexpression of Zeppo1 reduces cell-cell adhesion and stimulates migration and proliferation. Knockdown of Zeppo1 induces adhesion and lumen formation. Zeppo1 regulates transcription, complexing with Groucho and repressing E-cadherin expression and Wnt and TGFß reporter expression. Zeppo1 promotes expression of metastasis-associated p120-catenin isoform 1 and alters p120-catenin localization upon cell contact with the extracellular matrix. Significantly, Zeppo1 overexpression in a mouse breast cancer model increases lung metastases, while reducing Zeppo1 expression reduces both tumor size and the number of lung metastases. These results indicate that Zeppo1 is a key regulator of breast cancer progression.


Subject(s)
Cadherins/metabolism , Catenins/metabolism , Gene Expression Regulation, Neoplastic , Neoplasm Metastasis/genetics , Protein Transport/genetics , Repressor Proteins/metabolism , 3T3 Cells , Animals , Cell Adhesion/genetics , Cell Line , HEK293 Cells , Humans , Mice , Mice, Inbred BALB C , Protein Isoforms/metabolism , Repressor Proteins/genetics , Delta Catenin
13.
Retina ; 37(10): 1967-1976, 2017 Oct.
Article in English | MEDLINE | ID: mdl-28045850

ABSTRACT

PURPOSE: To evaluate construct and face validity of the Eyesi Binocular Indirect Ophthalmoscope Simulator. METHODS: The performance of 25 medical students (Group A) was compared with that of 17 ophthalmology and optometry trainees (Group B) on the Eyesi Binocular Indirect Ophthalmoscope Simulator. During the course of a single session, each participant viewed an orientation module followed by an instruction session and a demonstration case, and performed 6 cases of progressively increasing difficulty (4 levels) and a 10-question face validity questionnaire. Outcomes included total score, total examination time, percent retina examined, and duration of eye exposure to light. RESULTS: Group B achieved significantly better total scores than Group A on all difficulty levels (P = 0.02, P = 0.001, P = 0.001, and P = 0.0001, for Levels 1-4, respectively) and had a significantly faster mean duration of examination (8 minutes 58 seconds vs. 5 minutes 21 seconds, P < 0.0001). Medical students reported higher scores in the face validity questionnaire for the simulator experience being helpful at orienting them to true indirect ophthalmology, and that further training on the simulator would improve their skills in the clinic (P = 0.03 for all). CONCLUSION: The Eyesi Binocular Indirect Ophthalmoscope Simulator has significant construct and face validity and shows promise for medical education.


Subject(s)
Clinical Competence , Computer Simulation , Internship and Residency , Ophthalmology/education , Ophthalmoscopes , Reproducibility of Results , User-Computer Interface , Adult , Female , Humans , Male , Students, Medical
14.
Ophthalmic Plast Reconstr Surg ; 33(5): 372-375, 2017.
Article in English | MEDLINE | ID: mdl-27749618

ABSTRACT

PURPOSE: This study retrospectively reviews preseptal cellulitis and abscesses involving the eyebrow to elucidate the bacteriology and potential causative factors. METHODS: A retrospective chart review was conducted to identify patients who had been diagnosed with preseptal cellulitis or abscess involving the eyebrow at the Massachusetts Eye and Ear Infirmary between 2008 and 2015. Demographic, clinical, and microbiological data were collected. RESULTS: Eighty patients with eyebrow infections were identified, of whom 49 (61.3%) were female and 31 (38.7%) were male. The median age was 37 years (range 14-67 years). Eyebrow abscess was present in 54 cases (67.5%), while 26 cases (32.5%) were limited to preseptal cellulitis without abscess formation. Methicillin-resistant Staphylococcus aureus was found in 20 abscesses (39.2% of culture results), and methicillin-sensitive S. aureus was found in 12 abscesses (23.5% of culture results). Coagulase-negative staphylococci were present in 7 eyebrow abscesses (13.7% of culture results). Clinical history was remarkable for eyebrow hair removal (tweezing, waxing, threading, or shaving) in 17 cases (21.3%), manipulation of acne lesions ("popping," "picking," or "squeezing") in 6 cases (7.5%), and both brow hair removal and acne manipulation in 1 case (1.3%). CONCLUSIONS: There is a high incidence of methicillin-resistant Staphylococcus aureus in the bacteriology of eyebrow infections. Empirical antibiotic coverage for methicillin-resistant Staphylococcus aureus should be strongly considered in any patient with an eyebrow area abscess or preseptal cellulitis. Individuals who practice cosmetic eyebrow grooming should be encouraged to consider hygiene practices, which could reduce the risk of infection.


Subject(s)
Eye Infections, Bacterial/microbiology , Eyebrows/microbiology , Methicillin-Resistant Staphylococcus aureus/isolation & purification , Staphylococcal Infections/microbiology , Adolescent , Adult , Aged , Eye Infections, Bacterial/diagnosis , Female , Humans , Male , Massachusetts , Middle Aged , Retrospective Studies , Staphylococcal Infections/diagnosis , Young Adult
15.
J Biol Chem ; 290(6): 3803-13, 2015 Feb 06.
Article in English | MEDLINE | ID: mdl-25538248

ABSTRACT

The NET (nocA, Nlz, elB, TLP-1) subfamily of zinc finger proteins is an important mediator during developmental processes. The evolutionary conserved zinc finger protein ZNF503/Zeppo2 (zinc finger elbow-related proline domain protein 2, Zpo2) plays critical roles during embryogenesis. We found that Zpo2 is expressed in adult tissue and examined its function. We found that ZPO2 is a nuclearly targeted transcriptional repressor that is expressed in mammary epithelial cells. Elevated Zpo2 levels increase mammary epithelial cell proliferation. Zpo2 promotes cellular invasion through down-regulation of E-cadherin and regulates the invasive phenotype in a RAC1-dependent manner. We detect elevated Zpo2 expression during breast cancer progression in a MMTV-PyMT transgenic mouse model. Tumor transplant experiments indicated that overexpression of Zpo2 in MMTV-PyMT mammary tumor cell lines enhances lung metastasis. Our findings suggest that Zpo2 plays a significant role in mammary gland homeostasis and that deregulation of Zpo2 may promote breast cancer development.


Subject(s)
Carrier Proteins/metabolism , Cell Proliferation , Epithelial Cells/metabolism , Mammary Neoplasms, Experimental/metabolism , Nerve Tissue Proteins/metabolism , Nuclear Proteins/metabolism , Animals , Cadherins/genetics , Cadherins/metabolism , Carrier Proteins/genetics , Cell Line, Tumor , Cell Movement , Epithelial Cells/physiology , Female , Gene Expression Regulation, Neoplastic , Intracellular Signaling Peptides and Proteins , Mammary Neoplasms, Experimental/pathology , Mice , Neoplasm Invasiveness , Nerve Tissue Proteins/genetics , Nuclear Proteins/genetics , rac1 GTP-Binding Protein/metabolism
16.
Ophthalmic Plast Reconstr Surg ; 32(3): 199-203, 2016.
Article in English | MEDLINE | ID: mdl-25844505

ABSTRACT

PURPOSE: To evaluate the effect of camera flash position on the measurement of photographic margin reflex distances (MRD). METHODS: Subjects without any ophthalmic disease were prospectively enrolled after institutional review board approval. Clinical measurements of MRD1 and interpalpebral fissure were obtained. Photographs were then taken with a digital single lens reflex with built-in pop-up flash (dSLR-pop), a dSLR with lens-mounted ring flash (dSLR-ring), a point-and-shoot camera, and a smartphone, each in 4 positions: with the camera upright, rotated 90°, 180°, and 270°. The images were analyzed using ImageJ software to measure MRD1, interpalpebral fissure, horizontal white-to-white, and distance from nasal limbus to the corneal light reflex. RESULTS: Thirty-two eyes of 16 subjects were included (ages 27-65). When using the dSLR-ring, point-and-shoot, and smartphone, the difference between clinical and photographic MRD1 did not reach statistical significance. There was, however, a statistically significant difference in the upright position with dSLR-pop (mean difference 0.703 mm, σ = 0.984 mm, p = 0.0008). For dSLR-pop, photographic MRD1 in upright versus inverted position differed significantly (mean difference -0.562 mm, σ =0.348 mm, p < 0.0001). Photographic MRD1 between dSLR-pop and dSLR-ring showed significant difference in upright position (mean difference -0.572 mm, σ = 0.701 mm, p = 0.0002). There were no statistically significant differences between clinical and photographic interpalpebral fissure, and among white-to-white and nasal limbus to light reflex measurements in any position in all 4 cameras. CONCLUSIONS: When using photographs for measurement of MRD1, cameras with a near-coaxial light source and aperture have values that are most similar to clinical measurements.


Subject(s)
Blinking/physiology , Cornea/physiopathology , Eye Diseases/diagnosis , Light , Photography/instrumentation , Software , Adult , Aged , Eye Diseases/physiopathology , Female , Humans , Male , Middle Aged , Photic Stimulation , Prospective Studies
17.
Soft Matter ; 10(27): 4840-7, 2014 Jul 21.
Article in English | MEDLINE | ID: mdl-24860849

ABSTRACT

Using hydrodynamic focusing, we encapsulated polystyrene ellipsoidal particles in water droplets dispersed in an immiscible, continuous phase of light mineral oil. The axisymmetric shape of the drop partially encapsulating an elongated particle was computed as a function of the particle aspect ratio, droplet volume, and contact angle. When the droplet volume is within a certain range, pinned (partially engulfed) and fully engulfed equilibrium configurations coexist. Partial encapsulation may be preferred (has a lower free energy) even when the droplet's volume is sufficient to fully engulf the particle. The co-existence of multiple equilibrium states suggests possible hysteretic encapsulation behavior. We also estimate the axial capillary force exerted by the droplet on the particle as a function of volume and contact angle. The theoretical predictions are critically compared with experimental observations.

18.
Adv Exp Med Biol ; 801: 669-75, 2014.
Article in English | MEDLINE | ID: mdl-24664757

ABSTRACT

Diabetic Retinopathy is one of the hallmark microvascular diseases secondary to diabetes. Endothelial cells and pericytes are key players in the pathogenesis. Interaction between the two cell types is important in the regulation of vascular function and the maintenance of the retinal homeostatic environment. There are currently several approaches to analyze changes in morphology and function of the two cell types. Morphologic approaches include trypsin digest, while functional approaches include studying blood flow. This review explores the advantages and limitations of various methods and summarizes recent experimental studies of EC and pericyte dysfunction in rodent models of DR. An improved understanding of the role played by EC and pericyte dysfunction can lead to enhanced insights into retinal vascular regulation in DR and open new avenues for future treatments that reverse their dysfunction.


Subject(s)
Diabetic Retinopathy/pathology , Disease Models, Animal , Endothelial Cells/pathology , Oximetry/methods , Pericytes/pathology , Rodentia , Animals , Diabetic Retinopathy/physiopathology , Retinal Vessels/pathology , Retinal Vessels/physiopathology
19.
bioRxiv ; 2024 Jan 30.
Article in English | MEDLINE | ID: mdl-38352308

ABSTRACT

Lipids are primary metabolites that play essential roles in multiple cellular pathways. Alterations in lipid metabolism and transport are associated with infectious diseases and cancers. As such, proteins involved in lipid synthesis, trafficking, and modification, are targets for therapeutic intervention. The ability to rapidly detect these proteins can accelerate their biochemical and structural characterization. However, it remains challenging to identify lipid binding motifs in proteins due to a lack of conservation at the amino acids level. Therefore, new bioinformatic tools that can detect conserved features in lipid binding sites are necessary. Here, we present Structure-based Lipid-interacting Pocket Predictor (SLiPP), a structural bioinformatics algorithm that uses machine learning to detect protein cavities capable of binding to lipids in experimental and AlphaFold-predicted protein structures. SLiPP, which can be used at proteome-wide scales, predicts lipid binding pockets with an accuracy of 96.8% and a F1 score of 86.9%. Our analyses revealed that the algorithm relies on hydrophobicity-related features to distinguish lipid binding pockets from those that bind to other ligands. Use of the algorithm to detect lipid binding proteins in the proteomes of various bacteria, yeast, and human have produced hits annotated or verified as lipid binding proteins, and many other uncharacterized proteins whose functions are not discernable from sequence alone. Because of its ability to identify novel lipid binding proteins, SLiPP can spur the discovery of new lipid metabolic and trafficking pathways that can be targeted for therapeutic development.

20.
Elife ; 122024 Feb 08.
Article in English | MEDLINE | ID: mdl-38329015

ABSTRACT

Sterol lipids are widely present in eukaryotes and play essential roles in signaling and modulating membrane fluidity. Although rare, some bacteria also produce sterols, but their function in bacteria is not known. Moreover, many more species, including pathogens and commensal microbes, acquire or modify sterols from eukaryotic hosts through poorly understood molecular mechanisms. The aerobic methanotroph Methylococcus capsulatus was the first bacterium shown to synthesize sterols, producing a mixture of C-4 methylated sterols that are distinct from those observed in eukaryotes. C-4 methylated sterols are synthesized in the cytosol and localized to the outer membrane, suggesting that a bacterial sterol transport machinery exists. Until now, the identity of such machinery remained a mystery. In this study, we identified three novel proteins that may be the first examples of transporters for bacterial sterol lipids. The proteins, which all belong to well-studied families of bacterial metabolite transporters, are predicted to reside in the inner membrane, periplasm, and outer membrane of M. capsulatus, and may work as a conduit to move modified sterols to the outer membrane. Quantitative analysis of ligand binding revealed their remarkable specificity for 4-methylsterols, and crystallographic structures coupled with docking and molecular dynamics simulations revealed the structural bases for substrate binding by two of the putative transporters. Their striking structural divergence from eukaryotic sterol transporters signals that they form a distinct sterol transport system within the bacterial domain. Finally, bioinformatics revealed the widespread presence of similar transporters in bacterial genomes, including in some pathogens that use host sterol lipids to construct their cell envelopes. The unique folds of these bacterial sterol binding proteins should now guide the discovery of other proteins that handle this essential metabolite.


Subject(s)
Phytosterols , Sterols , Sterols/metabolism , Bacteria/genetics , Bacteria/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Biological Transport , Phytosterols/metabolism
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