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1.
Nature ; 628(8007): 416-423, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38538786

ABSTRACT

Antibody and chimeric antigen receptor (CAR) T cell-mediated targeted therapies have improved survival in patients with solid and haematologic malignancies1-9. Adults with T cell leukaemias and lymphomas, collectively called T cell cancers, have short survival10,11 and lack such targeted therapies. Thus, T cell cancers particularly warrant the development of CAR T cells and antibodies to improve patient outcomes. Preclinical studies showed that targeting T cell receptor ß-chain constant region 1 (TRBC1) can kill cancerous T cells while preserving sufficient healthy T cells to maintain immunity12, making TRBC1 an attractive target to treat T cell cancers. However, the first-in-human clinical trial of anti-TRBC1 CAR T cells reported a low response rate and unexplained loss of anti-TRBC1 CAR T cells13,14. Here we demonstrate that CAR T cells are lost due to killing by the patient's normal T cells, reducing their efficacy. To circumvent this issue, we developed an antibody-drug conjugate that could kill TRBC1+ cancer cells in vitro and cure human T cell cancers in mouse models. The anti-TRBC1 antibody-drug conjugate may provide an optimal format for TRBC1 targeting and produce superior responses in patients with T cell cancers.


Subject(s)
Immunoconjugates , Leukemia, T-Cell , Lymphoma, T-Cell , Receptors, Antigen, T-Cell, alpha-beta , T-Lymphocytes , Animals , Female , Humans , Mice , Immunoconjugates/immunology , Immunoconjugates/therapeutic use , Immunotherapy, Adoptive , Leukemia, T-Cell/drug therapy , Leukemia, T-Cell/immunology , Lymphoma, T-Cell/drug therapy , Lymphoma, T-Cell/immunology , Receptors, Antigen, T-Cell, alpha-beta/immunology , Receptors, Chimeric Antigen/immunology , T-Lymphocytes/immunology , Xenograft Model Antitumor Assays
2.
Proc Natl Acad Sci U S A ; 118(12)2021 03 23.
Article in English | MEDLINE | ID: mdl-33731480

ABSTRACT

Developing therapeutic agents with potent antitumor activity that spare normal tissues remains a significant challenge. Clonal loss of heterozygosity (LOH) is a widespread and irreversible genetic alteration that is exquisitely specific to cancer cells. We hypothesized that LOH events can be therapeutically targeted by "inverting" the loss of an allele in cancer cells into an activating signal. Here we describe a proof-of-concept approach utilizing engineered T cells approximating NOT-gate Boolean logic to target counterexpressed antigens resulting from LOH events in cancer. The NOT gate comprises a chimeric antigen receptor (CAR) targeting the allele of human leukocyte antigen (HLA) that is retained in the cancer cells and an inhibitory CAR (iCAR) targeting the HLA allele that is lost in the cancer cells. We demonstrate that engineered T cells incorporating such NOT-gate logic can be activated in a genetically predictable manner in vitro and in mice to kill relevant cancer cells. This therapeutic approach, termed NASCAR (Neoplasm-targeting Allele-Sensing CAR), could, in theory, be extended to LOH of other polymorphic genes that result in altered cell surface antigens in cancers.


Subject(s)
Biomarkers, Tumor , Immunotherapy , Loss of Heterozygosity , Molecular Targeted Therapy , Neoplasms/etiology , Neoplasms/therapy , Alleles , Antigens, Neoplasm/immunology , Cell- and Tissue-Based Therapy , HLA Antigens/genetics , HLA Antigens/immunology , Humans , Immunotherapy/methods , Immunotherapy, Adoptive , Molecular Targeted Therapy/adverse effects , Molecular Targeted Therapy/methods , Single-Chain Antibodies/pharmacology , Single-Chain Antibodies/therapeutic use
3.
Histopathology ; 82(3): 431-438, 2023 Feb.
Article in English | MEDLINE | ID: mdl-36226695

ABSTRACT

Myoid gonadal stromal tumours (MGST) represent a rare type of testicular sex cord-stromal tumour that has recently been recognised as a distinct entity by the World Health Organization (WHO) classification of genitourinary tumours. MGSTs affect adult men and have been reported to behave in an indolent fashion. Histologically, MGSTs are pure spindle cell neoplasms that coexpress SMA and S100 protein. Given that the molecular features of these neoplasms remain largely undescribed, we evaluated a multi-institutional series of MGSTs using DNA and RNA sequencing. This study included 12 tumours from 12 patients aged 28 to 57 years. Tumour sizes ranged from 0.6 to 4.3 cm. Aggressive histologic features, such as vascular invasion, necrosis, invasive growth, and atypical mitoses were invariably absent. Mitotic activity was low, with a median of less than 1 mitosis per 10 high power fields (HPF; maximum: 3 mitoses per 10 HPF). Molecular analyses did not identify recurrent mutations or gene fusions. All cases with interpretable copy number variant data (9/10 cases sequenced successfully) demonstrated a consistent pattern of chromosome arm-level and whole-chromosome-level copy number gains indicative of ploidy shifts, with recurrent gains involving chromosomes 3, 6, 7, 8, 9, 11, 12, 14q, 15q, 17, 18q, 20, and 21q. Similar findings have also been recognised in pure spindle cell and spindle-cell predominant sex cord-stromal tumours without S100 protein expression. MGSTs are characterised by ploidy shifts and may be part of a larger spectrum of spindle cell-predominant sex cord-stromal tumours, including cases without S100 protein expression.


Subject(s)
Sex Cord-Gonadal Stromal Tumors , Testicular Neoplasms , Adult , Humans , Male , Chromosomes/metabolism , DNA Copy Number Variations , S100 Proteins , Sex Cord-Gonadal Stromal Tumors/genetics , Sex Cord-Gonadal Stromal Tumors/pathology , Testicular Neoplasms/pathology , Middle Aged
4.
Histopathology ; 83(1): 31-39, 2023 Jul.
Article in English | MEDLINE | ID: mdl-37071396

ABSTRACT

AIMS: To elucidate the spectrum of metastatic tumours to the penis and their clinicopathologic features. METHODS: The databases and files of 22 pathology departments from eight countries on three continents were queried to identify metastatic solid tumours of the penis and to characterize their clinical and pathologic features. RESULTS: We compiled a series of 109 cases of metastatic solid tumours that secondarily involved the penis. The mean patient age at diagnosis was 71 years (range, 7-94 years). Clinical presentation commonly included a penile nodule/mass (48/95; 51%) and localised pain (14/95; 15%). A prior history of malignancy was known in 92/104 (89%) patients. Diagnosis was made mainly on biopsy (82/109; 75%), or penectomy (21/109; 19%) specimens. The most common penile locations were the glans (45/98; 46%) and corpus cavernosum (39/98; 39%). The most frequent histologic type was adenocarcinoma (56%). Most primary carcinomas originated in the genitourinary (76/108; 70%) and gastrointestinal (20/108; 18%) tracts, including prostate (38/108; 35%), urinary bladder (27/108; 25%), and colon/rectum (18/108; 17%). Concurrent or prior extrapenile metastases were identified in 50/78 (64%) patients. Clinical follow-up (mean 22 months, range 0-171 months) was available for 87/109 (80%) patients, of whom 46 (53%) died of disease. CONCLUSION: This is the largest study to date of metastatic solid tumours secondarily involving the penis. The most frequent primaries originated from the genitourinary and gastrointestinal tracts. Metastatic penile tumours usually presented with penile nodules/masses and pain, and they often occurred in the setting of advanced metastatic disease, portending poor clinical outcomes.


Subject(s)
Adenocarcinoma , Penile Neoplasms , Male , Humans , Child , Adolescent , Young Adult , Adult , Middle Aged , Aged , Aged, 80 and over , Penis/pathology , Penile Neoplasms/pathology , Adenocarcinoma/pathology , Biopsy
5.
Br J Clin Pharmacol ; 89(5): 1601-1616, 2023 05.
Article in English | MEDLINE | ID: mdl-36454221

ABSTRACT

AIMS: Tremelimumab, a cytotoxic T-lymphocyte-associated protein 4 human monoclonal antibody of the immunoglobulin G2 κ isotype, has been studied in oncology clinical trials as both monotherapy and in combination with durvalumab. This study characterized the pharmacokinetics of tremelimumab as monotherapy and in combination with durvalumab and evaluated the impact of patient covariates on pharmacokinetics. METHODS: A pooled-analysis population pharmacokinetics model was built using NONMEM methodology. Pharmacokinetic data from 5 studies spanning different tumour types and therapy regimens were pooled for model development (956 patients). A dataset pooled from 4 additional studies was used for external validation (554 patients). Demographic and relevant clinical covariates were explored during model development. RESULTS: Tremelimumab exhibited linear pharmacokinetics, well described by a 2-compartment model, with time-varying clearance (0.276 L/day at baseline) associated primarily with therapy regimen and linked with changes in disease status. As monotherapy and combination therapy, tremelimumab clearance over 1 year increased by ~16% and decreased by ~17%, respectively. Pharmacokinetic behaviour was consistent across patient demographics and cancer subtypes. Patients with higher bodyweight and lower albumin levels at baseline had significantly higher clearance; however, no dosage adjustments are warranted. A flat dose (75 mg) was projected to provide comparable exposure to weight-based dosing (1 mg/kg) in adults. CONCLUSION: Tremelimumab exhibited linear pharmacokinetics but consistently opposite trends of time-varying clearance as monotherapy and in combination with durvalumab. Baseline bodyweight and albumin were significant covariates, but conversion from weight-based dosing at 1 mg/kg to flat dosing at 75 mg had no clinically relevant impact.


Subject(s)
Neoplasms , Adult , Humans , Neoplasms/drug therapy , Neoplasms/pathology , Antibodies, Monoclonal, Humanized/therapeutic use , Antineoplastic Combined Chemotherapy Protocols/therapeutic use
6.
Environ Res ; 228: 115900, 2023 07 01.
Article in English | MEDLINE | ID: mdl-37059325

ABSTRACT

Recent years have seen a lot of interest in transition metal carbides/carbonitrides (MXenes), Which is one of newly proliferating two-dimensional (2D) materials.The advantages and applications of synthesizing MXenes-based biosensing systems are interesting. There is an urgent requirement for synthesis of MXenes. Through foliation, physical adsorption, and interface modification,it has been proposed that many biological disorders are related to genetic mutation. Majority of mutations were discovered to be nucleotide mismatches. Consequently, accurate -nucleotide mismatched discrimination is crucial for both diagnosing and treating diseases. To differentiate between such a sensitivealterations in the DNA duplex, several detection methods, particularly Electrochemical-luminescence (ECL) ones, have really been investigated.Mn+1XnTx is common name for MXenes, a novel family of two-dimensional (2D) transition metal carbides, nitrides, and carbonitrides, where T stands for interface termination units (i.e. = O, OH, and/or F). These electronic characteristics of MXenes may be changed between conductive to semiconducting due to abundant organometallic chemistry.Solid-state ECL sensors predicated on MXene would provide the facile nucleotide detection and convenience for usage with minimal training, mobility and possibly minimal cost.This study emphasizes upcoming requirements and possibilities in this area while describing the accomplishments achieved in the usage and employing of MXenes in the research and development of facile biomarkerdetection and their significance in designing electrochemical sensors. Opportunities are addressed for creating 2D MXene materials sensors and devices with incorporated biomolecule sensing. MXenes Carry out this process sensors, address the advantages of using MXenes and their variants as detecting materials for gathering different types of data, and attempt to clarify the design principles and operation of related MXene-based sensors, such as nucleotide detection, Single nucleotide detectors, Cancer theranostics, Biosensing capabilities, Gliotoxin detection, SARS-COV-2 nucleocapsid detection, electrochemical sensors, visual sensors, and humidity sensors. Finally, we examine the major issues and prospects for MXene-based materials used in various sensing applications.


Subject(s)
COVID-19 , Humans , Biomarkers , Nucleotides , SARS-CoV-2
7.
Lab Invest ; 102(5): 554-559, 2022 05.
Article in English | MEDLINE | ID: mdl-34963688

ABSTRACT

In clinical diagnostics and research involving histopathology, formalin-fixed paraffin-embedded (FFPE) tissue is almost universally favored for its superb image quality. However, tissue processing time (>24 h) can slow decision-making. In contrast, fresh frozen (FF) processing (<1 h) can yield rapid information but diagnostic accuracy is suboptimal due to lack of clearing, morphologic deformation and more frequent artifacts. Here, we bridge this gap using artificial intelligence. We synthesize FFPE-like images ("virtual FFPE") from FF images using a generative adversarial network (GAN) from 98 paired kidney samples derived from 40 patients. Five board-certified pathologists evaluated the results in a blinded test. Image quality of the virtual FFPE data was assessed to be high and showed a close resemblance to real FFPE images. Clinical assessments of disease on the virtual FFPE images showed a higher inter-observer agreement compared to FF images. The nearly instantaneously generated virtual FFPE images can not only reduce time to information but can facilitate more precise diagnosis from routine FF images without extraneous costs and effort.


Subject(s)
Formaldehyde , Gene Expression Profiling , Artificial Intelligence , Gene Expression Profiling/methods , Humans , Paraffin Embedding/methods , Tissue Fixation/methods
8.
Histopathology ; 81(5): 577-586, 2022 Nov.
Article in English | MEDLINE | ID: mdl-35971742

ABSTRACT

AIMS: Biphasic hyalinizing psammomatous (BHP) renal cell carcinoma (RCC) is a newly described emerging entity within the spectrum of papillary RCC in the WHO 2022 classification. Molecular analyses have discovered that BHP RCC consistently harbour somatic mutations in the neurofibromin 2 (NF2) gene. The NF2 gene product, merlin, is known to primarily function as a tumour suppressor. Merlin protein loss correlates closely with the presence of NF2 mutations in benign and malignant tumours arising in different sites. In the present study we explored the role of merlin immunohistochemistry (IHC) in tumours within the spectrum of BHP RCC to determine the diagnostic utility of this marker. MATERIALS AND METHODS: We performed merlin IHC in 13 BHP RCC, 18 papillary RCC, 10 TFE3-translocation RCC, 15 TFEB-altered RCC (including 13 TFEB-rearranged and 2 TFEB-amplified), and 10 mucinous tubular and spindle cell carcinomas of unknown mutational status. RESULTS: Unequivocal loss of merlin expression in >90% of the tumour cells was observed in 12/13 BHP-RCC (92%), with the remaining tumour demonstrating weak focal cytoplasmic expression in ~10% of the tumour. In contrast, merlin was diffusely or multifocally expressed in all papillary RCC, TFE3-translocation RCC, and TFEB-altered RCC, as well as in 70% of mucinous tubular and spindle carcinomas. CONCLUSIONS: In this study, merlin IHC was ~92% sensitive and ~94% specific for BHP RCC. These data suggest that merlin IHC is a reliable surrogate marker for the presence of underlying NF2 gene inactivation, being diagnostically useful to identify BHP RCC. CONCLUSIONS: In this study, merlin IHC was ~92% sensitive and ~94% specific for BHP RCC. These data suggest that merlin IHC is a reliable surrogate marker for the presence of underlying NF2 gene inactivation, being diagnostically useful to identify BHP RCC.


Subject(s)
Carcinoma, Renal Cell , Carcinoma , Kidney Neoplasms , Meningeal Neoplasms , Meningioma , Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/genetics , Carcinoma, Renal Cell/pathology , Humans , Immunohistochemistry , Kidney Neoplasms/pathology , Neurofibromin 2/genetics
9.
Histopathology ; 80(6): 922-927, 2022 May.
Article in English | MEDLINE | ID: mdl-35347739

ABSTRACT

AIMS: Formal depiction of granulomatous inflammation associated with renal neoplasms has mainly consisted of case reports. Herein, we investigate the clinicopathological features and potential significance of granulomas associated with renal tumours from a large multi-institutional cohort. METHODS AND RESULTS: One hundred and eleven study cases were collected from 22 institutions, including 57 partial nephrectomies and 54 radical nephrectomies. Patient ages ranged from 27 to 85 years (average = 60.1 years; male = 61%). Renal neoplasms included clear cell renal cell carcinoma (RCC; 86%), papillary RCC (8%), chromophobe RCC (3%), clear cell papillary RCC (1%), mixed epithelial stromal tumour (1%) and oncocytoma (1%). Granulomas were peritumoral in 36%, intratumoral in 24% and both in 40% of cases. Total granuloma count per case ranged from one to 300 (median = 15) with sizes ranging from 0.15 to 15 mm (mean = 1.9 mm). Necrotising granulomas were seen in 14% of cases. Histochemical stains for organisms were performed on 45% of cases (all negative). Sixteen cases (14%) had a prior biopsy/procedure performed, and eight patients had neoadjuvant immunotherapy or chemotherapy. Eleven patients (10%) had a confirmed diagnosis of sarcoidosis, including five in whom sarcoidosis was diagnosed after nephrectomy. CONCLUSION: Based on this largest case-series to date, peri-/intratumoral granulomas associated with renal neoplasms may be more common than initially perceived. The extent of granulomatous inflammation can vary widely and may or may not have necrosis with possible aetiologies, including prior procedure or immunotherapy/chemotherapy. Although a clinical association with sarcoidosis is infrequent it can still occur, and the presence of granulomas warrants mention in pathology reports.


Subject(s)
Carcinoma, Renal Cell , Kidney Neoplasms , Sarcoidosis , Adult , Aged , Aged, 80 and over , Carcinoma, Renal Cell/pathology , Female , Granuloma/pathology , Humans , Inflammation , Kidney Neoplasms/pathology , Male , Middle Aged , Sarcoidosis/pathology
10.
Opt Lett ; 47(1): 194-197, 2022 Jan 01.
Article in English | MEDLINE | ID: mdl-34951915

ABSTRACT

We propose a novel, to the best of our knowledge, plasmonic-based methodology for the purpose of fast DNA sequencing. The interband surface plasmon resonance and field-enhancement properties of graphene nanopore in the presence of the DNA nucleobases are investigated using a hybrid quantum/classical method (HQCM), which employs time-dependent density functional theory and a quasistatic finite difference time domain approach. In the strong plasmonic-molecular coupling regime where the plasmon and DNA absorption frequencies are degenerated, the optical response of DNA molecule in the vicinity of the nanopore is enhanced. In contrast, when the plasmon and nucleobases resonances are detuned the distinct peaks and broadening of the molecular resonances represent the inherent properties of the nucleobase. Due to the different optical properties of DNA nucleobases in the ultraviolet (UV) region of light, the signal corresponding to the replacement of nucleobases in a DNA block can be determined by considering the differential absorbance. Results show the promising capability of the present mechanism for practical DNA sequencing.


Subject(s)
Graphite , Nanopores , DNA , Sequence Analysis, DNA , Surface Plasmon Resonance
11.
J Biol Chem ; 294(50): 19322-19334, 2019 12 13.
Article in English | MEDLINE | ID: mdl-31690625

ABSTRACT

Mutations in CTNNB1, the gene encoding ß-catenin, are common in colon and liver cancers, the most frequent mutation affecting Ser-45 in ß-catenin. Peptides derived from WT ß-catenin have previously been shown to be presented on the cell surface as part of major histocompatibility complex (MHC) class I, suggesting an opportunity for targeting this common driver gene mutation with antibody-based therapies. Here, crystal structures of both the WT and S45F mutant peptide bound to HLA-A*03:01 at 2.20 and 2.45 Å resolutions, respectively, confirmed the accessibility of the phenylalanine residue for antibody recognition. Phage display was then used to identify single-chain variable fragment clones that selectively bind the S45F mutant peptide presented in HLA-A*03:01 and have minimal WT or other off-target binding. Following the initial characterization of five clones, we selected a single clone, E10, for further investigation. We developed a computational model of the binding of E10 to the mutant peptide-bound HLA-A3, incorporating data from affinity maturation as initial validation. In the future, our model may be used to design clones with maintained specificity and higher affinity. Such derivatives could be adapted into either cell-based (CAR-T) or protein-based (bispecific T-cell engagers) therapies to target cancer cells harboring the S45F mutation in CTNNB1.


Subject(s)
Histocompatibility Antigens Class I/genetics , Immunoglobulin Fragments/chemistry , Protein Engineering , beta Catenin/genetics , Cell Line , Histocompatibility Antigens Class I/chemistry , Humans , Models, Molecular , Mutation , beta Catenin/chemistry
12.
Am J Pathol ; 189(6): 1180-1189, 2019 06.
Article in English | MEDLINE | ID: mdl-31079810

ABSTRACT

Easily accessible biomarkers that may inform on the metastatic potential of localized prostate cancer are urgently needed. Herein, we show that syntaphilin (SNPH), a molecule originally identified as a negative regulator of mitochondrial dynamics in neurons, is abundantly expressed in prostate cancer. SNPH distribution in prostate cancer is spatially biphasic, with high expression at the invasive front, correlating with increased proliferative rates, as determined by Ki-67 labeling, and reduced levels in the central tumor bulk, which are further decreased in patients with distant metastases. Higher levels of SNPH are observed with increasing Gleason grade. Prostate tumors predominantly express a novel, extraneuronal isoform of SNPH that accumulates in mitochondria and maintains oxidative metabolism and tumor cell proliferation. These data suggest that SNPH is a novel marker of high Gleason grade prostate cancer, differentially expressed at the invasive front compared with the central tumor bulk, and is potentially down-regulated in metastatic disease. This biphasic pattern of expression may reflect a dual function of SNPH in controlling the balance between cell proliferation and invasion in tumors.


Subject(s)
Biomarkers, Tumor/biosynthesis , Gene Expression Regulation , Membrane Proteins/biosynthesis , Neoplasm Proteins/biosynthesis , Nerve Tissue Proteins/biosynthesis , Prostatic Neoplasms/metabolism , Aged , Aged, 80 and over , Humans , Male , Middle Aged , Neoplasm Grading , Neoplasm Metastasis , Prostatic Neoplasms/pathology , Protein Isoforms/biosynthesis
13.
Ann Diagn Pathol ; 48: 151593, 2020 Oct.
Article in English | MEDLINE | ID: mdl-32836180

ABSTRACT

The urinary bladder may be involved by a variety of secondary tumors that originate from other organs. Bladder secondary tumors are rare and may be mistaken as bladder primary tumors because of their overlapping morphologic features. To avoid the diagnostic pitfalls, we analyzed the clinicopathologic features of bladder secondary tumors in a large cohort of patients. Our patient cohort consisted of 45 females and 38 males with a mean age of 58.7 ± 15.4 years (range 10-87 years). The tumors involved the bladder via direct extension from adjacent organs (n = 42) and distant metastasis (n = 41). In females, the majority of secondary tumors originated from the gynecologic tract (n = 25), and other common origins included the colon/rectum (n = 5) and breast (n = 4). In males, the most common origin was the prostate (n = 18), followed by the colon/rectum (n = 4) and kidney (n = 3). 75.9% of the secondary tumors were adenocarcinoma (n = 63), and other common tumor types included sarcoma (n = 6), squamous cell carcinoma (n = 5), melanoma (n = 4), and neuroendocrine carcinoma (n = 3). 67.5% of patients (n = 56) died of the disease with a median overall survival of 23 months from the time of secondary involvement of the bladder. Patients with secondary tumors via direct extension had a median survival time of 20 months, which was not significantly different from that for patients with secondary involvement via distant metastasis (24 months) (p = 0.83). Median survival in cases with prostate primary was 20 months as compared to 23 months for all other tumor types (p = 0.68). The majority of secondary tumors are composed of adenocarcinoma, which highlights the importance of differentiating primary from secondary involvement in bladder adenocarcinoma. Regardless of the origin, bladder secondary tumors are associated with a poor prognosis.


Subject(s)
Adenocarcinoma/secondary , Urinary Bladder Neoplasms/mortality , Urinary Bladder Neoplasms/pathology , Urinary Bladder/pathology , Adenocarcinoma/diagnosis , Adult , Aged , Carcinoma, Neuroendocrine/diagnosis , Carcinoma, Neuroendocrine/secondary , Carcinoma, Squamous Cell/diagnosis , Carcinoma, Squamous Cell/secondary , Case-Control Studies , Diagnosis, Differential , Female , Humans , Male , Melanoma/diagnosis , Melanoma/secondary , Middle Aged , Outcome Assessment, Health Care , Prognosis , Sarcoma/diagnosis , Sarcoma/secondary , Survival Analysis , Urinary Bladder Neoplasms/secondary
14.
Proc Natl Acad Sci U S A ; 113(26): 7088-93, 2016 06 28.
Article in English | MEDLINE | ID: mdl-27298347

ABSTRACT

Single-nucleotide polymorphisms (SNPs) in a gene sequence are markers for a variety of human diseases. Detection of SNPs with high specificity and sensitivity is essential for effective practical implementation of personalized medicine. Current DNA sequencing, including SNP detection, primarily uses enzyme-based methods or fluorophore-labeled assays that are time-consuming, need laboratory-scale settings, and are expensive. Previously reported electrical charge-based SNP detectors have insufficient specificity and accuracy, limiting their effectiveness. Here, we demonstrate the use of a DNA strand displacement-based probe on a graphene field effect transistor (FET) for high-specificity, single-nucleotide mismatch detection. The single mismatch was detected by measuring strand displacement-induced resistance (and hence current) change and Dirac point shift in a graphene FET. SNP detection in large double-helix DNA strands (e.g., 47 nt) minimize false-positive results. Our electrical sensor-based SNP detection technology, without labeling and without apparent cross-hybridization artifacts, would allow fast, sensitive, and portable SNP detection with single-nucleotide resolution. The technology will have a wide range of applications in digital and implantable biosensors and high-throughput DNA genotyping, with transformative implications for personalized medicine.


Subject(s)
Biosensing Techniques/methods , DNA/genetics , Graphite/chemistry , Polymorphism, Single Nucleotide , Biosensing Techniques/instrumentation , Genotype , Humans
15.
Biomed Microdevices ; 20(2): 45, 2018 06 02.
Article in English | MEDLINE | ID: mdl-29858718

ABSTRACT

Detection of nucleic acid molecules is one of the most pervasive assays in biology, medicine, and agriculture applications. Currently, most comely used DNA/RNA detection platforms use fluorescence labeling and require lab-scale setting for performing the assay. There is a need for developing less expensive, label-free, and rapid detection of biomolecules with minimal utilization of resources. Use of electrical approaches for detection of biomolecules by utilizing their inherent charge is a promising direction for biosensing assays. Here, we report a 1024 × 1024 array of Ion Sensitive Field Effect Transistors (ISFET) as label free sensors for detection of nucleic acid molecules. Using PNA probe functionalized on these ISFET array, we robustly detected miRNA Let-7b by measuring changes in drain current after hybridization of target molecules with concentration as low as 1 nM. We demonstrate that mismatched or non-complementary target molecules resulted in statistically smaller changes. Most importantly, the high-density sensor array shows unprecedented reliability and robustness with P values <0.0001 for all experiments. Practical implementation of this platform could have a wide range of applications in high-throughput nucleic acid genotyping, detection of amplified pathogenic nucleic acid, detection of cell-free DNA, and electrical readouts for current hybridization-based DNA biomolecular assays.


Subject(s)
Biosensing Techniques/instrumentation , MicroRNAs/analysis , Transistors, Electronic , MicroRNAs/metabolism , Nucleic Acid Hybridization , Peptide Nucleic Acids/metabolism
16.
Proc Natl Acad Sci U S A ; 112(32): 9967-72, 2015 Aug 11.
Article in English | MEDLINE | ID: mdl-26216968

ABSTRACT

Mutant epitopes encoded by cancer genes are virtually always located in the interior of cells, making them invisible to conventional antibodies. We here describe an approach to identify single-chain variable fragments (scFvs) specific for mutant peptides presented on the cell surface by HLA molecules. We demonstrate that these scFvs can be successfully converted to full-length antibodies, termed MANAbodies, targeting "Mutation-Associated Neo-Antigens" bound to HLA. A phage display library representing a highly diverse array of single-chain variable fragment sequences was first designed and constructed. A competitive selection protocol was then used to identify clones specific for mutant peptides bound to predefined HLA types. In this way, we obtained two scFvs, one specific for a peptide encoded by a common KRAS mutant and the other by a common epidermal growth factor receptor (EGFR) mutant. The scFvs bound to these peptides only when the peptides were complexed with HLA-A2 (KRAS peptide) or HLA-A3 (EGFR peptide). We converted one scFv to a full-length antibody (MANAbody) and demonstrate that the MANAbody specifically reacts with mutant peptide-HLA complex even when the peptide differs by only one amino acid from the normal, WT form.


Subject(s)
Epitopes/genetics , Epitopes/immunology , HLA Antigens/genetics , HLA Antigens/immunology , Mutation/genetics , Single-Chain Antibodies/immunology , Cell Membrane/metabolism , Cell Surface Display Techniques , Clone Cells , Humans , Mutant Proteins/metabolism , Peptides/metabolism
17.
BMC Med Educ ; 18(1): 184, 2018 Aug 03.
Article in English | MEDLINE | ID: mdl-30075773

ABSTRACT

BACKGROUND: Residency prepares trainees to deliver clinical care. It's unknown if there is adequate career preparation, particularly for academic medicine. Prior literature has shown that interest in pursuing an academic career wanes during residency. Few trainees believe residency provides them with the necessary skills to be successful in academic medicine. Formalized areas of concentration may allow for deepened experience and mentorship in a specific field and may contribute to increased scholarly productivity which has been associated with selecting an academic career. Some training programs have instituted specialized tracks to allow residents to explore and develop an academic or clinical niche. The pervasiveness and characteristics of tracks currently available are unknown. A crucial first step in understanding how to best prepare residents for future careers is to understand current practice. The objective of this study was to identify the prevalence and characteristics of specialized tracks in emergency medicine (EM) training programs in the United States of America (USA). METHODS: Allopathic EM training programs in the USA were identified by the Society for Academic Emergency Medicine residency catalogue. Program websites were identified through this catalogue and an internet search. Each page of a program's website was dissected to identify basic program information and descriptions of their curricula including presence and descriptions of specialized tracks. Descriptive statistics are reported. RESULTS: 163 programs were identified, 156(95.7%) programs provided detailed descriptions of their curricula on their program website. 33/156(21.2%) offered dedicated tracks. Tracks were more common in four year programs (15/40;37.5%) compared to three years (18/116;15.5%). 23/33(70%) programs with tracks provided titles of their tracks and these commonly (20/23;87%) mirrored typical fellowships in EM. For programs that described the timing of tracks (15/33;45.5%), most spanned multiple years of training (12/15;80%). CONCLUSION: The presence of specialized tracks is not widespread in EM training programs in the USA, but is more commonly seen in four year programs. The timing of tracks varied but typically spanned multiple years of training. This information is a critical first step to allow future research to understand the impact of specialized tracks and their role in EM career choice and preparation for an academic career.


Subject(s)
Career Choice , Emergency Medicine/education , Internship and Residency , Specialization , Emergency Medicine/statistics & numerical data , Fellowships and Scholarships , Humans , Internship and Residency/statistics & numerical data , United States
18.
Nano Lett ; 17(9): 5193-5198, 2017 09 13.
Article in English | MEDLINE | ID: mdl-28771008

ABSTRACT

Circulating tumor cells (CTCs) contain molecular information on the primary tumor and can be used for predictive cancer diagnostics. Capturing rare live CTCs and their quantification in whole blood remain technically challenging. Here we report an aptamer-trigger clamped hybridization chain reaction (atcHCR) method for in situ identification and subsequent cloaking/decloaking of CTCs by porous DNA hydrogels. These decloaked CTCs were then used for live cell analysis. In our design, a DNA staple strand with aptamer-toehold biblocks specifically recognizes epithelial cell adhesion molecule (EpCAM) on the CTC surface that triggers subsequent atcHCR via toehold-initiated branch migration. Porous DNA hydrogel based-cloaking of single/cluster of CTCs allows capturing of living CTCs directly with minimal cell damage. The ability to identify a low number of CTCs in whole blood by DNA hydrogel cloaking would allow high sensitivity and specificity for diagnosis in clinically relevant settings. More significantly, decloaking of CTCs using controlled and defined chemical stimuli can release living CTCs without damages for subsequent culture and live cell analysis. We expect this liquid biopsy tool to open new powerful and effective routes for cancer diagnostics and therapeutics.


Subject(s)
Aptamers, Nucleotide/chemistry , Biosensing Techniques/methods , Breast Neoplasms/pathology , Epithelial Cell Adhesion Molecule/analysis , Hydrogels/chemistry , Neoplastic Cells, Circulating/pathology , Biomarkers, Tumor/analysis , Female , Humans , MCF-7 Cells
19.
Cancer ; 123(23): 4594-4607, 2017 Dec 01.
Article in English | MEDLINE | ID: mdl-28881377

ABSTRACT

BACKGROUND: The authors hypothesized that unilateral intensity-modulated radiotherapy (IMRT) would decrease toxicity compared with bilateral IMRT for patients with lateralized palatine tonsillar cancer and a neck classification of N0 to N2b, with similar oncological outcomes. METHODS: A total of 154 patients were treated with postoperative IMRT from 1997 through 2013. Data were collected prospectively from 2005 to 2013 and retrospectively collected before 2005. Of those patients with lateralized primary and N0 to N2b disease, 48 received unilateral IMRT (group 1) and 59 received bilateral IMRT (group 2); a total of 47 patients had nonlateralized primary or N2c to N3 disease and received bilateral IMRT (group 3). RESULTS: The median follow-up was 5.5 years. The 5-year locoregional control rates were similar in group 1, group 2, and group 3 (100%, 96%, and 94%, respectively; pooled comparison: P = .39 and group 1 vs group 2 comparison: P = .19). The 5-year overall survival rates were similar in group 1, group 2, and group 3 (85%, 79%, and 76%, respectively; pooled comparison: P = .60 and group 1 vs group 2 comparison: P = .25). There were no contralateral neck recurrences noted among unilaterally treated patients. Unilateral IMRT reduced acute toxicity and improved patient-reported quality of life compared with bilateral IMRT. CONCLUSIONS: Unilateral IMRT appears to reduce acute toxicity and achieves oncological outcomes similar to those of bilateral IMRT in selected patients with lateralized palatine tonsillar cancer with a neck classification of N0 to N2b. Cancer 2017;123:4594-4607. © 2017 American Cancer Society.


Subject(s)
Carcinoma, Squamous Cell/radiotherapy , Neoplasm Recurrence, Local/radiotherapy , Palatine Tonsil/radiation effects , Quality of Life , Radiotherapy, Intensity-Modulated/methods , Tonsillar Neoplasms/radiotherapy , Adult , Aged , Aged, 80 and over , Carcinoma, Squamous Cell/secondary , Carcinoma, Squamous Cell/surgery , Female , Follow-Up Studies , Humans , Lymphatic Metastasis , Male , Middle Aged , Neoplasm Invasiveness , Neoplasm Recurrence, Local/pathology , Neoplasm Recurrence, Local/surgery , Palatine Tonsil/pathology , Palatine Tonsil/surgery , Prognosis , Prospective Studies , Radiotherapy Dosage , Radiotherapy, Adjuvant , Retrospective Studies , Survival Rate , Tonsillar Neoplasms/pathology , Tonsillar Neoplasms/surgery
20.
Article in English | MEDLINE | ID: mdl-28893774

ABSTRACT

Fluconazole is an antifungal agent used for the treatment of invasive candidiasis, a leading cause of morbidity and mortality in premature infants. Population pharmacokinetic (PK) models of fluconazole in infants have been previously published by Wade et al. (Antimicrob Agents Chemother 52:4043-4049, 2008, https://doi.org/10.1128/AAC.00569-08) and Momper et al. (Antimicrob Agents Chemother 60:5539-5545, 2016, https://doi.org/10.1128/AAC.00963-16). Here we report the results of the first external evaluation of the predictive performance of both models. We used patient-level data from both studies to externally evaluate both PK models. The predictive performance of each model was evaluated using the model prediction error (PE), mean prediction error (MPE), mean absolute prediction error (MAPE), prediction-corrected visual predictive check (pcVPC), and normalized prediction distribution errors (NPDE). The values of the parameters of each model were reestimated using both the external and merged data sets. When evaluated with the external data set, the model proposed by Wade et al. showed lower median PE, MPE, and MAPE (0.429 µg/ml, 41.9%, and 57.6%, respectively) than the model proposed by Momper et al. (2.45 µg/ml, 188%, and 195%, respectively). The values of the majority of reestimated parameters were within 20% of their respective original parameter values for all model evaluations. Our analysis determined that though both models are robust, the model proposed by Wade et al. had greater accuracy and precision than the model proposed by Momper et al., likely because it was derived from a patient population with a wider age range. This study highlights the importance of the external evaluation of infant population PK models.


Subject(s)
Antifungal Agents/pharmacokinetics , Candida/drug effects , Candidiasis/drug therapy , Fluconazole/pharmacokinetics , Models, Statistical , Antifungal Agents/blood , Biological Availability , Candida/growth & development , Candida/pathogenicity , Candidiasis/microbiology , Candidiasis/pathology , Clinical Trials as Topic , Drug Administration Schedule , Female , Fluconazole/blood , Humans , Infant , Infant, Newborn , Infant, Premature , Male , Predictive Value of Tests
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