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Neuro-oncology Nov 2023The international, multicenter registry LOGGIC Core BioClinical Data Bank aims to enhance the understanding of tumor biology in pediatric low-grade glioma (pLGG) and...
BACKGROUND
The international, multicenter registry LOGGIC Core BioClinical Data Bank aims to enhance the understanding of tumor biology in pediatric low-grade glioma (pLGG) and provide clinical and molecular data to support treatment decisions and interventional trial participation. Hence, the question arises whether implementation of RNA sequencing (RNA-Seq) using fresh frozen (FrFr) tumor tissue in addition to gene panel and DNA methylation analysis improves diagnostic accuracy and provides additional clinical benefit.
METHODS
Analysis of patients aged 0 to 21 years, enrolled in Germany between April 2019 and February 2021, and for whom FrFr tissue was available. Central reference histopathology, immunohistochemistry, 850k DNA methylation analysis, gene panel sequencing, and RNA-Seq were performed.
RESULTS
FrFr tissue was available in 178/379 enrolled cases. RNA-Seq was performed on 125 of these samples. We confirmed KIAA1549::BRAF-fusion (n = 71), BRAF V600E-mutation (n = 12), and alterations in FGFR1 (n = 14) as the most frequent alterations, among other common molecular drivers (n = 12). N = 16 cases (13%) presented rare gene fusions (eg, TPM3::NTRK1, EWSR1::VGLL1, SH3PXD2A::HTRA1, PDGFB::LRP1, GOPC::ROS1). In n = 27 cases (22%), RNA-Seq detected a driver alteration not otherwise identified (22/27 actionable). The rate of driver alteration detection was hereby increased from 75% to 97%. Furthermore, FGFR1 internal tandem duplications (n = 6) were only detected by RNA-Seq using current bioinformatics pipelines, leading to a change in analysis protocols.
CONCLUSIONS
The addition of RNA-Seq to current diagnostic methods improves diagnostic accuracy, making precision oncology treatments (MEKi/RAFi/ERKi/NTRKi/FGFRi/ROSi) more accessible. We propose to include RNA-Seq as part of routine diagnostics for all pLGG patients, especially when no common pLGG alteration was identified.
Topics: Child; Humans; Proto-Oncogene Proteins B-raf; Pathology, Molecular; Protein-Tyrosine Kinases; RNA-Seq; Proto-Oncogene Proteins; Precision Medicine; Glioma; DNA-Binding Proteins; Transcription Factors
PubMed: 37075810
DOI: 10.1093/neuonc/noad078 -
Military Medical Research Mar 2022Traditional diagnostic strategies for infectious disease detection require benchtop instruments that are inappropriate for point-of-care testing (POCT). Emerging... (Review)
Review
Traditional diagnostic strategies for infectious disease detection require benchtop instruments that are inappropriate for point-of-care testing (POCT). Emerging microfluidics, a highly miniaturized, automatic, and integrated technology, are a potential substitute for traditional methods in performing rapid, low-cost, accurate, and on-site diagnoses. Molecular diagnostics are widely used in microfluidic devices as the most effective approaches for pathogen detection. This review summarizes the latest advances in microfluidics-based molecular diagnostics for infectious diseases from academic perspectives and industrial outlooks. First, we introduce the typical on-chip nucleic acid processes, including sample preprocessing, amplification, and signal read-out. Then, four categories of microfluidic platforms are compared with respect to features, merits, and demerits. We further discuss application of the digital assay in absolute nucleic acid quantification. Both the classic and recent microfluidics-based commercial molecular diagnostic devices are summarized as proof of the current market status. Finally, we propose future directions for microfluidics-based infectious disease diagnosis.
Topics: Communicable Diseases; Humans; Lab-On-A-Chip Devices; Microfluidic Analytical Techniques; Microfluidics; Pathology, Molecular
PubMed: 35300739
DOI: 10.1186/s40779-022-00374-3 -
Updates in Surgery Feb 2023Classification of adenocarcinomas (AC) arising around or within the gastroesophageal junction (GEJ) is hampered by major morphologic and phenotypic overlaps. We reviewed... (Review)
Review
Classification of adenocarcinomas (AC) arising around or within the gastroesophageal junction (GEJ) is hampered by major morphologic and phenotypic overlaps. We reviewed the surgical pathology of esophagectomy specimens of 115 primary resected AC of the esophagus as defined by the 5th edition of the WHO classification regarding the anatomical site of the tumor, with corresponding categorization according to the Siewert AEG Classification and the preceding 4th edition of the WHO (discriminating esophageal adenocarcinomas/EAC and adenocarcinomas of the gastroesophageal junction/AdGEJ), and further histology findings. In addition, immunohistochemistry (IHC) for CDX2, CK7, CK20, MUC2, MUC5AC and MUC6 was performed. Sixty-eight cases were Siewert AEG type I and 47 cases Siewert AEG type II. Out of the AEG I tumors, 26 were classified as AdGEJ. Regardless of the classification system, more proximally located tumors showed less aggressive behavior with lower rates of lymph node metastases, lymphatic, venous and perineural invasion, better histological differentiation (p < 0.05 each) and were more frequently associated with pre-neoplastic Barrett's mucosa (p < 0.001). Histologically, the tumors displayed intestinal morphology in the majority of cases. IHC showed non-conclusive patterns with a frequent CK7+/CK20+ immunophenotype in all tumors, but also a gastric MUC5AC+ and MUC6+ phenotype in some proximal tumors. In conclusion, histology of the tumors and IHC failed to distinguish reliably between more proximal and more distal tumors. The presence of Barrett's mucosa rather than location alone, however, may help to further differentiating adenocarcinomas arising in this region and may be indicative for a particular biologic type.
Topics: Humans; Barrett Esophagus; Pathology, Surgical; Stomach Neoplasms; Esophageal Neoplasms; Esophagogastric Junction; Adenocarcinoma
PubMed: 36001283
DOI: 10.1007/s13304-022-01360-z -
Nature Reviews. Genetics Nov 2021Synthetic biology seeks to redesign biological systems to perform novel functions in a predictable manner. Recent advances in bacterial and mammalian cell engineering... (Review)
Review
Synthetic biology seeks to redesign biological systems to perform novel functions in a predictable manner. Recent advances in bacterial and mammalian cell engineering include the development of cells that function in biological samples or within the body as minimally invasive diagnostics or theranostics for the real-time regulation of complex diseased states. Ex vivo and in vivo cell-based biosensors and therapeutics have been developed to target a wide range of diseases including cancer, microbiome dysbiosis and autoimmune and metabolic diseases. While probiotic therapies have advanced to clinical trials, chimeric antigen receptor (CAR) T cell therapies have received regulatory approval, exemplifying the clinical potential of cellular therapies. This Review discusses preclinical and clinical applications of bacterial and mammalian sensing and drug delivery platforms as well as the underlying biological designs that could enable new classes of cell diagnostics and therapeutics. Additionally, we describe challenges that must be overcome for more rapid and safer clinical use of engineered systems.
Topics: Animals; Bacteria; Cell- and Tissue-Based Therapy; Cell-Free System; Humans; Immunomodulation; Mammals; Microbiota; Neoplasms; Pathology, Molecular; Receptors, Antigen, T-Cell; Receptors, Chimeric Antigen; Synthetic Biology; T-Lymphocytes
PubMed: 34234299
DOI: 10.1038/s41576-021-00383-3 -
Neurobiology of Aging Oct 2022We investigated self-rating of cognitive task performance (self-appraisal) and the difference between self-rating and actual task performance (appraisal discrepancy) in...
We investigated self-rating of cognitive task performance (self-appraisal) and the difference between self-rating and actual task performance (appraisal discrepancy) in cognitively healthy older adults and their relationship with cortical thickness and Alzheimer's disease (AD) biomarkers, amyloid and tau. All participants (N = 151) underwent neuropsychological testing and 1.5T structural magnetic resonance imaging. A subset (N = 66) received amyloid-PET with [11C] PiB and tau-PET with [18F] Flortaucipir. We found that worse performers had lower self-appraisal ratings, but still overestimated their performance, consistent with the Dunning-Kruger effect. Self-appraisal rating and appraisal discrepancy revealed distinct relationships with cortical thickness and AD pathology. Greater appraisal discrepancy, indicating overestimation, was related to thinning of inferior-lateral temporal, fusiform, and rostral anterior cingulate cortices. Lower self-appraisal was associated with higher entorhinal and inferior temporal tau. These results suggest that overestimation could implicate structural atrophy beyond AD pathology, while lower self-appraisal could indicate early behavioral alteration due to AD pathology, supporting the notion of subjective cognitive decline prior to objective deficits.
Topics: Aged; Aging; Alzheimer Disease; Amyloid; Amyloid beta-Peptides; Cognitive Dysfunction; Humans; Magnetic Resonance Imaging; Metacognition; Positron-Emission Tomography; Tauopathies; tau Proteins
PubMed: 35868093
DOI: 10.1016/j.neurobiolaging.2022.06.007 -
EMBO Molecular Medicine May 2023Several promising plasma biomarkers for Alzheimer's disease have been recently developed, but their neuropathological correlates have not yet been fully determined. To...
Several promising plasma biomarkers for Alzheimer's disease have been recently developed, but their neuropathological correlates have not yet been fully determined. To investigate and compare independent associations between multiple plasma biomarkers (p-tau181, p-tau217, p-tau231, Aβ42/40, GFAP, and NfL) and neuropathologic measures of amyloid and tau, we included 105 participants from the Arizona Study of Aging and Neurodegenerative Disorders (AZSAND) with antemortem plasma samples and a postmortem neuropathological exam, 48 of whom had longitudinal p-tau217 and p-tau181. When simultaneously including plaque and tangle loads, the Aβ42/40 ratio and p-tau231 were only associated with plaques (ρ [95%CI] = -0.53[-0.65, -0.35], ρ [95%CI] = 0.28[0.10, 0.43]), GFAP was only associated with tangles (ρ [95%CI] = 0.39[0.17, 0.57]), and p-tau217 and p-tau181 were associated with both plaques (ρ [95%CI] = 0.40[0.21, 0.56], ρ [95%CI] = 0.36[0.15, 0.50]) and tangles (ρ [95%CI] = 0.52[0.34, 0.66]; ρ [95%CI] = 0.36[0.17, 0.52]). A model combining p-tau217 and the Aβ42/40 ratio showed the highest accuracy for predicting the presence of Alzheimer's disease neuropathological change (ADNC, AUC[95%CI] = 0.89[0.82, 0.96]) and plaque load (R = 0.55), while p-tau217 alone was optimal for predicting tangle load (R = 0.45). Our results suggest that high-performing assays of plasma p-tau217 and Aβ42/40 might be an optimal combination to assess Alzheimer's-related pathology in vivo.
Topics: Humans; Plaque, Amyloid; Alzheimer Disease; Autopsy; Neuropathology; Biomarkers; tau Proteins; Amyloid beta-Peptides
PubMed: 36912178
DOI: 10.15252/emmm.202217123 -
Clinics in Laboratory Medicine Jun 2022The COVID-19 pandemic has led to the rapid development of a plethora of molecular diagnostic assays with real-time polymerase chain reaction (RT-PCR) at the forefront.... (Review)
Review
The COVID-19 pandemic has led to the rapid development of a plethora of molecular diagnostic assays with real-time polymerase chain reaction (RT-PCR) at the forefront. In this review, we will discuss the history and utility of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) molecular diagnostics and the associated current and future regulatory process in Europe. We will assess the performance characteristics of a range of the most common SARS-CoV-2 molecular tests currently used in Europe with a focus on as rapid molecular platforms, stand-alone RT-PCR kits, the role of low-throughput and high-throughput end-to-end testing platforms, and the rapidly evolving field of SARS-CoV-2 variant of concern identification.
Topics: COVID-19; Europe; Humans; Pandemics; Pathology, Molecular; SARS-CoV-2
PubMed: 35636820
DOI: 10.1016/j.cll.2022.02.005 -
PLoS Pathogens Aug 2023Most humans have a lifelong imperceptible BK Polyomavirus (BKPyV) infection in epithelial cells lining the reno-urinary tract. In kidney transplant recipients,...
Most humans have a lifelong imperceptible BK Polyomavirus (BKPyV) infection in epithelial cells lining the reno-urinary tract. In kidney transplant recipients, unrestricted high-level replication of donor-derived BKPyV in the allograft underlies polyomavirus-associated nephropathy, a condition with massive epithelial cell loss and inflammation causing premature allograft failure. There is limited understanding on how BKPyV disseminates throughout the reno-urinary tract and sometimes causes kidney damage. Tubule epithelial cells are tightly connected and have unique apical and basolateral membrane domains with highly specialized functions but all in vitro BKPyV studies have been performed in non-polarized cells. We therefore generated a polarized cell model of primary renal proximal tubule epithelial cells (RPTECs) and characterized BKPyV entry and release. After 8 days on permeable inserts, RPTECs demonstrated apico-basal polarity. BKPyV entry was most efficient via the apical membrane, that in vivo faces the tubular lumen, and depended on sialic acids. Progeny release started between 48 and 58 hours post-infection (hpi), and was exclusively detected in the apical compartment. From 72 hpi, cell lysis and detachment gradually increased but cells were mainly shed by extrusion and the barrier function was therefore maintained. The decoy-like cells were BKPyV infected and could transmit BKPyV to uninfected cells. By 120 hpi, the epithelial barrier was disrupted by severe cytopathic effects, and BKPyV entered the basolateral compartment mimicking the interstitial space. Addition of BKPyV-specific neutralizing antibodies to this compartment inhibited new infections. Taken together, we propose that during in vivo low-level BKPyV replication, BKPyV disseminates inside the tubular system, thereby causing minimal damage and delaying immune detection. However, in kidney transplant recipients lacking a well-functioning immune system, replication in the allograft will progress and eventually cause denudation of the basement membrane, leading to an increased number of decoy cells, high-level BKPyV-DNAuria and DNAemia, the latter a marker of allograft damage.
Topics: Humans; Cytology; BK Virus; Polyomavirus; Kidney; Epithelial Cells; Polyomavirus Infections
PubMed: 37639485
DOI: 10.1371/journal.ppat.1011622 -
Archives of Pathology & Laboratory... Aug 2019Fatal dermatologic diseases and ones with high morbidity can occur in the inpatient setting. In such cases, prompt and accurate assessment of a bedside skin biopsy is... (Review)
Review
CONTEXT.—
Fatal dermatologic diseases and ones with high morbidity can occur in the inpatient setting. In such cases, prompt and accurate assessment of a bedside skin biopsy is required. This may be challenging for many pathologists who are not familiar with the complexity of skin pathology and skin terminology within the fields of dermatopathology and dermatology.
OBJECTIVE.—
To provide the pathologist with a practical, up-to-date, and "must-know" reference guide on dermatologic urgencies and emergencies from a real-world perspective, highlighting diagnostic pearls, diagnostic pitfalls, and commonly encountered practice gaps. This review will focus on key diseases with which every pathologist should be familiar, including angioinvasive fungal infections, Stevens-Johnson syndrome/toxic epidermal necrolysis, staph-scalded-skin syndrome, acute graft-versus-host disease, bullous pemphigoid, calciphylaxis, Sweet syndrome and its histiocytoid variant, pyoderma gangrenosum, and leukocytoclastic vasculitis, as well as those in their clinical and histopathologic differential.
DATA SOURCES.—
This review is based on peer-reviewed literature and our personal experiences with these diseases at major academic institutions, including one where a large number of stem cell transplants are performed. This review is unique as it represents collaborative expert opinion from both a dermatopathology and a dermatology standpoint.
CONCLUSIONS.—
This review outlines the critical role that the pathologist plays in the outcomes of patients with dermatologic urgencies and emergencies. Improved patient care will result from prompt and accurate histopathologic diagnoses as well as an open line of communication with the dermatologist.
Topics: Acute Disease; Biopsy; Dermatology; Graft vs Host Disease; Hematopoietic Stem Cell Transplantation; Humans; Pathologists; Pathology, Clinical; Skin; Skin Diseases
PubMed: 30785787
DOI: 10.5858/arpa.2018-0239-RA -
Archives of Pathology & Laboratory... Aug 2019Cutaneous metastases from a distant malignancy are a diagnostic challenge for pathologists. Secondary involvement of the skin by a metastatic process portends a much... (Review)
Review
CONTEXT.—
Cutaneous metastases from a distant malignancy are a diagnostic challenge for pathologists. Secondary involvement of the skin by a metastatic process portends a much worse clinical prognosis than any primary cutaneous malignant mimickers. Immunohistochemical staining methods continue to evolve and are of paramount importance in diagnosis.
OBJECTIVE.—
To review the clinical, histopathologic, and immunohistochemical staining patterns for commonly encountered entities and discuss potential pitfalls in diagnosis. A practical guide useful in approaching cutaneous metastases of unknown primary is outlined.
DATA SOURCES.—
An extensive search and review of literature in PubMed was performed, processed, and condensed.
CONCLUSIONS.—
Cutaneous metastases have broad histopathologic patterns. They are nearly always dermal based, with an overall foreign appearance. They can be single papules/nodules or multiple in number, mimicking an inflammatory or infectious process. Ultimately, immunohistochemistry remains an essential diagnostic tool, and clinical correlation is paramount in the workup of these entities.
Topics: Biomarkers, Tumor; Diagnosis, Differential; Humans; Immunohistochemistry; Neoplasms, Unknown Primary; Pathology, Clinical; Practice Guidelines as Topic; Skin; Skin Neoplasms
PubMed: 30605024
DOI: 10.5858/arpa.2018-0051-RA