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Nature Communications Jan 2024Highly multiplexed protein imaging is emerging as a potent technique for analyzing protein distribution within cells and tissues in their native context. However,...
Highly multiplexed protein imaging is emerging as a potent technique for analyzing protein distribution within cells and tissues in their native context. However, existing cell annotation methods utilizing high-plex spatial proteomics data are resource intensive and necessitate iterative expert input, thereby constraining their scalability and practicality for extensive datasets. We introduce MAPS (Machine learning for Analysis of Proteomics in Spatial biology), a machine learning approach facilitating rapid and precise cell type identification with human-level accuracy from spatial proteomics data. Validated on multiple in-house and publicly available MIBI and CODEX datasets, MAPS outperforms current annotation techniques in terms of speed and accuracy, achieving pathologist-level precision even for typically challenging cell types, including tumor cells of immune origin. By democratizing rapidly deployable and scalable machine learning annotation, MAPS holds significant potential to expedite advances in tissue biology and disease comprehension.
Topics: Humans; Pathologists; Machine Learning; Diagnostic Imaging; Proteomics
PubMed: 38167832
DOI: 10.1038/s41467-023-44188-w -
Arkhiv Patologii 2024The review presents key concepts and global developments in the field of artificial intelligence used in pathological anatomy. The work examines two types of artificial... (Review)
Review
The review presents key concepts and global developments in the field of artificial intelligence used in pathological anatomy. The work examines two types of artificial intelligence (AI): weak and strong ones. A review of experimental algorithms using both deep machine learning and computer vision technologies to work with WSI images of preparations, diagnose and make a prognosis for various malignant neoplasms is carried out. It has been established that weak artificial intelligence at this stage of development of computer (digital) pathological anatomy shows significantly better results in speeding up and refining diagnostic procedures than strong artificial intelligence having signs of general intelligence. The article also discusses three options for the further development of AI assistants for pathologists based on the technologies of large language models (strong AI) ChatGPT (PathAsst), Flan-PaLM2 and LIMA. As a result of the analysis of the literature, key problems in the field were identified: the equipment of pathology institutions, the lack of experts in training neural networks, the lack of strict criteria for the clinical viability of AI diagnostic technologies.
Topics: Humans; Artificial Intelligence; Deep Learning; Neural Networks, Computer; Algorithms; Machine Learning
PubMed: 38591909
DOI: 10.17116/patol20248602165 -
Pathologica Oct 2023Even if the SARS-CoV-2 pandemic has been declared over, several risks and clinical problems remain to be faced, including long-COVID sequelae and possible outbreaks of... (Review)
Review
Even if the SARS-CoV-2 pandemic has been declared over, several risks and clinical problems remain to be faced, including long-COVID sequelae and possible outbreaks of pathogenic variants. Intense research on COVID-19 has provided in these few years a striking amount of data covering different fields and disciplines, which can help to provide a knowledge shield against new potential infective spreads, and may also potentially be applied to other fields of medicine, including oncology and neurology. Nevertheless, areas of uncertainty still remain regarding the pathogenic mechanisms that subtend the multifaceted manifestations of the disease. To better clarify the pathogenesis of the disease, a systematic multidisciplinary evaluation of the many mechanisms involved in COVID-19 is mandatory, including clinical, physiological, radiological, immunological and pathological studies. In COVID-19 syndrome the pathological studies have been mainly performed on autopsy cases, and only a few studies are available on biopsies. Nevertheless, these studies have provided relevant information that can substantially contribute to decipher the complex scenario characterizing the different forms of COVID-19 and long-COVID-19. In this review the data provided by pathological investigations are recapitulated and discussed, in the light of different hypothesis and data provided by clinical, physiological and immunological data.
Topics: Humans; COVID-19; Pathologists; Post-Acute COVID-19 Syndrome; SARS-CoV-2; Biology
PubMed: 38054899
DOI: 10.32074/1591-951X-954 -
Surgical Pathology Clinics Dec 2023Malignancies of upper gastrointestinal tract are aggressive, and most locally advanced unresectable and metastatic cancers are managed by a combination of surgery and... (Review)
Review
Malignancies of upper gastrointestinal tract are aggressive, and most locally advanced unresectable and metastatic cancers are managed by a combination of surgery and neoadjuvant/adjuvant chemotherapy and radiotherapy. Current therapeutic recommendations include targeted therapies based on biomarker expression of an individual tumor. All G/gastro-esophageal junction (GEJ) cancers should be tested for HER2 status as a reflex test at the time of diagnosis. Currently, testing for PDL 1 and mismatch repair protein status is optional. HER2 testing is restricted to adenocarcinomas only and endoscopic biopsies, resections, or cellblocks. Facilities should be available for performing validated immunohistochemical stains and in-situ hybridization techniques, and importantly, pathologists should be experienced with preanalytical and analytical issues and scoring criteria. Genomic profiling via next-generation sequencing (NGS) is another strategy that assess numerous mutations and other molecular events simultaneously, including HER2 amplification, MSS status, tumor mutation burden, and neurotrophic tropomyosin-receptor kinases gene fusions.
Topics: Humans; Stomach Neoplasms; Receptor, ErbB-2; Pathologists; Biomarkers, Tumor; Esophageal Neoplasms; Esophagogastric Junction
PubMed: 37863558
DOI: 10.1016/j.path.2023.05.004 -
Human Pathology May 2024There is no shortage of comprehensive review articles on bone and soft tissue pathology, almost always representing a regurgitation of the literature with little to no...
Keeping it real: Merging traditional and contemporary practices in musculoskeletal pathology: A special issue of neoplastic and non-neoplastic bone and soft tissue pathology.
There is no shortage of comprehensive review articles on bone and soft tissue pathology, almost always representing a regurgitation of the literature with little to no guidance on personal "best practices," recommended applications of ancillary testing, and alternative points of view. This special issue of Human Pathology uniquely unites evidence-based medicine, where appropriate, with the collective personal experiences of a wide range of accomplished pathologists from varying institutions and backgrounds, addressing problematic areas, updated and sometimes imperfect classification systems, and their personal preferences for cost-effectively incorporating ancillary testing. For the preponderance of general pathologists (and specialists), whether academic or non-academic, non-neoplastic musculoskeletal diseases represent a far higher percentage of their practice than bone and soft tissue neoplasia. One of the most common frozen sections performed at many hospitals throughout the USA is revision arthroplasty, relying on the pathologist to help determine the presence (or absence) of periprosthetic joint infection, largely based on the hematoxylin & eosin (H&E) slide. Not every institution has access to the latest molecular techniques; fortunately, many of the current immunohistochemical antibodies serve as reliable surrogate markers of genetic mutations, allowing for cheaper but accurate diagnoses, when deemed necessary. Furthermore, molecular testing is often not necessary to establish a specific diagnosis, even among neoplasms with known underlying genetic abnormalities. It must be remembered that most bone and soft tissue tumors were recognized and classified correctly, before we uncovered and understood, among a subset, their underlying and unique molecular aberrations. Perhaps not surprisingly, in some cases, more than one molecular pathway may lead to the same histologic tumor subtype. Less commonly, an identical genetic driver/fusion may result in immunophenotypically and biologically distinct neoplasms, sometimes with entirely different clinical behaviors. "Dedifferentiation," a concept recognized among a variety of bone and soft tissue neoplasms, including but not limited to chondrosarcoma, parosteal osteosarcoma, and liposarcoma, needs to be objectively reassessed, particularly for liposarcoma. The following reviews attempt to address the above concepts, re-emphasizing the important role the practicing pathologist continues to (and must) play in the differential diagnoses of neoplastic and non-neoplastic musculoskeletal diseases.
Topics: Humans; Bone Neoplasms; Soft Tissue Neoplasms; Musculoskeletal Diseases; Predictive Value of Tests
PubMed: 38556003
DOI: 10.1016/j.humpath.2024.03.007 -
Seminars in Diagnostic Pathology Nov 2023The diagnostic work up and surveillance of germline disorders of bone marrow failure and predisposition to myeloid malignancy is complex and involves correlation between... (Review)
Review
The diagnostic work up and surveillance of germline disorders of bone marrow failure and predisposition to myeloid malignancy is complex and involves correlation between clinical findings, laboratory and genetic studies, and bone marrow histopathology. The rarity of these disorders and the overlap of clinical and pathologic features between primary and secondary causes of bone marrow failure, acquired aplastic anemia, and myelodysplastic syndrome may result in diagnostic uncertainty. With an emphasis on the pathologist's perspective, we review diagnostically useful features of germline disorders including Fanconi anemia, Shwachman-Diamond syndrome, telomere biology disorders, severe congenital neutropenia, GATA2 deficiency, SAMD9/SAMD9L diseases, Diamond-Blackfan anemia, and acquired aplastic anemia. We discuss the distinction between baseline morphologic and genetic findings of these disorders and features that raise concern for the development of myelodysplastic syndrome.
Topics: Humans; Anemia, Aplastic; Congenital Bone Marrow Failure Syndromes; Bone Marrow Diseases; Pathologists; Myeloproliferative Disorders; Myelodysplastic Syndromes; Bone Marrow Failure Disorders; Germ Cells; Neoplasms; Intracellular Signaling Peptides and Proteins
PubMed: 37507252
DOI: 10.1053/j.semdp.2023.06.006 -
Endoscopy International Open Aug 2023Barrett's esophagus (BE) with low-grade dysplasia (LGD) is considered usually endoscopically invisible and the endoscopic features are not well described. This study...
Barrett's esophagus (BE) with low-grade dysplasia (LGD) is considered usually endoscopically invisible and the endoscopic features are not well described. This study aimed to: 1) evaluate the frequency of visible BE-LGD; 2) compare rates of BE-LGD detection in the community versus a Barrett's referral unit (BRU); and 3) evaluate the endoscopic features of BE-LGD. This was a retrospective analysis of a prospectively observed cohort of 497 patients referred to a BRU with dysplastic BE between 2008 and 2022. BE-LGD was defined as confirmation of LGD by expert gastrointestinal pathologist(s). Endoscopy reports, images and histology reports were reviewed to evaluate the frequency of endoscopically identifiable BE-LGD and their endoscopic features. A total of 135 patients (27.2%) had confirmed BE-LGD, of whom 15 (11.1%) had visible LGD identified in the community. After BRU assessment, visible LGD was detected in 68 patients (50.4%). Three phenotypes were observed: (A) Non-visible LGD; (B) Elevated (Paris 0-IIa) lesions; and (C) Flat (Paris 0-IIb) lesions with abnormal mucosal and/or vascular patterns with clear demarcation from regular flat BE. The majority (64.7%) of visible LGD was flat lesions with abnormal mucosal and vascular patterns. Endoscopic detection of BE-LGD increased over time (38.7% (2009-2012) vs. 54.3% (2018-2022)). In this cohort, 50.4% of true BE-LGD was endoscopically visible, with increased recognition endoscopically over time and a higher rate of visible LGD detected at a BRU when compared with the community. BRU assessment of BE-LGD remains crucial; however, improving endoscopy surveillance quality in the community is equally important.
PubMed: 37564334
DOI: 10.1055/a-2102-7726 -
Archives of Pathology & Laboratory... Aug 2023Gene editing-based therapies are currently in development in the areas of oncology, inherited disease, and infectious disease. These potentially life-altering therapies...
CONTEXT.—
Gene editing-based therapies are currently in development in the areas of oncology, inherited disease, and infectious disease. These potentially life-altering therapies are derived from decades of research in both academic and industry settings that developed technologies rooted in principles and products of nature. However, with such technologic developments come many important considerations, including adverse risks, high cost, and ethical questions.
OBJECTIVE.—
To educate pathologists about gene editing technologies, inform them of potential indications and risks, outline regulatory and practical issues that could affect hospital-based practice and laboratory testing, and advocate that pathologists need to be present at discussions among industry and regulators pertaining to gene editing-based therapies.
DESIGN.—
A Gene Editing Workgroup, facilitated by the College of American Pathologists Personalized Health Care Committee and consisting of pathologists of various backgrounds, was convened to develop an educational paper to serve as a stimulus to increase pathologist involvement and inquiry in gene editing therapeutic and diagnostic implementation.
RESULTS.—
Through multiple discussions and literature review, the workgroup identified potential gaps in pathologists' knowledge of gene editing. Additional topics that could impact pathology and laboratory medicine were also identified and summarized in order to facilitate pathologists as stakeholders in gene editing therapy administration and monitoring and potential use in diagnostics.
CONCLUSIONS.—
Gene editing therapy is a complex but potentially transformative area of medicine. This article serves as an introduction to pathologists to assist them in future discussions with colleagues and potentially identify and alter pathology practices that relate to gene editing.
PubMed: 37610100
DOI: 10.5858/arpa.2022-0410-CP -
Zeitschrift Fur Rheumatologie May 2024The term Castleman's disease encompasses a group of rare lymphoproliferative diseases that show histopathological similarities in lymph node biopsy. Diagnostic criteria... (Review)
Review
The term Castleman's disease encompasses a group of rare lymphoproliferative diseases that show histopathological similarities in lymph node biopsy. Diagnostic criteria and a specific ICD-10 code have been available for a few years. Case studies listed at the beginning illustrate that close cooperation between clinicians and pathologists is required to enable a reliable diagnosis. For an optimal histopathological assessment, the pathologist is also dependent on the removal of a complete lymph node. Before distinguishing a potentially fatal multicentric idiopathic Castleman's disease from the resectable unicentric form, which is important in terms of prognosis and treatment, early diagnosis presupposes that Castleman's disease is considered in the differential diagnosis. Various immune phenomena and overlaps with autoimmune diseases can increase the probability of misdiagnosis or undetected cases in the clinical routine of rheumatologists. The intention of the present overview is therefore to point out the similarities with autoimmune diseases that are relevant for differential diagnoses and to point out situations that justify a review of the previous diagnosis.
Topics: Humans; Diagnosis, Differential; Castleman Disease; Rheumatology; Autoimmune Diseases
PubMed: 37624374
DOI: 10.1007/s00393-023-01393-8 -
Gastroenterology Nov 2023
Topics: Humans; Barrett Esophagus; Pathologists; Esophageal Neoplasms; Biomarkers
PubMed: 37659675
DOI: 10.1053/j.gastro.2023.08.041