Journal of Pathology and Translational Medicine

Volume 57(1); January 2023

Reviews

A standardized pathology report for gastric cancer: 2nd edition: Young Soo Park, Myeong-Cherl Kook, Baek-hui Kim, Hye Seung Lee, Dong-Wook Kang, Mi-Jin Gu, Ok Ran Shin, Younghee Choi, Wonae Lee, Hyunki Kim, In Hye Song, Kyoung-Mee Kim, Hee Sung Kim, Guhyun Kang, Do Youn Park, So-Young Jin, Joon Mee Kim, Yoon Jung Choi, Hee Kyung Chang, Soomin Ahn, Mee Soo Chang, Song-Hee Han, Yoonjin Kwak, An Na Seo, Sung Hak Lee, Mee-Yon Cho; J Pathol Transl Med. 2023;57(1):1-27. Published online January 15, 2023; DOI: https://doi.org/10.4132/jptm.2022.12.23

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The first edition of ‘A Standardized Pathology Report for Gastric Cancer’ was initiated by the Gastrointestinal Pathology Study Group of the Korean Society of Pathologists and published 17 years ago. Since then, significant advances have been made in the pathologic diagnosis, molecular genetics, and management of gastric cancer (GC). To reflect those changes, a committee for publishing a second edition of the report was formed within the Gastrointestinal Pathology Study Group of the Korean Society of Pathologists. This second edition consists of two parts: standard data elements and conditional data elements. The standard data elements contain the basic pathologic findings and items necessary to predict the prognosis of GC patients, and they are adequate for routine surgical pathology service. Other diagnostic and prognostic factors relevant to adjuvant therapy, including molecular biomarkers, are classified as conditional data elements to allow each pathologist to selectively choose items appropriate to the environment in their institution. We trust that the standardized pathology report will be helpful for GC diagnosis and facilitate large-scale multidisciplinary collaborative studies.

Citations

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Genomic and Transcriptomic Characterization of Gastric Cancer with Bone Metastasis
Sujin Oh, Soo Kyung Nam, Keun-Wook Lee, Hye Seung Lee, Yujun Park, Yoonjin Kwak, Kyu Sang Lee, Ji-Won Kim, Jin Won Kim, Minsu Kang, Young Suk Park, Sang-Hoon Ahn, Yun-Suhk Suh, Do Joong Park, Hyung Ho Kim
Cancer Research and Treatment.2024; 56(1): 219. CrossRef
Microscopic tumor mapping of post-neoadjuvant therapy pancreatic cancer specimens to predict post-surgical recurrence: A prospective cohort study
Yeshong Park, Yeon Bi Han, Jinju Kim, MeeYoung Kang, Boram Lee, Eun Sung Ahn, Saemi Han, Haeryoung Kim, Hee-Young Na, Ho-Seong Han, Yoo-Seok Yoon
Pancreatology.2024;[Epub] CrossRef
Effect of Neoadjuvant Chemotherapy on Tumor-Infiltrating Lymphocytes in Resectable Gastric Cancer: Analysis from a Western Academic Center
Elliott J. Yee, Danielle Gilbert, Jeffrey Kaplan, Sachin Wani, Sunnie S. Kim, Martin D. McCarter, Camille L. Stewart
Cancers.2024; 16(7): 1428. CrossRef
Pathological Interpretation of Gastric Tumors in Endoscopic Submucosal Dissection
Jung Yeon Kim
Journal of Digestive Cancer Research.2023; 11(1): 15. CrossRef
Histopathology of Gastric Cancer
Baek-hui Kim, Sung Hak Lee
The Korean Journal of Helicobacter and Upper Gastrointestinal Research.2023; 23(2): 143. CrossRef
Endoscopic submucosal dissection hands-on training with artificial mucosal layer EndoGEL
Tae-Se Kim, Jun Haeng Lee
Journal of Innovative Medical Technology.2023; 1(1): 5. CrossRef

Infections and immunity: associations with obesity and related metabolic disorders: Amitabha Ray, Melissa J. L. Bonorden, Rajashree Pandit, Katai J. Nkhata, Anupam Bishayee; J Pathol Transl Med. 2023;57(1):28-42. Published online January 15, 2023; DOI: https://doi.org/10.4132/jptm.2022.11.14

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Abstract PDF

About one-fourth of the global population is either overweight or obese, both of which increase the risk of insulin resistance, cardiovascular diseases, and infections. In obesity, both immune cells and adipocytes produce an excess of pro-inflammatory cytokines that may play a significant role in disease progression. In the recent coronavirus disease 2019 (COVID-19) pandemic, important pathological characteristics such as involvement of the renin-angiotensin-aldosterone system, endothelial injury, and pro-inflammatory cytokine release have been shown to be connected with obesity and associated sequelae such as insulin resistance/type 2 diabetes and hypertension. This pathological connection may explain the severity of COVID-19 in patients with metabolic disorders. Many studies have also reported an association between type 2 diabetes and persistent viral infections. Similarly, diabetes favors the growth of various microorganisms including protozoal pathogens as well as opportunistic bacteria and fungi. Furthermore, diabetes is a risk factor for a number of prion-like diseases. There is also an interesting relationship between helminths and type 2 diabetes; helminthiasis may reduce the pro-inflammatory state, but is also associated with type 2 diabetes or even neoplastic processes. Several studies have also documented altered circulating levels of neutrophils, lymphocytes, and monocytes in obesity, which likely modifies vaccine effectiveness. Timely monitoring of inflammatory markers (e.g., C-reactive protein) and energy homeostasis markers (e.g., leptin) could be helpful in preventing many obesity-related diseases.

Citations

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Theory of the Leaky Intestine: Gender Differences in Intestinal Parasitic Infections, Cytoskeletal Wall Dysfunctions, and Hypertension
Philip Njemanze, Anthonia Chioma Amadi, Joy E. Onuchukwu, Chinwendu C. Darlington, Nneoma E. Ukeje, Clinton O. Mezu, Clara C. Ofoegbu, Chidera Okuh, Chidimma O. Ukaegbu, Linda O. Uzoma, Marvis Amuchie, Faustina N. Ojilere, Lilian C. Mbara, Esther C. Nneke
Qeios.2024;[Epub] CrossRef
The potential of DNA methylation markers in the study of obesity
A. F. Nikolaeva, K. O. Petrova, O. V. Vasyukova, R. M. Guseinova, I. R. Minniakhmetov, R. I. Khusainova, N. G. Mokrysheva, V. O. Sigin
Obesity and metabolism.2024; 20(4): 301. CrossRef
Dysbiosis of the gut microbiota and its effect on α-synuclein and prion protein misfolding: consequences for neurodegeneration
Nasir Uddin Mahbub, Md Minarul Islam, Seong-Tshool Hong, Hea-Jong Chung
Frontiers in Cellular and Infection Microbiology.2024;[Epub] CrossRef
Sarcoma Size and Limb Dimensions Predict Complications, Recurrence, and Death in Patients with Soft Tissue Sarcoma in the Thigh: A Multidimensional Analysis
Rami Elmorsi, Luis Camacho, David D. Krijgh, Gordon S. Tilney, Heather Lyu, Raymond S. Traweek, Russell G. Witt, Margaret S. Roubaud, Christina L. Roland, Alexander F. Mericli
Annals of Surgical Oncology.2024;[Epub] CrossRef
Theory of the Leaky Intestine: Sex Differences in Intestinal Parasitic Infections, Cytoskeletal Wall Dysfunctions, and Hypertension
Philip Njemanze, Anthonia Chioma Amadi, Joy E. Onuchukwu, Chinwendu C. Darlington, Nneoma E. Ukeje, Clinton O. Mezu, Clara C. Ofoegbu, Chidera Okuh, Chidimma O. Ukaegbu, Linda O. Uzoma, Marvis Amuchie, Faustina N. Ojilere, Lilian C. Mbara, Esther C. Nneke
Qeios.2024;[Epub] CrossRef
Anti-Obesity Effects of Marine Macroalgae Extract Caulerpa lentillifera in a Caenorhabditis elegans Model
Kawita Chumphoochai, Preeyanuch Manohong, Nakorn Niamnont, Montakan Tamtin, Prasert Sobhon, Krai Meemon
Marine Drugs.2023; 21(11): 577. CrossRef
Obesity and consequent changes in the body
Bojana Kisić, Dragana Puhalo-Sladoje, Dijana Mirić, Dragiša Rašić, Tatjana Novaković
Praxis medica.2022; 51(3-4): 35. CrossRef

Single-cell and spatial sequencing application in pathology: Yoon-Seob Kim, Jinyong Choi, Sug Hyung Lee; J Pathol Transl Med. 2023;57(1):43-51. Published online January 10, 2023; DOI: https://doi.org/10.4132/jptm.2022.12.12

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Abstract PDF

Traditionally, diagnostic pathology uses histology representing structural alterations in a disease’s cells and tissues. In many cases, however, it is supplemented by other morphology-based methods such as immunohistochemistry and fluorescent in situ hybridization. Single-cell RNA sequencing (scRNA-seq) is one of the strategies that may help tackle the heterogeneous cells in a disease, but it does not usually provide histologic information. Spatial sequencing is designed to assign cell types, subtypes, or states according to the mRNA expression on a histological section by RNA sequencing. It can provide mRNA expressions not only of diseased cells, such as cancer cells but also of stromal cells, such as immune cells, fibroblasts, and vascular cells. In this review, we studied current methods of spatial transcriptome sequencing based on their technical backgrounds, tissue preparation, and analytic procedures. With the pathology examples, useful recommendations for pathologists who are just getting started to use spatial sequencing analysis in research are provided here. In addition, leveraging spatial sequencing by integration with scRNA-seq is reviewed. With the advantages of simultaneous histologic and single-cell information, spatial sequencing may give a molecular basis for pathological diagnosis, improve our understanding of diseases, and have potential clinical applications in prognostics and diagnostic pathology.

Citations

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Incorporating Novel Technologies in Precision Oncology for Colorectal Cancer: Advancing Personalized Medicine
Pankaj Ahluwalia, Kalyani Ballur, Tiffanie Leeman, Ashutosh Vashisht, Harmanpreet Singh, Nivin Omar, Ashis K. Mondal, Kumar Vaibhav, Babak Baban, Ravindra Kolhe
Cancers.2024; 16(3): 480. CrossRef
Potential therapeutic targets for hypotension in duchenne muscular dystrophy
Harshi Saxena, Neal L. Weintraub, Yaoliang Tang
Medical Hypotheses.2024; 185: 111318. CrossRef
A comparative analysis of single-cell transcriptomic technologies in plants and animals
Vamsidhar Reddy Netla, Harshraj Shinde, Gulshan Kumar, Ambika Dudhate, Jong Chan Hong, Ulhas Sopanrao Kadam
Current Plant Biology.2023; 35-36: 100289. CrossRef
Fibroblasts – the cellular choreographers of wound healing
Samuel Knoedler, Sonja Broichhausen, Ruiji Guo, Ruoxuan Dai, Leonard Knoedler, Martin Kauke-Navarro, Fortunay Diatta, Bohdan Pomahac, Hans-Guenther Machens, Dongsheng Jiang, Yuval Rinkevich
Frontiers in Immunology.2023;[Epub] CrossRef

Perspectives on single-nucleus RNA sequencing in different cell types and tissues: Nayoung Kim, Huiram Kang, Areum Jo, Seung-Ah Yoo, Hae-Ock Lee; J Pathol Transl Med. 2023;57(1):52-59. Published online January 10, 2023; DOI: https://doi.org/10.4132/jptm.2022.12.19

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Abstract PDF

Single-cell RNA sequencing has become a powerful and essential tool for delineating cellular diversity in normal tissues and alterations in disease states. For certain cell types and conditions, there are difficulties in isolating intact cells for transcriptome profiling due to their fragility, large size, tight interconnections, and other factors. Single-nucleus RNA sequencing (snRNA-seq) is an alternative or complementary approach for cells that are difficult to isolate. In this review, we will provide an overview of the experimental and analysis steps of snRNA-seq to understand the methods and characteristics of general and tissue-specific snRNA-seq data. Knowing the advantages and limitations of snRNA-seq will increase its use and improve the biological interpretation of the data generated using this technique.

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Mapping the cellular landscape of Atlantic salmon head kidney by single cell and single nucleus transcriptomics
Adriana M.S. Andresen, Richard S. Taylor, Unni Grimholt, Rose Ruiz Daniels, Jianxuan Sun, Ross Dobie, Neil C. Henderson, Samuel A.M. Martin, Daniel J. Macqueen, Johanna H. Fosse
Fish & Shellfish Immunology.2024; 146: 109357. CrossRef
Impaired cortical neuronal homeostasis and cognition after diffuse traumatic brain injury are dependent on microglia and type I interferon responses
Jonathan M. Packer, Chelsea E. Bray, Nicolas B. Beckman, Lynde M. Wangler, Amara C. Davis, Ethan J. Goodman, Nathaniel E. Klingele, Jonathan P. Godbout
Glia.2024; 72(2): 300. CrossRef
Adipose tissue macrophage heterogeneity in the single-cell genomics era
Haneul Kang, Jongsoon Lee
Molecules and Cells.2024; 47(2): 100031. CrossRef
Single-cell and spatially resolved transcriptomics for liver biology
Ping Lin, Xi Yan, Siyu Jing, Yanhong Wu, Yiran Shan, Wenbo Guo, Jin Gu, Yu Li, Haibing Zhang, Hong Li
Hepatology.2023;[Epub] CrossRef
Integrated analysis of single-cell and bulk RNA-seq establishes a novel signature for prediction in gastric cancer
Fei Wen, Xin Guan, Hai-Xia Qu, Xiang-Jun Jiang
World Journal of Gastrointestinal Oncology.2023; 15(7): 1215. CrossRef
Placental single cell transcriptomics: Opportunities for endocrine disrupting chemical toxicology
Elana R. Elkin, Kyle A. Campbell, Samantha Lapehn, Sean M. Harris, Vasantha Padmanabhan, Kelly M. Bakulski, Alison G. Paquette
Molecular and Cellular Endocrinology.2023; 578: 112066. CrossRef
Analyzing alternative splicing in Alzheimer’s disease postmortem brain: a cell-level perspective
Mohammad-Erfan Farhadieh, Kamran Ghaedi
Frontiers in Molecular Neuroscience.2023;[Epub] CrossRef
Single-nucleus transcriptome inventory of giant panda reveals cellular basis for fitness optimization under low metabolism
Shangchen Yang, Tianming Lan, Rongping Wei, Ling Zhang, Lin Lin, Hanyu Du, Yunting Huang, Guiquan Zhang, Shan Huang, Minhui Shi, Chengdong Wang, Qing Wang, Rengui Li, Lei Han, Dan Tang, Haimeng Li, Hemin Zhang, Jie Cui, Haorong Lu, Jinrong Huang, Yonglun
BMC Biology.2023;[Epub] CrossRef
Single-cell transcriptomics in thyroid eye disease
Sofia Ahsanuddin, Albert Y. Wu
Taiwan Journal of Ophthalmology.2023;[Epub] CrossRef

Inflammatory bowel disease–associated intestinal fibrosis: Ji Min Park, Jeongseok Kim, Yoo Jin Lee, Sung Uk Bae, Hye Won Lee; J Pathol Transl Med. 2023;57(1):60-66. Published online January 10, 2023; DOI: https://doi.org/10.4132/jptm.2022.11.02

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Abstract PDF

Fibrosis is characterized by a proliferation of fibroblasts and excessive extracellular matrix following chronic inflammation, and this replacement of organ tissue with fibrotic tissue causes a loss of function. Inflammatory bowel disease (IBD) is a chronic inflammation of the gastrointestinal tract, and intestinal fibrosis is common in IBD patients, resulting in several complications that require surgery, such as a stricture or penetration. This review describes the pathogenesis and various factors involved in intestinal fibrosis in IBD, including cytokines, growth factors, epithelial-mesenchymal and endothelial-mesenchymal transitions, and gut microbiota. Furthermore, histopathologic findings and scoring systems used for stenosis in IBD are discussed, and differences in the fibrosis patterns of ulcerative colitis and Crohn’s disease are compared. Biomarkers and therapeutic agents targeting intestinal fibrosis are briefly mentioned at the end.

Citations

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Resistance to apoptosis in complicated Crohn's disease: Relevance in ileal fibrosis
M. Seco-Cervera, D. Ortiz-Masiá, D.C. Macias-Ceja, S. Coll, L. Gisbert-Ferrándiz, J. Cosín-Roger, C. Bauset, M. Ortega, B. Heras-Morán, F. Navarro-Vicente, M. Millán, J.V. Esplugues, S. Calatayud, M.D. Barrachina
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Food additives impair gut microbiota from healthy individuals and IBD patients in a colonic in vitro fermentation model
Irma Gonza, Elizabeth Goya-Jorge, Caroline Douny, Samiha Boutaleb, Bernard Taminiau, Georges Daube, Marie–Louise Scippo, Edouard Louis, Véronique Delcenserie
Food Research International.2024; 182: 114157. CrossRef
Epigenetic Regulation of EMP/EMT-Dependent Fibrosis
Margherita Sisto, Sabrina Lisi
International Journal of Molecular Sciences.2024; 25(5): 2775. CrossRef
Disease clearance in ulcerative colitis: A new therapeutic target for the future
Syed Adeel Hassan, Neeraj Kapur, Fahad Sheikh, Anam Fahad, Somia Jamal
World Journal of Gastroenterology.2024; 30(13): 1801. CrossRef
Pathways Affected by Falcarinol-Type Polyacetylenes and Implications for Their Anti-Inflammatory Function and Potential in Cancer Chemoprevention
Ruyuf Alfurayhi, Lei Huang, Kirsten Brandt
Foods.2023; 12(6): 1192. CrossRef
Time to eRAASe chronic inflammation: current advances and future perspectives on renin-angiotensin-aldosterone-system and chronic intestinal inflammation in dogs and humans
Romy M. Heilmann, Georg Csukovich, Iwan A. Burgener, Franziska Dengler
Frontiers in Veterinary Science.2023;[Epub] CrossRef
Role of the epithelial barrier in intestinal fibrosis associated with inflammatory bowel disease: relevance of the epithelial-to mesenchymal transition
Dulce C. Macias-Ceja, M. Teresa Mendoza-Ballesteros, María Ortega-Albiach, M. Dolores Barrachina, Dolores Ortiz-Masià
Frontiers in Cell and Developmental Biology.2023;[Epub] CrossRef

Original Article

The proteomic landscape shows oncologic relevance in cystitis glandularis: Jun Yong Kim, Dohyun Han, Hyeyoon Kim, Minsun Jung, Han Suk Ryu; J Pathol Transl Med. 2023;57(1):67-74. Published online December 22, 2022; DOI: https://doi.org/10.4132/jptm.2022.10.24

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Abstract PDF: Background
The relationship between cystitis glandularis (CG) and bladder malignancy remains unclear.
Methods
We identified the oncologic significance of CG at the molecular level using liquid chromatography-tandem mass spectrometry-based proteomic analysis of 10 CG, 12 urothelial carcinoma (UC), and nine normal urothelium (NU) specimens. Differentially expressed proteins (DEPs) were identified based on an analysis of variance false discovery rate < 0.05, and their functional enrichment was analyzed using a network model, Gene Set Enrichment Analysis, and Gene Ontology annotation.
Results
We identified 9,890 proteins across all samples and 1,139 DEPs among the three entities. A substantial number of DEPs overlapped in CG/NU, distinct from UC. Interestingly, we found that a subset of DEP clusters (n = 53, 5%) was differentially expressed in NU but similarly between CG and UC. This “UC-like signature” was enriched for reactive oxygen species (ROS) and energy metabolism, growth and DNA repair, transport, motility, epithelial-mesenchymal transition, and cell survival. Using the top 10 shortlisted DEPs, including SOD2, PRKCD, CYCS, and HCLS1, we identified functional elements related to ROS metabolism, development, and transport using network analysis. The abundance of these four molecules in UC/CG than in NU was consistent with the oncologic functions in CG.
Conclusions
Using a proteomic approach, we identified a predominantly non-neoplastic landscape of CG, which was closer to NU than to UC. We also confirmed a small subset of common DEPs in UC and CG, suggesting that altered ROS metabolism might imply potential cancerous risks in CG.

Case Report

Metallic implant-associated lymphoma: ALK-negative anaplastic large cell lymphoma associated with total knee replacement arthroplasty: Jai-Hyang Go; J Pathol Transl Med. 2023;57(1):75-78. Published online January 10, 2023; DOI: https://doi.org/10.4132/jptm.2022.10.30

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Abstract PDF

Metallic implant-associated lymphomas are extremely rare. Only seven cases have been reported in association with knee joint arthroplasty, and all tumors were large B-cell lymphomas. This report is the first case of anaplastic large cell lymphoma occurring after total knee replacement arthroplasty. An 80‑year‑old female patient was admitted because of right knee pain for 2 years. She had undergone total knee replacement arthroplasty 10 years prior. Computed tomography showed an irregular osteolytic lesion in the right lateral femoral condyle, adjacent to the metallic prosthesis. Histologic findings reveal sheets of anaplastic tumor cells that were positive for CD2, CD4, CD5, CD43, and CD30 but negative for CD3, CD20, CD15, and anaplastic lymphoma kinase. Epstein-Barr encoding region in situ hybridization was negative. Analysis of T-cell receptor γ gene rearrangement studies using BIOMED-2–based multiplex polymerase chain reaction confirmed monoclonal T cell proliferation. The woman was finally diagnosed with ALK-negative anaplastic large cell lymphoma.

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Primary bone diffuse large B‐cell lymphoma (PB‐DLBCL): a distinct extranodal lymphoma of germinal centre origin, with a common EZB‐like mutational profile and good prognosis
Vanesa‐Sindi Ivanova, John Davies, Thomas Menter, Damian Wild, Anne Müller, Fatime Krasniqi, Frank Stenner, Alexandros Papachristofilou, Stefan Dirnhofer, Alexandar Tzankov
Histopathology.2024; 84(3): 525. CrossRef

Newsletter

What’s new in neuromuscular pathology 2022: myopathy updates and gene therapies: Chunyu Cai; J Pathol Transl Med. 2023;57(1):79-80. Published online December 20, 2022; DOI: https://doi.org/10.4132/jptm.2022.10.14

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Abstract PDF: This compilation of new changes in the diagnosis and treatment of muscle and nerve disease is extracted from the latest publications from the European Neuromuscular Centre International workshops, FDA.gov and clinicaltrials.gov.

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