Molecular Pathology Research Research Articles

Deep learning application in prediction of cancer molecular alterations based on pathological images: a bibliographic analysis via CiteSpace

BackgroundThe advancements in artificial intelligence (AI) technology for image recognition were propelling molecular pathology research into a new era.ObjectiveTo summarize the hot spots and research trends in the field of molecular pathology image recognition.MethodsRelevant articles from January 1st, 2010, to August 25th, 2023, were retrieved from the Web of Science Core Collection. Subsequently, CiteSpace was employed for bibliometric and visual analysis, generating diverse network diagrams illustrating keywords, highly cited references, hot topics, and research trends.ResultsA total of 110 relevant articles were extracted from a pool of 10,205 articles. The overall publication count exhibited a rising trend each year. The leading contributors in terms of institutions, countries, and authors were Maastricht University (11 articles), the United States (38 articles), and Kather Jacob Nicholas (9 articles), respectively. Half of the top ten research institutions, based on publication volume, were affiliated with Germany. The most frequently cited article was authored by Nicolas Coudray et al. accumulating 703 citations. The keyword "Deep learning" had the highest frequency in 2019. Notably, the highlighted keywords from 2022 to 2023 included “microsatellite instability”, and there were 21 articles focusing on utilizing algorithms to recognize microsatellite instability (MSI) in colorectal cancer (CRC) pathological images.ConclusionThe use of DL is expected to provide a new strategy to effectively solve the current problem of time-consuming and expensive molecular pathology detection. Therefore, further research is needed to address issues, such as data quality and standardization, model interpretability, and resource and infrastructure requirements.Graphical abstract

Dr. Wu Mengchao (1922-2021), founder and pioneer of Chinese hepatobiliary surgery.

Wu Mengchao had been engaged in basic and clinical research in hepatobiliary surgery since the 1950s and is recognised as the founder and pioneer of hepatobiliary surgery in China. In his career of over 60 years, Wu performed over 16,000 operations and made numerous breakthroughs in hepatobiliary surgery, liver cancer signal transduction, immunotherapy and molecular pathology research. Wu's series of achievements have driven the innovative development of basic theoretical research on the liver in China, establishing it as a long-term international leader in the field of hepatobiliary surgery. This biography elucidates Wu's outstanding contributions to the establishment and development of Chinese hepatobiliary surgery.

Poly(Ethylene Glycols) to Facilitate Celloidin Removal for Immunohistochemical Studies on Archival Human Brain and Temporal Bone Sections.

Pathology repositories worldwide store millions of celloidin-processed human brain and temporal bone (TB) sections vital for studying central nervous system diseases and sensory organs. However, accessing these sections for modern molecular-pathological research, like immunohistochemistry, is hindered by the challenge of removing celloidin without damaging tissue. In this study, we explored the use of polyethylene glycols (PEGs), a class of non-hazardous, ethylene glycol oligomers, combined with an improved section mounting technique, to gently and effectively dissolve celloidin from sections archived for up to 40 years. Optimizing our protocol involved exploring celloidin dissolution kinetics in PEGs of varying molecular weights and terminations, as well as different temperatures. Low molecular weight PEGs, particularly PEG 200, were the most efficient celloidin solvent. Nuclear magnetic resonance (NMR) spectroscopy of celloidin-PEG 200 dissolution products revealed no chemical alterations, suggesting pure solvation without chemical modification. Because the solvation of celloidin in PEG was inhibited by proteins, we further developed a protein-free mounting protocol allowing complete celloidin removal in 30 to 60 minutes by immersing in PEG 200. In summary, our approach overcomes major methodological hurdles, rendering decades-old archival celloidin sections viable for immunohistochemical and other molecular biological techniques, while enhancing safety and workflow efficiency.

Molecular pathology of colorectal cancer: The Saudi situation in perspective.

Colorectal cancer (CRC) is one of the most common cancers worldwide, and one of the most common causes of cancer deaths. In recent times, significant advancements have been made in elucidating the molecular alterations of the disease, and the results have been an improved understanding of CRC biology, as well as the discovery of biomarkers of diagnostic, prognostic, and therapeutic significance. In this review, an evaluation is carried out of the molecular pathology research of CRC emanating from Saudi Arabia. The verdict is that the data on the molecular alterations in CRC from Saudi patients is at best modest. This dearth of molecular pathology data is aptly reflected in the paucity of molecular markers recommended for testing by the Saudi National Cancer Centre guidelines for CRC management. Large scale multi-institutional and multiregional translational studies are required to generate molecular data that would inform diagnostic, prognostic, and risk-stratification guidelines for Saudi CRC patients.

Expression of DR4, DR5, FAS, Caspase-8 and, DDIAS Genes in AML Patients.

Acute myeloid leukemia (AML) is the most common acute leukemia in adults and accompanies a worse survival. In this study, gene expression levels of 5 key players of apoptosis, including DR4, DR5, FAS, caspase 8, and DNA damage-induced apoptosis suppressor (DDIAS), have been evaluated in AML patients compared with controls, aiming to evaluate their possible role and prognostic impact. This cross-sectional study was performed in the Cancer Molecular Pathology Research Center, Mashhad University of Medical Sciences. A total of 30 newly diagnosed AML cases as well as 30 healthy controls enrolled in the study. Real-time polymerase chain reaction was used to evaluate the expressions of DR4, DR5, FAS, DDIAS, and caspase 8 genes in cases and controls. Other necessary data, including cytogenetic findings, mutations, French-American-British (FAB) classification, and survival, were retrieved from hospital records and by direct contact with patients. Statistical analysis was done by SPSS software. When appropriate, the Mann-Whitney U, Pearson's correlation, and the t tests were utilized. Overall survival (OS) was estimated using the Kaplan-Meier method. The expression of all evaluated genes, including DDIAS (0.89 ± 0.20), DR4 (0.67 ± 0.24), DR5 (0.72 ± 0.24), FAS (0.70 ± 0.25), and Caspase 8 (0.77 ± 0.20) were significantly decreased in AML patients compared with the controls (P < 0.001). Patients with the t (16;16) or inv (16) expressed significantly higher amounts of the FAS gene and those with FLT3 mutation exhibited lower expression of caspase 8. Expression of the evaluated genes showed no significant effect on survival. The expression of DR4, DR5, FAS, and caspase 8 seems to be decreased in AML. Lower expression of these molecules may aid AML cells in avoiding apoptosis because they are involved in the initiation of apoptosis, making them potential targets for treatment.

Evaluation of FLT3-ITD Mutations and MDR1 Gene Expression in AML Patients.

Acute myeloid leukemia (AML) is a hematopoietic malignancy caused by genetic abnormalities. Currently, molecular and genetic factors are routinely used as diagnostic and prognostic markers. FLT-3 is one of the most known diagnostic factors in AML. MDR1 gene belongs to the ATP binding cassette family; it is known as one of the chemotherapy-resistant causes of AML. We aimed to study FLT-3ITD mutations and their association with MDR1 gene expression in AML individuals. For investigation, 80 AML individuals and 20 healthy controls were selected. This study was done in the Cancer molecular Pathology Research Center of Mashhad University of Medical Sciences (MUMS), Iran during 2017-2019. FLT3-ITD mutation was assessed by polymerase chain reaction (PCR); Real-time quantitative PCR was performed to measure the amount of MDR1 gene expression. Bone marrow and blood smears of patients were evaluated in terms of morphology. SPSS 16.0 was used for data analysis. FLT3-ITD mutation and MDR1 overexpression were found in 18.8% and 23.8% of AML patients, respectively. Statistical analysis did not show any relationship or association between these two markers. Cuplike morphology was observed in blast cells in 21.25% of AML cases, which was associated with the presence of FLT3-ITD mutation. FLT-3 and MDR1 function independently. Survival studies to determine the exact role of MDR1 overexpression in drug resistance issues would be suggested.

Advances in clinical molecular pathology research using organoid-based patient-derived models

Advances in clinical molecular pathology research using organoid-based patient-derived models

BMI-1 Gene Expression in Patients with Acute and Chronic Myeloid Leukemia in the Northeast of Iran

Background: The B-cell-specific Moloney murine leukemia virus integration site1 (BMI-1) is one of the famous members of the Polycomb ring finger group, which plays a crucial role in the gene transcription regulation through histone changes. Hence, it is believed to be necessary to further clarify the effects of the BMI-1 clinical. Method: This cross-sectional study was conducted on 70 acute myeloid leukemia (AML), 70 chronic myeloid leukemia (CML), and 20 healthy individuals, as the control group. We used Real-Time quantitative polymerase chain reaction (Real-Time PCR) in order to assess the BMI-1 level expression and its effect on prognosis in AML patients in the Molecular Pathology Research Center. Results: The results of the present work indicated that the BMI-1 overexpression was significantly higher in the AML and CML patients compared to that in the healthy controls (P < 0.001). Furthermore, a significant relationship was observed between the BMI-1 overexpression and poor prognosis in the AML patients (Hazard ratio=1.749, P < 0.001, 95% confidence interval = 1.31-2.32). Additionally, BMI-1high was found in chronic and blastic phase in the CML patients (P < 0.001). Conclusion: We concluded that investigation of BMI-1 gene expression pattern will be conducive to the prognosis and treatment of myeloid leukemia.

Comprehensive and Computable Molecular Diagnostic Panel (C2Dx) From Small Volume Specimens for Precision Oncology: Molecular Subtyping of Non-Small Cell Lung Cancer From Fine Needle Aspirates.

The Comprehensive, Computable NanoString Diagnostic gene panel (C2Dx) is a promising solution to address the need for a molecular pathological research and diagnostic tool for precision oncology utilizing small volume tumor specimens. We translate subtyping-related gene expression patterns of Non-Small Cell Lung Cancer (NSCLC) derived from public transcriptomic data which establish a highly robust and accurate subtyping system. The C2Dx demonstrates supreme performance on the NanoString platform using microgram-level FNA samples and has excellent portability to frozen tissues and RNA-Seq transcriptomic data. This workflow shows great potential for research and the clinical practice of cancer molecular diagnosis.

Application of artificial intelligence in toxicopathology

Traditionally, pathologists examine tissue slides under a microscope to find pathological lesions, and have the burden of finding the lesions among so many histopathology slides. Furthermore, inconsistency of diagnoses results differ corresponding to training among researchers. Therefore, accumulated research experience has led to the use of novel tools for increasing accuracy and consistency of diagnoses. With rapid transition from analog to digital methods and new developments in digital pathology, it is possible to use whole slide imaging (WSI) by scanning glass slides. Artificial intelligence (AI), including machine learning and deep learning using WSI, is starting to be applied to automatically classify and count microscope images, and this method has been expanded to include the field of medical image analysis. This review aims to define current trends toward AI application in the biomedical area, especially in the field of toxicopathology, outline current future business trends, and discuss multiple issues of diagnosis, quantification, three-dimensional reconstruction, molecular pathological research, and the future direction of AI in toxicopathology. Big data systems including a large amount of well-defined toxicopathological information will be highly useful for accuracy and corrections of diagnoses. In addition, the need for critical peer review is profound in the continuing educational process. Taken together, it is highly promising that AI model based on big data in the toxicopathological field could classify, detect, and segment pathological lesions in numerous organs of experimental animals and could help explain various biological mechanisms. This promising approach will provide an accurate and fast analysis of tissue structure and biological pathways using AI algorithms and big data.

Application of artificial intelligence in toxicopathology

Traditionally, pathologists examine tissue slides under a microscope to find pathological lesions, and have the burden of finding the lesions among so many histopathology slides. Furthermore, inconsistency of diagnoses results differ corresponding to training among researchers. Therefore, accumulated research experience has led to the use of novel tools for increasing accuracy and consistency of diagnoses. With rapid transition from analog to digital methods and new developments in digital pathology, it is possible to use whole slide imaging (WSI) by scanning glass slides. Artificial intelligence (AI), including machine learning and deep learning using WSI, is starting to be applied to automatically classify and count microscope images, and this method has been expanded to include the field of medical image analysis. This review aims to define current trends toward AI application in the biomedical area, especially in the field of toxicopathology, outline current future business trends, and discuss multiple issues of diagnosis, quantification, three-dimensional reconstruction, molecular pathological research, and the future direction of AI in toxicopathology. Big data systems including a large amount of welldefined toxicopathological information will be highly useful for accuracy and corrections of diagnoses. In addition, the need for critical peer review is profound in the continuing educational process. Taken together, it is highly promising that AI model based on big data in the toxicopathological field could classify, detect, and segment pathological lesions in numerous organs of experimental animals and could help explain various biological mechanisms. This promising approach will provide an accurate and fast analysis of tissue structure and biological pathways using AI algorithms and big data.

Potent mouse monoclonal antibodies that block SARS-CoV-2 infection

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has developed into a global pandemic since its first outbreak in the winter of 2019. An extensive investigation of SARS-CoV-2 is critical for disease control. Various recombinant monoclonal antibodies of human origin that neutralize SARS-CoV-2 infection have been isolated from convalescent patients and will be applied as therapies and prophylaxis. However, the need for dedicated monoclonal antibodies suitable for molecular pathology research is not fully addressed. Here, we produced six mouse anti-SARS-CoV-2 spike monoclonal antibodies that not only exhibit robust performance in immunoassays including western blotting, ELISA, immunofluorescence, and immunoprecipitation, but also demonstrate neutralizing activity against SARS-CoV-2 infection to VeroE6/TMPRSS2 cells. Due to their mouse origin, our monoclonal antibodies are compatible with the experimental immunoassay setups commonly used in basic molecular biology research laboratories, providing a useful tool for future research. Furthermore, in the hope of applying the antibodies of clinical setting, we determined the variable regions of the antibodies and used them to produce recombinant human/mouse chimeric antibodies.

Adi Gazdar, MD: one of the founders of the molecular pathology of cancer, a great scientist and a great man

Adi Gazdar, MD, a true giant in the field of lung cancer research, passed away aged 81 on December 29, 2018. Dr. Gazdar held the W. Ray Wallace Distinguished Chair in Molecular Pathology Research and was Professor of Pathology at the Hamon Center for Therapeutic Oncology Research and Department of Pathology at the University of Texas Southwestern Medical Center in Dallas, TX. Adi Gazdar was one of the first true “molecular pathologists” of lung cancer and help leaded the development of this area around the world through is publications, collaborations, and mentoring activities. He is survived by his wife of 49 years, Celia Gazdar.

The Role of Genetic Mutations in Gene PANK2 on Hallervorden-Spatz Syndrome

Shahin Asadi* Author Affiliations Director in the Division of Medical Genetics and Molecular Pathology Research, Iran Received: October 24, 2019 | Published: November 01, 2019 Corresponding author: Shahin Asadi, Director in the Division of Medical Genetics and Molecular Pathology Research, Iran DOI: 10.26717/BJSTR.2019.22.003753

Analysis of EVI1 Gene Expression in Acute Myeloid Leukemia Patients in the Northeast of Iran

Background: Acute myeloid leukemia (AML) is a heterogeneous disease characterized by increasing immature blood cells in the bone marrow. Aberrant expression of specific genes is a common finding in AML. The proto-oncogene EVI1 is located in a 3q26 position that encodes a zinc finger protein. In the present research, we analyzed the expression of EVI1 gene in 88 Iranian patients with AML. Method: This case-control study was performed in the Cancer Molecular Pathology Research Center of Mashhad University of Medical Sciences. Total RNA was extracted from the bone marrow or peripheral blood mononuclear cells of 88 AML patients and the same number of healthy cases. The expression level of EVI1 was investigated by real-time polymerase chain reaction (RT-PCR). Relative quantification analysis was performed by comparative CT (2−ΔΔCT) method. Results: AML patients expressed a high level of EVI1 (32.95%). In addition, a statistically significant relationship was detected between t (8;21) and EVI1 expression (P=0.049). No correlations were found between EVI1 expression and FAB (French American British) classification, and also between FLT3-ITD mutation and white blood cell count (P =0.6). Furthermore, no correlations were found between the level of EVI1 expression and overall survival (P=0.72). Conclusion:Although EVI1 is highly expressed in peripheral blood mononuclear cells of AML patient, it cannot be considered as an independent prognostic factor.

Longitudinal monitoring of cancer cell subpopulations in monolayers, 3D spheroids, and xenografts using the photoconvertible dye DiR

A central challenge in cancer biology is the identification, longitudinal tracking, and -omics analysis of specific cells in vivo. To this aim, photoconvertible fluorescent dyes are reporters that are characterized by a set of excitation and emission spectra that can be predictably altered, resulting in a distinct optical signature following irradiation with a specific light source. One such dye, DiR, is an infrared fluorescent membrane probe that can irreversibly undergo such a switch. Here, we demonstrate a method using DiR for the spatiotemporal labeling of specific cells in the context of cancer cell monolayer cultures, 3D tumor spheroids, and in vivo melanoma xenograft models to monitor the proliferation of cellular subpopulations of interest over time. Importantly, the photoconversion process is performed in situ, supporting the pursuit of novel avenues of research in molecular pathology.

New molecular pathological strategies for malignant iris tumors

Molecular pathological research offers new chances for the diagnostic and therapeutic management of malignant iris tumors. Besides immunohistological and polymerase chain reaction analyses further techniques, such as multiplex ligation-dependent probe amplification, microsatellite analyses and next-generation sequencing are able to detect various mutations in the tumor genome. An up to date review of new molecular pathological strategies for malignant iris tumors was carried out. This article provides a review of the recent literature based on a PubMed search and clinical experience with iris tumors. The diagnostic characteristics and targeted treatment options are presented, exemplified by iris melanoma and iris carcinoma metastases. In iris melanomas, mutations in the GNA11 and GNAQ genes (in approximately 85% of the cases) seem to be important. Furthermore, the monosomy-3 status should be investigated in these tumors. In iris lymphomas, molecular pathological analyses are essential for an exact diagnosis. Detection of mutations in MYD88, BRAF, KLF2, ID3, TCF3, STAT3, RHo, TET2, IDH2, CXCR4, CD79B and DNMT3A are helpful. In particular, the detection of the CD20 antigen is of therapeutic relevance because this lymphoma subgroup responds well to rituximab, aCD20 antibody treatment. In iris carcinoma metastases, investigations for mutations are helpful because then a targeted treatment seems to be possible. Molecular pathological analyses will become essential in the future management of iris tumors because they play akey role towards apersonalized treatment approach.

Updates on FIGO Staging Classification and the New WHO Classification for Cancer of the Ovary

Background: The knowledge of different subtypes of ovarian cancer is improving with the progress in molecular pathological research. The WHO classification was revised,in parallel with the implementation of the new FIGO staging classification. The former is mainly based on the histopathological findings and defines the actual type of tumor. It has an important impact on prognosis and therapy of the patient.&#x0D; Materials and methods: FIGO staging classification for cancer of the ovary, fallopian tube, and peritoneum published by Jaime Prat and the new WHO Classification of Ovarian Cancer published by Robert Kurman and coauthors in 2014 are summarized.&#x0D; Results: The International Federation of Gynecology and Obstetrics recently significantly revised staging criteria for cancer of the ovary. The latest revision was based on the concept that high-grade serous tubal intraepithelial carcinoma (STIC) may be the origin of some high-grade serous carcinomas of the ovary and peritoneum. Therefore, staging criteria for the ovary, fallopian tube, and peritoneum have been unified. Understanding this background and other important revised points are essential. The previous focus of mesothelial origin of ovarian cancer has been eliminated in new classification. Instead, a discussion of tubal carcinogenesis of hereditary and some other high-grade serous carcinomas is featured. Regarding serous cancers, the previously assumed pathogenesis pathway may be correct for some, but not for all. The earlier transitional cell type of ovarian cancer has been removed while seromucinous tumors have been added as a new entity. The role of some borderline tumors as one possible step in the progression from benign to invasive lesions is incorporated. The article summarizes the essential updates concerning serous, mucinous, seromucinous, endometrioid, clearcell, and Brenner tumors.&#x0D; Conclusion: The new WHO classification takes into account the recent findings on the origin, pathogenesis, and prognosis of different ovarian cancer subtypes. In both FIGO and WHO classification, the tubal origin of hereditary and some non-hereditary high-grade serous cancers is mentioned in contrast to the hitherto theory of mesothelial origin of tumors. Seromucinous tumors represent a new entity.&#x0D; Bangladesh J Obstet Gynaecol, 2017; Vol. 32(1): 33-41

Generation of an Abcc8 heterozygous mutation human embryonic stem cell line using CRISPR/Cas9

The gene of ATP-binding cassette subfamily C member 8 (Abcc8) is cytogenetically located at 11p15.1 and encodes the sulfonylurea receptor (SUR1). SUR1 is a subunit of ATP-sensitive potassium channel (KAPT) in the β-cell regulating insulin secretion. Mutations of ABCC8 are responsible for congenital hyperinsulinism (CHI). Here we reported that an Abcc8 heterozygous mutant cell line was generated by CRISPR/Cas9 technique with 1bp insertion resulting in abnormal splicing on human embryonic stem cell line H1. The phenotypic characteristics of this cell line reveal defective KATP channel and diazoxide-responsive that provides ideal model for molecular pathology research and drug screening for CHI.

Generation of an Abcc8 homozygous mutation human embryonic stem cell line using CRISPR/Cas9

The gene of ATP-binding cassette subfamily C member 8 (Abcc8) is cytogenetically located at 11p15.1 and encodes the sulfonylurea receptor (SUR1). SUR1 is a subunit of ATP-sensitive potassium channel (KAPT) in the β-cell regulating insulin secretion. Mutations of ABCC8 are responsible for congenital hyperinsulinism (CHI). Here we generated an Abcc8 homozygous mutant cell line by CRISPR/Cas9 technique with 22bp deletion resulting in abnormal splicing on human embryonic stem cell line H1. The phenotypic characteristics of this cell line reveal defective KATP channel and diazoxide-unresponsive that provides an ideal model for molecular pathology research and drug screening for CHI.