Journal of Pathology Clinical Research最新文献

{"title":"Exosome-derived ANXA9 functions as an oncogene in breast cancer","authors":"Cuiping Lu,&nbsp;Ying Zhan,&nbsp;Yunshan Jiang,&nbsp;Jianrong Liao,&nbsp;Zidan Qiu","doi":"10.1002/cjp2.334","DOIUrl":"10.1002/cjp2.334","url":null,"abstract":"<p>Breast cancer (BCA) is one of the most prevalent cancers among women. Emerging evidence has revealed that Annexin A-9 (<i>ANXA9</i>) plays a crucial function in the development of some cancers. Notably, <i>ANXA9</i> has been reported to be a new prognostic biomarker for gastric and colorectal cancers. However, its expression and biological function in BCA have not yet been investigated. Using online bioinformatics tools such as TIMER, GEPIA, HPA, and UALCAN, we predicted <i>ANXA9</i> expression and its correlation with the clinicopathological characteristics of BCA patients. RT-qPCR and western blot were utilized to measure <i>ANXA9</i> mRNA and ANXA9 protein expression in BCA patient tissues and cells. BCA-derived exosomes were identified by transmission electron microscopy. Functional assays were employed to evaluate the biological role of <i>ANXA9</i> in BCA cell proliferation, migration, invasion, and apoptosis. A tumor xenograft <i>in vivo</i> model was utilized to assess the role of <i>ANXA9</i> in tumor growth in mice. Bioinformatics and functional screening analysis revealed that <i>ANXA9</i> was highly expressed in BCA patient tissues, with median <i>ANXA9</i> expression 1.5- to 2-fold higher than in normal tissues (<i>p</i> &lt; 0.05). RT-qPCR confirmed that <i>ANXA9</i> expression in BCA tissues was around 1.5-fold higher than the adjacent normal tissues (<i>p</i> &lt; 0.001). <i>ANXA9</i> expression in different subtypes of BCA also showed a difference, and <i>ANXA9</i> was found to be mostly significantly upregulated in luminal BCA relative to normal tissues or other histological subtypes (<i>p</i> &lt; 0.001). Moreover, <i>ANXA9</i> expression was elevated in different races, ages, clinical stages, node metastasis status, and menopause status groups relative to the normal group (<i>p</i> &lt; 0.001). Furthermore, <i>ANXA9</i> was found to be secreted by BCA tissue-derived exosomes and its expression was upregulated 1- to 7-fold in BCA cells treated with exosomes (<i>p</i> &lt; 0.001), while its expression in MCF10A cells was not significantly altered by treatment with exosomes (<i>p</i> &gt; 0.05). <i>ANXA9</i> silencing induced a significant decrease of around 30% in the colony number of BCA cells (<i>p</i> &lt; 0.01). The number of migrated and invaded BCA cells also decreased by around 65 and 68%, respectively, after silencing <i>ANXA9</i> (<i>p</i> &lt; 0.01). Tumor size was significantly reduced (nearly half) in the LV-sh-<i>ANXA9</i> group relative to the LV-NC group in the xenograft model (<i>p</i> &lt; 0.01), suggesting that <i>ANXA9</i> silencing repressed tumor progression in BCA progression <i>in vitro</i> and <i>in vivo</i>. In conclusion, exosome-derived <i>ANXA9</i> functions as an oncogene that facilitates the proliferation, migration, and invasiveness of BCA cells and enhances tumor growth in BCA development, which may provide a new prognostic and therapeutic biomarker for BCA patients.</p>","PeriodicalId":48612,"journal":{"name":"Journal of Pathology Clinical Research","volume":"9 5","pages":"378-390"},"PeriodicalIF":4.1,"publicationDate":"2023-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pathsocjournals.onlinelibrary.wiley.com/doi/epdf/10.1002/cjp2.334","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9959583","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Post-operative mortality and recurrence patterns in pancreatic cancer according to KRAS mutation and CDKN2A, p53, and SMAD4 expression","authors":"Yohei Masugi,&nbsp;Manabu Takamatsu,&nbsp;Mariko Tanaka,&nbsp;Kensuke Hara,&nbsp;Yosuke Inoue,&nbsp;Tsuyoshi Hamada,&nbsp;Tatsunori Suzuki,&nbsp;Junichi Arita,&nbsp;Yuki Hirose,&nbsp;Yoshikuni Kawaguchi,&nbsp;Yousuke Nakai,&nbsp;Atsushi Oba,&nbsp;Naoki Sasahira,&nbsp;Gaku Shimane,&nbsp;Tsuyoshi Takeda,&nbsp;Keisuke Tateishi,&nbsp;Sho Uemura,&nbsp;Mitsuhiro Fujishiro,&nbsp;Kiyoshi Hasegawa,&nbsp;Minoru Kitago,&nbsp;Yu Takahashi,&nbsp;Tetsuo Ushiku,&nbsp;Kengo Takeuchi,&nbsp;Michiie Sakamoto,&nbsp;for the GTK Pancreatic Cancer Study Group in Japan","doi":"10.1002/cjp2.323","DOIUrl":"10.1002/cjp2.323","url":null,"abstract":"<p>Alterations in <i>KRAS</i>, <i>CDKN2A</i> (<i>p16</i>), <i>TP53</i>, and <i>SMAD4</i> genes have been major drivers of pancreatic carcinogenesis. The clinical course of patients with pancreatic cancer in relation to these driver alterations has not been fully characterised in large populations. We hypothesised that pancreatic carcinomas with different combinations of <i>KRAS</i> mutation and aberrant expression of CDKN2A, p53, and SMAD4 might show distinctive recurrence patterns and post-operative survival outcomes. To test this hypothesis, we utilised a multi-institutional cohort of 1,146 resected pancreatic carcinomas and assessed <i>KRAS</i> mutations by droplet digital polymerase chain reaction and CDKN2A, p53, and SMAD4 expression by immunohistochemistry. Multivariable hazard ratios (HRs) and 95% confidence intervals (CIs) for disease-free survival (DFS) and overall survival (OS) were computed according to each molecular alteration and the number of altered genes using the Cox regression models. Multivariable competing risks regression analyses were conducted to assess the associations of the number of altered genes with specific patterns of recurrence. Loss of SMAD4 expression was associated with short DFS (multivariable HR, 1.24; 95% CI, 1.09–1.43) and OS times (multivariable HR, 1.27; 95% CI, 1.10–1.46). Compared to cases with 0–2 altered genes, cases with three and four altered genes had multivariable HRs for OS of 1.28 (95% CI, 1.09–1.51) and 1.47 (95% CI, 1.22–1.78), respectively (<i>p</i>_trend &lt; 0.001). Patients with an increasing number of altered genes were more likely to have short DFS time (<i>p</i>_trend = 0.003) and to develop liver metastasis (<i>p</i>_trend = 0.006) rather than recurrence at local or other distant sites. In conclusion, loss of SMAD4 expression and an increasing number of altered genes were associated with unfavourable outcomes in pancreatic cancer patients. This study suggests that the accumulation of the four major driver alterations can confer a high metastatic potential to the liver, thereby impairing post-operative survival among patients with pancreatic cancer.</p>","PeriodicalId":48612,"journal":{"name":"Journal of Pathology Clinical Research","volume":"9 5","pages":"339-353"},"PeriodicalIF":4.1,"publicationDate":"2023-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/1b/22/CJP2-9-339.PMC10397380.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9957561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dual epigenetic changes in diabetes mellitus-associated pancreatic ductal adenocarcinoma correlate with downregulation of E-cadherin and worsened prognosis","authors":"Yutaro Hara,&nbsp;Hiroki Mizukami,&nbsp;Keisuke Yamazaki,&nbsp;Takahiro Yamada,&nbsp;Akiko Igawa,&nbsp;Yuki Takeuchi,&nbsp;Takanori Sasaki,&nbsp;Hanae Kushibiki,&nbsp;Kotaro Murakami,&nbsp;Kazuhiro Kudoh,&nbsp;Keinosuke Ishido,&nbsp;Kenichi Hakamada","doi":"10.1002/cjp2.326","DOIUrl":"10.1002/cjp2.326","url":null,"abstract":"<p>Diabetes mellitus (DM) is a risk factor for pancreatic ductal adenocarcinoma (PDAC) that promotes the promoter methylation of <i>CDH1</i>. It is still unclear whether DM can exert other epigenetic effects, such as altering microRNA (miR) expression, in PDAC. The expression of miR-100-5p is known to be changed in DM patients and can suppress the expression of E-cadherin. In this study, the correlation between DM status and dual epigenetic changes was evaluated in PDAC specimens from patients who underwent radical surgical resection. A total of 132 consecutive patients with PDAC were clinicopathologically evaluated. E-cadherin and nuclear β-catenin expression was measured using immunohistochemistry. DNA and miRs were extracted from the main tumor site on formalin-fixed paraffin-embedded tissue sections. TaqMan miR assays were applied to assess miR-100-5p expression. Bisulfite modification was conducted on the extracted DNA, which was then subjected to methylation-specific polymerase chain reaction. Immunohistochemistry revealed that decreased E-cadherin expression and increased nuclear β-catenin expression were significantly associated with DM and poor tumor cell differentiation. The presence of long-duration DM (≥3 years)  was a significant factor contributing to <i>CDH1</i> promoter methylation (<i>p</i> &lt; 0.01), while miR-100-5p expression was proportionally correlated with the preoperative HbA1c level (<i>R</i> = 0.34, <i>p</i> &lt; 0.01), but not the duration of DM. The subjects with high miR-100-5p expression and <i>CDH1</i> promoter methylation showed the highest level of vessel invasion and prevalence of tumor size ≥30 mm. PDAC subjects with dual epigenetic changes showed poorer overall survival (OS) than those with a single epigenetic change. miR-100-5p expression ≥4.13 and <i>CDH1</i> promoter methylation independently predicted poor OS and disease-free survival (DFS) in the multivariate analysis. OS and DFS worsened in DM subjects with both HbA1c ≥ 6.5% and DM duration ≥3 years. Thus, DM is associated with two modes of epigenetic change by independent mechanisms and worsens prognosis.</p>","PeriodicalId":48612,"journal":{"name":"Journal of Pathology Clinical Research","volume":"9 5","pages":"354-366"},"PeriodicalIF":4.1,"publicationDate":"2023-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/92/06/CJP2-9-354.PMC10397378.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9947974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"KLF2 inhibits colorectal cancer progression and metastasis by inducing ferroptosis via the PI3K/AKT signaling pathway","authors":"Jia Li,&nbsp;Ji Ling Jiang,&nbsp;Yi Mei Chen,&nbsp;Wei Qi Lu","doi":"10.1002/cjp2.325","DOIUrl":"10.1002/cjp2.325","url":null,"abstract":"<p>Krüppel-like factor 2 (KLF2) belongs to the zinc finger family and is thought to be a tumor suppressor gene due to its low expression in various cancer types. However, its functional role and molecular pathway involvement in colorectal cancer (CRC) are not well defined. Herein, we investigated the potential mechanism of KLF2 in CRC cell invasion, migration, and epithelial–mesenchymal transition (EMT). We utilized the TCGA and GEPIA databases to analyze the expression of KLF2 in CRC patients and its correlation with different CRC stages and CRC prognosis. RT-PCR, western blot, and immunohistochemistry assays were used to measure KLF2 expression. Gain-of-function assays were performed to evaluate the role of KLF2 in CRC progression. Moreover, mechanistic experiments were conducted to investigate the molecular mechanism and involved signaling pathways regulated by KLF2. Additionally, we also conducted a xenograft tumor assay to evaluate the role of KLF2 in tumorigenesis. KLF2 expression was low in CRC patient tissues and cell lines, and low expression of KLF2 was associated with poor CRC prognosis. Remarkably, overexpressing KLF2 significantly inhibited the invasion, migration, and EMT capabilities of CRC cells, and tumor growth in xenografts. Mechanistically, KLF2 overexpression induced ferroptosis in CRC cells by regulating glutathione peroxidase 4 expression. Moreover, this KLF2-dependent ferroptosis in CRC cells was mediated by inhibiting the PI3K/AKT signaling pathway that resulted in the suppression of invasion, migration, and EMT of CRC cells. We report for the first time that KLF2 acts as a tumor suppressor in CRC by inducing ferroptosis via inhibiting the PI3K/AKT signaling pathway, thus providing a new direction for CRC prognosis assessment and targeted therapy.</p>","PeriodicalId":48612,"journal":{"name":"Journal of Pathology Clinical Research","volume":"9 5","pages":"423-435"},"PeriodicalIF":4.1,"publicationDate":"2023-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/b5/8a/CJP2-9-423.PMC10397377.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10313948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"NTRK gene aberrations in triple-negative breast cancer: detection challenges using IHC, FISH, RT-PCR, and NGS","authors":"Federica Zito Marino,&nbsp;Simona Buono,&nbsp;Marco Montella,&nbsp;Rosa Giannatiempo,&nbsp;Francesco Messina,&nbsp;Giovanni Casaretta,&nbsp;Grazia Arpino,&nbsp;Giulia Vita,&nbsp;Francesco Fiorentino,&nbsp;Luigi Insabato,&nbsp;Alessandro Sgambato,&nbsp;Michele Orditura,&nbsp;Renato Franco,&nbsp;Marina Accardo","doi":"10.1002/cjp2.324","DOIUrl":"10.1002/cjp2.324","url":null,"abstract":"<p>Triple-negative breast cancer (TNBC) is usually an aggressive disease with a poor prognosis and limited treatment options. The neurotrophic tyrosine receptor kinase (NTRK) gene fusions are cancer type-agnostic emerging biomarkers approved by the Food and Drug Administration (FDA), USA, for the selection of patients for targeted therapy. The main aim of our study was to investigate the frequency of <i>NTRK</i> aberrations, i.e. fusions, gene copy number gain, and amplification, in a series of TNBC using different methods. A total of 83 TNBCs were analyzed using pan-TRK immunohistochemistry (IHC), fluorescence <i>in situ</i> hybridization (FISH), real-time polymerase chain reaction (RT-PCR), and RNA-based next-generation sequencing (NGS). Of 83 cases, 16 showed pan-TRK positivity although no cases had <i>NTRK</i>-fusions. Indeed, FISH showed four cases carrying an atypical <i>NTRK1</i> pattern consisting of one fusion signal and one/more single green signals, but all cases were negative for fusion by NGS and RT-PCR testing. In addition, FISH analysis showed six cases with <i>NTRK1</i> amplification, one case with <i>NTRK2</i> copy number gain, and five cases with <i>NTRK3</i> copy number gain, all negative for pan-TRK IHC. Our data demonstrate that IHC has a high false-positive rate for the detection of fusions and molecular testing is mandatory; there is no need to perform additional molecular tests in cases negativity for NTRK by IHC. In conclusion, the <i>NTRK</i> genes are not involved in fusions in TNBC, but both copy number gain and amplification are frequent events, suggesting a possible predictive role for other NTRK aberrations.</p>","PeriodicalId":48612,"journal":{"name":"Journal of Pathology Clinical Research","volume":"9 5","pages":"367-377"},"PeriodicalIF":4.1,"publicationDate":"2023-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pathsocjournals.onlinelibrary.wiley.com/doi/epdf/10.1002/cjp2.324","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9956671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Defining triple-negative breast cancer with neuroendocrine differentiation (TNBC-NED)","authors":"Sean M Hacking,&nbsp;Evgeny Yakirevich,&nbsp;Yihong Wang","doi":"10.1002/cjp2.318","DOIUrl":"10.1002/cjp2.318","url":null,"abstract":"<p>Primary breast neuroendocrine (NE) neoplasms are uncommon, and definitions harbor controversy. We retrospectively collected 73 triple-negative breast cancers (TNBC) and evaluated NE biomarker expression along with p53 aberrant staining (which correlates with <i>TP53</i> gene mutation) and Rb protein loss by immunohistochemistry. In the study cohort, we found 11 (15%) cases of TNBC with neuroendocrine differentiation (TNBC-NED) showing positivity for one or more NE markers (synaptophysin/chromogranin/insulinoma-associated protein 1 [INSM1]). We also identified one separate small cell neuroendocrine carcinoma. Histologic types for these 11 TNBC-NED cases were as follows: 8 invasive ductal carcinoma (IDC) not otherwise specified (NOS), 2 IDC with apocrine features, 1 IDC with solid papillary features. INSM1 had the highest positivity and was seen in all 11 carcinomas. Seven (64%) cases showed p53 aberrant staining, 6 (55%) had Rb protein loss, while 6 (55%) had p53/Rb co-aberrant staining/protein loss. TNBC-NED was associated with Rb protein loss (<i>p</i> &lt; 0.001), as well as p53/Rb co-aberrant staining/protein loss (<i>p</i> &lt; 0.001). In 61 cases negative for NE markers, 37 (61%) showed p53 aberrant staining, while 5 (8%) had Rb protein loss. We also analyzed genomic and transcriptomic data from The Cancer Genome Atlas (TCGA) PanCancer Atlas of 171 basal/TNBC patients. Transcriptomic analysis revealed mRNA expression of <i>RB1</i> to be correlated negatively with <i>SYN1</i> mRNA expression (<i>p</i> = 0.0400) and <i>INSM1</i> mRNA expression (<i>p</i> = 0.0106) in this cohort. We would like to highlight the importance of these findings. TNBC-NED is currently diagnosed as TNBC, and although it overlaps morphologically with TNBC without NED, the unique p53/Rb signature highlights a genetic overlap with NE carcinomas of the breast.</p>","PeriodicalId":48612,"journal":{"name":"Journal of Pathology Clinical Research","volume":"9 4","pages":"313-321"},"PeriodicalIF":4.1,"publicationDate":"2023-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pathsocjournals.onlinelibrary.wiley.com/doi/epdf/10.1002/cjp2.318","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9622183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cell-by-cell quantification of the androgen receptor in benign and malignant prostate leads to a better understanding of changes linked to cancer initiation and progression","authors":"Seta Derderian,&nbsp;Tarik Benidir,&nbsp;Eleonora Scarlata,&nbsp;Turki Altaylouni,&nbsp;Lucie Hamel,&nbsp;Fatima Zahra Zouanat,&nbsp;Fadi Brimo,&nbsp;Armen Aprikian,&nbsp;Simone Chevalier","doi":"10.1002/cjp2.319","DOIUrl":"10.1002/cjp2.319","url":null,"abstract":"<p>The androgen receptor (AR) plays a crucial role in the development and homeostasis of the prostate and is a key therapeutic target in prostate cancer (PCa). The gold standard therapy for advanced PCa is androgen deprivation therapy (ADT), which targets androgen production and AR signaling. However, resistance to ADT develops via AR-dependent and AR-independent mechanisms. As reports on AR expression patterns in PCa have been conflicting, we performed cell-by-cell AR quantification by immunohistochemistry in the benign and malignant prostate to monitor changes with disease development, progression, and hormonal treatment. Prostates from radical prostatectomy (RP) cases, both hormone-naïve and hormone-treated, prostate tissues from patients on palliative ADT, and bone metastases were included. In the normal prostate, AR is expressed in &gt;99% of luminal cells, 51% of basal cells, and 61% of fibroblasts. An increase in the percentage of AR negative (%AR−) cancer cells along with a gradual loss of fibroblastic AR were observed with increasing Gleason grade and hormonal treatment. This was accompanied by a parallel increase in staining intensity of AR positive (AR+) cells under ADT. Staining AR with N- and C-terminal antibodies yielded similar results. The combination of %AR− cancer cells, %AR− fibroblasts, and AR intensity score led to the definition of an AR index, which was predictive of biochemical recurrence in the RP cohort and further stratified patients of intermediate risk. Lastly, androgen receptor variant 7 (ARV7)+ cells and AR− cells expressing neuroendocrine and stem markers were interspersed among a majority of AR+ cells in ADT cases. Altogether, the comprehensive quantification of AR expression in the prostate reveals concomitant changes in tumor cell subtypes and fibroblasts, emphasizing the significance of AR− cells with disease progression and palliative ADT.</p>","PeriodicalId":48612,"journal":{"name":"Journal of Pathology Clinical Research","volume":"9 4","pages":"285-301"},"PeriodicalIF":4.1,"publicationDate":"2023-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/91/88/CJP2-9-285.PMC10240153.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9997095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Explainability and causability in digital pathology","authors":"Markus Plass,&nbsp;Michaela Kargl,&nbsp;Tim-Rasmus Kiehl,&nbsp;Peter Regitnig,&nbsp;Christian Geißler,&nbsp;Theodore Evans,&nbsp;Norman Zerbe,&nbsp;Rita Carvalho,&nbsp;Andreas Holzinger,&nbsp;Heimo Müller","doi":"10.1002/cjp2.322","DOIUrl":"10.1002/cjp2.322","url":null,"abstract":"<p>The current move towards digital pathology enables pathologists to use artificial intelligence (AI)-based computer programmes for the advanced analysis of whole slide images. However, currently, the best-performing AI algorithms for image analysis are deemed black boxes since it remains – even to their developers – often unclear why the algorithm delivered a particular result. Especially in medicine, a better understanding of algorithmic decisions is essential to avoid mistakes and adverse effects on patients. This review article aims to provide medical experts with insights on the issue of explainability in digital pathology. A short introduction to the relevant underlying core concepts of machine learning shall nurture the reader's understanding of why explainability is a specific issue in this field. Addressing this issue of explainability, the rapidly evolving research field of explainable AI (XAI) has developed many techniques and methods to make black-box machine-learning systems more transparent. These XAI methods are a first step towards making black-box AI systems understandable by humans. However, we argue that an explanation interface must complement these explainable models to make their results useful to human stakeholders and achieve a high level of causability, i.e. a high level of causal understanding by the user. This is especially relevant in the medical field since explainability and causability play a crucial role also for compliance with regulatory requirements. We conclude by promoting the need for novel user interfaces for AI applications in pathology, which enable contextual understanding and allow the medical expert to ask interactive ‘what-if’-questions. In pathology, such user interfaces will not only be important to achieve a high level of causability. They will also be crucial for keeping the human-in-the-loop and bringing medical experts' experience and conceptual knowledge to AI processes.</p>","PeriodicalId":48612,"journal":{"name":"Journal of Pathology Clinical Research","volume":"9 4","pages":"251-260"},"PeriodicalIF":4.1,"publicationDate":"2023-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pathsocjournals.onlinelibrary.wiley.com/doi/epdf/10.1002/cjp2.322","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9622160","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Altered cytoplasmic and nuclear ADP-ribosylation levels analyzed with an improved ADP-ribose binder are a prognostic factor in renal cell carcinoma","authors":"Peter Schraml,&nbsp;Fabio Aimi,&nbsp;Martin Zoche,&nbsp;Domingo Aguilera-Garcia,&nbsp;Fabian Arnold,&nbsp;Holger Moch,&nbsp;Michael O Hottiger","doi":"10.1002/cjp2.320","DOIUrl":"10.1002/cjp2.320","url":null,"abstract":"<p>ADP-ribosylation (ADPR) of proteins is catalyzed by ADP-ribosyltransferases, which are targeted by inhibitors (i.e. poly(ADP-ribose) polymerase inhibitors [PARPi]). Although renal cell carcinoma (RCC) cells are sensitive <i>in vitro</i> to PARPi, studies on the association between ADPR levels and somatic loss of function mutations in DNA damage repair genes are currently missing. Here we observed, in two clear cell RCC (ccRCC) patient cohorts (<i>n</i> = 257 and <i>n</i> = 241) stained with an engineered ADP-ribose binding macrodomain (eAf1521), that decreased cytoplasmic ADPR (cyADPR) levels significantly correlated with late tumor stage, high-ISUP (the International Society of Urological Pathology) grade, presence of necrosis, dense lymphocyte infiltration, and worse patient survival (<i>p</i> &lt; 0.01 each). cyADPR proved to be an independent prognostic factor (<i>p</i> = 0.001). Comparably, absence of nuclear ADPR staining in ccRCC correlated with absence of PARP1 staining (<i>p</i> &lt; 0.01) and worse patient outcome (<i>p</i> &lt; 0.05). In papillary RCC the absence of cyADPR was also significantly associated with tumor progression and worse patient outcome (<i>p</i> &lt; 0.05 each). To interrogate whether the ADPR status could be associated with genetic alterations in DNA repair, chromatin remodeling, and histone modulation, we performed DNA sequence analysis and identified a significant association of increased <i>ARID1A</i> mutations in ccRCC^{cyADPR+++/PARP1+} compared with ccRCC^{cyADPR−/PARP1−} (31% versus 4%; <i>p</i> &lt; 0.05). Collectively, our data suggest the prognostic value of nuclear and cytoplasmic ADPR levels in RCC that might be further influenced by genetic alterations.</p>","PeriodicalId":48612,"journal":{"name":"Journal of Pathology Clinical Research","volume":"9 4","pages":"273-284"},"PeriodicalIF":4.1,"publicationDate":"2023-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/42/02/CJP2-9-273.PMC10240151.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9996631","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"KRAS mutations and endometriosis burden of disease","authors":"Natasha L Orr,&nbsp;Arianne Albert,&nbsp;Yang Doris Liu,&nbsp;Amy Lum,&nbsp;JooYoon Hong,&nbsp;Catalina L Ionescu,&nbsp;Janine Senz,&nbsp;Tayyebeh M Nazeran,&nbsp;Anna F Lee,&nbsp;Heather Noga,&nbsp;Kate Lawrenson,&nbsp;Catherine Allaire,&nbsp;Christina Williams,&nbsp;Mohamed A Bedaiwy,&nbsp;Michael S Anglesio,&nbsp;Paul J Yong","doi":"10.1002/cjp2.317","DOIUrl":"10.1002/cjp2.317","url":null,"abstract":"<p>The clinical phenotype of somatic mutations in endometriosis is unknown. The objective was to determine whether somatic <i>KRAS</i> mutations were associated with greater disease burden in endometriosis (i.e. more severe subtypes and higher stage). This prospective longitudinal cohort study included 122 subjects undergoing endometriosis surgery at a tertiary referral center between 2013 and 2017, with 5–9 years of follow-up. Somatic activating <i>KRAS</i> codon 12 mutations were detected in endometriosis lesions using droplet digital PCR. <i>KRAS</i> mutation status for each subject was coded as present (<i>KRAS</i> mutation in at least one endometriosis sample in a subject) or absent. Standardized clinical phenotyping for each subject was carried out via linkage to a prospective registry. Primary outcome was anatomic disease burden, based on distribution of subtypes (deep infiltrating endometriosis, ovarian endometrioma, and superficial peritoneal endometriosis) and surgical staging (Stages I–IV). Secondary outcomes were markers of surgical difficulty, demographics, pain scores, and risk of re-operation. <i>KRAS</i> mutation presence was higher in subjects with deep infiltrating endometriosis or endometrioma lesions only (57.9%; 11/19) and subjects with mixed subtypes (60.6%; 40/66), compared with those with superficial endometriosis only (35.1%; 13/37) (<i>p</i> = 0.04). <i>KRAS</i> mutation was present in 27.6% (8/29) of Stage I cases, in comparison to 65.0% (13/20) of Stage II, 63.0% (17/27) of Stage III, and 58.1% (25/43) of Stage IV cases (<i>p</i> = 0.02). <i>KRAS</i> mutation was also associated with greater surgical difficulty (ureterolysis) (relative risk [RR] = 1.47, 95% CI: 1.02–2.11) and non-Caucasian ethnicity (RR = 0.64, 95% CI: 0.47–0.89). Pain severities did not differ based on <i>KRAS</i> mutation status, at either baseline or follow-up. Re-operation rates were low overall, occurring in 17.2% with <i>KRAS</i> mutation compared with 10.3% without (RR = 1.66, 95% CI: 0.66–4.21). In conclusion, <i>KRAS</i> mutations were associated with greater anatomic severity of endometriosis, resulting in increased surgical difficulty. Somatic cancer-driver mutations may inform a future molecular classification of endometriosis.</p>","PeriodicalId":48612,"journal":{"name":"Journal of Pathology Clinical Research","volume":"9 4","pages":"302-312"},"PeriodicalIF":4.1,"publicationDate":"2023-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pathsocjournals.onlinelibrary.wiley.com/doi/epdf/10.1002/cjp2.317","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9624779","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}