Browsing by Author "Idrees, Muhammad T."
Now showing 1 - 10 of 18
Results Per Page
Sort Options
Item Artificial intelligence-based multi-class histopathologic classification of kidney neoplasms(Elsevier, 2023-02-16) Gondim, Dibson D.; Al-Obaidy, Khaleel I.; Idrees, Muhammad T.; Eble, John N.; Cheng, Liang; Pathology and Laboratory Medicine, School of MedicineArtificial intelligence (AI)-based techniques are increasingly being explored as an emerging ancillary technique for improving accuracy and reproducibility of histopathological diagnosis. Renal cell carcinoma (RCC) is a malignancy responsible for 2% of cancer deaths worldwide. Given that RCC is a heterogenous disease, accurate histopathological classification is essential to separate aggressive subtypes from indolent ones and benign mimickers. There are early promising results using AI for RCC classification to distinguish between 2 and 3 subtypes of RCC. However, it is not clear how an AI-based model designed for multiple subtypes of RCCs, and benign mimickers would perform which is a scenario closer to the real practice of pathology. A computational model was created using 252 whole slide images (WSI) (clear cell RCC: 56, papillary RCC: 81, chromophobe RCC: 51, clear cell papillary RCC: 39, and, metanephric adenoma: 6). 298,071 patches were used to develop the AI-based image classifier. 298,071 patches (350 × 350-pixel) were used to develop the AI-based image classifier. The model was applied to a secondary dataset and demonstrated that 47/55 (85%) WSIs were correctly classified. This computational model showed excellent results except to distinguish clear cell RCC from clear cell papillary RCC. Further validation using multi-institutional large datasets and prospective studies are needed to determine the potential to translation to clinical practice.Item Clinicopathologic and molecular spectrum of testicular sex cord-stromal tumors not amenable to specific histopathologic subclassification(Elsevier, 2022-12) Siegmund , Stephanie E.; Sholl , Lynette M.; Tsai , Harrison K.; Yang, Yiying; Vasudevaraja, Varshini; Tran, Ivy; Snuderl, Matija; Fletcher, Christopher D. M.; Cornejo, Kristine M.; Idrees, Muhammad T.; Al-Obaidy, Khaleel I.; Collins , Katrina; Gordetsky, Jennifer B.; Wobker, Sara E.; Hirsch, Michelle S.; Trpkov , Kiril; Yilmaz , Asli; Anderson, William J.; Quiroga-Garza, Gabriela; Magi-Galluzzi, Cristina; Canete-Portillo, Sofia; Acosta , Andres M.; Pathology and Laboratory Medicine, School of MedicineA subset of testicular sex cord-stromal tumors (SCST), which includes neoplasms with mixed histology, cannot be classified into a specific histologic subtype. This study evaluated the clinicopathologic, immunophenotypic and molecular features of 26 SCST not amenable to specific classification by expert uropathologists. Median age at diagnosis was 43 years and median tumor size was 2.4 cm. Follow-up information was available for 18 (69%) patients, with evidence of an aggressive clinical course in 6 patients (4 alive with disease, 2 dead of disease 3 months and 6 months after orchiectomy). Microscopically, SCST not amenable to specific classification demonstrated monophasic epithelioid (9/26, 35%), monophasic spindle cell (5/26, 19%), and biphasic or mixed histology (12/26, 46%). One or more aggressive histopathologic features were seen in 11 cases. DNA sequencing was successful in 22 tumors. Pathogenic CTNNB1 and APC alterations were seen in 7 (33%) and 2 (10%) cases, respectively, with additional variants (e.g., CDKN2A, RB1, TP53, BRCA2) being identified in individual cases. Combined evaluation of morphology, sequencing data and beta-catenin immunohistochemistry resulted in reclassification of 6 (23%) tumors as Sertoli cell tumor, not otherwise specified. This was supported by comparing the methylation profiles of a subset of these tumors and those of typical Sertoli cell tumors. Additionally, a subset of 5 neoplasms (19%) with spindle cell or biphasic histology and SMA expression was characterized by hyperdiploid genomes with recurrent chromosomal gains and absence of driver mutations, possibly representing a distinct tumor type. The SCST that remained not amenable to specific histologic classification (15/26, 58%) were enriched for aggressive histologic features and malignant clinical behavior. In conclusion, this study demonstrated that a subset of testicular SCST that were originally not amenable to specific classification could be reclassified by combined evaluation of morphology, immunohistochemistry and molecular data.Item Comparing oncologic outcomes in patients undergoing surgery for oncocytic neoplasms, conventional oncocytoma, and chromophobe renal cell carcinoma(Elsevier, 2019-11) Flack, Chandra K.; Calaway, Adam C.; Miller, Brady L.; Picken, Maria M.; Gondim, Dibson D.; Idrees, Muhammad T.; Abel, E. Jason; Gupta, Gopal N.; Boris, Ronald S.; Urology, School of MedicineIntroduction Oncocytic neoplasms are renal tumors similar to oncocytoma, but their morphologic variations preclude definitive diagnosis. This somewhat confusing diagnosis can create treatment and surveillance challenges for the treating urologist. We hypothesize that these subtle morphologic variations do not drastically affect the malignant potential of these tumors, and we sought to demonstrate this by comparing clinical outcomes of oncocytic neoplasms to those of classic oncocytoma and chromophobe. Methods We gathered demographic and outcomes data for patients with variant oncocytic tumors. Oncologic surveillance was conducted per institutional protocol in accordance with NCCN guidelines. Descriptive statistics were used to compare incidence of metastasis and death against those for patients with oncocytoma and chromophobe. Three hundred and fifty-one patients were analyzed: 164 patients with oncocytoma, 28 with oncocytic neoplasms, and 159 with chromophobe tumors. Results Median follow-up time for the entire cohort was 32.4 months, (interquartile range 9.2–70.0). Seventeen total patients (17/351, 4.9%) died during the course of the study. In patients with oncocytoma or oncocytic neoplasm, none were known to metastasize or die of their disease. Only chromophobe tumors >6 cm in size in our series demonstrated metastatic progression and approximately half of these metastasized tumors demonstrated sarcomatoid changes. Conclusion Variant oncocytic neoplasms appear to have a natural course similar to classic oncocytoma. These tumors appear to have no metastatic potential, and oncologic surveillance may not be indicated after surgery.Item DOG1 immunohistochemical staining of testicular biopsies is a reliable tool for objective assessment of infertility(Elsevier, 2019-06) Salama, Rasha; Al-Obaidy, Khaleel I.; Perrino, Carmen M.; Grignon, David J.; Ulbright, Thomas M.; Idrees, Muhammad T.; Pathology and Laboratory Medicine, School of MedicineTesticular biopsy may be a component of the work-up of male infertility. However, no reliable diagnostic tools are available for objective quantitative assessment of spermatogenic cells. It is well known that MAGE-A4 is selectively expressed in spermatogonia and our group has previously demonstrated that DOG1 differentially stains germ cells. Therefore, we performed DOG1 and a double stain cocktail (DOG1 and 57b murine monoclonal anti-MAGE-A4) immunohistochemical stains on 40 testicular infertility biopsies (10 each with active spermatogenesis, Sertoli cell-only, hypospermatogenesis, and maturation arrest), 25 benign seminiferous tubules from radical orchiectomies, and 5 spermatocytic tumors (ST). In biopsies/resections with active spermatogenesis, DOG1 stained spermatocytes and spermatids and was absent in spermatogonia, while MAGE-A4 stained spermatogonia and primary spermatocytes (weak). In hypospermatogenesis, DOG1 highlighted decreased spermatocytes/spermatids and MAGE-A4 highlighted decreased spermatogonia. DOG1 staining confirmed decreased to absent spermatocytes in maturation arrest and MAGE-A4 staining established the presence of preserved spermatogonia in all cases. All STs were negative for DOG1 and positive for MAGE-A4, while all Sertoli cell-only cases were negative for DOG1 and the double stain cocktail. In conclusion, we confirmed that DOG1 is expressed in spermatocytes and spermatids and MAGE-A4 highlights primarily spermatogonia. Usage of these stains facilitates confirmation of maturation arrest, assessment of the percentage of testis involvement in hypospermatogenesis and identification of mixed patterns. Finally, this study supports that the differentiation of STs is more closely related to spermatogonia than the more mature spermatocytes.Item Eosinophilic Esophagitis Symptom Scores Are High in Children Without Eosinophilic Disease(Wolters Kluwer, 2021-10) Bose, Paroma; Albright, Eric; Idrees, Muhammad T.; Perkins, Anthony; Sawyers, Cindy; Gupta, Sandeep K.; Hon, Emily C.; Biostatistics, School of Public HealthObjectives: The Pediatric Eosinophilic Esophagitis (EoE) Symptom Score version 2 (PEESSv2.0) is an EoE-specific validated metric for disease monitoring, but its use has not been explored outside of EoE. Our aim was to determine if PEESSv2.0 scores differentiate between children with EoE and non-EoE esophageal dysfunction undergoing initial esophagogastroduodenoscopy (EGD). Methods: A prospective cohort study of pediatric subjects was conducted. Children ages 1–18 undergoing initial EGD for esophageal dysfunction were enrolled. Demographics, clinical history, and child self-report and parent-proxy report PEESSv2.0 symptom scores were collected at the time of EGD. Esophageal biopsies were reviewed, and EoE was defined as >15 eosinophils/high powered field (hpf) seen in any level of the esophagus. Non-EoE was defined as <15 eosinophils/hpf. Results: Seventy-one children were included in the study from 2015 to 2018 [59% (42/71) males; mean age 9.2 years; range 1–17 years]. Fifty-eight percent (41/71) met criteria for EoE, and 42% (30/71) were labeled non-EoE. Non-EoE children and their parents had higher/worse median PEESSv2.0 total scores than those with EoE [47.0 vs 28.0 (P = 0.001) and 40.5 vs 26.5 (P = 0.012), respectively]. Non-EoE children reported higher median GERD [9.0 vs 4.0 (P = 0.003)], nausea/vomiting [9.0 vs 4.0 (P = 0.003)], and pain [11.0 vs 6.0 (P = 0.001)] subdomain scores compared to those with EoE. PEESSv2.0 dysphagia subdomain scores (child and parent-proxy) did not differ between EoE and non-EoE groups [22.0 vs 15.0 (P = 0.184) and 18.5 vs 17.4 (P = 0.330), respectively]. Discussion: Total PEESSv2.0 scores were worse in non-EoE group compared to EoE group. Although PEESSv2.0 is validated for use in monitoring EoE therapy, it does not distinguish children with EoE from non-EoE esophageal dysfunction at the time of diagnostic EGD.Item Identification of a common polymorphism in COQ8B acting as a modifier of thoracic aortic aneurysm severity(Elsevier, 2022-01-13) Landis, Benjamin J.; Lai, Dongbing; Guo, Dong-Chuan; Corvera, Joel S.; Idrees, Muhammad T.; Stadler, Henry W.; Cuevas, Christian; Needler, Gavin U.; Vujakovich, Courtney E.; Milewicz, Dianna M.; Hinton, Robert B.; Ware, Stephanie M.; Pediatrics, School of MedicineThoracic aortic aneurysm (TAA) predisposes to sudden, life-threatening aortic dissection. The factors that regulate interindividual variability in TAA severity are not well understood. Identifying a molecular basis for this variability has the potential to improve clinical risk stratification and advance mechanistic insight. We previously identified COQ8B, a gene important for biosynthesis of coenzyme Q, as a candidate genetic modifier of TAA severity. Here, we investigated the physiological role of COQ8B in human aortic smooth muscle cells (SMCs) and further tested its genetic association with TAA severity. We find COQ8B protein localizes to mitochondria in SMCs, and loss of mitochondrial COQ8B leads to increased oxidative stress, decreased mitochondrial respiration, and altered expression of SMC contractile genes. Oxidative stress and mitochondrial cristae defects were prevalent in the medial layer of human proximal aortic tissues in patients with TAA, and COQ8B expression was decreased in TAA SMCs compared with controls. A common single nucleotide polymorphism (SNP) rs3865452 in COQ8B (c.521A>G, p.H174R) was associated with decreased rate of aortic root dilation in young patients with TAA. In addition, the SNP was less frequent in a second cohort of early-onset thoracic aortic dissection cases compared with controls. COQ8B protein levels in aortic SMCs were increased in TAA patients homozygous for rs3865452 compared with those homozygous for the reference allele. Thus, COQ8B is important for aortic SMC metabolism, which is dysregulated in TAA, and rs3865452 may decrease TAA severity by increasing COQ8B level. Genotyping rs3865452 may be useful for clinical risk stratification and tailored aortopathy management.Item Idiopathic gastroparesis is associated with specific transcriptional changes in the gastric muscularis externa(Wiley, 2018-04) Herring, B. Paul; Hoggatt, April M.; Gupta, Anita; Griffith, Sarah; Nakeeb, Attila; Choi, Jennifer N.; Idrees, Muhammad T.; Nowak, Thomas; Morris, David L.; Wo, John M.; Cellular and Integrative Physiology, School of MedicineBACKGROUND: The molecular changes that occur in the stomach that are associated with idiopathic gastroparesis are poorly described. The aim of this study was to use quantitative analysis of mRNA expression to identify changes in mRNAs encoding proteins required for the normal motility functions of the stomach. METHODS: Full-thickness stomach biopsy samples were collected from non-diabetic control subjects who exhibited no symptoms of gastroparesis and from patients with idiopathic gastroparesis. mRNA was isolated from the muscularis externa and mRNA expression levels were determined by quantitative reverse transcriptase (RT)-PCR. KEY RESULTS: Smooth muscle tissue from idiopathic gastroparesis patients had decreased expression of mRNAs encoding several contractile proteins, such as MYH11 and MYLK1. Conversely, there was no significant change in mRNAs characteristic of interstitial cells of Cajal (ICCs) such as KIT or ANO1. There was also a significant decrease in mRNA-encoding platelet-derived growth factor receptor α (PDGFRα) and its ligand PDGFB and in Heme oxygenase 1 in idiopathic gastroparesis subjects. In contrast, there was a small increase in mRNA characteristic of neurons. Although there was not an overall change in KIT expression in gastroparesis patients, KIT expression showed a significant correlation with gastric emptying whereas changes in MYLK1, ANO1 and PDGFRα showed weak correlations to the fullness/satiety subscore of patient assessment of upper gastrointestinal disorder-symptom severity index scores. CONCLUSIONS AND INFERENCES: Our findings suggest that idiopathic gastroparesis is associated with altered smooth muscle cell contractile protein expression and loss of PDGFRα+ cells without a significant change in ICCs.Item Immunophenotypic Characterization of Germ Cell Tumor-Derived Primitive Neuroectodermal Tumors: Evidence for Frequent Neuronal and/or Glial Differentiation(Allen Press, 2021) Magers, Martin J.; Perrino, Carmen M.; Ulbright, Thomas M.; Idrees, Muhammad T.; Pathology and Laboratory Medicine, School of MedicineContext: Primitive neuroectodermal tumors (PNETs) may arise as a somatic-type malignancy in germ cell tumors. In this setting, most PNETs resemble those of the central nervous system and lack chromosome 22 translocations. However, description of the morphologic and differentiation spectrum of PNETs arising from germ cell tumors is lacking. Objective: To investigate the morphologic and immunohistochemical features of these tumors, concentrating on neuronal and glial features. Design: We selected cases based on a morphologically identifiable glial and/or differentiated neuronal component in association with the undifferentiated PNET. Immunohistochemistry for glial fibrillary acidic protein, S100 protein, synaptophysin, chromogranin A, and SOX11 was performed on tumors with available material, with the scoring of both staining intensity (0-3) and extent (0-3). Thirteen qualifying PNETs of testicular origin with available immunohistochemical stains or stainable material were identified. The complete stain panel was performed in 10 tumors. Results: SOX11 demonstrated positive staining in the undifferentiated PNET component of all tumors (10 of 10) and was rarely positive in the differentiated (ie, neuronal/glial) component (1 of 10; focal and weak); synaptophysin was slightly less sensitive in the undifferentiated component (12 of 13; often focal and weak) and also showed positivity in the neuronal/glial component (5 of 13). Glial fibrillary acidic protein and S100 were more frequently positive in the differentiated areas (83% and 77%, respectively) compared with undifferentiated areas (25% and 17%, respectively). Conclusions: SOX11 is a sensitive immunohistochemical marker for testicular PNET, particularly those lacking differentiation. Testicular PNETs often demonstrate glial and/or neuronal differentiation. Differentiation is marked by the acquisition of S100 and glial fibrillary acidic protein expression and SOX11 loss.Item Merlin immunohistochemistry is useful in diagnosis of tumours within the spectrum of biphasic hyalinizing psammomatous renal cell carcinoma(Wiley, 2022-11) Collins, Katrina; Hwang, Michael; Antic, Tatjana; Paintal, Ajit; Argani, Pedram; Matoso, Andres; Gopinath, Arun; Baskovich, Brett; Mehra, Rohit; Williamson, Sean R.; Idrees, Muhammad T.; Barletta, Justine A.; Anderson, William J.; Hirsch, Michelle S.; Hornick , Jason L.; Acosta, Andres M.; Pathology and Laboratory Medicine, School of MedicineAims: Biphasic hyalinizing psammomatous (BHP) renal cell carcinoma (RCC) is a newly described emerging entity within the spectrum of papillary RCC in the WHO 2022 classification. Molecular analyses have discovered that BHP RCC consistently harbour somatic mutations in the neurofibromin 2 (NF2) gene. The NF2 gene product, merlin, is known to primarily function as a tumour suppressor. Merlin protein loss correlates closely with the presence of NF2 mutations in benign and malignant tumours arising in different sites. In the present study we explored the role of merlin immunohistochemistry (IHC) in tumours within the spectrum of BHP RCC to determine the diagnostic utility of this marker. Materials and methods: We performed merlin IHC in 13 BHP RCC, 18 papillary RCC, 10 TFE3-translocation RCC, 15 TFEB-altered RCC (including 13 TFEB-rearranged and 2 TFEB-amplified), and 10 mucinous tubular and spindle cell carcinomas of unknown mutational status. Results: Unequivocal loss of merlin expression in >90% of the tumour cells was observed in 12/13 BHP-RCC (92%), with the remaining tumour demonstrating weak focal cytoplasmic expression in ~10% of the tumour. In contrast, merlin was diffusely or multifocally expressed in all papillary RCC, TFE3-translocation RCC, and TFEB-altered RCC, as well as in 70% of mucinous tubular and spindle carcinomas. Conclusions: In this study, merlin IHC was ~92% sensitive and ~94% specific for BHP RCC. These data suggest that merlin IHC is a reliable surrogate marker for the presence of underlying NF2 gene inactivation, being diagnostically useful to identify BHP RCC.Item Molecular pathology of urogenital tumors : Recommendations from the 2019 International Society of Urological Pathology (ISUP) Consensus Conference(SpringerLink, 2021-05) Hommerding, Oliver; Allory, Yves; Argani, Pedram; Bismar, Tarek A.; Bubendorf, Lukas; Canete-Portillo, Sofía; Chaux, Alcides; Chen, Ying-Bei; Cheng, Liang; Cubilla, Antonio L.; Egevad, Lars; Gill, Anthony J.; Grignon, David J.; Hartmann, Arndt; Hes, Ondrej; Idrees, Muhammad T.; Kao, Chia-Sui; Knowles, Margaret A.; Looijenga, Leendert H.J.; Lotan, Tamara L.; Pritchard, Colin C.; Rubin, Mark A.; Tomlins, Scott A.; Van der Kwast, Theodorus H.; Velazquez, Elsa F.; Warrick, Joshua I.; Williamson, Sean R.; Kristiansen, Glen; Pathology and Laboratory Medicine, School of MedicineComprehensive understanding of molecular principles in cancer and the diversification of oncological therapy promise individual therapeutic concepts, which have not yet found their way into urogenital cancer therapy. In March 2019 the International Society of Urogenital Pathology (ISUP) therefore held a consensus conference on recommendations for molecular diagnostics of genitourinary tumors, which were published in five separate manuscripts and are summarized in this article.In preparation for the conference, a comprehensive survey of current practices for molecular testing of urogenital tumors was carried out by members of the ISUP. At the conference, the results and the corresponding background information were presented by five working groups and recommendations for action for diagnostics were developed. An agreement between 66% of the conference participants was defined as consensus.