Browsing by Subject "Histology"
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Item A Clinical Severity Index for Eosinophilic Esophagitis: Development, Consensus, and Future Directions(Elsevier, 2022) Dellon, Evan S.; Khoury, Paneez; Muir, Amanda B.; Liacouras, Chris A.; Safroneeva, Ekaterina; Atkins, Dan; Collins, Margaret H.; Gonsalves, Nirmala; Falk, Gary W.; Spergel, Jonathan M.; Hirano, Ikuo; Chehade, Mirna; Schoepfer, Alain M.; Menard-Katcher, Calies; Katzka, David A.; Bonis, Peter A.; Bredenoord, Albert J.; Geng, Bob; Jensen, Elizabeth T.; Pesek, Robert D.; Feuerstadt, Paul; Gupta, Sandeep K.; Lucendo, Alfredo J.; Genta, Robert M.; Hiremath, Girish; McGowan, Emily C.; Moawad, Fouad J.; Peterson, Kathryn A.; Rothenberg, Marc E.; Straumann, Alex; Furuta, Glenn T.; Aceves, Seema S.; Pediatrics, School of MedicineBackground & aims: Disease activity and severity of eosinophilic esophagitis (EoE) dictate therapeutic options and management, but the decision-making process for determining severity varies among practitioners. To reduce variability in practice patterns and help clinicians monitor the clinical course of the disease in an office setting, we aimed to create an international consensus severity scoring index for EoE. Methods: A multidisciplinary international group of adult and pediatric EoE researchers and clinicians, as well as non-EoE allergy immunology and gastroenterology experts, formed 3 teams to review the existing literature on histology, endoscopy, and symptoms of EoE in the context of progression and severity. A steering committee convened a 1-day virtual meeting to reach consensus on each team's opinion on salient features of severity across key clinicopathologic domains and distill features that would allow providers to categorize disease severity. Results: Symptom features and complications and inflammatory and fibrostenotic features on both endoscopic and histologic examination were collated into a simplified scoring system-the Index of Severity for Eosinophilic Esophagitis (I-SEE)-that can be completed at routine clinic visits to assess disease severity using a point scale of 0-6 for mild, 7-14 for moderate, and ≥15 for severe EoE. Conclusions: A multidisciplinary team of experts iteratively created a clinically usable EoE severity scoring system denominated "I-SEE" to guide practitioners in EoE management by standardizing disease components reflecting disease severity beyond eosinophil counts. I-SEE should be validated and refined using data from future clinical trials and routine clinical practice to increase its utilization and functionality.Item Clinicopathological and Treatment Patterns of Combined Small-Cell Lung Carcinoma with Future Insight to Treatment: A Population-Based Study(MDPI, 2023-01-28) Ullah, Asad; Saeed, Omer; Karki, Nabin Raj; Goodbee, Mya; Yasinzai, Abdul Qahar Khan; Waheed, Abdul; Heneidi, Saleh; Thomas, Anish; Karim, Nagla Abdel; Johnson, Joyce; Del Rivero, Jaydira; Khan, Jaffar; Pathology and Laboratory Medicine, School of MedicineBackground: Primary lung cancer is the most common cause of cancer-related mortality in the United States (US). Approximately 90% of lung cancers are associated with smoking and the use of other tobacco products. Based on histology, lung cancers are divided into small-cell lung carcinomas (SCLCs) and non-small-cell lung carcinomas (NSCLCs). Most SCLCs are of the pure subtype, while the rare combined SCLCs contain elements of both small-cell and non-small-cell morphologies. This study sought to evaluate the demographics, clinical factors, molecular abnormalities, treatment approaches, and survival outcomes with combined SCLC and NSCLCs. Materials and methods: Data on 2126 combined SCLC patients was extracted from the Surveillance Epidemiology and End Result (SEER) database from 2000 to 2018. Data extracted for analyses included age, sex, race, tumor size, tumor location, metastasis status, stage at diagnosis, treatment received, and treatment outcomes. Multivariate analysis was performed using Statistical Product and Service Solutions (SPSS) software. Results: The patients had a median age of 68 years; 43.9% of the patients were female and 56.1% were male; 84.5% were White and 11.7% were African Americans. The majority of patients had a poorly differentiated disease at 29.6%; 17% were undifferentiated, 3.2% were moderately differentiated, and 0.8% were well differentiated. Chemotherapy was the most common treatment modality (45.3%); 17% underwent surgery only, 10.3% underwent surgery followed by adjuvant chemotherapy, and 10% underwent radiation after surgery. Five-year cancer-specific survival was 15.2% with surgery alone, and combined surgery and chemotherapy provided the highest percentages (38.3% and 34.7%, respectively). Females had significantly higher 1- and 5-year cancer-specific survival rates compared to males (59.3% and 29.9% vs. 48.0% and 23.7, respectively; p < 0.001). Well-differentiated tumors had significantly higher survival compared to other gradings (p < 0.001). Survival decreased as tumor staging moved distally from localized to regional to distant (p < 0.001). Metastasis to bone, liver, brain, and lung significantly decreased survival in comparison to patients who did not have any metastasis (p < 0.001). Females had significantly shorter survival compared to their counterparts when metastasis was to the bone, brain, or liver (p < 0.001). Multivariate analysis identified male sex (Hazard Ratio (HR) = 1.2), undifferentiated grade (HR = 1.9), regional extent of disease (HR = 1.7), distant extent of disease (HR = 3.7), and metastasis to liver (HR = 3.5) as variables associated with worse survival. Conclusion: Combined SCLC is overall very rare. However, the frequency of presentation with combined SCLC is on the rise, in part due to improvements in diagnostic techniques. Despite advances in therapies, treating combined SCLC is challenging, and novel therapies are not utilized, owing to low rates of targetable mutations. Combined SCLC has higher survival rates if well differentiated.Item DNA/RNA Degradation Rate in Long Term Fixed Museum Specimens(2014-04-11) Cook, Shannon; Dodge, Chelsea; Morgan, Randy; Sandusky, George E.In today’s research driven society, it has become commonplace for institutions to rely upon DNA and RNA extraction techniques to help obtain genomic data from old specimens. Generally, specimens were commonly preserved for future gross examination and/or teaching. Using histological examination of specimens from museum jars from the Pathology Department at the Indiana University School of Medicine, the sequential and chronological degradation of DNA and RNA has been studied. We examined gross specimens from nine decades from 1920 until 2000. We evaluated histologic preservation of kidney, liver, heart, lung, spleen, uterus, and brain for nuclear structure in these samples. Nuclear preservation was based on amount of nuclei per 20x microscopic field and the crispness of the nuclear membrane and internal features. The nuclei in high lipid tissues such as the brain were found to degrade at a quicker rate than dense tissues such as the heart and uterus. Our study has shown specimens preserved beyond fifty years were likely to have little to no nuclei left, thus indicating that there was little to no DNA and RNA remaining. This technique of histologic evaluation first is an important finding and a general guideline which may save research institutions from the expensive process of DNA and RNA extraction.Item The Efficacy of Team-Based Learning in Histology(2010) Brokaw, James J.; Condon, Keith W.Team-Based Learning (TBL) is an instructional strategy in which traditional lectures are replaced with in-class activities that promote group discussion and active learning. Students are expected to master the basic facts and concepts of the subject matter prior to coming to class. We sought to determine whether the knowledge obtained using TBL is comparable to that obtained using traditional lectures, and whether students have a preference for either instructional method. From 2006-2008, the students in a graduate histology course were taught the structure and function of the basic tissues using TBL. Other topics in the course were taught using lectures, so the students experienced both instructional methods. Using the same 59 multiple-choice questions, we tested the students’ knowledge about the basic tissues, and compared the results to those obtained in 2005, when the basic tissue material was taught using lectures. In 2006-2008, the mean ± SD exam performance after TBL (87.5 ± 7.5, n = 32; 83.9 ± 11.1, n = 36; 78.9 ± 13.2, n = 24) was similar to that observed in 2005 after lectures (82.7 ± 12.0, n = 39). When asked to respond to the statement, “I prefer TBL sessions rather than traditional lectures”, 40.4% of the students agreed or strongly agreed, 23.4% disagreed or strongly disagreed, and 36.0% had no opinion (89 of 92 students responding). These results suggest that TBL and lectures produce comparable learning outcomes, at least as measured on a multiple-choice exam, and that students have a mild preference for the TBL format.Item Histological Quantification to Determine Lung Fungal Burden in Experimental Aspergillosis(JoVE, 2018-03-09) Stolz, Dylan J.; Sands, Ethan M.; Amarsaikhan, Nansalmaa; Tsoggerel, Angar; Templeton, Steven P.; Microbiology and Immunology, School of MedicineThe quantification of lung fungal burden is critical for the determination of the relative levels of immune protection and fungal virulence in mouse models of pulmonary fungal infection. Although multiple methods are used to assess fungal burden, quantitative polymerase chain reaction (qPCR) of fungal DNA has emerged as a technique with several advantages over previous culture-based methods. Currently, a comprehensive assessment of lung pathology, leukocyte recruitment, fungal burden, and gene expression in mice with invasive aspergillosis (IA) necessitates the use of a significant number of experimental and control animals. Here the quantification of lung histological staining to determine fungal burden using a reduced number of animals was examined in detail. Lung sections were stained to identify fungal structures with Gomori's modified methanamine silver (GMS) staining. Images were taken from the GMS-stained sections from 4 discrete fields of each formalin-fixed paraffin-embedded lung. The GMS stained areas within each image were quantified using an image analysis program, and from this quantification, the mean percentage of stained area was determined for each sample. Using this strategy, eosinophil-deficient mice exhibited decreased fungal burden and disease with caspofungin therapy, while wild-type mice with IA did not improve with caspofungin. Similarly, fungal burden in mice lacking γδ T cells were also improved by caspofungin, as measured by qPCR and GMS quantification. GMS quantification is therefore introduced as a method for the determination of relative lung fungal burden that may ultimately reduce the quantity of experimental animals required for comprehensive studies of invasive aspergillosisItem Integrated Case-Based Learning Session for Breast and Upper Limb Anatomy(Association of American Medical Colleges, 2024-05-10) Merritt, Emily; McNulty, Margaret A.; Byram, Jessica N.; Anatomy, Cell Biology and Physiology, School of MedicineIntroduction: Medical students are frequently introduced to medical school curricula through anatomy coursework, which often includes histology and embryology content. As medical education has increasingly emphasized integration of content areas, use of activities such as case-based learning (CBL) sessions has grown. Little published work has demonstrated the effectiveness of CBL sessions in integrating anatomy, embryology, and histology on first-year medical students' ability to improve content mastery and adapt their study techniques. Methods: We developed a CBL session that included anatomy, embryology, and histology content covering the upper extremity and breast pathology that was taught to incoming first-year medical students (N = 51) during a prematriculation program in the summers of 2022 and 2023. The session involved completion of an individual pre- and postsession quiz; group completion of clinical cases involving image interpretation, matching exercises, and construction of diagrams, flowcharts, or tables; and a postsession survey with Likert-style and free-response questions about preparation and session effectiveness. Results: Postsession quiz scores significantly improved (p < .001). On the postsession survey (response rate: 59%), students commented that they enjoyed the real-life application and integration of the cases and that the sessions improved their understanding of the connections between content areas. Other comments demonstrated that students were evaluating and adapting their study approach in preparation for the sessions, often using techniques introduced and practiced in the sessions. Discussion: CBL sessions can provide opportunities to incoming first-year medical students to practice, adapt, and evaluate study techniques while delivering integrated content.Item Intrahepatic HBV DNA as a predictor of antivirus treatment efficacy in HBeAg-positive chronic hepatitis B patients(Baishideng Publishing Group, 2007-05-28) Lu, Hai-Ying; Zhuang, Li-Wei; Yu, Yan-Yan; Ivan, Hadad; Si, Chong-Wen; Zeng, Zheng; Li, Jun; Hou, Dong-Ming; Chen, Xin-Yue; Han, Zhong-Hou; Chen, Yong; Department of Medicine, IU School of MedicineAIM: To evaluate the effect of antiviral agents on intrahepatic HBV DNA in HBeAg-positive chronic hepatitis B patients. METHODS: Seventy-one patients received treatment with lamivudine, interferon alpha (IFN-alpha 2b) or sequential therapy with lamivudine-IFN-alpha 2b for 48 wk. All subjects were followed up for 24 wk. Serum and intrahepatic HBV DNA were measured quantitatively by PCR. HBV genotypes were analyzed by PCR-RFLP. RESULTS: At the end of treatment, the intrahepatic HBV DNA level in 71 patients decreased from a mean of (6.1 +/- 1.0) log10 to (4.9 +/- 1.4) log10. Further, a larger decrease was seen in the intrahepatic HBV DNA level in patients with HBeAg seroconversion. Intrahepatic HBV DNA level (before and after treatment) was not significantly affected by the patients' HBV genotype, or by the probability of virological flare after treatment. CONCLUSION: Intrahepatic HBV DNA can be effectively lowered by antiviral agents and is a significant marker for monitoring antivirus treatment. Low intrahepatic HBV DNA level may achieve better efficacy of antivirus treatment.Item Label-free imaging of non-deparaffinized sections of the human kidney to determine tissue quality and signatures of disease(Wiley, 2022) Sabo, Angela R.; Winfree, Seth; Bledsoe, Sharon B.; Phillips, Carrie L.; Lingeman, James E.; Eadon, Michael T.; Williams, James C., Jr.; El-Achkar, Tarek M.; Anatomy, Cell Biology and Physiology, School of MedicineLabel-free fluorescence imaging of kidney sections can provide important morphological information, but its utility has not been tested in a histology processing workflow. We tested the feasibility of label-free imaging of paraffin-embedded sections without deparaffinization and its potential usefulness in generating actionable data. Kidney tissue specimens were obtained during percutaneous nephrolithotomy or via diagnostic needle biopsy. Unstained non-deparaffinized sections were imaged using widefield fluorescence microscopy to capture endogenous fluorescence. Some samples were also imaged with confocal microscopy and multiphoton excitation to collect second harmonic generation (SHG) signal to obtain high-quality autofluorescence images with optical sectioning. To adjudicate the label-free signal, the samples or corresponding contiguous sections were subsequently deparaffinized and stained with Lillie's allochrome. Label-free imaging allowed the recognition of various kidney structures and enabled morphological qualification for adequacy. SHG and confocal imaging yielded quantifiable high-quality images for tissue collagens and revealed specific patterns in glomeruli and various tubules. Disease specimens from patients with diabetic kidney disease and focal segmental glomerulosclerosis showed distinctive signatures compared to specimens from healthy controls with normal kidney function. Quantitative cytometry could also be performed when DAPI is added in situ before imaging. These results show that label-free imaging of non-deparaffinized sections provides useful information about tissue quality that could be beneficial to nephropathologists by maximizing the use of scarce kidney tissue. This approach also provides quantifiable features that could inform on the biology of health and disease.Item Mission SpaceX CRS-19 RRRM-1 space flight induced skin genomic plasticity via an epigenetic trigger(Elsevier, 2024-11-14) Singh, Kanhaiya; Verma, Priyanka; Srivastava, Rajneesh; Rustagi, Yashika; Kumar, Manishekhar; Verma, Sumit S.; Mohanty, Sujit; Beheshti, Afshin; Warren, Liz; Sen, Chandan K.; Surgery, School of MedicineGenomic plasticity helps adapt to extreme environmental conditions. We tested the hypothesis that exposure to space environment (ESE) impacts the epigenome inducing genomic plasticity. Murine skin samples from the Rodent Research Reference Mission-1 were procured from the International Space Station (ISS) National Laboratory. Targeted RNA sequencing to test differential gene expression between the skin of ESE versus ground controls revealed upregulation of VEGF-mediated angiogenesis pathways secondary to promoter hypomethylation in responders. Methylome sequencing identified ESE-sensitive hypomethylated genes including developmental angiogenic genes Araf, Vegfb, and Vegfr1. Based on differentially expressed genes, the angiogenesis biofunction was enriched in responders. The induction of genomic plasticity in response to ESE, as reported herein, may be viewed as a mark of biological resilience that is evident in a minority of organisms, responders but not in non-responders, exposed to the same stressor. Inducible genomic plasticity may be implicated in natural resilience to ESE.Item Molecular signatures of inherited and acquired sporadic late onset nemaline myopathies(BMC, 2023-01-26) Nicolau, Stefan; Dasgupta, Aneesha; Dasari, Surendra; Charlesworth, M. Cristine; Johnson, Kenneth L.; Pandey, Akhilesh; Doles, Jason D.; Milone, Margherita; Anatomy, Cell Biology and Physiology, School of MedicineAcquired sporadic late onset nemaline myopathy (SLONM) and inherited nemaline myopathy (iNM) both feature accumulation of nemaline rods in muscle fibers. Unlike iNM, SLONM is amenable to therapy. The distinction between these disorders is therefore crucial when the diagnosis remains ambiguous after initial investigations. We sought to identify biomarkers facilitating this distinction and to investigate the pathophysiology of nemaline rod formation in these different disorders. Twenty-two muscle samples from patients affected by SLONM or iNM underwent quantitative histological analysis, laser capture microdissection for proteomic analysis of nemaline rod areas and rod-free areas, and transcriptomic analysis. In all iNM samples, nemaline rods were found in subsarcolemmal or central aggregates, whereas they were diffusely distributed within muscle fibers in most SLONM samples. In SLONM, muscle fibers harboring nemaline rods were smaller than those without rods. Necrotic fibers, increased endomysial connective tissue, and atrophic fibers filled with nemaline rods were more common in SLONM. Proteomic analysis detected differentially expressed proteins between nemaline rod areas and rod-free areas, as well as between SLONM and iNM. These differentially expressed proteins implicated immune, structural, metabolic, and cellular processes in disease pathophysiology. Notably, immunoglobulin overexpression with accumulation in nemaline rod areas was detected in SLONM. Transcriptomic analysis corroborated proteomic findings and further revealed substantial gene expression differences between SLONM and iNM. Overall, we identified unique pathological and molecular signatures associated with SLONM and iNM, suggesting distinct underlying pathophysiological mechanisms. These findings represent a step towards enhanced diagnostic tools and towards development of treatments for SLONM.