Outcome of lung transplantation in patients with pulmonary alveolar microlithiasis in the era of COVID-19 infection.

Lung transplant recipients are at higher risk of developing COVID-19 infection compared to other solid organ transplants. The risk further increases in the unvaccinated patients. We present a case of a 43-year-old male who underwent bilateral sequential lung transplantation for pulmonary alveolar microlithiasis (PAM) and had an uneventful recovery. However, two years post-transplantation, the patient developed chronic lung allograft dysfunction (CLAD) with bronchiolitis obliterans syndrome and two episodes of COVID-19 infection. During the second episode of COVID-19 infection, the patient developed sepsis and multi-organ dysfunction ultimately resulting in death. Our case report highlights the increased susceptibility of PAM patients' post-lung transplant to COVID-19 infection. Continuous follow-up of PAM patients' post-lung transplantation is necessary to prevent unfavorable outcomes.

Identification of Glandular (Acinar)/Tubule Formation in Invasive Carcinoma of the Breast: A Study to Determine Concordance Using the World Health Organization Definition.

CONTEXT.­: The Nottingham Grading System (NGS) developed by Elston and Ellis is used to grade invasive breast cancer (IBC). Glandular (acinar)/tubule formation is a component of NGS. OBJECTIVE.­: To investigate the ability of pathologists to identify individual structures that should be classified as glandular (acinar)/tubule formation. DESIGN.­: A total of 58 hematoxylin-eosin photographic images of IBC with 1 structure circled were classified as tubules (41 cases) or nontubules (17 cases) by Professor Ellis. Images were sent as a PowerPoint (Microsoft) file to breast pathologists, who were provided with the World Health Organization definition of a tubule and asked to determine if a circled structure represented a tubule. RESULTS.­: Among 35 pathologists, the κ statistic for assessing agreement in evaluating the 58 images was 0.324 (95% CI, 0.314-0.335). The median concordance rate between a participating pathologist and Professor Ellis was 94.1% for evaluating 17 nontubule cases and 53.7% for 41 tubule cases. A total of 41% of the tubule cases were classified correctly by less than 50% of pathologists. Structures classified as tubules by Professor Ellis but often not recognized as tubules by pathologists included glands with complex architecture, mucinous carcinoma, and the "inverted tubule" pattern of micropapillary carcinoma. A total of 80% of participants reported that they did not have clarity on what represented a tubule. CONCLUSIONS.­: We identified structures that should be included as tubules but that were not readily identified by pathologists. Greater concordance for identification of tubules might be obtained by providing more detailed images and descriptions of the types of structures included as tubules.

Cytologic-Histologic Correlation Practices for Nongynecologic Cytology Specimens: A Survey by the College of American Pathologists Cytopathology Committee.

CONTEXT.­: Cytologic-histologic correlation (CHC) is a Clinical Laboratory Improvement Amendments-mandated requirement for gynecologic cytology, but no similar requirement exists for nongynecologic cytology. This study presents the findings from a College of American Pathologists' survey of nongynecologic cytology practice patterns. OBJECTIVE.­: To survey the current CHC practices for nongynecologic cytology. DESIGN.­: Data were analyzed from a survey developed by the committee and distributed to participants in the Nongynecologic Cytopathology Education Program mailing. RESULTS.­: Adoption of CHC for nongynecologic cytology cases is worldwide, with 88.5% of institutions performing CHC on these specimens, a substantial increase from previous years. Performance of CHC varied by institution type, with clinic or regional/local independent laboratories and national/corporate laboratories performing CHC significantly less frequently than hospitals, university hospitals/academic medical centers, and Veterans Administration/Department of Defense hospital institutions. Most CHC was performed concurrently in real time, when the corresponding surgical specimen was reviewed. Selection for real-time concurrent CHC was by the interpreting pathologist, the pathologist diagnosing the surgical biopsy sample or cytopathology case, or both. Sampling was by far the most common reason for discordance. A 2-step difference was the most frequent threshold for discordance between cytology and surgical specimens, but this criterion varied among institutions, with no majority definition. The positive predictive value of a positive cytology finding was calculated rarely in North American institutions but was calculated more frequently in international institutions. CONCLUSIONS.­: CHC practices for nongynecologic cytopathology mirror those found for CHC of gynecologic cytopathology.

Molecular analysis with pancreaseq® in evaluation and management of pancreatic cysts: A cohort of 28 patients.

Objectives: Herein, we present the PancreaSeq® results of 28 patients and emphasize the usefulness of molecular testing in evaluation of pancreatic cysts. Material and Methods: A total of 10 (35.7%) non-diagnostic, 6 (21.4%) negative, 5 (17.8%) atypical, and 7 (25%) were positive for mucinous cystic neoplasm (MCN) pancreatic cyst aspirates were analyzed with PancreaSeq® at Mayo Clinic, Jacksonville between September 2021 and February 2023. Results: Three non-diagnostic, two negative, three atypical, and two positive for MCN cysts were positive for KRAS and GNAS mutations. They were interpreted as intraductal papillary mucinous neoplasm (IPMN) with low risk for progression to high-grade dysplasia/adenocarcinoma. One negative case was positive for KRAS and GNAS mutation and RNF43 copy number alteration. It was interpreted as IPMN with a low risk of progression. Two non-diagnostic, one negative, and two positive for MCN cysts were positive for KRAS mutation. All were interpreted as IPMN/MCNs with low risk of progression. One positive for MCN case was positive for GNAS mutation and ALK fusion and one positive for MCN case was positive for GNAS mutation, ALK fusion, and RNF43 copy number alteration. Both were interpreted as IPMN and their risk of progression was interpreted as not well understood. One atypical case was positive for KRAS and TP53 mutation and was interpreted as IPMN/ MCNs with a high risk of progression. VHL mutation was present in one non-diagnostic case. It was interpreted as serous cystadenoma and the risk for progression was low. Conclusion: Molecular analysis of pancreatic cysts with PancreaSeq® is useful in accurate diagnosis, especially when cytologic material is non-diagnostic and helps improve patient management.

Artificial Intelligence Advances in Transplant Pathology.

Transplant pathology plays a critical role in ensuring that transplanted organs function properly and the immune systems of the recipients do not reject them. To improve outcomes for transplant recipients, accurate diagnosis and timely treatment are essential. Recent advances in artificial intelligence (AI)-empowered digital pathology could help monitor allograft rejection and weaning of immunosuppressive drugs. To explore the role of AI in transplant pathology, we conducted a systematic search of electronic databases from January 2010 to April 2023. The PRISMA checklist was used as a guide for screening article titles, abstracts, and full texts, and we selected articles that met our inclusion criteria. Through this search, we identified 68 articles from multiple databases. After careful screening, only 14 articles were included based on title and abstract. Our review focuses on the AI approaches applied to four transplant organs: heart, lungs, liver, and kidneys. Specifically, we found that several deep learning-based AI models have been developed to analyze digital pathology slides of biopsy specimens from transplant organs. The use of AI models could improve clinicians' decision-making capabilities and reduce diagnostic variability. In conclusion, our review highlights the advancements and limitations of AI in transplant pathology. We believe that these AI technologies have the potential to significantly improve transplant outcomes and pave the way for future advancements in this field.

Evaluating Low HER2 Status in Invasive Breast Carcinoma via HER2 Immunohistochemistry, with HER2 FISH Correlation: A Cohort of 112 Patients.

Introduction: Recent trials demonstrated clinically significant benefits in HER2-nonamplified breast cancer with HER2-low expression using novel anti-HER2 antibody-drug conjugates. Thus, HER2-low breast cancer was proposed as a separate diagnostic entity. Herein, we reclassify HER2-negative cancers according to the new HER2-low category using a modified system and further investigate HER2-very-low expression. Methods: 114 HER2 immunohistochemistry (IHC)-negative invasive breast tumors were identified from the pathology database of Mayo Clinic, Jacksonville, FL, between January 2019 and August 2022. Two blinded breast pathologists (BP) independently rescored HER2 IHC slides at 200x and 400x magnification. Discordant cases between the two BPs were rescored together. The most recent 2018 ASCO/CAP HER2 scoring criteria were used. HER2 (0) was subdivided into HER2 (absent) and HER2 (very low). HER2 FISH testing was performed in all cases. Results: The cohort comprised of 38 (33.3%) HER2 (0) and 76 (66.7%) HER2 (1+) tumors. The first round of rescoring at 200x and 400x magnification resulted in 17 (14.9%) HER2 (absent), 31 (27.2%) HER2 (very low), and 64 (56.2%) HER2 (1+) and 2 (1.8%) HER2 (2+) tumors by BP1 and 20 (17.5%) HER2 (absent), 33 (28.9%) HER2 (very low), and 61 (53.5%) HER2 (1+) tumors by BP2. The combined final rescoring by BP1 and BP2 was as follows: 15 (13.2%) HER2 (absent), 35 (30.7%) HER2 (very low), 63 (55.3%) HER2 (1+), and 1 (0.9%) HER2 (2+) cases. A comparison of the first round of rescoring between two BPs showed substantial agreement with Cohen's kappa value of 0.67. Both comparisons of first rescoring by BP1 and by BP2 to combined final rescoring showed almost perfect agreement with Cohen's kappa value of 0.83.Follow-up FISH studies showed one amplified tumor. Conclusion: Our data support the need for finer granularity, classification, and understanding of HER2-low breast cancers. We also show that reproducibility between trained BP can be obtained, albeit with scoring at high power and low threshold for showing challenging interpretations.

First Report of Management of Sequential Small Cell Transformation and ALK I1171T Mutation as Resistance Mechanisms in a Patient With ALK-EML4 Fused Non-Small Cell Lung Adenocarcinoma With a Novel Combination of Temozolomide and Lorlatinib: A Case Report.

ALK-EML4 fusion-positive lung adenocarcinomas (LUADs) are effectively treated with ALK tyrosine kinase inhibitors, but most patients eventually develop resistance to these drugs owing to ALK-dependent or independent mechanisms. Endothelial to mesenchymal transformation with SCLC development is an ALK-independent mechanism of resistance that has not been previously reported with sequential ALK I1171T mutation while the patient is on treatment for the SCLC. Here, we report the first case of sequential SCLC transformation followed by ALK I1171T mutation in a patient with ALK-EML4 fusion-positive LUAD. After progression on multiple lines of therapy, we describe our experience of managing ALK-mutant LUAD and transformed SCLC with a novel combination of lorlatinib and temozolomide. We also briefly summarize cases of endothelial to mesenchymal transformation ALK-mutant LUAD from the literature.

Classification of fungal genera from microscopic images using artificial intelligence.

Microscopic image examination is fundamental to clinical microbiology and often used as the first step to diagnose fungal infections. In this study, we present classification of pathogenic fungi from microscopic images using deep convolutional neural networks (CNN). We trained well-known CNN architectures such as DenseNet, Inception ResNet, InceptionV3, Xception, ResNet50, VGG16, and VGG19 to identify fungal species, and compared their performances. We collected 1079 images of 89 fungi genera and split our data into training, validation, and test datasets by 7:1:2 ratio. The DenseNet CNN model provided the best performance among other CNN architectures with overall accuracy of 65.35% for top 1 prediction and 75.19% accuracy for top 3 predictions for classification of 89 genera. The performance is further improved (>80%) after excluding rare genera with low sample occurrence and applying data augmentation techniques. For some particular fungal genera, we obtained 100% prediction accuracy. In summary, we present a deep learning approach that shows promising results in prediction of filamentous fungi identification from culture, which could be used to enhance diagnostic accuracy and decrease turnaround time to identification.

Two unique cases of metastatic malignant melanoma of the gastrointestinal tract.

INTRODUCTION AND IMPORTANCE: Gastrointestinal tract (GIT) is a common site for malignant melanoma metastasis, with small bowel being the most common. It is usually difficult to diagnose at an early stage because of the anatomical location of the disease. It is also challenging for pathologists to diagnose due to the small amount of biopsy samples. Survival rates of melanoma patients with distant metastasis are very poor. CASE PRESENTATION: This study presents two males, aged 67 and 69 years old, who have metastatic melanoma within the GIT. One was metastasis to the esophagus and another with metastasis to the jejunum presenting as intraluminal masses. Their clinical history and pathologic features of the metastasis are evaluated to give an insight into this disease. CLINICAL DISCUSSION: Gastrointestinal melanoma is hard to detect due to its anatomical location and limited ability to biopsy. Typically, they present at an advanced stage when diagnosed. Approximately 60 % of patients with cutaneous melanoma will have GIT metastasis at the time of autopsy. The small bowel was found to have an affinity for malignant melanoma due to the expression of the CCR9 ligand, CCL25. BRAF mutations are much less observed in GIT mucosal melanomas as compared to cutaneous melanomas. Furthermore, AKAP13-NTRK3 fusion has been reported specifically in the GIT mucosal melanomas. NTRK fusions in general can be observed in metastatic melanomas and have been reported in GIT metastatic melanomas. CONCLUSION: GIT malignant melanomas are difficult to detect due to their anatomical location, with poor prognosis, and have a unique genetic profile.

Metastatic Thyroid Carcinoma to the Kidneys Presenting Initially as Bilateral Renal Masses: A Rare Case Report and Literature Review.

Thyroid cancers exist in multiple forms. Papillary and follicular carcinomas of the thyroid are often referred to as well-differentiated thyroid cancers. Well-differentiated thyroid cancers rarely present as a distant metastatic cancer on initial diagnosis. Papillary thyroid cancer tends to have a good prognosis; however, if distant metastasis of PTC is present, there is usually a poor clinical outcome with a less favorable prognosis. In this study, we report a 90-year-old female who presented with right-sided abdominal discomfort. A renal ultrasound revealed bilateral upper pole renal masses. A percutaneous biopsy was ordered, and the microscopic examination revealed bilateral renal metastasis with a follicular variant of papillary thyroid carcinoma. The patient underwent thyroidectomy and sustained radiation therapy for her bilateral renal metastases. She died 6 years after her initial diagnosis, due to sepsis. This is the second study in literature to report bilateral renal metastasis of follicular variant of papillary thyroid cancer.

A rare case of BK virus non-hemorrhagic cystitis following lung transplant.

BK virus cystitis is known to occur following hematopoietic stem cell transplant (HSCT), but few cases exist in the literature following lung transplant. Because of the rarity of this presentation, patients may have missed diagnoses and prescribed ineffective treatments. We present our case of an atypical presentation of BK virus cystitis appearing as bladder carcinoma in situ in a lung transplant patient.

Use of Self-Collected Saliva Samples for the Detection of SARS-CoV-2.

OBJECTIVE: Using a US Food and Drug Administration (FDA) emergency use authorization (EUA) reverse transcription polymerase chain reaction (RT-PCR) method, we examined the analytic performance accuracy of saliva specimens as compared to nasopharyngeal (NP) specimens in symptomatic patients. Correlation between test results and symptoms was also evaluated. METHODS: Over a 5-week period in 2020, 89 matched saliva and nasopharyngeal swabs were collected from individuals exhibiting symptoms consistent with SARS-CoV-2. Specimens were tested with an FDA EUA-approved RT-PCR method, and performance characteristics were compared. RESULTS: The concordance rate between saliva and nasopharyngeal testing was 93.26%. The mean cycle threshold value of saliva when compared to the NP specimen was 3.56 cycles higher. As compared to NP swab, saliva testing demonstrates acceptable agreement but lower sensitivity. CONCLUSION: When compared to a reference method using NP swabs, the use of saliva testing proved to be a reliable method. Self-collected saliva testing for SARS-CoV-2 allows for a viable option when trained staff or collection materials are in short supply.

Performance Accuracy of a Laboratory-Developed Real-Time RT-PCR Method for Detection of SARS-CoV-2 in Self-Collected Saliva Specimens.

OBJECTIVE: The ongoing COVID-19 pandemic caused by SARS-CoV-2 has challenged diagnostic laboratories to re-examine traditional methods for collecting specimens and sample types used in molecular testing. Our goal was to demonstrate that saliva can be used for detecting SARS-CoV-2 and correlates well with established molecular methods using nasopharyngeal (NP) swabs. METHODS: We examined use of a saliva collection device in conjunction with a laboratory-developed real-time reverse transcription-polymerase chain reaction (LDPCR) method for detecting SARS-CoV-2 in a symptomatic population and compared results with 2 US Food and Drug Administration (FDA)-approved methods (emergency use authorization [EUA]) that use specimens from NP swabs. RESULTS: The sensitivity of LDPCR compared with the reference methods was 75.0% (21/28); specificity, 98.1% (104/106). When cycle threshold values were compared between paired specimens using the LDPCR and a EUA reverse transcription PCR method, both targeting the open-reading frame gene, the mean value for saliva was 4.66 cycles higher than for NP specimens. CONCLUSION: Use of self-collected saliva in conjunction with an LDPCR for SARS-CoV-2 compared favorably with 2 FDA EUA methods using NP swabs. The use of an alternative sample type and assay method will aid in expanding the availability of testing during the ongoing COVID-19 pandemic.

Fat Necrosis Mimicking Renal Cell Carcinoma Recurrence Following Cryotherapy, Partial Nephrectomy, and Nephrectomy.

OBJECTIVE: To present our experience with three patients surgically treated for suspected recurrent renal cell carcinoma whose final pathology was consistent with tumefactive fat necrosis. METHODS: Three patients underwent definitive therapy for biopsy proven renal cell carcinoma (cryoablation, partial nephrectomy, and nephrectomy) and later demonstrated evidence of recurrent renal cell carcinoma on follow up imaging. All three patients underwent surgical resection of the suspected recurrences with final pathology consistent with tumefactive fat necrosis. RESULTS: The three patients were 60, 74, and 39-years old, respectively. The previous definitive therapies for renal cell carcinoma were percutaneous ablation, RAPN, and nephrectomy. Each patient had previous surgical pathology that confirmed prior renal cell carcinoma. Signs of recurrence on diagnostic imaging occurred 2 years, 23 months, and 8 months post-definitive therapy. CONCLUSION: In patients with a history of renal cell carcinoma, consideration of fat necrosis should be taken into account upon seeing imaging concerning for tumor recurrence. Continued analysis of cases with such a diagnosis will be beneficial in recognizing this possibility to avoid unnecessary surgery or therapy when possible.

Prevalence of SARS-CoV-2 Antibodies in a Multistate Academic Medical Center.

OBJECTIVE: To estimate the seroprevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies in health care personnel. METHODS: The Mayo Clinic Serology Screening Program was created to provide a voluntary, two-stage testing program for SARS-CoV-2 antibodies to health care personnel. The first stage used a dried blood spot screening test initiated on June 15, 2020. Those participants identified as reactive were advised to have confirmatory testing via a venipuncture. Venipuncture results through August 8, 2020, were considered. Consent and authorization for testing was required to participate in the screening program. This report, which was conducted under an institutional review board-approved protocol, only includes employees who have further authorized their records for use in research. RESULTS: A total of 81,113 health care personnel were eligible for the program, and of these 29,606 participated in the screening program. A total of 4284 (14.5%) of the dried blood spot test results were "reactive" and warranted confirmatory testing. Confirmatory testing was completed on 4094 (95.6%) of the screen reactive with an overall seroprevalence rate of 0.60% (95% CI, 0.52% to 0.69%). Significant variation in seroprevalence was observed by region of the country and age group. CONCLUSION: The seroprevalence for SARS-CoV-2 antibodies through August 8, 2020, was found to be lower than previously reported in other health care organizations. There was an observation that seroprevalence may be associated with community disease burden.

Addressing the Challenge of COVID-19: One Health Care Site's Leadership Response to the Pandemic.

The coronavirus disease 2019 (COVID-19) pandemic created an extremely disruptive challenge for health care leaders that required a rapid, dynamic, and innovative response. The purpose of this manuscript is to share the leadership actions and decisions at Mayo Clinic in Florida during the first 6 months of the pandemic (February to July 2020). We note 4 strategies that contributed to an effective response: (1) leverage experience with disaster preparedness and mobilize regional and national networks; (2) use surge models to anticipate and to address supply chain issues as well as practical and financial effects of the pandemic; (3) adapt creatively to establish new safety and procedural protocols in various areas for various populations; and (4) communicate timely information effectively and be the common source of truth. Mayo Clinic in Florida was able to address the surges of patients with COVID-19, to provide ongoing tertiary care, and to restore function within the first 6 months with new, strengthened practices and protocols.

PLEKHA7, an Apical Adherens Junction Protein, Suppresses Inflammatory Breast Cancer in the Context of High E-Cadherin and p120-Catenin Expression.

Inflammatory breast cancer is a highly aggressive form of breast cancer that forms clusters of tumor emboli in dermal lymphatics and readily metastasizes. These cancers express high levels of E-cadherin, the major mediator of adherens junctions, which enhances formation of tumor emboli. Previous studies suggest that E-cadherin promotes cancer when the balance between apical and basolateral cadherin complexes is disrupted. Here, we used immunohistochemistry of inflammatory breast cancer patient samples and analysis of cell lines to determine the expression of PLEKHA7, an apical adherens junction protein. We used viral transduction to re-express PLEKHA7 in inflammatory breast cancer cells and examined their aggressiveness in 2D and 3D cultures and in vivo. We determined that PLEKHA7 was deregulated in inflammatory breast cancer, demonstrating improper localization or lost expression in most patient samples and very low expression in cell lines. Re-expressing PLEKHA7 suppressed proliferation, anchorage independent growth, spheroid viability, and tumor growth in vivo. The data indicate that PLEKHA7 is frequently deregulated and acts to suppress inflammatory breast cancer. The data also promote the need for future inquiry into the imbalance between apical and basolateral cadherin complexes as driving forces in inflammatory breast cancer.

Oncotype DX and Prosigna in breast cancer patients: A comparison study.

BACKGROUND: Oncotype Dx® (ODX) is the most used prognostic and predictive assay for ER + breast cancer (BCa) and is categorized into low (< 18), intermediate (18 to 30), or high (≥31) risk of recurrence. Prosigna® is a prognostic signature to estimate distant recurrence-free survival for stage I/II, ER+ cancer in postmenopausal women treated with adjuvant therapy. The goal of the study is to assess the agreement between ODX and Prosigna®. MATERIALS AND METHODS: 100 previously ODX classified peri and postmenopausal, early-stage (I or II) BCa patients were retrieved and Prosigna assay was performed on archived tumor blocks on a NanoString nCounter® DX Analysis System. RESULTS: ODX assay was assigned as follows: 57% low, 39% intermediate, and 4% high. There were 8% two-step disagreements (high to low or vice versa) between ODX and Prosigna®; and 42% one-step disagreement (low to intermediate or vice versa). 78% were classified by Prosigna as luminal A and 22% as luminal B. The majority of luminal A cases (67/78; 85.9%) had low ROR score whereas ODX classified almost two-thirds (50/78~ 64%) as low RS. An insignificant percentage of luminal B cases (1/22 - 4.5%) were classified as high RS by ODX, and a modest percentage were classified as high ROR by Prosigna (15/22 ~68%). According to our follow up results, recurrence was detected in three cases. In all three cases; Prosigna was a better indicator of recurrence. CONCLUSIONS: The agreement between ODX and Prosigna® is low, and this has management implications, especially when chemotherapy is needed.

Utility of p16 and HPV testing in oropharyngeal squamous cell carcinoma: An institutional review.

In the US, 60% to 80% of oropharyngeal squamous cell carcinomas (OPSCCs) are associated with human papillomavirus (HPV). However, until recently, no consensus existed about when and how to test for HPV in patients with head and neck cancers. We aimed to evaluate the use of p16 and HPV testing at our institution because p16 immunohistochemistry is reportedly a reliable surrogate marker for HPV detection in OPSCCs. METHODS: We identified all cases at our institution of primary or metastatic squamous cell carcinoma (SCC) of the head and neck with a concurrent p16 immunostain analysis from January 1, 2013, through August 31, 2018. Patient demographic data, tumor characteristics, p16 result, and any HPV result (in situ hybridization and E6 and E7 RNA test) were captured. RESULTS: We identified 104 patients. Most primary tumors (53/57 [93.0%]) and metastases (40/47 [85.1%]) were positive for p16. Thirty-seven cases (35.6%) had reflex high-risk HPV (HR HPV) testing performed. Of the 35 p16-positive cases, 6 had discrepant HR HPV results (p16+ /HPV- ). We identified 47 p16 immunostains that were performed on lymph nodes with primary tumors of unknown origin. Most were cytology cases (34/47 [72.3%]), and most were p16 positive (40/47 [85.1%]). Neither tumor differentiation nor tumor keratinization was predictive of p16 positivity. Tumors with basaloid differentiation were universally p16 positive. CONCLUSION: p16 immunohistochemistry accurately identifies HPV-positive OPSCC. Cytology specimens have an important role in characterizing SCC of unknown origin. HR HPV testing is not routinely required, and results may be discrepant with p16 findings.