bluuebunny/crossref_metadata_2025 huggingface dataset:
Comprehensive Analysis of Complex Copy Number Variations in the Plasmodium falciparum Genome via Long-Read Sequencing: Implications for Antimalarial Resistance and Broad Genomic Insights
Authors: Luniewski A , Guler J
Published: October 2024

Introduction/Objective

The genome of Plasmodium falciparum, characterized by a high AT content and a propensity for copy number variations (CNVs), presents a model for understanding how genomes adapt to stress. Our research focused on the prevalence and distribution of CNVs highlights long-read sequencing as a tool for detecting complex structural variants in other models.

Methods/Case Report

P. falciparum parasites were cultured and treated with DSM1 and aphidicolin that induce replication stress. Long-read sequencing was conducted using the Oxford Nanopore Technology Minion, with an emphasis on an optimizing DNA extraction method for preserving intact chromosomes. Visualization of CNVs, including tandem and inverted duplications, was achieved through a custom R Shiny application that allowed both quantitative and qualitative assessments.

Results (if a Case Study enter NA)

Long read sequencing identified an enrichment of multiple CNV types in treated samples, with a significant enrichment of inverted duplications as well as other types of structural variants. Aphidicolin and DSM1-treated samples demonstrated significant accumulation of these variations compared to controls (2.0 and 5.6-fold, respectively with a p value of < 0.0001 in both treatment groups). These occurred mainly in core genomic regions that do not contain variable gene copies. An increase in the number of inverted duplications may be related to stress response to the treatment and may be a potential adaptive mechanism of the parasite. Our manual single-read visualization technique made it possible to visualize the structure of various CNV types, which provides unique insight on CNVs as they arise in single genomes.

Conclusion

We hypothesize that inverted duplications represent stalled replication forks, and we are currently assessing their frequency in replicating and non-replicating cells. This study highlights the role of long-read sequencing in detecting complex genomic structures in P. falciparum, which may influence the parasite’s resistance to drug treatment. These findings not only advance our understanding of malaria pathology but also aid our comprehension of how cancer cells might react to drug-induced stress and the mechanisms behind CNV formation in neoplastic cells.
Clinical Validation and Comparison of Bacterial Vaginosis Detection
Authors: Figueroa C I , Moore N , Flaws M
Published: October 2024

Introduction/Objective

Bacterial vaginosis (BV) is considered a top reason for women’s gynecological visits, causing symptoms such as vaginal discharge, foul odor, itching, and burning associated with the alteration of the normal vaginal microbiome. It is often presented as a decrease in Lactobacillus spp. and an increase in anaerobic organisms such as Gardnerella vaginalis and Atopobium vaginae. In response to the demand for more automated and less subjective testing, molecular methods have recently been developed to aid in BV testing. The objectives of this study are to validate and compare the molecular Aptima® Bacterial Vaginosis Assay by Hologic® to the established BV Screen via a Gram stained vaginal smear graded through Nugent scoring at RUSH University Medical Center in Chicago, IL and perform a cost analysis between the testing methods.

Methods/Case Report

Samples of known BV value were tested on the Panther® instrument to validate the Aptima® Bacterial Vaginosis Assay for accuracy and precision. Clinical samples of vaginal swabs were used to make a Gram stained BV screen for Nugent scoring, then afterwards were placed into Hologic Multitest Aptima® probes for molecular testing on the Panther® instrument. Nugent scoring was performed blind by the molecular test. Molecular results of negative, positive, and invalid were then compared to the Nugent scores: scores of 0-3 for negative/normal vaginal flora, 7-10 for positive BV, and 4-6 for intermediate/altered scores were screened for discrepancy.

Results (if a Case Study enter NA)

The Aptima® BV Assay tested 52 known samples with 97% accuracy and 100% precision. A total of 80 clinical samples of vaginal swabs used for Gram stained BV screens were run on the Aptima® BV Assay; 61 provided conclusive data for comparative analysis. When compared to the original Nugent scores, the positive percent agreement (PPA) was 77.0% and negative percent agreement (NPA) was 92.9%.

Conclusion

The Aptima® BV Assay proved to be both accurate and precise in its validation testing. Clinically, it was able to screen for BV in vaginal samples with a good percent agreement to Gram stained BV screens. Further testing of additional clinical samples are to be done to continue analysis. Although the supplies needed to perform a Gram stain cost less than molecular testing, the reimbursement payment for molecular testing is much greater and overall reduces employee time costs for performing the test, making it the more cost effective choice for the laboratory.
Lack of Diagnostic Value from Fungal and Mycobacterial Cultures in Cases of Suspected Prosthetic Joint Infection
Authors: Nava A , Graf E , Burnett K
Published: October 2024

Introduction/Objective

Infections of prosthetic joints cause significant morbidity and often result in removal of the infected joint. In many cases, an infectious etiology can be difficult to definitively identify. As a result, providers suspecting prosthetic joint infections (PJI) often place large order sets of microbiology tests, including fungal and mycobacterial cultures. Fungal and mycobacterial cultures are labor-intensive for the laboratory taking up to 28 days and 42 days, respectively, to complete. As a potential area for a diagnostic stewardship intervention, we wanted to evaluate how often a fungal or mycobacterial culture produced actionable information in cases of suspected PJI.

Methods/Case Report

Data reports were retrieved from both the Electronic Health Record (EHR) and the Laboratory Information System (LIS) from May 2022 to May 2023. As sources submitted by the provider often do not specify that the joint is prosthetic, data from LIS was evaluated to identify microbiology culture test sets ordered on joint sources, while data from EHR was examined to isolate patients with implanted joints. Using Microsoft Excel, data from both systems was compared in order to match microbiology culture test sets to the known implanted joints. LIS data from implanted joint sources was assessed to record negative (no growth) and positive (growth) cultures, and to register all organisms isolated.

Results (if a Case Study enter NA)

Of 794 order sets for cultures collected from prosthetic joint sources, 430 included requests for fungal culture and 79 included requests for mycobacterial culture. Of these 79 requests for mycobacterial culture, 0 organisms were isolated (0%). Of these 430 requests for fungal culture, 7 grew yeast (1.6%) and 7 out of 7 (100%) of these yeasts were also isolated on general (aerobic bacterial) culture. No molds were isolated.

Conclusion

Discontinuing the routine practice of ordering fungal and mycobacterial culture for prosthetic joint sources would have no negative impact on patient care but would reduce unnecessary work in the microbiology laboratory and potentially avoid additional costs to the patient. Education to the orthopedic provider group as well as best practice alerts in the EHR will be pursued, based on the findings from this study, in order to reduce unnecessary culture orders.
Increasing Burden of Antibiotic Resistance in Children Suffering from Septicemia in Tertiary Care Hospitals
Authors: Khan H , Mazhar K , Ullah R , Sajjad Naqvi S , Noorul Hasan T
Published: October 2024

Introduction/Objective

Invasion of the bloodstream by microorganisms constitutes one of the most serious situations in infectious disease. Children are the most susceptible groups to contract diseases specifically Blood Stream Infections (BSIs). BSIs have been considered to be the main cause of morbidity and mortality in children. It is associated with a high mortality rate of 20%–50%. The emerging causative agents and resistance to various antimicrobial agents are increasing from time to time.

Methods/Case Report

The present study was carried out to confirm the causative agents and their antibacterial susceptibility pattern in children with septicemia at Tertiary Care Hospitals, Peshawar, KP, Pakistan. This cross- sectional study involved about 873 pediatric patients (≤ 13 years). BACTEC BD 9050 system was used to identify the causative organism, and sub-cultures were done on MacConkey Agar and Blood Agar. The antibiotic susceptibility test was done using the Kirby Bauer Disk diffusion method as per CLSI guidelines.

Results (if a Case Study enter NA)

Among 873 study subjects 568 (65.06 %) were males followed by 305 (34.93 %) females. Out of the 873 tested blood samples, blood cultures were positive in 83 (9.51%) followed by 122 (13.98%) skin contaminants, and no growth was observed in 668 (76.51%) cases. The majority 43 (51.80 %) of them were neonates (≤ 28 days). Gram-positive and Gram-negative bacteria constituted 58 (69.87%) and 25 (30.13%), respectively. The most frequent pathogen found was Staphylococcus aureus 54 (65.06 %), followed by Klebsiella spp., E. coli, and Pseudomonas aeruginosa 6 (7.22 %), Salmonella spp. 5 (6.02 %) Enterococcus faecalis 3 (3.61 %), Acinetobacter baumannii 2 (2.40 %) and Staphylococcus epidermidis 1 (1.20 %). In Staphylococcus aureus about 6 (11.11) were MRSA. The majority of bacterial isolates showed high resistance to Ciprofloxacin, Ceftazidime, Cefuroxime, Co-trimoxazole, Cefepime, Cefotaxime, Minocycline, Tobramycin, Cefoxitin and Cephradine that are commonly used in the study area.

Conclusion

The majority of the isolates were multidrug resistant. These higher percentages of multi-drug resistant emerged isolates urge us to take infection prevention measures and to conduct other large studies for appropriate empiric antibiotic choice.
Case Series: Emerging Pathogens Aerococcus urinae and Aerococcus sanguinicola at a Canadian tertiary care hospital
Authors: Tariq J , Kakodkar P , Scott J , LU L , Wu F , Mehta N , Hamula C
Published: October 2024

Introduction/Objective

Background: Aerococcus urinae and sanguinicola are emerging opportunistic pathogen linked with urinary tract infections. Unmanaged Aerococcus infections have the propensity to precipitated into urosepsis. The ongoing gestalt of managing these infections needs standardization. We reviewed A. urinae and sanguinicola isolates from our clinical microbiology laboratory to better characterize its spectrum of clinical presentation, sources of infection, microbiological characteristics, and antimicrobial management.

Methods/Case Report

Methods: The electronic microbiology database was utilized to review the retrospective clinical data of patients that grew positive cultures for Aerococcus urinae and sanguinicola on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) in Saskatchewan from January to July 2023.

Demographic variables, site of presentation, microbiological parameters surrounding culture and sensitivities, and antimicrobial management were recorded. The results were analyzed on SPSS 28 software.

Results (if a Case Study enter NA)

Results: This cohort (n=115) had a median age 82 years [Range: 7 to 103] with a female predilection (F:M = 78:37). A. urinae and sanguinicola were primarily involved in UTI (n=96), obstructive uropathy (n=9), and urosepsis (n=6). The hypothyroidism (26.9%, n = 31) rate in this population was 3-fold higher than the age-matched background rate for our province. Aerococcus infections were predominantly monomicrobial (73.9%, n= 85 out of 115) and showed sensitivity for ceftriaxone, penicillin G, and vancomycin. Antimicrobials were seldom used in the UTI cohort (31.2%, n=30 out of 96). Amoxicillin-clavulanate (29.8%, n=25 out 84) was the most popular choice at patient discharge in monomicrobial Aerococcus infections only.

Conclusion

Conclusion: Aerococcus urinae and sanguinicola are emerging uropathogen. Despite this, the clinical significance of these Aerococcus species remains undervalued. Our case series shows that untreated or recurrent A. urinae and A. sanguinicola infections can precipitate into urosepsis. Clinicians should utilize the antimicrobial susceptibility profiles for these Aerococcus species to provide appropriate antimicrobial coverage and manage these pathogens effectively. Further studies should explore the link between hypothyroidism and these aerococcal infections.
Molecular Characterization of Endophytic Fungal Strains for Green Synthesis of ZnO and Au Nanoparticles
Authors: Abdelmonem M , EL-Rouby M N , Hammad S E , Elshikh H H , Mostafa M A , Wasim H , Abdelmageed M , Eldaly R
Published: October 2024

Introduction/Objective

Introduction: Traditional methods for nanoparticle synthesis often involve hazardous compounds, posing environmental risks and limiting their biomedical applications due to instability. The exploration of green synthesis approaches using natural products and eco-friendly solvents presents a challenging yet imperative pursuit in nanoparticle research.

Methods/Case Report

Methods: Endophytic fungi were isolated from healthy Eucalyptus sideroxylon plants collected from the Desert Research Center. Cultivation of fungi in malt extract broth was conducted at 28°C with agitation for 96 hours. Subsequently, fungal DNA was extracted, and ITS-rDNA regions were PCR-amplified for identification. Sequencing and phylogenetic analysis were performed to characterize the fungal isolates. Fungal filtrates were utilized for the biosynthesis of ZnO and Au nanoparticles (NPs) from ZnSO4 and HAuCl4 solutions, respectively.

Results (if a Case Study enter NA)

Results: Among the 13 fungal isolates, Fusarium chlamydosporum (FI-03) exhibited the most efficient synthesis of ZnO and Au NPs. Sequencing confirmed the identity of the fungal strain. The synthesized NPs displayed uniform spherical shapes, with ZnO NPs averaging 19.3 nm and Au NPs averaging 22.1 nm in size. Transmission electron microscopy (TEM) analysis further elucidated the morphology of the NPs.

Conclusion

Conclusion: Fusarium chlamydosporum emerged as a promising candidate for the green synthesis of ZnO and Au NPs. This environmentally friendly approach offers a cost-effective and biocompatible alternative to conventional nanoparticle synthesis methods.
Novel Effects of Chlorhexidine Gluconate on Gram-Positive vs Gram-Negative Microorganisms
Authors: Patel H V
Published: October 2024

Introduction/Objective

Chlorhexidine Gluconate (CHG) is a widely used antiseptic for the skin, oral areas, and cleansing oneself for surgery. Uses of CHG throughout healthcare centers have proven to reduce potential pathogens and lessen risks of central venous catheter blood infections. Gram-positive and gram-negative microorganisms can lead to major diseases such as prostatitis, candidiasis, endocarditis, and more. It is crucial to understand the effects that CHG has on these organisms so we can accurately apply it to treat these various illnesses. It also allows us to better understand the source of surgical site infections (SSIs) and prevent them.

Methods/Case Report

A minimum bactericidal concentration (MBC) was employed to see how various CHG concentrations (0% (control), 1%, 3%, 5%, 7%, and 9%) would affect the gram-positive (C. albicans and S. aureus) and gram-negative (P. aeruginosa and E. coli) microorganisms. First, a 1.0 McFarland suspension was created for each organism. Then, the various CHG concentration wells for each microorganism would be created within 96 well plates. In each well, there was always 300 μL of solution (containing the McFarland suspension and CHG liquid formula (HibiClensTM). After 4 minutes of CHG exposure in each well, an inoculating loop was used to streak a petri dish. One trial was completed after all concentrations were done for each microoganism. Each trial was incubated for 24 hours and there were a total of 6 trials.

Results (if a Case Study enter NA)

The substantial results challenged the previously assumed hypothesis that gram- negative microorganisms are more resistant to CHG. The separation between the two types of microorganisms became evident at even the 1% CHG concentration. C. albicans and S. aureus are thriving with averages of approximately 74,333 CFU/mL and 70,333.3 CFU/mL respectively for 1% CHG in comparison to the 1% CHG concentration for P. aeruginosa (2,500 CFU/mL) and E. coli (22,334.3 CFU/mL). Additionally. P. aeruginosa and E. coli had no colonies in any of the trials at 7% and 9% CHG, while C. albicans and S. aureus were present in numerous amounts.

Conclusion

Through numerous trials using an MBC as a new method, dose response curves for E. coli, P. aeruginosa, S. aureus, and C. albicans were deduced. The curves displayed how gram-positive microorganisms are more resistant to CHG than gram-negative microorganisms, defying what was previously assumed. In regards to various diseases and infections caused by these various bacteria, CHG may now be assesed for potential forms of treatment.
Anticancer Efficacy of Biosynthesized Zinc Oxide and Gold Nanoparticles
Authors: Abdelmonem M , Hammad S E , Elshikh H H , Mostafa M A , EL-Rouby M N , Wasim H , Abdelmageed M
Published: October 2024

Introduction/Objective

Introduction: Advancements in nanoscale materials have led to the exploration of metal oxides for cancer diagnosis and therapy. Zinc oxide nanoparticles (ZnO NPs) and gold nanoparticles (Au NPs) are particularly promising due to their biocompatibility and anticancer properties demonstrated across various cancer cell lines.

Objectives

This study aimed to isolate fungal endophytes from Eucalyptus sideroxylon leaves and utilize them for the biosynthesis of nanoparticles (ZnO NPs and Au NPs) to assess their anticancer activity.

Methods/Case Report

Methods: Healthy Eucalyptus sideroxylon samples were collected from a desert research center, and endophytes were isolated and cultivated. The fungal biomass was processed to synthesize ZnO NPs and Au NPs. Cell lines were propagated for cytotoxicity experiments using the MTT assay in a 96-well plate format.

Results (if a Case Study enter NA)

Results: Biosynthesized ZnO and Au NPs exhibited anticancer activity against HCT-116 and CACO2 cell lines. The IC50 values for ZnO NPs were 5.06 μg/mL for HCT-116 and 6.07 μg/mL for CACO2, while Au NPs showed IC50 values of 5.9 μg/mL for HCT-116 and 1.1 μg/mL for CACO2. ZnO NPs demonstrated dose-dependent toxicity on HCT-116 cells, with increasing concentrations leading to a reduction in cell viability. Similarly, Au NPs exhibited dose-dependent cytotoxicity on both cell lines.

Conclusion

Conclusion: This study underscores the potential of endophytic fungi for biosynthesizing metal nanoparticles with significant anticancer effects. ZnO NPs displayed superior efficacy against colon cancer cells compared to Au NPs, indicating their potential as therapeutic agents. The findings highlight the importance of exploring natural sources for nanoparticle synthesis and their application in cancer therapy.
Synchronous endometrial and minor salivary gland carcinomas – role of molecular diagnostics amid lack of clinical suspicion
Authors: Singh P , Stewart J , Nelson A , Mogrovejo D O
Published: October 2024

Introduction/Objective

Synchronous malignancies account for 3-5% of all tumor diagnoses but can be challenging to detect if one or both tumors are rare histologic subtypes and clinical suspicion is lacking. Molecular diagnostics are critical for accurate diagnosis in these difficult cases to guide appropriate patient care.

Methods/Case Report

We report the case of a 49-year-old female who was diagnosed with a high-grade, mixed- histology endometrial adenocarcinoma a few years back. She was found to have hilar and mediastinal nodal carcinoma of uncertain differentiation a couple of months after her initial diagnosis, clinically labelled as metastatic endometrial carcinoma. Following neoadjuvant chemotherapy, her hysterectomy showed complete pathologic response, and was found to be POLE ultramutated on NGS. Follow-up PET scan in 2023 showed progression of hilar/endobronchial thickening, as well as interval increase in size of mediastinal nodes, again presumed to be endometrial metastases, despite the POLE mutant status. Repeat sampling was performed from both the sites, along with comprehensive molecular profiling. Cytology from the nodes and surgical pathology from the endobronchial lesion showed similar morphology consisting of hyperchromatic basaloid cells in cribriform arrangement with tubular structures containing myxoid stromal material, negative for PAX-8, ER, p40, and TTF1 immunostains, inconsistent with endometrial metastasis. Molecular studies including FISH and NGS showed MYB1::NFIB fusion characteristic of adenoid cystic carcinoma and absence of POLE mutation, definitively refuting the clinically suspected progression of endometrial metastasis. Molecular testing confirmed that the endobronchial tumor and mediastinal nodal involvement were caused by a second primary, distinct from her POLE-ultramutated endometrial carcinoma which disappeared with chemotherapy. Her extended molecular workup also revealed a pathogenic mutation in BRIP1, suggesting a genetic cancer predisposition syndrome requiring referral for genetic counseling.

Results (if a Case Study enter NA)

NA

Conclusion

Molecular pathology is an invaluable tool for unravelling diagnostic complexity. Pathologists must integrate cytomorphology, molecular genetics and knowledge of cancer biology to steer the clinical teams towards the best patient care.
Malignant Rhabdoid Tumor masquerading as Neuroblastoma: A rare Case-report
Authors: Rahman J , Wei E , Knowles K
Published: October 2024

Introduction/Objective

Malignant rhabdoid tumors (MRT) predominantly impact infants and young children, typically occurring around the age of 15 months. While they can emerge from soft tissues throughout the body, but commonly initiate in the kidneys. Neuroblastoma-like characteristics are seldom observed within the varied phenotypes of malignant rhabdoid tumors. Here, we present an exceptionally rare and distinctive subtype of malignant rhabdoid tumor exhibiting features akin to neuroblastoma localized within the unusal parapharyngeal space.

Methods/Case Report

A 2-month-old female presented to the ED with an enlarging right cervical neck mass. The mother reported a one-week history of upper respiratory tract symptoms and noticed an enlarging mass of her right neck. CT reported a “parapharyngeal abscess with airway compression”. The patient was started on Augmentin with no significant improvement. Repeat CT with contrast demonstrated an enlarging rim-enhancing 3 cm mass involving the right parapharyngeal space, trachea, and right carotid arteries. Laryngoscopy and incisional biopsy of right neck lymph nodes demonstrated a high-grade malignancy with prominent nucleoli, high N/C ratio and scant cytoplasm. The tumor tested positive for CD 99, synaptophysin, and neurofilament, leading to the initial diagnosis of neuroblastoma. However, molecular analysis uncovered the loss of INI-1 on 22q11.2, prompting a reevaluation and a final diagnosis of MRT with neuroblastoma-like characteristics was made.

Results (if a Case Study enter NA)

NA

Conclusion

A range of tumors displaying distinct “rhabdoid” cytological features are collectively termed as malignant rhabdoid tumors (MRTs). Conventional immunohistochemistry (IHC) staining for CD99, synaptophysin, neurofilament, and myogenin might suggest neuroblastoma, Ewing sarcoma, or rhabdomyosarcoma. However, the absence of INI-1 expression provides a definitive diagnosis. INI-1 loss, a purported tumor suppressor gene located on chromosome 22q11.2, solidifies the tumor’s classification as malignant rhabdoid tumor (MRT). Additionally, a positive neurofilament stain in MRT is crucial for diagnostic and therapeutic assessments. This differentiation is vital, given the dismal prognosis of MRT with a 5-year survival rate of less than 10%.
Bladder cancer`s genetic Tapestry: Insights from two Cases with Ataxia Telangiectasia Mutated Gene Alterations
Authors: Elsafy H , Sami F I , Lack M , Hamza A
Published: October 2024

Introduction/Objective

Ataxia-telangiectasia mutated (ATM) plays a central role in the cellular response to DNA damage and is common in several tumor types including bladder cancer. The specific impact of ATM alterations on prognosis and therapy response in bladder cancer is uncertain. However, some data suggests shorter overall survival and benefit in patients treated with immune checkpoint inhibitors. This abstract explores the clinicopathologic features of two young patients of bladder cancer, harboring the ATM gene mutation.

Methods/Case Report

The institutional database was searched for diagnosis of urothelial carcinoma from January 2020 to December 2023. Only patients under the age of 30 years were included. Two cases were identified. Data such as patient age, gender, clinical history and presentation, histologic features, and gene mutations were collected.

Results (if a Case Study enter NA)

One patient was a 21-year-old male who presented with hematuria and the other was 17-year-old female who presented for work up vaginal bleeding. Both were non-smokers and had no family history of bladder cancer. Cystoscopy showed papillary tumors in both patients and TURBT specimens showing low grade non-invasive urothelial carcinoma in both patients. Genetic testing revealed ATM mutation in both patients. The male patient had recurrent disease twice and received intravesical BCG therapy, the female patient remains without recurrence 12 months later. Both patients remain under surveillance cystoscopy every three months.

Conclusion

These cases contribute to the growing body of evidence emphasizing the need for personalized therapeutic approaches and further research to unravel the complexities of bladder cancer in the context of ATM gene mutation among young patients.
Novel Approach for Detection of BRAF and KRAS Mutations Using ARMS (amplification refractory mutation system) Primers for Colon Cancer Therapeutic Response Prediction
Authors: Moon J J
Published: October 2024

Introduction/Objective

KRAS and BRAF V600E mutations are confirmed predictive biomarkers for anti-EGFR monoclonal antibody therapy response and prognosis for colorectal cancer and often considered mutually exclusive with few exceptions (0.05% of mCRC cases). We have developed a multiplex PCR assay utilizing ARMS (amplification refractory mutation system) Primers and Probes for screening and further testing of BRAF mutation status in a 2 step process.

Methods/Case Report

The Multiplex PCR Assay or BRAF/KRAS mutation was designed as a 5 color assay. Primers and Probes consisted of Wild Type Kras and wild and mutant (V600E/V600K) type BRAF primers and probes. For specimen, Positive and negative control standards made of engineered positive control plasmids for wild type KRAS & BRAF and mutant type V600E & V600K BRAF as well as internal control of bet actin and 2 Patient samples with known BRAF V600E mutant status were run. Mutant type V600E & V600K BRAF were mixed with wild type V600 controls in different ratios as well. Results were interpreted as BRAF wild KRAS wild/ BRAF wild KRAS mutant/ BRAF V600E KRAS wild/BRAF V600K KRAS wild type and NGS was recommended in cases of concurrent BRAF and KRAS mutations.

Results (if a Case Study enter NA)

Positive/negative/internal control standards for wild type KRAS & BRAF and mutant type V600E & V600K BRAF showed expected results in both CFX 96 and ABI 7500 runs in triplicates. Graphs were able to determine separate Ct values and sigmoidal amplification plots that readily differentiated KRAS wild/BRAF wild/ BRAF V600E types. Mutant type V600E & V600K BRAF that were mixed with wild type V600 controls in different ratios all showed expected results and were able to differentiate between wild and mutant types with accuracy. Also, the 2 patient samples with known (Sanger sequencing-diagnosed) V600E mutation status showed positive Ct values for KRAs wild and V600E probes and negative CT values for V600 wild/V600K probes. No invalid runs or unexpected control results were observed.

Conclusion

The ARMS BRAF/KRAS multiplex test is a efficient, accurate 2 step assay. In the patients and positive and negative controls prepared, it was able to reliably diagnose KRAS and BRAF mutation status in a matter of 4 hours running time. Given the fact that this is a cost effective assay that can utilize most commonly used Real time PCR machines this test may be clinically implemented if larger clinical trials utilizing tissue samples from a larger number of colon cancer patients are conducted.
Molecular Testing Prevents Overdiagnosis of Epithelioid Hemangioma
Authors: Gabutan E , Salahi N , Alejandro N , Gupta R , Mendoza R P , Li Z
Published: October 2024

Introduction/Objective

Epithelioid hemangiomas (EH) are mostly solitary benign vascular tumors commonly involving the dermal and subcutaneous areas of the head and neck. However, reports of multifocality are increasing, specially in same anatomic region. Some reported cases of EH show morphologic features that may mimic malignant vascular tumors such as hemangioendotheliomas or angiosarcomas. However, there are no reported overlaps in the molecular characteristics of these tumors. We describe a multifocal EH with atypical features, suspicious for angiosarcoma, which needed molecular testing to resolve the diagnosis.

Methods/Case Report

The patient is a previously healthy 42-year-old male with a 5-month history of multiple growing painless penile nodules. Biopsy of one of the nodules was done. Histologic examination showed multifocal dermal- based ill-circumscribed nodules with interspersed inflammatory infiltrates and focal areas of necrosis. Tumor periphery shows vasoformative growth with intraluminal and extravasated red blood cells. Neoplastic cells were large and ovoid with abundant eosinophilic cytoplasm, large vesicular pleomorphic nuclei and prominent nucleoli.

Immunohistochemical stains showed strong expression of ERG, FLI-1, and CD31 and negativity for AE1/AE3, CD34, HHV8 and EMA. The morphologic and immunohistochemical features of the specimen showed significant overlap of two primary differential diagnoses - epithelioid angiosarcoma and epithelioid hemangioma. Ultimately, molecular testing revealed ZFP36-FOSB fusion, confirming the diagnosis of EH.

Results (if a Case Study enter NA)

NA

Conclusion

Differentiating benign and malignant epithelioid vascular neoplasms can sometimes be challenging. There can be overlap in terms of architectural variety, presence of necrosis, vasoformation, inflammatory cell components and cytologic features, especially in EH with atypical features and epithelioid angiosarcoma (EA). Both of these tumors show positive immunoreactivity for CD31, CD34, FLI1 and ERG, and negativity for most keratins.

Currently, the most reliable way to distinguish each tumor is molecular testing, with EH having FOS/FOSB rearrangements and EA with MYC or FLT4 amplification. Benign and malignant epithelioid vascular tumors can be indistinguishable morphologically and immunohistochemically. Molecular tests can help differentiate these neoplasms to better tailor patient management.
Thyroid Lesion with a Novel Concurrent ETV6-NTRK3 Translocation and DICER1 Mutation
Authors: Gabutan E , Salahi N , Cilento J , Gupta R , Mendoza R P
Published: October 2024

Introduction/Objective

Understanding of the behavior of thyroid tumors expand as the basis of their classification gradually move from morphologic to molecular/genetic. The use of molecular methods in detecting mutations in fine needle aspiration (FNA) specimens further helped in tailoring patient management. Here, we describe a case of a thyroid lesion which was diagnosed with atypia of undetermined significance (AUS) on FNA and discovered to have an unreported concurrent mutation pattern.

Methods/Case Report

The patient is a 26 year-old female with long standing history of prominent anterior neck mass. New onset of neck pain prompted sonographic analysis which revealed a 1.1 cm hypoechoic left thyroid nodule with microcalcification. FNA was done, and was signed out as AUS which initiated molecular genetic testing. The lesion was found to have both ETV6/NTRK3 translocation and DICER1 p.P375R mutation. Existing literature on NTRK3 rearrangements in thyroid tumors confer a >95% risk of malignancy. It is commonly associated with BRAF-negative papillary thyroid carcinomas (PTC) with both in BRAF-like behavior in terms of nodal metastases and extrathyroidal extension. On the other hand, there are no existing literature specifying the malignancy risk of the exact DICER1 mutation identified since it has been linked to follicular neoplasms in general. Furthermore, isolated DICER1 mutations in the thyroid showed RAS-like behavior. Subsequent resection of the thyroid revealed that the tumor is morphologically a PTC, with lymphovascular invasion.

Results (if a Case Study enter NA)

NA

Conclusion

Molecular testing in thyroid lesions with morphologically indeterminable features on FNA significantly aided in prognostication of patients and prediction of malignancy risk. In this case with a previously unreported combination of mutations, existing literature helped in describing the probable behavior of the patient’s tumor. Thus, the researchers emphasize the importance of databases of identified mutations in tumors and their associated characteristics such as The Cancer Genomic Atlas (TCGA) and The Catalogue of Somatic Mutations in Cancer (COSMIC).
DICER1 Mutations Enable Rare Tumor Formation
Authors: Bhuiyan T A , Velasquez-Zarate L
Published: October 2024

Introduction/Objective

DICER1 is a tumor suppressor gene that imparts a slight increase in tumor formation when mutated. The protein plays a role in processing miRNA that silences transcription. Germline mutations of DICER1 predispose to tumors in a known set of organs and rarely in other locations. However the presence of additional genetic aberrations further increases the likelihood of tumor formation. Acting as a compounding factor, DICER1 mutations can present a constantly shifting cancer phenotype of affected patients. Of particular interest here is the development of both Pineoblastoma and Malignant spindle cell sarcoma in a young patient. Sarcomas are estimated to make up only 10% of pediatric cancers and Pineal masses only 3%.

Methods/Case Report

This case involves an 8 year old male with a history of Pineoblastoma who originally presented with slowly worsening ataxia. A screening ultrasound on following visits identified an abdominal mass that was confirmed with computed tomography. Subsequent biopsies showed malignant spindle cells arranged in a herringbone pattern. Additionally these cells displayed high mitotic activity and hyperchromatic nuclei. Surprisingly, they also demonstrated extramedullary hematopoiesis. Multiple stains were performed however no significant conclusion could be made. The appearance of this tumor and its rarity prompted a request for a Complete Comprehensive Sarcoma Panel via Next Generation Sequencing. This confirmed the presence of pathologic BRAF and DICER1 genes. From that the diagnosis of DICER1 associated Malignant Spindle Cell Sarcoma was made. BRAF V600E is the most common genetic variant and is seen in multiple cancers but only seen in 1-3% of sarcomas.

Pathologic variants of the DICER1 gene exist on exons 13 and 25. The presence of these exon mutations in some way affect DICER1 protein function and compound the effects of the mutated BRAF gene. This situation is unique as such neoplasms are rarely found in the anterior abdominal wall and showcases the effects of DICER1 on rare tumor phenotypes.

Results (if a Case Study enter NA)

NA

Conclusion

Continuing research into both DICER1 protein pathways is essential for isolating a diagnosis and guiding treatment. It would seem screening images and genetic testing would benefit pediatric or even adult patients with common and rare cancers. Extra effort made toward this would not be outside the norm as personalized medicine is gradually becoming the standard for cancer treatment.
A Curious Case of Pancreatoblastoma in an Older Age Woman
Authors: Talreja S , Laury R , Kumar S
Published: October 2024

Introduction/Objective

Pancreatoblastoma is a malignant epithelial neoplasm of the pancreas and displays multiple lines of differentiation with acinar differentiation as the predominant pattern. The squamoid nests are considered a defining component of pancreatoblastoma. Pancreatoblastoma is seen most often in children, however, rare cases in adults have been described in the literature. In children, most pancreatoblastomas are indolent and curable, however, the prognosis is worse in adults due to the presence of frequent metastasis.

Methods/Case Report

We report an interesting case of pancreatoblastoma in a 65-year-old woman with no pertinent medical history who presented with abdominal discomfort. MRI abdomen showed an 11.3 cm mass with central necrosis within the head of the pancreas. Fine-needle aspiration (FNA) of the mass showed monotonous cells with neuroendocrine differentiation and FNA was signed out as a low-grade neuroendocrine tumor (NET). The patient underwent a Whipple resection for a presumed NET.

On gross examination, a 14 cm large solid, fleshy, lobulated, partially encapsulated mass was noted in the head of the pancreas. H&E slides on low power showed the tumor composed of highly cellular lobules separated by fibrous bands. Within the lobules, the neoplastic cells predominantly had an acinar differentiation with focal trabecular or solid areas. Dispersed within the tumor were squamoid nests composed of plump to spindle-shaped cells with abundant eosinophilic cytoplasm arranged in whorls. Immunohistochemical stains demonstrated squamoid nests being positive for CK5/6 and had a nuclear-staining pattern with beta-catenin. The remaining tumor was positive for trypsin, chymotrypsin, BCL-10, synaptophysin (focal), chromogranin (focal), and INSM-1 (patchy). On MSK-Impact (next- generation sequencing), a mutation in CTNNB1 was detected.

Results (if a Case Study enter NA)

NA

Conclusion

In adults, it is important to consider pancreatoblastoma in the differential diagnoses of solid pancreatic tumors while being cautious not to confuse it with neuroendocrine tumor or acinar cell carcinoma. The presence of squamoid nests is critical for its diagnosis. Making a diagnosis of pancreatoblastoma through FNA or pancreatic biopsy can be exceptionally challenging in cases lacking squamoid nests.
A fetus with a mass in the oral cavity: a rare case of large oral immature teratoma
Authors: Siddiqui H F , Anjum S
Published: October 2024

Introduction/Objective

Oral teratoma is a rare congenital neoplastic lesion composed of variable amounts of all three germ cell layers, comprising 2-9% of all teratomas. Teratomas are classified into subtypes depending upon the presence of immature components. Sacrococcygeal and head and neck regions are the most common sites, with slight female predominance. Mortality increases if diagnosed in the fetal or neonatal period.

Methods/Case Report

We report a case of male fetus diagnosed radiologically as ultrasound at 20 weeks of gestation revealed abnormal facial characteristics. A huge lump protruding from face measuring 10.8 x 6.7 cm was observed. Grossly a grey-white, multilobulated lesion was seen with cystic spaces originating from midline soft palate. Histologically an immature teratoma comprising bone, skin adnexae, glandular tissue and immature neuroepithelial tissue was identified. The case was distinguished as immature teratoma of the oropharynx.

Results (if a Case Study enter NA)

NA

Conclusion

Prenatal diagnosis with modalities including ultrasound, MRI, alpha fetoprotein concentrations, fetoscopy and fetal karyotyping is possible in early pregnancy which can aid in risk stratification and planning therapeutic interventions. Delayed diagnosis and treatment increase the likelihood of malignant transformation. Intrapartum intubation and resection of the tumor at the time of the cesarean section has shown better outcomes. However, despite all efforts, survival rates are low.
Calretinin Staining Pattern is Variable in Hirschsprung Disease Occurring in Patients with Down Syndrome
Authors: Prasad V , Conces M , Zinnen A
Published: October 2024

Introduction/Objective

Hirschsprung disease (HD), a congenital absence of enteric ganglion cells, affects 2-10% of patients with Down syndrome (DS). Submucosal nerve hypertrophy (SNH) and abnormal calretinin immunohistochemistry (IHC) support a diagnosis of HD, but the concordance of these findings can be variable in DS. Recognizing differences in HD occuring in DS can provide insight into the disease and help to improve outcomes and reduce delays in diagnosis for these patients. We sought to describe the histologic and calretinin staining patterns in HD occurring in patients with DS.

Methods/Case Report

From 2017-2023, 22 rectal biopsies from 20 patients with DS were retrospectively collected and reviewed. Subsequent pull-through (PT) resections were evaluated from 8 patients. Biopsies were evaluated for ganglion cells and SNH. Calretinin IHC was qualitatively evaluated for intensity (strong, weak) and density (many, partial, rare). Quantitative analysis used a calculation of the percent area above threshold (%AAT) function of the NIH ImageJ software version 2.1.0. Representative areas of the PT resections were also evaluated by ImageJ %AAT analysis.

Results (if a Case Study enter NA)

HD biopsies (12/22, 54.5%) were from male patients (age 3 days-6 weeks) and showed SNH in 11/12 (91.7%) with a mean nerve diameter of 57.3 microns (range 25-89 microns). Ganglionated biopsies (10/22, 45.5%) were collected from patients 3 days to 12 years old (M:F ratio 1:1.5) and showed SNH in 6/10 (60%) with a mean nerve diameter of 44.4 microns (range 10-70 microns). Strong normal calretinin staining was only seen in ganglionated biopsies (7/10 non-HD versus 0/12 HD). Negative calretinin staining was only seen in HD (0/10 non-HD vs 7/12 HD). Abnormal staining was seen in both non-HD (3/10, 30%) and HD (5/12, 41.7%) as partial strong positivity and rare weak positivity, respectively. ImageJ %AAT quantitative analysis revealed an average of 1.71 in biopsies with strong calretinin expression, 0.130 with weak staining, and 0.033 with negative staining. Evaluation of 8 PT resections (mean length of aganglionosis 7.1 cm) showed a mean nerve diameter in the aganglionic segment of 88.3 microns, 49.6 microns in the TZ, and 32.7 microns in the ganglionated segment. ImageJ %AAT quantitative analysis of calretinin revealed a mean of 0.044 in the aganglionic area, 0.66 in the TZ, and 1.56 in the ganglionated segment.

Conclusion

Recognition of the variable calretinin patterns seen in rectal biopsies from patients with DS can assist in accurate and timely diagnosis of HD.
Tumefactive Pulmonary amyloidosis in an elderly male: A Diagnostic Dilemma
Authors: siddiqui F , Alam A , Muzaffar S , Qureshi P M
Published: October 2024

Introduction/Objective

Tumefactive pulmonary amyloidosis is a rare variant of pulmonary amyloidosis characterized by the extracellular deposition of abnormal protein fibrils in the lung parenchyma, forming tumor-like masses called amyloidomas. Although most cases are clinically silent, it may present with findings that mimic a wide range of respiratory conditions (eg. primary or metastatic malignant nodules, granulomatous disease, multiple pulmonary hamartomas etc), thereby necessitating a comprehensive and broad-based approach to differential diagnosis.

Methods/Case Report

We present a case of an 88-year-old male with a history of smoking and multiple comorbidities. He presented with numerous bilateral pulmonary nodules identified on a CT scan, concerning for malignancy. A biopsy from a left upper lobe lesion revealed necrotic tissue and was non-diagnostic. A PET scan to assess for metastatic disease was unremarkable, and demonstrated mild hypermetabolic activity, confined to the lungs, with standardized uptake values (SUV) ranging from 4.3 to a maximum SUV of 8.9. A subsequent right lung biopsy was positive for amyloid, confirmed by Congo red staining. A Mass spectrometry analysis further identified the amyloid as AL type. Serum, and urine protein electrophoresis with immunofixation were negative for M protein and the serum free light chain assay was normal as well. Significantly, the bone marrow biopsy also yielded normal results, and the patient was diagnosed with a localized form of AL amyloidosis.

Results (if a Case Study enter NA)

NA

Conclusion

This case highlights how tumefactive pulmonary amyloidosis poses a diagnostic challenge due to its rarity and resemblance to malignancy on imaging. Careful histopathological examination, including immunohistochemical stains and amyloid typing, was pivotal in establishing the correct diagnosis and underscores the essential role of pathology and laboratory medicine in differentiating rare pulmonary conditions, along with the need for a multidisciplinary approach in complex diagnostic scenarios.
The Potential Health Risks of Catha edulis Forsk (Khat) Consumption on Some Vital Organs
Authors: Abdelmonem M , Abo-Zaid M A , Alfattah M A , Ismail A H , El-Agamy S A , El-Azab K , Amin A H , Wasim H , Abdelmageed M , Saleh Abdelfattah M
Published: October 2024

Introduction/Objective

Introduction: Catha edulis Forsk (Khat) leaves are widely chewed by adults in the Arabian Peninsula and the Horn of Africa for their mild stimulating properties.

Objectives

To investigate the impact of an aqueous extract of Catha edulis Forsk leaves on the proper functioning of vital organs.

Methods/Case Report

Methods: Materials and methods: Twenty-five female albino rats were divided into two groups: a control group and a treated group which received a daily gavage of 1 ml of aqueous Khat extract with a concentration of 700 mg/kg body weight for four weeks. The effects of this treatment on selected organs, including the brain, hippocampus, heart, and ovaries, were assessed using various measurements and analyses.

Results (if a Case Study enter NA)

Results: Results: The antioxidant evaluation showed a significant increase in MDA levels in the khat group and a significant decrease in GSH, SOD, and CAT levels compared to the control group. There was a significant decrease in IL-4 and a significant increase in TNF-α and TGF-β1 compared to the control group. In contrast, the cardiac enzymes; Troponin, CK, CPK, and GOT showed a significant increase compared to the control group. The results of the hormonal assay indicated a significant increase in LH, FSH, and testosterone levels, along with a significant decrease in estrogen in the khat group compared to the control group. Furthermore, the histological investigations revealed significant changes in tissue architecture in the studied organs. In the heart, the treated group exhibited an intact, thick pericardium, along with markedly apoptotic cardiac muscle fibers and others with pyknotic nuclei and mildly congested blood vessels and capillaries. The examination of brain tissues in the treated group showed thick meninges with mild inflammatory infiltrate, marked astrogliosis with degenerated neurons in the cerebral cortex, inflammatory infiltrate with abscess formation and mildly congested blood vessels and eosinophilic plaque-like area in the deep cortex, and scattered degenerated neurons and some neurons with nuclear vacuoles and average glial cells in the white matter. In the ovaries, sections showed primary, secondary, and antral follicles, scattered cystically dilated follicles with atrophied lining, and multiple corpora lutea in the edematous stroma with scattered apoptotic stromal cells.

Conclusion

Based on these findings, long-term use of khat as a chewing material may harm vital organs.