Archival Specimens Research Articles

A Robust FISH Assay to Detect FGFR2 Translocations in Intrahepatic Cholangiocarcinoma Patients.

FGFR fusions retaining the FGFR kinase domain are active kinases that are either overexpressed or constitutively activated throughout diverse cancer types. The presence of FGFR translocations enhances tumor cell proliferation and contributes to significant sensitivity to FGFR kinase inhibitors. FGFR2 as an actionable target in intrahepatic cholangiocarcinoma (iCCA) has been tested in many clinical trials. FISH (fluorescence in situ hybridization) and NGS (next-generation sequence) are well-known tools to investigate the translocations of FGFR with multiple or unknown translocation partners. A rapid and robust FISH assay was developed and validated to detect FGFR2 translocations from FFPE specimens in iCCA. The analytical performance of the FISH assay was evaluated for probe localization, probe sensitivity and specificity, and assay precision. Twenty-five archival FFPE specimens from local iCCA patients were tested for FGFR2 translocations. FISH results were correlated with that of NGS on some samples. Biallelic translocations and a novel FGFR2 translocation involving the partner gene, SHROOM3, t(4;10) (q21;q26), were identified in a local iCCA patient.

Prospective phase I study of checkpoint blockade for the treatment of patients with newly diagnosed high-grade glioma prior to radiochemotherapy: Results of nivolumab plus ipilimumab treatment arm.

2057 Background: The limited success of checkpoint inhibitors (CPI) targeting the programmed death-1 (PD-1) axis in the adjuvant setting for glioblastoma has prompted a deeper understanding of the brain tumor and immune microenvironment and evaluating how the sequence of immunotherapy administration impacts antitumor response. We initiated a feasibility study (NCT03425292) of postoperative nivolumab (anti-PD-1) monotherapy and combination therapy in adults with newly diagnosed high-grade gliomas (HGG) prior to radiotherapy. Methods: Within six weeks from surgical resection of newly diagnosed HGG, patients in study Arm 3 received nivolumab 300 mg every 2 weeks and ipilimumab 1 mg/kg every 6 weeks until disease progression or unacceptable toxicity. The primary endpoint was the rate of dose-limiting toxicities (DLT). Secondary objectives included adverse events, antitumor activity and pharmacodynamic effects of study treatment. Next-generation sequencing (NGS) was performed on archival tumor specimens before treatment and at the time of subsequent surgery. Results: Fifteen patients were treated with nivolumab plus ipilimumab. 27% (4/15) of patients were receiving dexamethasone at treatment initiation. MGMT promoter was methylated in 5 tumors, unmethylated in 9, and equivocal in one. The most common treatment-related adverse events (AEs) were rash, pruritus, fatigue, nausea, and anorexia. Grade 3 AEs were lipase increased (n = 2), anorexia (n = 1), pruritus (n = 1), and rash (n = 3), and Grade 4 cerebral edema occurred in 1 patient. Median progression-free survival (mPFS) was 1.3 months and median overall survival (mOS) was 19.3 months. Paired tumor specimens obtained before and after treatment were analyzed in six patients and revealed molecular changes in response to treatment as well as differences between patients with shrinking tumors versus progressing tumors. Conclusions: We show that nivolumab plus ipilimumab can be safely administered prior to radiation. To our knowledge, this is the first study in which checkpoint blockade therapy was administered for newly diagnosed glioblastoma prior to standard radiotherapy. Despite the short mPFS, mOS was suggestive of a potential long-term benefit from early CPI exposure, and three patients deferred chemoradiation greater than seven months. Analysis of other study arms is ongoing. Clinical trial information: NCT03425292 .

A phase I trial of sequential dosing of sonidegib and pembrolizumab in advanced solid tumors (aST) and non–small-cell lung cancer (NSCLC).

9093 Background: Pembrolizumab interrupts PD-1/-L1 interaction and is efficacious in many cancers. However, resistance invariably emerges in the majority of patients. Potential mechanisms include activation of compensatory pathways. The inhibition of sonic hedgehog signaling (sHH) was previously shown to induce intra-tumoral (IT) infiltration by CD4+, CD8+ and HLA-DR class II cells. Our preclinical data showed sHH inhibitor enhanced IT penetration by monoclonal antibodies and induced PD-L1 expression. We conducted a phase I study using a novel sequential pulse dosing of sonedegib followed by pembrolizumab in aST with an expansion cohort to determine the maximum tolerated dose (MTD), tolerability and preliminary efficacy. Methods: The dose escalation utilized a 3+3 design to determine the MTD and proceeded to expansion cohort upon determination of the MTD. Patients enrolled to each dose level were observed for dose limiting toxicities (DLTs) during the 1st cycle. The expansion cohort consisted of NSCLC and head/neck squamous cell carcinoma (HNSCC) previously treated by anti-PD1/-L1. The recommended phase 2 dose (RP2D) was determined following the review of the toxicity profile of the combination from all cycles. The study treatment consisted of sonidegib oral daily from day 1 to 8 and pembrolizumab I.V. 200 mg on day 8 on an every 3-week cycle. The sonidegib dose levels explored were 400, 600 and 800 mg. Archival tumor and blood specimens were collected for correlative studies. Adverse events (AEs) were categorized and graded per CTCAE v5.0, and tumor response by RECIST v1.1. Results: The study enrolled a total of 33 patients and 29 received treatment (13 in escalation and 16 in expansion), including patients with NSCLC, HNSCC, skin cancer, gastric cancer and melanoma. The enrollment to the NSCLC cohort is complete and HNSCC continues. No DLT was encountered during dose escalation and the MTD was not reached. The highest planned dose level was selected to proceed to expansion (sonidegib 800mg days 1-8 in combination with pembrolizumab I.V. 200 mg on day 8 on an every 3-week cycle). The expansion cohort proceeded to enroll 15 patients evaluable for AEs (10 NSCLC and 5 HSNCC). Grade 3 and above treatment-related AEs across all patients were hyperglycemia, fatigue, dyspepsia, abdominal pain. The mature efficacy data will be reported at the meeting. Conclusions: The study successfully determined the RP2D of sonidegib when dosed sequentially with pembrolizumab in advanced solid tumors. The AE profile of the combination is similar to that for respective agents given individually. The efficacy data among anti-PD1/-PDL1-treated NSCLC will be reported at the meeting. Clinical trial information: NCT04007744 .

A proteomic signature associated with prognosis in HPV-related locally advanced oropharyngeal squamous cell carcinoma (LA-OPSCC).

6055 Background: Although HPV-related LA-OPSCC is associated with better prognosis than HPV-negative disease, ~30% of cases relapse despite curative-intent chemoradiotherapy. New prognostic biomarkers are needed to rationalise curative-intent treatment without compromising efficacy. We aimed to develop a proteomic signature associated with risk of recurrence from diagnostic biopsies of patients with HPV-positive OPSCC. Methods: We analysed 139 formalin fixed paraffin embedded archival core biopsy specimens from 124 patients with HPV-related (p16 IHC positive) T1-4N0-3M0 LA-OPSCC tumours. All patients were treated with definitive chemoradiotherapy at the Princess Alexandra Hospital (Brisbane, Australia) between 2007-2019. The cohort included 50 patients with recurrence less than five years from diagnosis and 74 age/performance-status matched patients with no recurrence. Proteomic analysis was performed utilizing data-independent acquisition mass spectrometry (DIA-MS). A proteomic prognostic signature associated with recurrence free survival (RFS) at five years was the primary endpoint of interest. It was developed using a computational pipeline comprising an initial univariate Cox model step, followed by multiple runs of multivariate Cox models with Least Absolute Shrinkage and Selection Operator (LASSO) regularization, and then a final step of recursive feature selection. Results: A total of 7,597 proteins were quantified and 665 were differentially expressed proteins between tumour and normal adjacent tissues. There were 5,199 proteins remaining in the tumour samples after filtering. RFS was significantly (q-value < 0.05) associated with 252 proteins, whose functions are enriched in adaptive and innate immunity and MAPK6/MAPK4 signalling pathways. A 16-protein signature associated with RFS stratified patients into low, intermediate, or high-risk groups (C-index = 0.885, p < 0.0001). The 16-protein signature outperformed clinico-pathological covariates including age, stage, ECOG and smoking history with the highest area under the receiver operating characteristic curve (AUROC 0.95). Conclusions: DIA-MS-based proteomics on core biopsies can be used to risk stratify HPV-related OPSCC patients. A 16-protein signature associated with RFS was successfully identified as a basis for future studies. Validation of this proteomic prognostic signature in independent cohorts is required and may be used to inform future clinical trials to better tailor upfront therapy.

Identifying small non-coding RNAs as biomarkers for cervical cancer.

e17507 Background: Small non-coding RNAs (sncRNAs) that control post-transcriptional gene expression are attractive candidate molecular targets for cancer screening tests. We evaluated whether sncRNAs expression are markedly different in benign, precancerous, and cancerous cervical tissue. Methods: We examined the expression of six sncRNA species: circular RNAs (circRNAs) microRNAs (miRNAs), piwi-interacting RNA (piRNAs), small nuclear RNA (snRNAs), small nucleolar RNA (snoRNAs), and transfer RNA (tRNA), from archival formalin-fixed paraffin-embedded cervical specimen obtained from 172 women (74 benign, 58 high-grade squamous intraepithelial lesion (HSIL) and 40 invasive cervical cancer). We used DESeq2 to identify differentially expressed sncRNA molecules with adjusted p-value < 0.05 and at least 2-fold up- or down-regulation. Results: Comparing benign to HSIL samples, we foundseveral statistically significant, differentially expressed sncRNAs: 906 circRNAs (*circ_0066810, p=3.76x10-16), 87 miRNAs (*miR-149-5p, p=1.30x10-14), 11 piRNAs (*piR_016945, p=8.32x10-13), 32 snRNAs (*RNU1-17P, p=1.90x10-10), 5 snoRNAs (*SCARNA18, p=1.35x10-5), and 24 tRNA (*tRNA-Glu-TTC-8-1, p=6.45x10-17). Comparing benign to invasive cervical cancer samples, we also foundseveral statistically significant, differentially expressed sncRNAs: 3,192 circRNAs (*circ_0123115, p=7.46x10-50), 325 miRNAs (*miR-7-5p, p=6.72x10-36), 82 piRNAs (*piR-hsa-27513, p=1.44x10-15), 71 snRNAs (*RNU1-20P, p=1.37x10-45), 52 snoRNAs (*SNORD95, p=1.68x10-23), and 68 tRNA (*tRNA-Cys-GCA-9-3, p=1.01x10-21). * Indicates the sncRNA with the smallest p-value, for each specie. Conclusions: Our results identify sncRNAs with potential utility of as diagnostic and prognostic biomarkers, and therapeutic targets for cervical precancer and cancer.

Dissociation protocols used for sarcoma tissues bias the transcriptome observed in single-cell and single-nucleus RNA sequencing

BackgroundSingle-cell RNA-seq has emerged as an innovative technology used to study complex tissues and characterize cell types, states, and lineages at a single-cell level. Classification of bulk tumors by their individual cellular constituents has also created new opportunities to generate single-cell atlases for many organs, cancers, and developmental models. Despite the tremendous promise of this technology, recent evidence studying epithelial tissues and diverse carcinomas suggests the methods used for tissue processing, cell disaggregation, and preservation can significantly bias gene expression and alter the observed cell types. To determine whether sarcomas – tumors of mesenchymal origin – are subject to the same technical artifacts, we profiled patient-derived tumor explants (PDXs) propagated from three aggressive subtypes: osteosarcoma (OS), Ewing sarcoma (ES), desmoplastic small round cell tumor (DSRCT). Given the rarity of these sarcoma subtypes, we explored whether single-nuclei RNA-seq from more widely available archival frozen specimens could accurately be identified by gene expression signatures linked to tissue phenotype or pathognomonic fusion proteins.ResultsWe systematically assessed dissociation methods across different sarcoma subtypes. We compared gene expression from single-cell and single-nucleus RNA-sequencing of 125,831 whole-cells and nuclei from ES, DSRCT, and OS PDXs. We detected warm dissociation artifacts in single-cell samples and gene length bias in single-nucleus samples. Classic sarcoma gene signatures were observed regardless of the dissociation method. In addition, we showed that dissociation method biases could be computationally corrected.ConclusionsWe highlighted transcriptional biases, including warm dissociation and gene-length biases, introduced by the dissociation method for various sarcoma subtypes. This work is the first to characterize how the dissociation methods used for sc/snRNA-seq may affect the interpretation of the molecular features in sarcoma PDXs.

Abstract CT177: A phase I, first in human study of CBA-1205, glycoengineered humanized anti-DLK-1 monoclonal antibody in patients with advanced solid tumors

Abstract Background: CBA-1205 is a novel humanized anti-delta-like 1 homolog (DLK-1) antibody. It is a glycoengineered antibody by GlymaxX® technology to potentiate antibody-dependent cellular cytotoxicity activity. DLK-1 is a membrane protein with 6 tandem EGF-like motifs in extracellular region. Overexpression of DLK-1 has been reported in variety of cancer types including hepatocellular carcinoma (HCC), suggesting that DLK-1 could be an ideal target for cancer therapy. Methods: This is a first in human, multicenter, open-label Phase I study. The purpose of part 1 is to evaluate the safety and tolerability in patients with advanced solid tumors who had no standard therapy or were refractory or intolerant to standard therapies and to determine the starting dose for part 2 in HCC patients. The standard 3+3 dose escalation design was utilized in seven cohorts (0.1, 0.3, 1, 3, 10, 20, 30 mg/kg). CBA-1205 was administered at 2-week intervals in a 28-day cycle. If the patient had no Dose Limiting Toxicity (DLT) during 28 days after the first two doses, CBA-1205 administration will be continued for further cycles unless any of the criteria for discontinuation. Serum DLK-1 concentration before the start of CBA-1205 administration was analyzed using the Human Pref-1/DLK1/FA1 DuoSet ELISA (R&D Systems, Inc.). Immunohistochemical analysis of DLK-1 expression in the archival tumor specimen was determined in FFPE tissue sections using mouse anti-hDLK-1 antibody (clone DI-2-20, Chiome Bioscience). Results: 22 patients with advanced solid tumors were enrolled. CBA-1205 was well tolerated in these patients and no DLT was observed even at the highest dose tested. No ≥ Grade 3 treatment related adverse events was observed throughout the study periods. The serum concentration of CBA-1205 increased dose-proportionally. The exposure to CBA-1205 exceeded the effective concentrations observed in a mouse xenograft model. No serum anti-CBA-1205 antibody was detected. The disease control was seen in 8 patients (38.1%, all with SD). Especially, long SD was observed in 3 patients with invasive thymoma, malignant melanoma, and pancreatic carcinoma, where progression free survival (PFS) was 39, 72(ongoing, at data cutoff), and 41 weeks, respectively. The serum concentration of soluble DLK-1 was detected in 6 out of 22 patients. Patients with SD by the best overall response had a higher rate of detectable serum DLK-1 concentration and a higher mean concentration than patients with PD. No DLK-1 expression in tumor was detected by IHC method, in 14 patients who consented to use the archival tumor specimens. Conclusions: CBA-1205 was well tolerated without any severe toxicity in patients with advanced solid tumors.Part 2 of this Phase I study with two cohorts (20, 30 mg/kg) in patients with unresectable advanced/recurrent HCC refractory or intolerable to the standard therapy has been initiated. Citation Format: Masafumi Ikeda, Nobuaki Matsubara, Chihiro Kondoh, shose taoka, Yuki Katsuya, Takafumi Koyama, Noboru Yamamoto. A phase I, first in human study of CBA-1205, glycoengineered humanized anti-DLK-1 monoclonal antibody in patients with advanced solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr CT177.

Tissue Microarray Lipidomic Imaging Mass Spectrometry Method: Application to the Study of Alcohol-Related White Matter Neurodegeneration.

Central nervous system (CNS) white matter pathologies accompany many diseases across the lifespan, yet their biochemical bases, mechanisms, and consequences have remained poorly understood due to the complexity of myelin lipid-based research. However, recent advances in matrix-assisted laser desorption/ionization-imaging mass spectrometry (MALDI-IMS) have minimized or eliminated many technical challenges that previously limited progress in CNS disease-based lipidomic research. MALDI-IMS can be used for lipid identification, semi-quantification, and the refined interpretation of histopathology. The present work illustrates the use of tissue micro-arrays (TMAs) for MALDI-IMS analysis of frontal lobe white matter biochemical lipidomic pathology in an experimental rat model of chronic ethanol feeding. The use of TMAs combines workload efficiency with the robustness and uniformity of data acquisition. The methods described for generating TMAs enable simultaneous comparisons of lipid profiles across multiple samples under identical conditions. With the methods described, we demonstrate significant reductions in phosphatidylinositol and increases in phosphatidylcholine in the frontal white matter of chronic ethanol-fed rats. Together with the use of a novel rapid peak alignment protocol, this approach facilitates reliable inter- and intra-group comparisons of MALDI-IMS data from experimental models and could be extended to human disease states, including using archival specimens.

Abstract 3405: Changes in HER3 expression associated with chemotherapy for pancreatic cancer

Abstract Background: Currently, intense efforts towards the development of targeted therapy, including anti-HER3 strategies for cancer treatment, are being made. Recently, HER3 activation was linked to resistance to targeted therapies (EGFR/HER2/MEK/RAF) and hormonal therapy by upregulating HER3 expression after those treatments in several cancer types. However, HER3 expression profile in pancreatic cancer treatment is still unknown. Here, we evaluated the status of HER3 expression after chemotherapy for pancreatic cancer. Methods: Patients with pancreatic cancer who underwent chemotherapy between January 2010 and June 2020 and from whom post-treatment archival tissue specimens were collected were included in this study. All resectable and locally advanced cases were evaluated using resected specimens, and all metastatic cases were evaluated using biopsy specimens. In patients from whom both pre- and post-chemotherapy specimens were collected, changes in HER3 expression status before and after treatment were immunohistochemically evaluated by using HER3/ErbB3 (D22C5) XP Rabbit mAb (Cell Signaling Technology) as a primary antibody. IHC scoring (0, 1+, 2+, 3+) of membranous staining intensity was performed according to HER2 IHC gastric scoring guideline. Results: Post-chemotherapy HER3 expression was evaluable in 41 patients, comprising 12, 14, 14, and 1 case as HER3 3+, 2+, 1+ and 0, respectively. In the HER3 3+/2+ and 1+/0 groups, tumor localization was 69%/67% in the pancreatic head, 23%/13% in the pancreatic body, and 8%/20% in the pancreatic tail; tumor stage was resectable (post-neoadjuvant status) 46%/20%, locally advanced 42%/47%, and metastatic 12%/33%; the median tumor size was 30 mm/35 mm; CEA elevation was 23%/20% and CA19-9 elevation was 69%/73%; treatment regimens were FOLFIRINOX 23%/40%, gemcitabine + nab-paclitaxel 19%/0%, gemcitabine + S-1 (neoadjuvant setting) 42%/27%, and the other chemotherapy 4%/20%, respectively. HER3 expression was able to be evaluated before and after chemotherapy in 5 cases: HER3 IHC score changed from 3+/2+ to 1+/0 for 1 case, from 1+/0 to 3+/2+ for 1 case and maintained at 3+/2+ for 3 cases. The median overall survival was 19.6 and 20.5 months in the HER3 3+/2+ and HER3 1+/0 groups, respectively (P = 0.965). Conclusion: HER3 expression with 3+/2+ is observed in 63% of pancreatic cancer patients, and HER3-expressing pancreatic cancer is of great interest as a therapeutic target. HER3 expression status may change before and after cytotoxic combination therapy in some cases of pancreatic cancer. Citation Format: Tomoyuki Satake, Chigusa Morizane, Mao Okada, Mariko Nishioka, Nobuyoshi Hiraoka, Satoshi Nara, Tomoya Kakegawa, Maki Kobayashi, Kumiko Koyama, Minoru Esaki, Takuji Okusaka. Changes in HER3 expression associated with chemotherapy for pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3405.

Molecular characterization of the parasitic nematode genus Crassicauda; larvae parasitic on the firefly squid and adults on beaked whales off the coast of Japan.

The Spirurina type X larvae, which infect firefly squid (Watasenia scintillans), are known to cause cutaneous creeping eruption and intestinal obstruction in humans. Although it has been reported that the adult of this larva is Crassicauda giliakiana, which was recovered from a Baird's beaked whale (Berardius bairdii), it is not well known internationally. In this study, to reconfirm the identification of this species, we determined the mitochondrial cox1 gene and the partial sequence of 18S-28S ribosomal DNA from larvae recovered from firefly squid. As the results, we confirmed that the larvae were C. giliakiana, and partial ribosomal DNA sequences were also performed for phylogenetic analysis. Furthermore, to determine the distribution of the genus Crassicauda in Japan as a definitive host, DNA was extracted from archival specimens of adult worms recovered from the kidneys of family Ziphiidae that had stranded on the coast in Japan, and phylogenetic analysis using ITS2 region was conducted. As a result, C. giliakiana were detected from not only B. bairdii but also Mesoplodon stejnegeri, and Ziphius cavirostris, and C. anthonyi was also detected in Z. cavirostris. Furthermore, the kidney parasitic nematoda Crassicauda sp., which is not registered in the database, was found in both M. densirostris and M. gingkodens. This study provides new insights into the distribution and the lifecycle of genus Crassicauda in Japan based on the phylogenetic relationship between larvae and adults.

Revalidation of Phalangomyia Dyar & Knab as a subgenus of Culex L. (Diptera: Culicidae) based on morphological and molecular evidence

Culex apicinus Philippi, 1865 and its synonyms, Phalangomyia debilis Dyar & Knab, 1914, Cx. escomeli Brèthes, 1920 and Cx. alticola Martini, 1931, were re-examined employing molecular and morphological phylogenetic methods. Archival and fresh specimens were used for morphological diagnosis and to generate fragments of two single-copy nuclear genes (CAD, HB) and one mitochondrial gene (COI). Additional sequences of Cx. apicinus and species of the subgenus Culex of Culex Linnaeus, 1758 and other subgenera of the genus were obtained from GenBank for molecular analysis. Diagnostic morphological characteristics of Cx. apicinus and other species of the subgenus Culex were contrasted. Phylogenetic relationships were generated using DNA sequences of protein coding genes under both Maximum Likelihood and Bayesian approaches. Culex apicinus showed unique morphological traits that allow its classification in a separate subgenus. The subspecific status is supported by its recovery as a monophyletic clade within the genus Culex based on morphological and molecular characters. The synonymous Phalangomyia debilis provides an available subgeneric name. Consequently, Phalangomyia Dyar & Knab, 1914 is resurrected from synonymy with Culex Linnaeus, 1758 as a monobasic subgenus of Culex.

Differential Spatial Gene and Protein Expression Associated with Recurrence Following Chemoradiation for Localized Anal Squamous Cell Cancer.

The identification of transcriptomic and protein biomarkers prognosticating recurrence risk after chemoradiation of localized squamous cell carcinoma of the anus (SCCA) has been limited by a lack of available fresh tissue at initial presentation. We analyzed archival FFPE SCCA specimens from pretreatment biopsies prior to chemoradiation for protein and RNA biomarkers from patients with localized SCCA who recurred (N = 23) and who did not recur (N = 25). Tumor cells and the tumor microenvironment (TME) were analyzed separately to identify biomarkers with significantly different expression between the recurrent and non-recurrent groups. Recurrent patients had higher mean protein expression of FoxP3, MAPK-activation markers (BRAF, p38-MAPK) and PI3K/Akt activation (phospho-Akt) within the tumor regions. The TME was characterized by the higher protein expression of immune checkpoint biomarkers such as PD-1, OX40L and LAG3. For patients with recurrent SCCA, the higher mean protein expression of fibronectin was observed in the tumor and TME compartments. No significant differences in RNA expression were observed. The higher baseline expression of immune checkpoint biomarkers, together with markers of MAPK and PI3K/Akt signaling, are associated with recurrence following chemoradiation for patients with localized SCCA. These data provide a rationale towards the application of immune-based therapeutic strategies to improve curative-intent outcomes beyond conventional therapies for patients with SCCA.

Morphometric Analysis and Linear Measurements of the Scala Tympani and Implications in Cochlear Implant Electrodes.

The objective of this study was to perform detailed height and cross-sectional area measurements of the scala tympani in histologic sections of nondiseased human temporal bones and correlate them with cochlear implant electrode dimensions. Previous investigations in scala tympani dimensions have used microcomputed tomography or casting modalities, which cannot be correlated directly with microanatomy visible on histologic specimens. Three-dimensional reconstructions of 10 archival human temporal bone specimens with no history of middle or inner ear disease were generated using hematoxylin and eosin histopathologic slides. At 90-degree intervals, the heights of the scala tympani at lateral wall, midscala, and perimodiolar locations were measured, along with cross-sectional area. The vertical height of the scala tympani at its lateral wall significantly decreased from 1.28 to 0.88 mm from 0 to 180 degrees, and the perimodiolar height decreased from 1.20 to 0.85 mm. The cross-sectional area decreased from 2.29 (standard deviation, 0.60) mm 2 to 1.38 (standard deviation, 0.13) mm 2 from 0 to 180 degrees ( p = 0.001). After 360 degrees, the scala tympani shape transitioned from an ovoid to triangular shape, corresponding with a significantly decreased lateral height relative to perimodiolar height. Wide variability was observed among the cochlear implant electrode sizes relative to scala tympani measurements. The present study is the first to conduct detailed measurements of heights and cross-sectional area of the scala tympani and the first to statistically characterize the change in its shape after the basal turn. These measurements have important implications in understanding locations of intracochlear trauma during insertion and electrode design.

Impact of CD34-dependent Micro Vessel Density on Periapical Odontogenic Cysts.

Odontogenic cysts belong to a type of lesions with endodontic origin that in some cases mimic even aggressive odontogenic tumors sharing with them similar radiographic features. Periapical cysts (PCs) belong to the inflammatory odontogenic cysts sub-category and rarely squamous cell carcinoma arises from their hyperplastic/ dysplastic epithelia. This study aimed to explore the impact of cluster differentiation 34 (CD34) protein expression combined with micro vessel density (MVD) on PCs. Forty-eight (n=48) archival, formalin-fixed, and paraffin-embedded PC tissue specimens were included in the study. Immunohistochemistry (IHC) was performed in the corresponding tissue sections using an anti- CD34 antibody. CD34 expression levels and also MVD in the examined cases were measured by implementing a digital image analysis protocol. CD34 over-expression (moderate to high staining intensity levels) were detected in 29/48 (60.4%) cases, whereas the rest of them (19/48-39.6%) were characterized by low levels of expression. Extended MVD was identified in 26/48 (50.1%) cases correlated with CD34 over-expression, epithelial hyperplasia (p-value=0.001), and marginally with inflammatory infiltration level in the examined lesions (p-value=0.056). CD34 over-expression combined with increased MVD is associated with a neoplastic-like (hyperplastic) phenotype in PCs as a result of increased neo-angiogenic activity. These histopathological characteristics rarely form an eligible substrate for squamous cell carcinoma onset in untended cases.

Abstract P4-01-15: Preliminary results from a phase 2 study of praluzatamab ravtansine (CX-2009) in patients with advanced breast cancer (ABC)

Abstract Background: CD166 is broadly expressed in normal epithelium and overexpressed in many types of malignancies, including breast cancer. Probody® therapeutic candidates are masked antibodies, conditionally activated by tumor-associated proteases, which restricts their activity to the tumor microenvironment and minimizes ‘off-tumor’ toxicity. CX-2009 is a conditionally activated humanized anti-CD166 monoclonal antibody conjugated to DM4 that showed clinical activity in ABC patients in a phase 1 study (Boni et al. Clin Cancer Res. 2022). This phase 2 study (NCT04596150) evaluates CX-2009 as monotherapy in patients with advanced HR+/HER2− BC (Arm A) and TNBC (Arm B), and in combination with pacmilimab (a conditionally activated PD-L1) in TNBC (Arm C). Methods: Key eligibility criteria for all cohorts include: ECOG 0-1, acceptable end-organ function, measurable disease, willingness to receive ocular prophylaxis for DM-4 related toxicity, and available tumor tissue for CD166 evaluation. Eligibility criteria for HR+ BC include: 2-4 prior regimens (excluding single-agent hormonal therapy with up to 2 prior cytotoxic regimens) and a prior CDK 4/6 inhibitor in the metastatic setting; eligibility criteria for TNBC include CD166 by IHC >1% by central assessment, 1-3 prior regimens in the metastatic setting and prior taxane. All patients initially received 7 mg/kg Q3W; the protocol was subsequently amended to enroll patients at 6 mg/kg Q3W. The primary endpoint was overall response rate (ORR) using RECIST v1.1 assessed by central review. Other key endpoints include ORR by investigator assessment, clinical benefit rate at 24 weeks (CBR24; defined as any response, confirmed or unconfirmed, or SD for 24 weeks), duration of response, and progression-free survival by investigator. Archival tumor specimens and blood samples were collected for correlative research including genomic analyses. Results: As of 13 May 2022, 60 patients were enrolled in Arm A (all patients started at 7 mg/kg); 52 were evaluable for efficacy by investigator. Median duration of follow-up was 29.1 weeks (range: 3.6-60.7). Median age was 60.5 years (36, 83); pts received a median of 3.5 (1, 6) prior treatments for ABC. CD166 H-Score > 200 was reported in 53.3% of patients. Arm A met the primary efficacy endpoint with a confirmed ORR by central radiology of 14.9% (n=47); by investigator, ORR was similar at 15.4% (n=52); an additional 9 patients (17.3%) had an unconfirmed response. CBR24 was 40.4%; using only confirmed responses, CBR24 was 23.1%. Median PFS was 11.4 weeks (95% CI 9.0, 13.9). Common treatment-related all-grade adverse events (TRAEs) included blurred vision (42%), nausea (35%), fatigue (35%), diarrhea (25%), peripheral neuropathy (27%), infusion-related reaction (23%) and decreased appetite (20%). Grade ≥3 ocular and neuropathic TRAEs were 15% and 10%, respectively. AEs resulting in treatment discontinuation (AEDC) were 25%. For Arm B and C, 55 and 10 patients were enrolled (the majority received a starting dose of 6 mg/kg). For Arm B, the futility boundary was crossed (ORR < 10%). Grade ≥3 ocular and neuropathic TRAEs and AEDC at 7 mg/kg in Arm B were similar to Arm A (11%, 11% and 21% respectively); whereas at 6 mg/kg, they were reduced at 3%, 0% and 0%, respectively. Biomarker data and correlation with outcomes will be presented. Conclusions: Praluzatamab ravtansine demonstrated single-agent activity in unselected heavily pretreated patients with HR+/HER2- ABC. Time to event analyses, such as PFS, were confounded by higher-than-expected toxicity at a starting dose of 7 mg/kg. The toxicity profile was generally consistent with a DM4 payload. The lower dose of 6 mg/kg appears to be better tolerated. Additional clinical studies in HR+ABC, incorporating a starting dose of 6 mg/kg and potentially including a biomarker strategy, are warranted. Citation Format: Kathy Miller, Sara Tolaney, Leisha A. Emens, Sung-Bae Kim, Erika Hamilton, Cristina Saura, Lucia Sanz, Valentina Boni, Filipa Lynce, Juan Miguel Cejalvo, Jennifer Crozier, Shirley Wang, Hirdesh Uppal, Alison L. Hannah, Sara Hurvitz. Preliminary results from a phase 2 study of praluzatamab ravtansine (CX-2009) in patients with advanced breast cancer (ABC) [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P4-01-15.

Improving sarcoma classification by using RNA hybridisation capture sequencing in sarcomas of uncertain histogenesis of young individuals

Our aim was to utilise a 241-gene RNA hybridisation capture sequencing (CaptureSeq) gene panel to identify unexpected fusions in undifferentiated, unclassified or partly classified sarcomas of young individuals (<40 years). The purpose was to determine the utility and yield of a large, targeted fusion panel as a tool for classifying tumours that do not fit typical diagnostic entities at the time of the original diagnosis. RNA hybridisation capture sequencing was performed on 21 archival resection specimens. Successful sequencing was obtained in 12 of 21 samples (57%), two of which (16.6%) harboured translocations. A novel NEAT1::GLI1 fusion, not previously reported in the literature, presented in a young patient with a tumour in the retroperitoneum, which displayed low grade epithelioid cells. The second case, a localised lung metastasis in a young male, demonstrated a EWSR1::NFATC2 translocation. No targeted fusions were identified in the remaining 83.4% (n=10) of cases. Forty-three per cent of the samples failed sequencing as a result of RNA degradation. RNA-based sequencing is an important tool, which helps to redefine the classification of unclassified or partly classified sarcomas of young adults by identifying pathogenic gene fusions in up to 16.6% of the cases. Unfortunately, 43% of the samples underwent significant RNA degradation, falling below the sequencing threshold. As CaptureSeq is not yet available in routine pathology practice, increasing awareness of the yield, failure rate and possible aetiological factors for RNA degradation is fundamental to maximise laboratory procedures to improve RNA integrity, allowing the potential identification of significant gene alterations in solid tumours.

First isolation and molecular characterization of canine parvovirus-type 2b (CPV-2b) from red foxes (Vulpes vulpes) living in the wild habitat of Turkey

BackgroundThe canine parvovirus, with its many variants, is responsible for a pivotal and common viral infection affecting millions of dogs and other carnivore species worldwide, particularly the wild ones, which are considered as the main reservoir hosts. To that end, this study investigated the presence of canine parvovirus (CPV) in red foxes (Vulpes vulpes) living in wild habitats of several regions of Turkey.MethodsWe randomly collected 630 archival fox stool specimens from rural areas of 22 provinces and used real-time PCR to detect CPV.ResultsTwo of the 630 (0.3%) stool samples were positive for CPV-DNA, named Tr-Fox/128(Aydın) and Tr-Fox/159(Manisa). We attempted to isolate the virus in a MDCK cell line, and cytopathic effects were observed four days post-inoculation. Three regions corresponding to the CPV capsid protein VP2 gene from extracted DNA of positive samples were amplified by conventional PCR, and the products were visualised, purified, and Sanger sequenced. Three overlapping DNA raw sequence fragments, were read, assembled, and aligned to obtain approximately 1.5 kb-long regions that cover most of the VP2 gene, then deposited in GenBank. After comparing the isolates with parvovirus sequences data of domestic and wild carnivores by BLAST processing, our isolates' similarity rate with each other was 99.40%, with base differences in 9 nucleotide positions. They were classified as 2b variant closely related to isolates from dogs in Turkey, Egypt, Iraq, Italy, Thailand, and China.ConclusionThis study presents evidence of interspecies transmission of CPV, of which there are no reports on prevalence in wildlife carnivores of our country. Identification of CPV in red foxes threatens local and hunting dogs, which may contract the infection or disseminate it to other wild animal species or vice-versa.

Metallothionein expression in feline injection site fibrosarcomas

BackgroundFeline injection site fibrosarcoma is an aggressive and infiltrative tumour arising in the background of chronic inflammation. The aim of this study was to evaluate the expression of metallothionein (I-II) in feline injection site fibrosarcomas and to assess its possible relationships with Ki67 index, inflammation score and tumour grade. The study included 40 feline fibrosarcomas, located in the common injection sites (i.e., interscapular area, thigh, flank), constituting archival diagnostic specimens collected between 2019–2020. Tumours were graded histologically according to the newly proposed soft-tissue sarcoma grading system in cats. Immunohistochemistry was performed to evaluate the expression of Ki67 and metallothionein in tumour cells.ResultsThe cytoplasmic and sometimes nuclear expression of metallothionein was observed in all tumours grade I, 66.67% of tumours grade II and 55% of tumours grade III. The expression of metallothionein was negatively correlated with tumour grade and inflammation score, while the Ki67 index was positively correlated with tumour grade, inflammation score and necrosis score.ConclusionThe downregulation of MT expression in feline injection site fibrosarcomas seems to be connected with an increase in the inflammatory infiltration, hence tumour progression. This is the first study describing metallothionein expression in feline injection site fibrosarcomas.

Use of distinct molecular signatures of appendiceal cancer subtypes to assess biomarker development.

189 Background: Appendiceal Neoplasms are diverse entities which have a variety of clinical presentations, histologic subtypes, biologic behavior, and patient outcomes. Advanced disease at initial diagnosis is not uncommon and therapeutic options are limited. This study aims to identify potential targets to develop epigenetics-based therapeutics/biomarkers. Methods: Archival (FFPE) specimens were collected from 25 patients with histologically confirmed and subtyped appendiceal neoplasia and 16 age-matched non-neoplastic controls. Four appendiceal neoplastic processes identified: Low grade appendiceal neoplasm (LAMN), pseudomyxoma peritonei (intra-peritoneal spread of LAMN), conventional-type adenocarcinoma and goblet cell adenocarcinoma. Gene expression profiling was performed using the HTG EdgeSeq Oncology Biomarker panel. Differentially expressed genes (DEGs) were selected with cut-off threshold FDR&lt;0.05 and analyzed using Qlucore Explorer and functional analyses via Ingenuity Pathway Analysis (IPA). Results: Four appendiceal neoplastic processes identified: pseudomyxoma peritonei (20%), low-grade appendiceal mucinous neoplasm (24%), adenocarcinoma (24%), and goblet cell adenocarcinoma (32%). Unsupervised hierarchical clustering identified 498 DEGs (424 up, 74 down) between all appendiceal cancer versus age-matched controls that showed enrichment in B-cell inflammatory signaling, senescence, cell cycle regulation, PI3K/AKT signaling, cell cycle checkpoint control pathways, and sets relating to NANOG in stem cell pluripotency (all p0.001). G1/S checkpoint, apoptosis, ATM, and PTEN signaling are downregulated (p0.001). TP53, E2F1, IL6, IFNG, TNF, and HGF (p0.001) regulated overlapping genes. Four-subgroups comparison found 67 DEGs involved in T-helper cell differentiation, immune-mediated apoptosis, T-cell fatigue, and PD1/PDL1 signaling to be dysregulated (p0.001). IFNG, FGF2, POU5F1, TNF, and MYC (p0.001) were upstream regulators. Conclusions: In this study, downregulated gene expressions in appendiceal cancers are related to cell proliferation and death control mechanisms, with a trend towards overexpression of inflammatory and cell cycle pathways. It is postulated that genes involved in these pathways are hypermethylated. More research is being undertaken on epigenetics-based biomarkers for diagnosis and prognosis. Given PI’s decades of experience in biomarker research, we aim to develop a "single blood test" to expand bedside monitoring alternatives that align with the National Cancer Moonshot Initiative to discover cancer early, when the likelihood of a cure is highest.

SLC-0111, an inhibitor of carbonic anhydrase IX, attenuates hepatoblastoma cell viability and migration.

In response to hypoxia, tumor cells undergo transcriptional reprogramming including upregulation of carbonic anhydrase (CA) IX, a metalloenzyme that maintains acid-base balance. CAIX overexpression has been shown to correlate with poor prognosis in various cancers, but the role of this CA isoform in hepatoblastoma (HB) has not been examined. We surveyed the expression of CAIX in HB specimens and assessed the impact of SLC-0111, a CAIX inhibitor, on cultured HB cells in normoxic and hypoxic conditions. CAIX immunoreactivity was detected in 15 out of 21 archival pathology HB specimens. The CAIX-positive cells clustered in the middle of viable tumor tissue or next to necrotic areas. Tissue expression of CAIX mRNA was associated with metastasis and poor clinical outcome of HB. Hypoxia induced a striking upregulation of CAIX mRNA and protein in three HB cell models: the immortalized human HB cell line HUH6 and patient xenograft-derived lines HB-295 and HB-303. Administration of SLC-0111 abrogated the hypoxia-induced upregulation of CAIX and decreased HB cell viability, both in monolayer and spheroid cultures. In addition, SLC-0111 reduced HB cell motility in a wound healing assay. Transcriptomic changes triggered by SLC-0111 administration differed under normoxic vs. hypoxic conditions, although SLC-0111 elicited upregulation of several tumor suppressor genes under both conditions. Hypoxia induces CAIX expression in HB cells, and the CAIX inhibitor SLC-0111 has in vitro activity against these malignant cells.