Characteristics Of Tumor Tissue Research Articles

Characterization of testicular embryonic-type neuroectodermal tumor and embryonic-type neuroectodermal tissue admixed with mature neuro-glial tissue using a broad immunohistochemical panel.

Embryonic-type neuroectodermal tumor (ENT) is a somatic-type malignancy characterized by overgrowth of embryonic-type neuroectodermal tissue (EtNT). In germ cell tumors, EtNT is frequently intermingled with other components that may exhibit significant morphologic overlap [mature neuro-glial tissue (MNGT), nephroblastomatous tissues, and primitive endodermal-type glands]. Therefore, the quantification of EtNT (crucial for the diagnosis of ENT) can be challenging. In this study, we investigated the immunohistochemical profile of ENT, EtNT, and MNGT using a broad immunohistochemical panel. We found that SOX2 was the most sensitive marker for EtNT (100%), but it also stained MNGT (28.6%). GFAP and S100 were relatively sensitive (71.4%) and highly specific (GFAP 100%, S100 85.8%) for MNGT, whereas synaptophysin stained both. Combining our results with those of previous studies, we propose that a combination of SOX11, SOX2, GFAP, S100, AFP, villin, CDX2, PAX8, and nuclear WT1 may help to identify and quantify EtNT in germ cell tumors.

Optimizing ctDNA: An Updated Review of a Promising Clinical Tool for the Management of Uveal Melanoma.

Uveal melanoma (UM) is the most common primary malignant intraocular tumor in adults. Distant metastasis is common, affecting around 50% of patients. Prognostic accuracy relies on molecular characterization of tumor tissue. In these patients, however, conventional biopsy can be challenging due to the difficulty of obtaining sufficient tissue for the analysis due to the small tumor size and/or post-brachytherapy shrinkage. An alternative approach is liquid biopsy, a non-invasive technique that allows for real-time monitoring of tumor dynamics. Liquid biopsy plays an increasingly prominent role in precision medicine, providing valuable information on the molecular profile of the tumor and treatment response. Liquid biopsy can facilitate early detection and can be used to monitor progression and recurrence. ctDNA-based tests are particularly promising due to their ease of integration into clinical practice. In this review, we discuss the application of ctDNA in liquid biopsies for UM. More specifically, we explore the emerging technologies in this field and the advantages and disadvantages of using different bodily fluids for liquid biopsy. Finally, we discuss the current barriers to routine clinical use of this technique.

NIMG-03. IMPACT OF CONCURRENT IMMUNOTHERAPY AND STEREOTACTIC RADIOSURGERY ON METASTATIC BRAIN DISEASE: A THREE-DIMENSIONAL MAGNETIC RESONANCE FINGERPRINTING RADIOMIC ANALYSIS

Abstract BACKGROUND Unlike traditional chemotherapy (limited by the blood-brain barrier), the central nervous system penetrance of immunotherapy allows for synergy with stereotactic radiosurgery (SRS), the standard-of-care management of limited brain metastases. Magnetic resonance fingerprinting (MRF) is a novel technology allowing for simultaneous imaging quantification of multiple tissue properties. We present the first serial MRF results in concomitant SRS/immunotherapy for metastatic brain disease. METHODS A patient with known history of small cell lung cancer (SCLC) presented with a seizure. MRI revealed a solitary 1 cm right occipital metastasis, subsequently receiving SRS rather than whole-brain radiation therapy to optimize cognition preservation. Durvalumab (with carboplatin/etoposide) was given one week before SRS (22 Gy single-fraction). Pre-SRS MRF scans were obtained with the Gamma Knife stereotactic headframe in place. Post-SRS MRF scans were obtained at 1, 3, and 5 months. MRF data was processed and region of interest analysis was performed to measure T1 and T2 values within the lesion using MATLAB. RESULTS The mean T1 and T2 values of the solid tumor (ST) in precontrast MRF maps decreased over time with a slight increase at final follow-up. Specifically, the T1 values decreased from 2131 ms (Pre-SRS) to 1018 ms, then 996 ms followed by a slight increase to 1296 ms. Similarly, the T2 values progressively decreased from 143 ms (Pre-SRS) to 45 ms (first follow-up) to 43 ms (3-month follow-up), with an increase (51 ms) at last follow-up. CONCLUSIONS In this first report of MRF in concomitant immunotherapy/Gamma Knife SRS (and the first in a SCLC patient). MRF demonstrated serial drop in T1 and T2 over time followed by slight increase at 5 months follow-up. The alterations observed in T1 and T2 MRF are compatible with post-treatment effects in the tumor's tissue characteristics, including decreased cellularity, water content, and presence of paramagnetic substances.

SURG-10. DEVELOPMENT OF 2 COMPLEMENTARY INNOVATIVE APPROACHES FOR REAL-TIME, LABEL-FREE INTRAOPERATIVE TUMOR DETECTION TO ENHANCE EXTENT OF RESECTION OF LOW GRADE GLIOMAS

Abstract Brain tumor surgery aims to maximize tumor resection while avoiding neurological deficits. Accurate characterization of tissue and delineation of resection margins are essential to achieve optimal surgical outcome. Hyperspectral imaging (HSI) and Real-time Rapid Evaporative Ionization Mass Spectrometry ( REIMS) are both novel technological adjuncts able to accurately detect intraoperatively zones of low grade glioma without substantially altering the surgical work flow. For HSI, we successfully demonstrate how an HSI system can interface with a clinically approved surgical microscope making use of the microscope’s available light sources and optical ports. We integrated the HSI system into the clinical workflow during brain surgery, specifically for resections of low-grade gliomas (LGG). During the study the acquired dataset was used to train an AI algorithm to detect LGG, providing 81% accuracy on unseen data. Real-time Rapid Evaporative Ionization Mass Spectrometry (REIMS) enables in-situ tissue characterization based on the mass spectrometric analysis of electrosurgical vapors generated during dissection. We demonstrate the use of REIMS for the molecular characterization of brain tumor tissue, thereby providing quasi real-time assessment of tumor type. A classification model containing 31 sampling points in normal brain tissue and 93 in glial tumor tissue provided 89.3% sensitivity and 91.1% specificity. Both techniques, HSI and REIMS display a high intraoperative diagnostic accuracy in terms of glioma tissue detection and are complementary, real-time and label-free methods which we developed and tested up to the stage of high Technology Readiness levels (TRL) of 7 and 5 respectively.

Abstract 18453: Giant Right Atrial Lipoma Inducing Atrial Flutter and Tachycardia-Mediated Cardiomyopathy: The Value of Multimodality Cardiac Imaging

Case Presentation: A 60-year-old male who presented with progressive dyspnea on exertion and atrial flutter with rapid ventricular response. His TTE showed a large (5.1 x 3.9 cm) right atrial (RA) mass occupying 80% of a severely dilated RA attached to the lateral wall (Fig A) and severe global LV hypokinesis with an ejection fraction of 20 - 25%. A TEE was then performed to further characterize this mass and showed a large (6.3 x 5.5 x 3.7 cm), heterogeneously echoreflectant, bi-lobed, and partially mobile RA mass attached to the lateral wall (Fig B,C) just below the superior vena cava and extending near the tricuspid valve annulus with sparing of the leaflets and only mild tricuspid regurgitation. At last, a chest CT scan showed a large (5.5 x 4.5 x 3.3 cm) mass which was tissue characterized as RA lipoma (Fig D). Therefore, patient underwent an uncomplicated surgical resection of the mass with partial removal of RA free wall (Fig D,E) repaired with a pericardial patch. Pathology confirmed a RA lipoma. Patient’s atrial flutter was then ablated, and patient was discharged home in stable condition. Discussion: This case illustrates an unreported cavitary giant RA lipoma inducing atrial flutter and tachycardia-mediated cardiomyopathy and emphasizes the importance of multimodality cardiac imaging in its diagnosis and management. Cardiac lipomas are rare benign tumors usually of small size and therefore mostly incidentally detected. They can rarely lead to embolization, conduction abnormalities, and flow obstruction requiring surgical resection. In this patient, pre-operative echocardiography and CT imaging were critical in the assessment of the tumor size, tissue characterization, location, motion, relation or extension to other cardiac structures, and obstruction or dysfunction of heart valves. Pre-and-intraoperative echocardiography were also essential in planning and performing the successful surgical resection of the RA lipoma.

Prevalence of pathogenic germline variants in a cohort of patients with early onset non-small cell lung cancer (EOLUNG).

10630 Background: Patients with early onset lung cancer might be more likely to carry pathogenic (or likely-pathogenic) germline variants (PGV) in genes associated with cancer predisposition. However, germline testing is not recommended in this population. We designed this study to determine the prevalence of PGVs in patients with early onset lung cancer. Methods: This prospective, multicenter cohort study assessed PGV in patients younger than 51 years diagnosed with non-small cell lung cancer (NSCLC) in 3 sites at the Catalan Institute of Oncology between June 2018 to May 2022. Genomic DNA was sequenced using a custom-designed NGS panel covering 164 cancer-predisposing genes and results were discussed in a multidisciplinary tumor board. Results: 138 patients were included. Median age was 45.5 (28-50) years; 49% were females; 79% were ever-smokers with a median packs-year of 24 and median age of tobacco initiation of 16 years old. Most patients had non-squamous histology (88%) and had stage IV (62%) at diagnosis. Somatic oncogenic drivers were found in 74 patients (54%): EGFR 27 (20%); ALK 22 (16%); KRAS 20 (14%); RET 3 (2%); ROS1 1 (1%); BRAF V600E 1 (1%). Only 4% had past personal history of cancer and 50% had family history of cancer in a first-degree relative, being lung and breast cancer the most common tumors. Overall, 20 patients (14%) carried PGVs involving 12 genes associated with cancer predisposition: PARK2 (n=4); SBDS (n=3); NBN (n=2); ATM (n=2); TSC1 (n=2) and BLM, FANCA, MCPH1, PMS2, POLH, SDHA, RECQL4 (n=1, each). Four patients (3%) fulfilled criteria to be referred to genetic counseling clinic. There were no significant differences in clinical and molecular characteristics among patients with PGVs compared to their counterparts (Table). Conclusions: In this prospective cohort, 14% of patients with early onset NSCLC harbored germline PGVs. As clinicopathological and genomic features were not associated with PGVs, germline testing might be considered in addition to comprehensive genomic characterization of tumor tissue in young patients with NSCLC. However, only a minority of PGVs were deemed clinically actionable.[Table: see text]

Relevant Membrane Transport Proteins as Possible Gatekeepers for Effective Pharmacological Ascorbate Treatment in Cancer.

Despite the increasing number of newly diagnosed malignancies worldwide, therapeutic options for some tumor diseases are unfortunately still limited. Interestingly, preclinical but also some clinical data suggest that the administration of pharmacological ascorbate seems to respond well, especially in some aggressively growing tumor entities. The membrane transport and channel proteins are highly relevant for the use of pharmacological ascorbate in cancer therapy and are involved in the transfer of active substances such as ascorbate, hydrogen peroxide, and iron that predominantly must enter malignant cells to induce antiproliferative effects and especially ferroptosis. In this review, the relevant conveying proteins from cellular surfaces are presented as an integral part of the efficacy of pharmacological ascorbate, considering the already known genetic and functional features in tumor tissues. Accordingly, candidates for diagnostic markers and therapeutic targets are mentioned.

Lipidomic study and diagnosis of hepatocellular carcinoma tumor with rapid evaporative ionization mass spectrometry.

Liver cancer is generally considered the leading cause of cancer deaths worldwide, and hepatocellular carcinoma (HCC) contributes to more than 90% of liver cancers. The altered lipid metabolism for rapid cancer cell growth and tumor formation has been frequently proven. In this study, an ambient ionization mass spectrometry technique, rapid evaporative ionization mass spectrometry (REIMS) using a monopolar electric knife, called iKnife, was systematically optimized and employed for ex vivo analysis of 12 human HCC tumor tissue specimens together with the paired paracancerous tissue (PT) and noncancerous liver tissue (NCT) specimens. Nine free fatty acids and 34 phospholipids were tentatively identified according to their extract masses and/or tandem mass spectra. With the help of statistical methods, 7 free fatty acids and 10 phospholipids were distributed differently in 3 types of liver tissue specimens (95% confidence interval). The box plots showed these characterized lipid metabolites varied in PT, HCC, and NCT. Compared with PT and NCT, the upregulations of four common fatty acids FA 18:0, FA 20:4, FA 16:0, and FA 18:1, together with phospholipids PC 36:1, PE 38:3, PE (18:0/20:4), PA (O-36:1), PC (32:1), PC 32:0, PE 34:0, and PC (16:0/18:1), were found in HCC specimens. The sensitivity and specificity of the established statistic model for real-time HCC tumor diagnosis were 100% and 90.5%, respectively. This study demonstrated that the described REIMS technique is a potential method for rapid lipidomic analysis and characterization of HCC tumor tissue.

Abstract 46: High-plex spatial transcriptomic characterization of canine tumor tissue

Abstract Background: Combination therapy to treat hematological and solid malignancies including chemotherapy, radiation, targeted and immunotherapy all hold huge potential for eliciting clinical responses. Informative pre-clinical testing of these approaches can be greatly facilitated using immune competent animals with spontaneous tumors. Pet dogs are immunologically outbred, immune competent and develop spontaneous tumors such as non Hodgkin’s lymphoma, glioblastoma, osteosarcoma, urothelial carcinoma and melanoma that share remarkable clinical, biological and genetic features with their human counterparts. As such, pre clinical testing of therapeutic approaches in dogs with cancer promises to accurately inform human clinical trial design. For this comparative approach to provide maximum information to accelerate human clinical translation of novel combination therapies and identify correlative biomarkers of therapeutic response, it is necessary to develop research tools for deep interrogation of the canine tumor microenvironment (TME). Here we present spatial transcriptomic analysis of multiple canine tumor and tissue types using GeoMx® digital spatial profiler (DSP) Canine Cancer Atlas (CCA) panel. Methods: FFPE slides or tissue microarrays were used to profile tumor and normal tissue from canines. Each slide was stained with tissue specific immunofluorescent antibodies, including Pan-cytokeratin, CD45, Vimentin, IBA1, CD3, and/or CD68. Regions of interest were selected to assess the TME and normal tissue as possible. Slides were then run on the DSP using the CCA panel that contains 1900-canine specific genes using standard DSP methods. Results: We were able to spatially detect over 1700 genes across multiple tissue types from canines, including osteosarcoma, glioblastoma, melanoma and normal tissues. Genes were detected in spatial compartments including malignant tumor, tumor stroma and normal tissue. Conclusions: Together the GeoMx CCA allow for interrogation of the TME of multiple tumor types and has the potential to inform spatial biomarkers for response to therapy, as well as translate the effectiveness of these therapies to humans. Citation Format: Sarah E. Church, Cheryl London, Christine M. Toedebusch, Ben Sutton, Sarah Weigel, Erin Piazza. High-plex spatial transcriptomic characterization of canine tumor tissue [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 46.

Genetic Characterization of Ovarian Tumor Tissues from Patients with Epithelial Ovarian Cancer in a Philippine Tertiary Hospital: A Descriptive Study.

This study identified genetic variations in ovarian tumor specimens from Filipino epithelial ovarian cancer (EOC) patients using next-generation sequencing. Genomic DNA was isolated from formalin-fixed paraffin-embedded ovarian specimens from 8 chemosensitive and 8 chemoresistant EOC patients. Targeted next-generation sequencing was done to identify mutations in hotspot regions of common oncogenes and tumor-suppressor genes. The mutations were cross-referenced with dbSNP and ClinVar databases to identify previously reported alterations, and potentially damaging variants were predicted using PolyPhen-2. Our study has identified 85 unique variants, 35 in chemosensitive EOC, 22 in chemoresistant EOC, and 28 in both. Chemosensitive EOC specimens had more exonic single nucleotide variants than chemoresistant EOC specimens. Of the 50 oncogenes and tumor suppressor genes, KDR gene had the most frequent variations in EOC patients. Two of the unique KDR variants identified were novel mutations. Thirty-nine unique protein-modifying genetic variants were identified in all specimens, the majority of which have been previously reported in dbSNP and ClinVar. This study was the first non-BRCA genetic analysis done on ovarian cancer in Filipino patients. Next-generation sequencing was able to identify previously reported alterations with known therapeutic implications which may benefit from targeted therapy instead of standard chemotherapy regimen.

Quantitative Phosphoproteomics Analysis Uncovers PAK2- and CDK1-Mediated Malignant Signaling Pathways in Clear Cell Renal Cell Carcinoma

Clear cell Renal Cell Carcinoma (ccRCC) is among the 10 most common cancers in both men and women and causes more than 140,000 deaths worldwide every year. In order to elucidate the underlying molecular mechanisms orchestrated by phosphorylation modifications, we performed a comprehensive quantitative phosphoproteomics characterization of ccRCC tumor and normal adjacent tissues. Here, we identified 16,253 phosphopeptides, of which more than 9000 were singly quantified. Our in-depth analysis revealed 600 phosphopeptides to be significantly differentially regulated between tumor and normal tissues. Moreover, our data revealed that significantly up-regulated phosphoproteins are associated with protein synthesis and cytoskeletal re-organization which suggests proliferative and migratory behavior of renal tumors. This is supported by a mesenchymal profile of ccRCC phosphorylation events. Our rigorous characterization of the renal phosphoproteome also suggests that both epidermal growth factor receptor and vascular endothelial growth factor receptor are important mediators of phospho signaling in RCC pathogenesis. Furthermore, we determined the kinases p21-activated kinase 2, cyclin-dependent kinase 1 and c-Jun N-terminal kinase 1 to be master kinases that are responsible for phosphorylation of many substrates associated with cell proliferation, inflammation and migration. Moreover, high expression of p21-activated kinase 2 is associated with worse survival outcome of ccRCC patients. These master kinases are targetable by inhibitory drugs such as fostamatinib, minocycline, tamoxifen and bosutinib which can serve as novel therapeutic agents for ccRCC treatment.

Establishment of 6 pediatric rhabdomyosarcoma patient's derived xenograft models closely recapitulating patients' tumor characteristics.

The prognosis for patients with metastatic and recurrent pediatric rhabdomyosarcoma (RMS) remains poor. The availability of preclinical models is essential to identify promising treatments We established a series of pediatric RMS patient derived xenografts (PDXs), all faithfully mirroring primary tumor characteristics and representing a unique tool for clarifying the biological processes underlying RMS progression and relapse. Fresh tumor samples from 12 RMS patients were implanted subcutaneously in both flanks of immunocompromised mice. PDXs were considered as grafted after accomplishing three passages in mice. Characterization of tumor tissues and models was performed by comparing both morphology and immunoistochemical and fluorescence in situ hybridization (FISH) characteristics. Six PDXs were established, with a successful take rate of 50%. All models closely mirrored parental tumor characteristics. An increased grafting rate for tumors derived from patients with worse outcome (p = 0.006) was detected. For 50% PDXs grafting occurred when the corresponding patient was still alive. Our findings increase the number of available RMS PDX models and strengthen the role of PDXs as useful preclinical tools for patients with unmet medical needs and to develop personalized therapies.

Abstract 2470: Comparison of H-scan ultrasound and diffusion-weighted magnetic resonance imaging of head and neck cancer undergoing neoadjuvant chemotherapy

Abstract Introduction: The use of ultrasound (US) for tumor tissue characterization remains an exciting prospect. The purpose of this research project was to introduce a 3-dimensional (3-D) H-scan US imaging system, which links information in the backscattered US signals to various-sized tissue structures in volume space, and evaluate use for monitoring early response of head and neck cancer to neoadjuvant chemotherapy. Methods: Studies were conducted using female mice (N = 20) implanted in the mammary fat pad with 1 million breast cancer cells (MDA-MB-231). Once tumors reached about 0.8 cm in size, animals were divided into three groups so that mean tumor size in each were comparable. Animals underwent H-scan US and diffusion-weighted magnetic resonance imaging (DW-MRI) at baseline and again at days 1, 3, and 7. After baseline imaging, animals were administered neoadjuvant treatment injections, namely: (1) 0.3 mg sterile saline (control), (2) 5 mg/kg of cisplatin, or (3) 25 mg/kg cisplatin. In vivo US imaging was performed using a Vevo 3100 system (FUJIFILM VisualSonics Inc) equipped with an MX201 linear array transducer. Volume acquisitions contained 400 frames of US image data spaced 50 μm apart. To generate the H-scan US images, Gaussian-weighted Hermite polynomial filters were convolved with the radiofrequency (RF) data to measure the relative strength of the backscattered US signals. In short, the lower frequency signals were assigned to a red (R) channel and the higher frequency components to a blue (B) channel. The unfiltered original RF signal was assigned to the green (G) channel to complete the RGB colormap. Animals were also imaged using a preclinical MRI scanner (BioSpec 3T, Bruker) using a DW-MRI sequence for generation of apparent diffusion coefficient (ADC) maps as a measure of intratumoral water diffusion. After the last day of imaging, animals were euthanized and tumor tissue excised for ex vivo analysis. Results: In vivo results demonstrated that 3-D H-scan US imaging was considerably more sensitive to tumor changes after neoadjuvant treatment as compared to B-scan US. While there was no difference at baseline (p > 0.60), H-scan US images from the cisplatin treated tumors exhibited increased intensity at day 7 (15.6 ± 1.9% and 17.2 ± 3.2% for low and high dosed groups, respectively; p < 0.05) indicating a decrease in aggregate US scatterer size. Furthermore, longitudinal trends found using H-scan US imaging matched those from DW-MRI (p < 0.05). Collectively, these observations were attributed to cancer cell nuclear condensation and apoptotic activity as confirmed by histological analysis. Conclusions: 3-D H-scan US imaging is a promising new tool for monitoring cancer response to neoadjuvant therapy. In vivo results matched those found using DW-MRI, which is an established modality for assessing anticancer treatment using apoptosis-inducing drugs. Citation Format: Haowei Tai, Ryan Margolis, Junjie Li, Brian Trinh, Jane Song, Kenneth Hoyt. Comparison of H-scan ultrasound and diffusion-weighted magnetic resonance imaging of head and neck cancer undergoing neoadjuvant chemotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2470.

Fat Attenuation Index of Renal Cell Carcinoma Reveals Biological Characteristics and Survival Outcome.

PurposeThe computed tomography fat attenuation index (FAI) is an ideal quantifiable imaging factor to identify the inflammation degree of peri-tumor adipose tissue. We aimed to verify whether FAI could reflect peri-tumor adipose inflammation, predict the survival outcome of renal cell carcinoma (RCC), and discover transcriptomic features of tumor tissues and adjacent adipocytes.Materials and MethodsTwo clinical cohorts (Fudan University Shanghai Cancer Center [FUSCC] cohort [n=129] and TCGA cohort [n=218]) were used to explore the association between FAI and clinical outcome. A prospective cohort (n = 19) was used to discover the molecular phenotyping of peri-tumor adipose tissue and tumor tissue according to their FAI value. A clinical cohort (n = 32) in which patients received cyto-reductive surgery was used to reveal the dynamic change of FAI.ResultsA high peri-tumor FAI was significantly associated with a worse outcome in both the FUSCC (HR = 2.28, p = 0.01) and the TCGA cohort (HR = 2.24, p <0.001). The analysis of the RNA expression of paired RCC tissue and peri-tumor fat tissue showed synchronized alterations in pathways such as cytokine–cytokine receptor interaction and complement and coagulation cascades. RCC tissues showed significant alterations in the neuroactive ligand–receptor interaction pathway. Immune deconvolution analysis showed enhanced infiltration of macrophages in high FAI tumor tissues with a lower angiogenesis level. We also observed synchronous dynamic changes in FAI and tumor size after targeted therapy.ConclusionIn summary, FAI could be used in RCC to reflect the biological characteristics and tumor immune micro-environment of both the tumor and the peri-tumor adipose. High peri-tumor FAI had the potential to predict a worse survival outcome in various cohorts. This study demonstrates that the crosstalk exists between a tumor and its micro-environment and could be reflected easily by imaging procedures, which could facilitate clinical decision making.

Colorectal Cancer Heterogeneity and the Impact on Precision Medicine and Therapy Efficacy.

Novel targeted therapies for metastatic colorectal cancer are needed to personalize treatments by guiding specific biomarkers selected on the genetic profile of patients. RAS and BRAF inhibitors have been developed for patients who become unresponsive to standard therapies. Sotorasib and adagrasib showed promising results in phase I/II basket trial and a phase III trial was planned with a combination of these RAS inhibitors and anti-EGFR monoclonal antibodies. Encorafenib and binimetinib were administered in phase II clinical trials for BRAF mutated patients. Pembrolizumab is now recommended in patients exhibiting microsatellite instability. Larotrectinib and entrectinib showed a fast and durable response with few and reversible adverse events in cases with NTRK fusions. Trastuzumab and trastuzumab deruxtecan exhibited promising and durable activity in HER-2-positive patients. In this review, the reasons for an extension of the molecular profile of patients were assessed and placed in the context of the advancements in the understanding of genetics. We highlight the differential effect of new targeted therapies through an ever-deeper characterization of tumor tissue. An overview of ongoing clinical trials is also provided.

Integrative proteomic characterization of trace FFPE samples in early-stage gastrointestinal cancer

BackgroundThe surveillance and therapy of early-stage cancer would be better for patients’ prognosis. However, the extreme trace amount of tissue samples in different stages have limited in portraying the characterization of early-stage cancer. Therefore, we focused on and presented comprehensive proteomic and phosphoproproteomic profiling of the trace FFPE samples from early-stage gastrointestinal cancer, and then explored the potential biomarkers of early-stage gastrointestinal cancer.MethodsIn this study, a quantitative proteomic method with chromatography with mass spectrometry (LC-MS/MS) was used to analyse the proteomic difference between the trace early-stage esophageal squamous cell carcinoma (EESCC) and early-stage duodenum adenocarcinoma cancer (EDAC).ResultsWe identified ~ 6000 proteins and > 10,000 phosphosites in single trace FFPE samples. Comparative analysis disclosed the diverse proteomic features of tumor tissues compared with paired normal tissue of EESCC and EDAC, and revealed the difference of EESCC and EDAC was derived from their origin normal tissue. The distinct separation of EESCC and EDAC illustrated the functions of cell cycle (RB1 T373, EGFR T693) in EESCC, and the positive impacts of apoptosis, metabolic processes (MTOR and MTOR S1261) in EDAC. Furthermore, we deconvoluted the immune infiltration of early-stage gastrointestinal cancer, in which higher immune cell signatures were detected in EDAC, and showed the specific cytokines in EESCC and EDAC. We performed kinases-substates relationship analysis and elucidated the specific proteomic kinase characterization of EESCC and EDAC, and proposed the medicative effects and corresponding drugs for EESCC and EDAC at the clinic.ConclusionWe disclosed the specific immune characterization of the early-stage gastrointestinal cancer, and presented potential makers of EESCC (EGFR, PDGFRB, CDK4, WEE1) and EDAC (MTOR, MAP2K1, MAPK3). This study represents a major stepping stone towards investigating the carcinogenesis mechanism of gastrointestinal cancer, and providing a rich resource for medicative strategy in the clinic.Graphical

Prognostic Value of Postoperative Circulating Tumor DNA in Patients With Early- and Intermediate-Stage Hepatocellular Carcinoma.

Majority of patients with resected early- and intermediate-stage liver cancer will experience postoperative recurrence. This study aimed to investigate the application of ctDNA sequencing in the postoperative period of hepatocellular carcinoma. A total of 96 patients with liver cancer were enrolled in this study. Postoperative peripheral blood samples were collected from all patients after surgery and analyzed using hybridization capture-based next-generation sequencing. Identification of at least one somatic mutation in the peripheral blood was defined as ctDNA+. Five genetic features in tumor tissues were associated with disease-free survival (DFS) using Lasso-Cox model. The area under the receiver operating characteristic curve was 0.813 and 0.882 in training and validation cohorts, respectively. The recurrence rate in ctDNA+ and ctDNA- groups was 60.9% and 27.8%, respectively. Multivariate Cox regression analysis showed that the postoperative ctDNA was an independent prognostic predictor of DFS (HR [hazard ratio]: 6.074, 95% Cl [confidence interval]: 2.648-13.929, P<0.001) and overall survival (OS) (HR: 4.829, 95% CI: 1.508-15.466, P=0.008). Combined ctDNA with AFP improved prediction performance. The median DFS was 2.0, and 8.0 months in ctDNA+/AFP-H and ctDNA+/AFP-L groups, respectively; while ctDNA-/AFP-H and ctDNA-/AFP-L groups had not reached the median time statistically (Log-rank test, P < 0.0001). Furthermore, ctDNA- patients had better prognosis than ctDNA+ patients irrespective of tumor stage. Postoperative ctDNA sequencing has great prognostic value in patients with liver cancer. Patients with positive ctDNA should receive more intensive disease monitoring and more aggressive treatment strategies to improve the survival time.

Spatially resolved transcriptomics of high-grade serous ovarian carcinoma

SummaryBulk and single-cell RNA sequencing do not provide full characterization of tissue spatial diversity in cancer samples, and currently available in situ techniques (multiplex immunohistochemistry and imaging mass cytometry) allow for only limited analysis of a small number of targets. The current study represents the first comprehensive approach to spatial transcriptomics of high-grade serous ovarian carcinoma using intact tumor tissue. We selected a small cohort of patients with highly annotated high-grade serous ovarian carcinoma, categorized them by response to neoadjuvant chemotherapy (poor or excellent), and analyzed pre-treatment tumor tissue specimens. Our study uncovered extensive differences in tumor composition between the poor responders and excellent responders to chemotherapy, related to cell cluster organization and localization. This in-depth characterization of high-grade serous ovarian carcinoma tumor tissue from poor and excellent responders showed that spatial interactions between cell clusters may influence chemo-responsiveness more than cluster composition alone.

ECM Mechanoregulation in Malignant Pleural Mesothelioma.

Malignant pleural mesothelioma is a relatively rare, but devastating tumor, because of the difficulties in providing early diagnosis and effective treatments with conventional chemo- and radiotherapies. Patients usually present pleural effusions that can be used for diagnostic purposes by cytological analysis. This effusion cytology may take weeks or months to establish and has a limited sensitivity (30%–60%). Then, it is becoming increasingly urgent to develop alternative investigative methods to support the diagnosis of mesothelioma at an early stage when this cancer can be treated successfully. To this purpose, mechanobiology provides novel perspectives into the study of tumor onset and progression and new diagnostic tools for the mechanical characterization of tumor tissues. Here, we report a mechanical and biophysical characterization of malignant pleural mesothelioma cells as additional support to the diagnosis of pleural effusions. In particular, we examined a normal mesothelial cell line (Met5A) and two epithelioid mesothelioma cell lines (REN and MPP89), investigating how malignant transformation can influence cellular function like proliferation, cell migration, and cell spreading area with respect to the normal ones. These alterations also correlated with variations in cytoskeletal mechanical properties that, in turn, were measured on substrates mimicking the stiffness of patho-physiological ECM.

Data-driven separation of MRI signal components for tissue characterization

PurposeMRI can be utilized for quantitative characterization of tissue. To assess e.g. water fractions or diffusion coefficients for compartments in the brain, a decomposition of the signal is necessary. Imposing standard models carries the risk of estimating biased parameters if model assumptions are violated. This work introduces a data-driven multicomponent analysis, the monotonous slope non-negative matrix factorization (msNMF), tailored to extract data features expected in MR signals. MethodsThe msNMF was implemented by extending the standard NMF with monotonicity constraints on the signal profiles and their first derivatives. The method was validated using simulated data, and subsequently applied to both ex vivo DWI data and in vivo relaxometry data. Reproducibility of the method was tested using the latter. ResultsThe msNMF recovered the multi-exponential signals in the simulated data and showed superiority to standard NMF (based on the explained variance, area under the ROC curve, and coefficient of variation). Diffusion components extracted from the DWI data reflected the cell density of the underlying tissue. The relaxometry analysis resulted in estimates of edema water fractions (EWF) highly correlated with published results, and demonstrated acceptable reproducibility. ConclusionThe msNMF can robustly separate MR signals into components with relation to the underlying tissue composition, and may potentially be useful for e.g. tumor tissue characterization.