Resected Tumor Samples Research Articles

Multiplex immune profiling reveals the role of serum immune proteomics in predicting response to preoperative chemotherapy of gastric cancer

Responses toward preoperative chemotherapy are heterogeneous in patients with gastric adenocarcinoma. Existing studies in the field focus heavily on the tumor microenvironment (TME), whereas little is known about the relationship between systemic immunity and chemotherapy response. In this study, we collect serum samples from patients with gastric adenocarcinoma before, on, and after preoperative chemotherapy and study their immune proteomics using an antibody-based proteomics panel. We also collect surgically resected tumor samples and incorporate multiple methods to assess their TME. We find that both local and systemic immune features are associated with treatment response. Preoperative chemotherapy induces a sophisticated systemic immune response indicated by dynamic serum immune proteomics. A pretreatment serum protein scoring system is established for response prediction. Together, these findings highlight the fundamental but largely underestimated role of systemic immunity in the treatment of gastric cancer, suggesting a patient stratification strategy based on pretreatment serum immune proteomics.

Prognostic and predictive value of Immunoscore and its correlation with ctDNA in stage II colorectal cancer

ABSTRACT This study aimed to validate the prognostic value of Immunoscore (IS) in stage II colorectal cancer (CRC), and explore the roles of IS and circulating tumor DNA (ctDNA) in the adjuvant treatment for early-stage CRC. Resected tumor samples from stage II CRC patients were collected from the Sun Yat-sen University Cancer Center. The densities of CD3+ and CD8+ lymphocytes were quantified and converted to IS and classified into Low, Intermediate (Int), and High groups according to predefined cutoffs. A total of 113 patients were included in the study. Patients with IS-High, Int, and Low were 43 (38%), 62 (55%), and 8 (7%), respectively. Patients with IS-High had an excellent clinical outcome, with none recurring during a median follow-up of 3 years, including 15 (35%) clinical high-risk patients. The 3-year disease-free survival (DFS) was 100% for IS-High, 76% for IS-Int, and 47% for IS-Low (P < .001). In the multivariate Cox analysis, IS was the only significant parameter associated with DFS. IS-Int and IS-Low patients with adjuvant chemotherapy had improved DFS compared to those who did not receive adjuvant chemotherapy (HR = 0.3; 95% CI 0.1–0.92; P = .026). Among the 49 patients with postoperative ctDNA data, IS-High patients had the lowest ctDNA positivity rate, suggesting that they were most eligible for chemotherapy-free treatment. IS had a strong prognostic value in Chinese patients with stage II CRC and demonstrates its clinical utility. IS and ctDNA will jointly optimize the adjuvant treatment strategies for early-stage CRC.

Spatial meta-transcriptomics reveal associations of intratumor bacteria burden with lung cancer cells showing a distinct oncogenic signature

BackgroundThe lung intratumor microbiome influences lung cancer tumorigenesis and treatment responses, but detailed data on the extent, location, and effects of microbes within lung tumors are missing, information needed for...

Abstract 5546: Inflamed lymph nodes mark active tumor immune response in colorectal cancer patients

Abstract Background Tumor-infiltrating lymphocytes (TILs) can be used to predict immune response in multiple tumors. Currently, the evaluation of TILs relies on pathological and molecular examine on resected tumor samples. Enlarged regional lymph nodes could be attributed to tumor involvement or local inflammation with active immune response. We therefore aimed to investigate the role of inflamed lymph nodes in distinguishing the hot tumor from cold tumor. Methods Fresh-frozen tumor samples from pathologically-confirmed node-negative colorectal cancer patients with inflamed nodes (n= 22) and non-inflamed nodes (n= 23) were used to generate the genome-wide DNA methylation profile using Infinium Methylation EPIC BeadChip. The inflamed and non-inflamed nodes were defined as the pathologically-confirmed negative regional lymph nodes with enlarged size (≥ 5mm) and normal size (&amp;lt; 5mm) in radiological imaging, respectively. A MeTIL algorithm that integrates CD3+ T cell-specific differentially methylated positions was constructed and validated by immunohistochemical assay to evaluate TIL-based tumor immune response in bulk tumor samples. Results The baseline characteristics were balanced between patients with inflamed and non-inflamed nodes. The high abundance of TILs was significantly associated with inflamed nodes (P= 0.025). In addition, we identified a subgroup of superhot tumors characterized by inflamed nodes, enriched TILs and favorable overall survival outcomes (HR 0.53, 95% CI: 0.36-0.97; P = 0.032). Conclusions Inflamed regional lymph nodes in radiological imaging indicate potential active immune response in tumor. Our findings provide an easily accessible biomarker for cancer immunotherapy. Citation Format: Dingcheng Shen, Xiaolin Wang, Meijin Huang, Yanxin Luo, Huichuan Yu. Inflamed lymph nodes mark active tumor immune response in colorectal cancer patients [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 5546.

Gut microbiota composition and outcomes following neoadjuvant therapy in patients with localized pancreatic cancer: A prospective biomarker study.

4143 Background: The prognostic role of the gut microbiome, which modulates cancer development and therapeutic response, is unknown in patients with pancreatic ductal adenocarcinoma (PDAC). With increasing utilization of neoadjuvant therapy (NAT) prior to pancreatic cancer surgery, identification of patient-specific biologic signatures associated with NAT response a priori could help inform PDAC precision medicine. Thus, we assessed the influence of the baseline gut microbiome on clinical outcomes in patients with PDAC receiving NAT. Methods: Stool samples were collected at diagnosis from 42 consenting patients with localized PDAC intending to undergo NAT and surgical resection between 2018 and 2020. 16S rRNA sequencing was completed on pre-NAT stool and resected tumor samples. Microbiota alpha diversity and log transformed taxonomic classifications were utilized in multiple regression analyses to predict oncologic outcomes. Results: Five patients progressed during NAT and eight of the 37 operated patients were deemed NAT responders, demonstrating pathologic near complete or partial response (CAP 0-2), T1N0 AJCC 8th staging, and ≥ 80% CA 19-9 reduction. Compared to the gut, the tumor microbiota demonstrated remarkably reduced Shannon diversity (2.4±0.5 vs 1.5±0.4, p&lt; 0.0001) and distinct taxa (75.2±19.7 vs 8.0±4.5, p&lt; 0.0001) and, accordingly, was not associated with clinical outcomes. Overall, several taxa, including Bacteroides and Akkermansia, were enriched in the gut relative to the tumor ( p&lt; 0.001). The gut microbiota of NAT non-responders had an increased proportion of the gemcitabine metabolizing Enterobacteriaceae (additive log ratio (ALR) -3.4±2.0 vs -8.7±0.8, p= 0.0004). NAT responders, by contrast, had an increased proportion of the adaptive immune cell activating Akkermansia (ALR -0.9±1.2 vs -6.2±3.3, p= 0.0004). The incidence of jaundice or biliary stent placement was associated with relative increases in Enterobacteriaceae (+3.3 ALR, p&lt; 0.01 and +4.9 ALR, p&lt; 0.0001) and decreases in Akkermansia (-3.2 ALR, p= 0.02 and -2.4 ALR, p= 0.057), without altering total gut microbiota diversity. Age, sex, BMI, comorbidities, receipt of pre-NAT antibiotics, diagnostic EUS tumor size, resectability, and pre-NAT CA 19-9 were not predictive of NAT response or survival in a univariate regression model. However, inclusion of gut microbiota data improved the ability of the model to predict NAT response ( p= 0.016, adjusted R2 0.76) and survival ( p= 0.001, adjusted R2 0.89), with Enterobacteriaceae (FDR p= 0.012) and Akkermansia (FDR p= 0.015) being significant negative and positive predictors of NAT response, respectively. Conclusions: The baseline gut microbiota could be leveraged as a biomarker of NAT response and prognosis in patients with pancreatic cancer and warrants further investigation.

Deep Learning-Based Protein Features Predict Overall Survival and Chemotherapy Benefit in Gastric Cancer.

Gastric cancer (GC) is one of the most common malignant tumors with a high mortality rate worldwide and lacks effective methods for prognosis prediction. Postoperative adjuvant chemotherapy is the first-line treatment for advanced gastric cancer, but only a subgroup of patients benefits from it. Here, we used 833 formalin-fixed, paraffin-embedded resected tumor samples from patients with TNM stage II/III GC and established a proteomic subtyping workflow using 100 deep-learned features. Two proteomic subtypes (S-I and S-II) with overall survival differences were identified. S-I has a better survival rate and is sensitive to chemotherapy. Patients in the S-I who received adjuvant chemotherapy had a significant improvement in the 5-year overall survival rate compared with patients who received surgery alone (65.3% vs 52.6%; log-rank P = 0.014), but no improvement was observed in the S-II (54% vs 51%; log-rank P = 0.96). These results were verified in an independent validation set. Furthermore, we also evaluated the superiority and scalability of the deep learning-based workflow in cancer molecular subtyping, exhibiting its great utility and potential in prognosis prediction and therapeutic decision-making.

Enriching for tumor-reactive CD8 TIL (AGX148) leads to effective tumor clearance in a patient-derived xenograph model

Abstract Adoptive Cell Therapy (ACT) with Tumor Infiltrating Lymphocytes (TIL) can induce durable clinical responses in a subset of patients with melanoma; however, the efficacy of standard bulk TIL therapy can be limited. We hypothesize that the therapeutic efficacy of TIL ACT is dependent on the frequency and functionality of tumor-reactive T cells when infused back into patients. Our approach enhances the activity of the ACT product by enriching for the tumor-reactive CD8 TIL prior to ex vivo expansion by sorting on cells that co-express CD103 and CD39. The CD103/CD39 double positive (DP) CD8 TIL can be found in most human solid tumors but at varying frequencies in any given patient. Surgically resected human tumor samples were provided through a collaboration with the EACRI. Tumor samples were flow sorted and expanded ex vivo and patient-matched autologous tumor lines were generated. Tumors were then cocultured with the expanded autologous ACT product (AGX148) in vitro or used in xenograph mouse experiments. The AGX148 TIL products are effective at recognizing and killing autologous tumor cells, in vitro. Upon adoptive transfer into patient-derived tumor-bearing huIL-2 NOG mice, the transferred human T cells increased in frequency, migrated to the tumor, became activated in the tumor and recognized/destroyed established tumors. Interestingly there was little to no in vivo activity of CD8 TIL that did not express these two markers. We have generated a potent therapeutic ACT TIL product (AGX148) through the selective isolation and expansion of tumor-reactive T cells. This TIL product effectively induces durable curative responses in hosts harboring autologous tumors providing rationale for clinical investigation.

Comparison of tumor and two types of paratumoral tissues highlighted epigenetic regulation of transcription during field cancerization in non-small cell lung cancer

BackgroundField cancerization is the process in which a population of normal or pre-malignant cells is affected by oncogenic alterations leading to progressive molecular changes that drive malignant transformation. Aberrant DNA methylation has been implicated in early cancer development in non-small cell lung cancer (NSCLC); however, studies on its role in field cancerization (FC) are limited. This study aims to identify FC-specific methylation patterns that could distinguish between pre-malignant lesions and tumor tissues in NSCLC.MethodsWe enrolled 52 patients with resectable NSCLC and collected resected tumor (TUM), tumor-adjacent (ADJ) and tumor-distant normal (DIS) tissue samples, among whom 36 qualified for subsequent analyses. Methylation levels were profiled by bisulfite sequencing using a custom lung-cancer methylation panel.ResultsADJ and DIS samples demonstrated similar methylation profiles, which were distinct from distinct from that of TUM. Comparison of TUM and DIS profiles led to identification of 1740 tumor-specific differential methylated regions (DMRs), including 1675 hypermethylated and 65 hypomethylated (adjusted P < 0.05). Six of the top 10 tumor-specific hypermethylated regions were associated with cancer development. We then compared the TUM, ADJ, and DIS to further identify the progressively aggravating aberrant methylations during cancer initiation and early development. A total of 332 DMRs were identified, including a predominant proportion of 312 regions showing stepwise increase in methylation levels as the sample drew nearer to the tumor (i.e. DIS < ADJ < TUM) and 20 regions showing a stepwise decrease pattern. Gene set enrichment analysis (GSEA) for KEGG and GO terms consistently suggested enrichment of DMRs located in transcription factor genes, suggesting a central role of epigenetic regulation of transcription factors in FC and tumorigenesis.ConclusionWe revealed distinct methylation patterns between pre-malignant lesions and malignant tumors, suggesting the essential role of DNA methylation as an early step in pre-malignant field defects. Moreover, our study also identified differentially methylated genes, especially transcription factors, that could potentially be used as markers for lung cancer screening and for mechanistic studies of FC and early cancer development.

Evaluation of the impact of pre-operative stereotactic radiotherapy on the acute changes in histopathologic and immune marker profiles of brain metastases

The unique acute effects of the large fractional doses that characterize stereotactic radiosurgery (SRS) or radiotherapy (SRT), specifically in terms of antitumor immune cellular processes, vascular damage, tumor necrosis, and apoptosis on brain metastasis have yet to be empirically demonstrated. The objective of this study is to provide the first in-human evaluation of the acute biological effects of SRS/SRT in resected brain metastasis. Tumor samples from patients who underwent dose-escalated preoperative SRT followed by resection with available non-irradiated primary tumor tissues were retrieved from our institutional biorepository. All primary tumors and irradiated metastases were evaluated for the following parameters: tumor necrosis, T-cells, natural killer cells, vessel density, vascular endothelial growth factor, and apoptotic factors. Twenty-two patients with irradiated and resected brain metastases and paired non-irradiated primary tumor samples met inclusion criteria. Patients underwent a median preoperative SRT dose of 18 Gy (Range: 15–20 Gy) in 1 fraction, with 3 patients receiving 27–30 Gy in 3–5 fractions, followed by resection within median interval of 67.8 h (R: 18.25–160.61 h). The rate of necrosis was significantly higher in irradiated brain metastases than non-irradiated primary tumors (p < 0.001). Decreases in all immunomodulatory cell populations were found in irradiated metastases compared to primary tumors: CD3 + (p = 0.003), CD4 + (p = 0.01), and CD8 + (p = 0.01). Pre-operative SRT is associated with acute effects such as increased tumor necrosis and differences in expression of immunomodulatory factors, an effect that does not appear to be time dependent, within the limited intervals explored within the context of this analysis.

347 Cancer-associated Fibroblasts Affect GBM Progression

INTRODUCTION: Glioblastoma is an extremely aggressive form of brain cancer and despite the many advances made in therapeutic options, outcome and quality of life remains poor. Fibroblasts have been demonstrated to play a role in various systemic cancers by remodeling and reprogramming the tumor microenvironment immunologically and metabolically. Recently, cancer-associated fibroblasts (CAFs) have been identified in glioblastoma (GBM) patients and there is reason to believe that CAFs may have a protumoral effect in GBM progression. METHODS: Nine patients with resected GBM tumor samples were identified by pathology reports and embedded in paraffin, sectioned, and then stained with antibodies for alpha-SMA and GFAP. Ten 40x high-power fields per slide were visualized by a Zeiss Axio Observer microscope and counted by two independent researchers and verified by a board-certified neuropathologist. For in vivo work, 6-week C57BL/6J wild-type female mice were intracranially implanted with either Gl261-luciferase (Gl261-luc) tagged cells alone or in combination with NIH3T3 embryonic fibroblasts. Tumor burden was assessed on post-implantation day 7 via bioluminescent IVIS imaging. RESULTS: We found that fibroblasts were consistently present in human glioblastoma samples albeit in minute quantities of &lt;1%. We then discovered on IVIS that Gl261 cells mixed with NIH3T3 fibroblasts produced larger tumors on day 7 post-implantation. Implantation of these exogenous fibroblasts significantly worsened survival although this effect was not dose-dependent. CONCLUSION: Fibroblasts are present in glioblastoma patient samples. Despite their scarcity, they may still have the ability to affect the tumor microenvironment. Exogenous intracranial implantation of fibroblasts led to increased proliferation of gl261-luc tumor cells. As expected, these larger tumors had a negative effect on mouse survival and suggest that fibroblasts may be a potential avenue of glioblastoma therapy that needs further exploration.

Droplet digital polymerase chain reaction for detection and quantification of cell-free DNA TP53 target somatic mutations in oral cancer.

BACKGROUND: TP53 mutation is a driver mutation of oral carcinogenesis. This study investigated cancerous and cell-free DNA (cfDNA) in patients with oral squamous cell carcinoma (OSCC) to detect the target hotspot somatic mutation of TP53.OBJECTIVE: TP53 target hotspot mutations were determined in surgically resected primary tumor samples from 107 OSCC patients.METHODS: Cancerous and cfDNA samples were examined for mutations through droplet digital polymerase chain reaction (ddPCR) by using mutation-specific assays. The ddPCR results were evaluated alongside clinicopathological data.RESULTS: In total, 23 cases had target TP53 mutations in varying degrees. We found that OSCC had relatively low cfDNA shedding, and mutations were at low allele frequencies. Of these 23 cases, 13 had target TP53 mutations in their corresponding cfDNA. Target somatic mutations in cancerous DNA and cfDNA are related to cervical lymph node metastasis. The cfDNA concentration is related to primary tumor size, lymph node metastasis, and OSCC stage.CONCLUSIONS: Our results show that the detection of TP53 target somatic mutations in OSCC patients by using ddPCR is technically feasible. Low levels of cfDNA may produce different results between cancerous tissue and cfDNA analyses. Future research on cfDNA may quantify diagnostic biomarkers in the surveillance of OSCC patients.

EXTH-20. SINGLE-CELL DRUG ACTIVITY MAPPING IN GLIOBLASTOMA IDENTIFIES EXTENDED DRUG RESPONSE HETEROGENEITY AND THERAPY-INDUCED CELLULAR PLASTICITY

Abstract Glioblastoma (GBM) remains a highly malignant and incurable brain tumour. The inability to achieve clinical improvements in GBM treatment can be attributed to the excessive heterogeneity and plasticity of GBM cells, which is reflected by the presence of various cellular states within each tumour. How each of these tumour cell subtypes respond to therapy remains largely unknown. In this work, we developed a functional diagnostic analysis pipeline to measure therapeutic activity in GBM tumour cells at single-cell resolution using mass cytometry by time-of-flight (CyTOF). By applying an optimised GBM-specific and therapy-tailored antibody panel, we measured therapeutic activity upon exposure to ionising radiation (RT) or a small molecule MDM2 inhibitor (AMG232) in a cohort of patient-derived GBM cell lines (n=14). As such, extended heterogeneity in drug responsiveness was reflected by diverse degrees of alterations in cell cycle progression and apoptotic signalling, in addition to shifts in tumoral phenotypic states implying therapy-induced plasticity. A similar approach was used to measure drug activity in freshly resected tumour samples (n=18) harvested from different tumour regions (core or invasive front) within hours following surgery. Accordingly, we identified highly variable fractions of responsive tumour and microenvironmental cell populations in a patient-specific way. The ability to measure drug activity at single-cell resolution in a patient-tailored manner by applying a genotype-agnostic method, paves the way for advanced precision cancer medicine in GBM by offering a novel approach to more precisely select eligible patients for prospective clinical trials.

Use of Elastic Stain Technique to Detect Histologically Occult Vascular Invasion in Resected Colorectal Carcinomas at Danbury Hospital

Abstract Introduction/Objective Colorectal carcinoma (CRC) represents a leading cause of cancer related death in the western world and is by far the most common malignancy of the gastrointestinal tract. Vascular invasion (VI), in particular extramural VI by tumor is recognized as a feature of colorectal cancer progression, and the latter is an independent prognostic indicator of disease recurrence and survival in colorectal carcinoma. The purpose of this study is to detect VI in resected colorectal tumor samples and compare sensitivity of elastic staining to routine H&amp;E staining at Danbury Hospital. Methods/Case Report A total of 50 colorectal cancer specimens from segmental colon resection or endoscopic polypectomy performed at Danbury Hospital over a 3-year period were included. Histologic sections of each tumor were assessed for the presence of VI by routine H&amp;E staining. Superficial recuts of each tumor were subjected to elastic Von Giesen staining and reassessed for the presence of vascular invasion. Sensitivity of routine H&amp;E staining for the detection of VI was calculated with elastic stain serving as the “gold standard”. Results (if a Case Study enter NA) In this study, VI by carcinoma was identified by H&amp;E stain and/or elastic stain in 17 (34%) out of 50 cases. H&amp;E stain and elastic stain detected VI in 12 (24%) and 16 (32%) out of 50 cases, respectively. There was a single case for which H&amp;E stain showed vascular invasion that was not confirmed by elastic stain, representing a false negative for the H&amp;E technique. Elastic staining detected VI in 5 cases for which the corresponding H&amp;E stain was falsely negative for VI. Overall, vascular invasion status (absent or present) was concordant in 44 (88 %) of the 50 cases. With elastic stain deemed the “gold standard” for VI detection, the sensitivity, specificity, negative predictive value, and positive predictive value of H&amp;E stain were found to be 68.7%, 97.0%, 86.8%, and 91.6%, respectively. Conclusion Although H &amp; E staining of colorectal carcinoma tissue sections have a very good specificity and positive predictive value for the detection of VI, this technique suffers from a suboptimal sensitivity. For these reasons, we agree with previously published literature reports that the use of elastic stain as a supplement to H &amp; E staining should be strongly considered for the proper evaluation and prognostication of colorectal carcinoma specimens.

JCGA: the Japanese version of the Cancer Genome Atlas and its contribution to the interpretation of gene alterations detected in clinical cancer genome sequencing

With the emergence of next-generation sequencing (NGS)-based cancer gene panel tests in routine oncological practice in Japan, an easily interpretable cancer genome database of Japanese patients in which mutational profiles are unaffected by racial differences is needed to improve the interpretation of the detected gene alterations. Considering this, we constructed the first Japanese cancer genome database, called the Japanese version of the Cancer Genome Atlas (JCGA), which includes multiple tumor types. The database includes whole-exome sequencing data from 4907 surgically resected primary tumor samples obtained from 4753 Japanese patients with cancer and graphically provides genome information on 460 cancer-associated genes, including the 336 genes that are included in two NGS-based cancer gene panel tests approved by the Pharmaceuticals and Medical Devices Agency. Moreover, most of the contents of this database are written in Japanese; this not only helps physicians explain the results of NGS-based cancer gene panel tests but also enables patients and their families to obtain further information regarding the detected gene alterations.

Colonic Stent as Bridge to Surgery for Malignant Obstruction Induces Gene Expressional Changes Associated with a More Aggressive Tumor Phenotype.

Colonic stent is recommended as a bridge to elective surgery for malignant obstruction to improve short-term clinical outcomes for patients with colorectal cancer. However, since the oncological outcomes remain controversial, this study aimed to investigate the impact of self-expandable metallic stent (SEMS) on the tumor microenvironment. Patients treated with colonic stent as a bridge to surgery from 2010 to 2015 were identified from hospital records. Tumor biopsies and resected tumor samples of the eligible patients were retrieved retrospectively. Gene expression analysis was performed using the NanoString nCounter PanCancer IO 360 gene expression panel. Of the 164 patients identified, this study included 21 who underwent colonic stent placement as a bridge to elective surgery. Gene expression analysis revealed 82 differentially expressed genes between pre- and post-intervention specimens, of which 72 were upregulated and 10 downregulated. Among the significantly upregulated genes, 46 are known to have protumor functions, of which 26 are specifically known to induce tumorigenic mechanisms such as proliferation, migration, invasion, angiogenesis, and inflammation. In addition, ten differentially expressed genes were identified that are known to promote antitumor functions. SEMS induces gene expressional changes in the tumor microenvironment that are associated with tumor progression in colorectal cancer and may potentiate a more aggressive phenotype. Future studies are warranted to establish optimal timing of surgery after SEMS insertion in patients with obstructive colorectal cancer.

Spatial distribution of immune checkpoint proteins in histological subtypes of lung adenocarcinoma

The most prevalent histological type of non-small cell lung cancer (NSCLC) is adenocarcinoma. The WHO classifies this tumor into subtypes according to the predominant growth pattern such as lepidic, acinar, papillary, solid or micropapillary, each harboring specific molecular features. NSCLC adenocarcinoma heterogeneity is discussed to be a reason for therapy failure using targeted therapy or immune checkpoint inhibitors. For successful therapy of immune checkpoint inhibitors the expression and distribution of the involved immune checkpoint proteins is essential. Therefore, we aimed to investigate the distribution of five prominent immune checkpoint proteins in regard of the histological growth patterns of lung adenocarcinoma. We performed immunohistochemical staining of 84 tumor segments from 22 resected tumor samples to evaluate the expression of PD-L1, PD-1, Nectin-2, PVR, and TIGIT in distinct growth patterns of lung adenocarcinoma. We determined a distinct heterogeneity between and within different tumor segments regarding morphological growth patterns. Furthermore, expression of immune checkpoint proteins varied between different growth pattern areas as well as within one distinct growth pattern. Expression of PVR was significantly higher in solid compared to acinar growth pattern (p= 0.00736). Of note, we detected TIGIT not only on tumor infiltrating lymphocytes but also on tumor cells, whereas non-neoplastic lung tissue was consistently TIGIT-negative. The immune checkpoint protein distribution in histologic subtypes of pulmonary adenocarcinoma displays an considerable intra- and intertumoral heterogeneity implying the requirement of either a multiregion or an adjusted analysis when determining the expression status of PD-1:PD-L1 and the TIGIT:PVR/Nectin-2 checkpoint proteins as predictive markers.

Large-scale molecular epidemiological analysis of AAV in a cancer patient population.

Recombinant adeno-associated viruses (rAAVs) are well-established vectors for delivering therapeutic genes. However, previous reports have suggested that wild-type AAV is linked to hepatocellular carcinoma, raising concern with the safety of rAAVs. In addition, a recent long-term follow-up study in canines, which received rAAVs for factor VIII gene therapy, demonstrated vector integration into the genome of liver cells, reviving the uncertainty between AAV and cancer. To further explore this relationship, we performed large-scale molecular epidemiology of AAV in resected tumor samples and non-lesion tissues collected from 413 patients, reflecting nine carcinoma types: breast carcinoma, rectal cancer, pancreas carcinoma, brain tumor, hepatoid adenocarcinoma, hepatocellular carcinoma, gastric carcinoma, lung squamous, and adenocarcinoma. We found that over 80% of patients were AAV-positive among all nine types of carcinoma examined. Importantly, the AAV sequences detected in patient-matched tumor and adjacent non-lesion tissues showed no significant difference in incidence, abundance, and variation. Additionally, no specific AAV sequences predominated in tumor samples. Our data shows that AAV genomes are equally abundant in tumors and adjacent normal tissues, but lack clonality. The finding critically adds to the epidemiological profile of AAV in humans, and provides insights that may assist rAAV-based clinical studies and gene therapy strategies.

Multiplexed Immunohistochemistry and Digital Pathology as the Foundation for Next-Generation Pathology in Melanoma: Methodological Comparison and Future Clinical Applications.

The state-of-the-art for melanoma treatment has recently witnessed an enormous revolution, evolving from a chemotherapeutic, “one-drug-for-all” approach, to a tailored molecular- and immunological-based approach with the potential to make personalized therapy a reality. Nevertheless, methods still have to improve a lot before these can reliably characterize all the tumoral features that make each patient unique. While the clinical introduction of next-generation sequencing has made it possible to match mutational profiles to specific targeted therapies, improving response rates to immunotherapy will similarly require a deep understanding of the immune microenvironment and the specific contribution of each component in a patient-specific way. Recent advancements in artificial intelligence and single-cell profiling of resected tumor samples are paving the way for this challenging task. In this review, we provide an overview of the state-of-the-art in artificial intelligence and multiplexed immunohistochemistry in pathology, and how these bear the potential to improve diagnostics and therapy matching in melanoma. A major asset of in-situ single-cell profiling methods is that these preserve the spatial distribution of the cells in the tissue, allowing researchers to not only determine the cellular composition of the tumoral microenvironment, but also study tissue sociology, making inferences about specific cell-cell interactions and visualizing distinctive cellular architectures - all features that have an impact on anti-tumoral response rates. Despite the many advantages, the introduction of these approaches requires the digitization of tissue slides and the development of standardized analysis pipelines which pose substantial challenges that need to be addressed before these can enter clinical routine.

Expression Status of Serine Protease 27: A Prognostic Marker for Esophageal Squamous Cell Carcinoma Treated with Preoperative Chemotherapy/Chemoradiotherapy.

A previous study conducted a transcriptome analysis of paired normal and esophageal squamous cell carcinoma (ESCC) tissue samples. The results showed that the expression of serine protease 27 (PRSS27) was perturbed in tumor samples. Hence, this retrospective study aimed to validate the prognostic significance of PRSS27 in patients with preoperative treatment for ESCC. We enrolled 86 patients who received preoperative treatment before esophagectomy for ESCC. The expression of PRSS27 in resected ESCC and biopsy tissue samples obtained before preoperative treatment was evaluated via immunostaining, and its relationship with clinicopathological features and prognosis was analyzed. In normal esophageal mucosa tissue samples, PRSS27 was expressed in the cytoplasm of spinous cells in the suprabasal layer and basal cells in the basal layer. Of 64 resected ESCC tissue samples, 35 (54.7%) expressed PRSS27 and 29 (45.3%) did not. Moreover, ectopic nuclear expression of PRSS27 was observed. Based on multivariate analysis, PRSS27 expression in resected tumor samples was a predictor of poor prognosis. In cases in which PRSS27 expression was observed in biopsy samples, patients with PRSS27-negative resected tumors had a better postoperative prognosis than those with PRSS27-positive resected tumors. PRSS27 expression in resected ESCC tissue samples is a poor prognostic factor in ESCC patients with preoperative treatment. Furthermore, conversion of PRSS27 expression from positive in biopsy samples to negative in resected tumor samples is a predictor of good prognosis in these patients. Hence, PRSS27 status is an effective tool for decision making regarding adjuvant treatment in ESCC patients.

Achieving the Best RNA Quality in Urologic Tumor Samples Intended for Transcriptome Analysis

Purpose: To conduct research on the molecular oncology, physiology, and immunology of urologic tumors requires dissociated viable samples. Improper collection compromises the quality of data attained in molecular and functional assays due to the increased quantities of degraded proteins and RNA. We sought to improve the methods for tissue collection which can avoid generating considerable loss in the viability of cells for further analyses. Materials and Methods: Fifty resected tumor samples from 35 patients were obtained with different surgical techniques and at various time points for viability and RNA quality evaluation. The degradation of RNA was evaluated by its Qubit IQ score, OD 260/280 ratio, total yield, and quantity of β-actin. Results: Snap-frozen tissue samples obtained within 30 min showed better cell viability (P &lt; 0.0001), RNA total yield (P = 0.0081), Qubit ratio (P = 0.003), OD 260/280 ratio (P = 0.4213), and quantity of β-actin (P = 0.0015). Moreover, the bladder tumor samples collected from transurethral biopsy presented more satisfied cell viability results than the ones resected by transurethral electroresection (P &lt; 0.0001). Conclusion: Tumor samples should be processed or frozen freshly within 30 min once removed from human body. Furthermore, transurethral biopsy of bladder tumor is considered a better method for collecting samples for further molecular oncology studies. The high-quality RNA produced enable researchers to conduct more reliable studies by avoiding the experimental artifacts due to the presence of cellular debris or dead cells.