Cancer Specimens Research Articles

A comprehensive investigation of associations between cell death pathways and molecular and clinical features in pan-cancer.

Regulated cell death (RCD) pathways play significant roles in tumorigenesis. However, systematic investigation into correlations between RCD and various molecular and clinical features, particularly anti-tumor immunity and immunotherapy response in pan-cancer remains lacking. Using the single-sample gene set enrichment analysis, we quantified the activities of six RCD pathways (apoptosis, autophagy, ferroptosis, cuproptosis, necroptosis, and pyroptosis) in each cancer specimen. Then, we explored associations of these six RCD pathways with tumor immunity, genomic instability, tumor phenotypes and clinical features, and responses to immunotherapy and targeted therapies in pan-cancer by statistical analyses. Our results showed that the RCD (except autophagy) activities were oncogenic signatures, as evidenced by their hyperactivation in late stage or metastatic cancer patients, positive correlations with tumor proliferation, stemness, genomic instability and intratumor heterogeneity, and correlation with worse survival outcomes in cancer. In contrast, autophagy was a tumor suppressive signature as its associations with molecular and clinical features in cancer shows an opposite pattern compared to the other RCD pathways. Furthermore, heightened RCD (except cuproptosis) activities were correlated with increased sensitivity to immune checkpoint inhibitors. Additionally, elevated activities of pyroptosis, autophagy, cuproptosis and necroptosis were associated with increased drug sensitivity in a broad spectrum of anti-tumor targeted therapies, while the elevated activity of ferroptosis was correlated with decreased sensitivity to numerous targeted therapies. RCD (except autophagy) activities correlate with unfavorable cancer prognosis, while the autophagy activity correlate with favorable clinical outcomes. RCD (except cuproptosis) activities are positive biomarkers for anti-tumor immunity and immunotherapy response.

A RADD analysis of DNA damage in endometrial cancer specimens

A RADD analysis of DNA damage in endometrial cancer specimens

Prevalence of targetable and potentially targetable alterations in metastatic/recurrent cervical cancer specimens in a large genomic dataset

Prevalence of targetable and potentially targetable alterations in metastatic/recurrent cervical cancer specimens in a large genomic dataset

Evaluating stiffness of gastric wall using laser resonance frequency analysis for gastric cancer.

Tumor stiffness is drawing attention as a novel axis that is orthogonal to existing parameters such as pathological examination. We developed a new diagnostic method that focuses on differences in stiffness between tumor and normal tissue. This study comprised a clinical application of laser resonance frequency analysis (L-RFA) for diagnosing gastric cancer. L-RFA allows for precise and contactless evaluation of tissue stiffness. We used a laser to create vibrations on a sample's surface that were then measured using a vibrometer. The data were averaged and analyzed to enhance accuracy. In the agarose phantom experiments, a clear linear correlation was observed between the Young's modulus of the phantoms (0.34-0.71 MPa) and the summation of normalized vibration peaks (Score) in the 1950-4050 Hz range (R2 = 0.93145). Higher Young's moduli also resulted in lower vibration peaks at the excitation frequency, signal-to-noise (S/N) ratios, and harmonic peaks. We also conducted L-RFA measurements on gastric cancer specimens from two patients who underwent robot-assisted distal gastrectomy. Our results revealed significant waveform differences between tumor and normal regions, similar to the findings in agarose phantoms, with tumor regions exhibiting lower vibration peaks at the excitation frequency, S/N ratios, and harmonic peaks. Statistical analysis confirmed significant differences in the score between normal and tumor regions (p = 0.00354). L-RFA was able to assess tumor stiffness and holds great promise as a noninvasive diagnostic tool for gastric cancer.

Assessment of Inter-observer Reproducibility of the Residual Cancer Burden Index and Neoadjuvant Chemotherapy Response in Breast Carcinoma

Background : Locally advanced breast cancers are nowadays treated with neoadjuvant chemotherapy (NAC) to downstage the tumor. One way to assess the NAC response is to use “Residual cancer burden index (RCB).” The aim of the study was to assess inter-pathologist reproducibility of residual cancer burden index and to evaluate different clinico-pathological parameters that determine the pathological response. Methods: In this retrospective cohort study, surgically excised specimens of 49 NAC treated breast cancer were examined by histopathology and immunohistochemistry over a period of one and half years. Four pathologists with different level of experience reviewed the reports (unaware of original RCB index) and slides and assigned the RCB indices for each case. Clinical, histopathological and immunohistochemical parameters were evaluated.. Fleiss- Kappa statistics was applied to assess interobserver reproducibility of RCB index. Results: No significant relationship was observed between RCB index (of original report) with age, largest tumor dimension and number of chemotherapy cycles . The RCB index of 49 cases as assigned by four pathologists was calculated by Fleiss-kappa statistics and it showed good overall agreement (82.6%). Conclusion: It has been observed that there is no significant relation between pathological response to NAC with age, largest tumor dimension and number of chemotherapy cycles of breast carcinoma. It can also be concluded that RCB can be reliably used to report neoadjuvant chemotherapy treated specimens of breast cancer.

Transgelin 2 guards T cell lipid metabolism and antitumour function.

Mounting effective immunity against pathogens and tumours relies on the successful metabolic programming of T cells by extracellular fatty acids1-3. Fatty-acid-binding protein 5 (FABP5) has a key role in this process by coordinating the efficient import and trafficking of lipids that fuel mitochondrial respiration to sustain the bioenergetic requirements of protective CD8+ T cells4,5. However, the mechanisms that govern this immunometabolic axis remain unexplored. Here we report that the cytoskeletal organizer transgelin 2 (TAGLN2) is necessary for optimal fatty acid uptake, mitochondrial respiration and anticancer function in CD8+ T cells. TAGLN2 interacts with FABP5 to facilitate its cell surface localization and function in activated CD8+ T cells. Analyses of ovarian cancer specimens revealed that endoplasmic reticulum (ER) stress responses induced by the tumour microenvironment repress TAGLN2 in infiltrating CD8+ T cells, thereby enforcing their dysfunctional state. Restoring TAGLN2 expression in ER-stressed CD8+ T cells increased their lipid uptake, mitochondrial respiration and cytotoxic capacity. Accordingly, chimeric antigen receptor T cells overexpressing TAGLN2 bypassed the detrimental effects of tumour-induced ER stress and demonstrated therapeutic efficacy in mice with metastatic ovarian cancer. Our study establishes the role of cytoskeletal TAGLN2 in T cell lipid metabolism and highlights the potential to enhance cellular immunotherapy in solid malignancies by preserving the TAGLN2-FABP5 axis.

The Debated Issue on Tissue Copper Levels in Colorectal Cancer Patients: A Meta-analysis and Replication Study.

Colorectal cancer (CRC) is a growing public health problem. Several clinical studies have shown a potentially oncogenic role of copper in CRC progression, but the reports are inconsistent. To examine published evidence on the association between tissue copper status and CRC, we carried out a systematic review and meta-analysis, searching Cochrane Library, EBSCOhost, Embase, ProQuest, PubMed/Medline, Scopus, and Web of Science for studies reporting colon tumor and matched non-cancerous tissue copper concentrations in CRC patients for articles published till June 2023. Based on a random effects model, standardized mean differences (SMD) were assessed. We also completed a replication study on 17 CRC patients that analyzed copper levels in both cancer tissue specimens and healthy mucosa dissected from the same patient. Thirteen studies investigating copper levels (including the replication study) in colorectal specimens from a pooled total of 312 CRC and 298 healthy mucosa were selected. Our meta-analysis estimated a high between-study heterogeneity (I2 = 96%) and lower levels of copper in CRC tissue cancer specimens than in matched healthy mucosa: the decrease was equal to - 0.74 (95% CI, - 2.18; 0.71) but was not significant. The replication study showed a significant decrease in tissue cancer specimens. Sensitivity analyses of the meta-analysis revealed that pre-analytical methodology for tissue preparation significantly reduced the between-study heterogeneity strongly influencing copper levels (p < 0.01), indicating a copper decrease in the cytoplasmic copper pool of the tumor tissue suggesting a rapid turnover of the metal in cancer cells.

Multiwavelength Surface-Enhanced Raman Scattering Fingerprints of Human Urine for Cancer Diagnosis.

Label-free surface-enhanced Raman spectroscopy (SERS) is capable of capturing rich compositional information from complex biosamples by providing vibrational spectra that are crucial for biosample identification. However, increasing complexity and subtle variations in biological media can diminish the discrimination accuracy of traditional SERS excited by a single laser wavelength. Herein, we introduce a multiwavelength SERS approach combined with machine learning (ML)-based classification to improve the discrimination accuracy of human urine specimens for bladder cancer (BCa) diagnosis. This strategy leverages the excitation-wavelength-dependent SERS spectral profiles of complex matrices, which are mainly attributed to wavelength-related vibrational changes in individual analytes and differences in the variation ratios of SERS intensity across different wavelengths among various analytes. By capturing SERS fingerprints under multiple excitation wavelengths, we can acquire more comprehensive and unique chemical information on complex samples. Further experimental examinations with clinical urine specimens, supported by ML algorithms, demonstrate the effectiveness of this multiwavelength strategy and improve the diagnostic accuracy of BCa and staging of its invasion with SERS spectra from increasing numbers of wavelengths. The multiwavelength SERS holds promise as a convenient, cost-effective, and broadly applicable technique for the precise identification of complex matrices and diagnosis of diseases based on body fluids.

N-linked fucosylated glycans are biomarkers for prostate cancer with a neuroendocrine and metastatic phenotype.

Prostate cancer (PCa) is a heterogeneous disease with a spectrum of pathology and outcomes ranging from indolent to lethal. Although there have been recent advancements in prognostic tissue biomarkers, limitations still exist. We leveraged Matrix Assisted Laser Desorption Ionization (MALDI) imaging of formalin-fixed, paraffin embedded (FFPE) prostate cancer specimens to determine if N-linked glycans expressed in the extracellular matrix of lethal neuroendocrine prostate cancer were also expressed in conventional prostate adenocarcinomas that were associated with poor outcomes. We found that N-glycan fucosylation was abundant in neuroendocrine prostate cancer as well as adenocarcinomas at time of prostatectomy that eventually developed recurrent metastatic disease. Analysis of patient derived xenografts revealed that this fucosylation signature was enriched differently across metastatic disease organ sites, with the highest abundance in liver metastases. These data suggest that N-linked fucosylated glycans could be an early tissue biomarker for poor PCa outcomes. Implications: These studies identify that hyper-fucosylated N-linked glycans are enriched in neuroendocrine prostate cancer and conventional prostate adenocarcinomas that progress to metastatic disease, thus advancing biomarker discovery and providing insights into mechanisms underlying metastatic disease.

Evaluating glycocalyx morphology and composition in frozen and formalin-fixed liver tumor sections

BackgroundThe glycocalyx (GCX) is a glycan structure on the vascular endothelium and cancer cells. It is crucial for blood flow regulation, tumor invasion, and cancer drug resistance. Understanding the role of GCX in human tumors could help develop new cancer biomarkers and therapies. AimThis study aimed to demonstrate microstructural changes in human primary and metastatic liver tumors (henceforth termed liver tumors) by visualizing GCX using surgical specimens and comparing formalin-fixed paraffin-embedded sections (FFPEs) with frozen sections. The results of lectin staining were also compared between frozen and FFPE specimens to determine which was more useful for accurately assessing GCX structure and composition. MethodsLiver tumors and normal tissue samples from three patients were collected and processed into FFPEs and frozen sections, respectively. Lanthanum nitrate staining and scanning electron microscopy (SEM) were used to assess the GCX structures. Twenty lectins were analyzed for their glycan components in the samples. ResultsSEM revealed significant differences in GCX morphology among the cancer specimens. Frozen sections provided a more accurate GCX evaluation than FFPEs, showing distinct glycan compositions in hepatocellular carcinoma, colorectal carcinoma liver metastases, and melanoma liver metastases. Hepatocellular carcinoma samples exhibited a loss of N-acetylgalactosamine-related lectins. ConclusionThe results revealed that liver tumors have distinct and bulky GCX compared to normal liver tissue, while frozen sections are more reliable for GCX evaluation. These findings highlight glycan alterations in liver tumors and contribute to the development of new cancer therapies targeting GCX on tumor cell surfaces.

Molecular Tumor Testing on Colorectal Adenocarcinoma Specimens in a Large Community-Based Healthcare System.

This study aimed to describe the adherence of National Comprehensive Cancer Network guidelines to perform genetic screening for all colorectal cancer (CRC) specimens with molecular tumor testing, eg, immunohistochemical (IHC) testing, in a large community-based healthcare setting. The study also identified trends involving characteristics of CRC, individual reporting physician, and physician location and examined the potential impact of these trends on the performance of molecular tumor testing. This was a retrospective, multi-center study using a centralized pathology database to assess molecular testing on CRC specimens. The primary endpoint was whether tumor testing of a CRC specimen was performed. Secondary endpoints included tumor location within the colon (ie, the right or left side), year of CRC diagnosis, and location of the pathologist within the Advocate Aurora Health (AAH) system. The data were collected from 2016 to 2020. A total of 2469 CRC cases, reviewed by 47 pathologists practicing in five separate hospitals, were identified within the AAH system for the selected five-year time period. IHC testing was performed in 1666 of these specimens (67.5%). There was no statistical difference between CRC sidedness and IHC testing performed (p = 0.9). There were no discernible features or trends for the ordering of IHC testing among different pathologists. Molecular tumor testing for CRC specimens in this large community-based healthcare setting was inconsistent and below the ideal adherence rate of 100%. Secondary findings offered neither explanation nor trends in likelihood to send samples for IHC testing. Education would be beneficial for pathologists and all physicians who care for patients with CRC in community-based health care settings.

Association of glutaminase expression with immune-suppressive tumor microenvironment, clinicopathologic features, and clinical outcomes in endometrial cancer

ObjectiveIncreased glutamine metabolism by cancer cells via upregulation of the drug-targetable enzyme glutaminase may contribute to an immune-suppressive tumor microenvironment. Inhibiting glutamine metabolism can not only suppress tumor growth, but...

Ex vivo fluorescence-guided resection margin assessment in breast cancer surgery using a topically applied, cathepsin-activatable imaging agent

Up to 40 % of breast cancer patients have a tumor-positive resection margin (TPRM) – defined as cancer cells at the surface of the resected specimen – after breast-conserving surgery (BCS), necessitating re-resection or boost radiation. To prevent these additional treatments, intraoperative near-infrared (NIR) fluorescence imaging with the topically applied, cathepsin-activatable imaging agent AKRO-6qcICG might be used to detect TPRMs and guide additional resection. Here, to validate its performance, the agent is topically applied to all surfaces of freshly resected breast cancer specimens (n = 11 patients) and to 3–5 mm thick tissue slices of the specimens (n = 26 patients). NIR fluorescence images of the resection surfaces and tissue slices are acquired and correlated to final histopathology. AKRO-6qcICG detects TPRMs with a sensitivity, specificity, PVV, and NPV of 100 %, 67 %, 10 %, and 100 %, respectively. On the tissue slices, the fluorescence signal has a median tumor-to-background ratio of 1.8. These findings indicate that topically applied AKRO-6qcICG can visualize TPRMs ex vivo with a high sensitivity and NPV, with sufficient contrast to adjacent healthy breast tissue.

Methylation patterns at the adjacent CpG sites within enhancers are a part of cell identity

BackgroundIt is generally accepted that methylation status of CpG sites spaced up to 50 bp apart is correlated, and accumulation of locally disordered methylation at adjacent CpG sites is involved in neoplastic transformation, acting in similar way as stochastic accumulation of mutations.ResultsWe used EPIC microarray data from 596 samples, representing 12 healthy tissue and cell types, as well as 572 blood cancer specimens to analyze methylation status of adjacent CpG sites across human genome, and subsequently validated our findings with NGS and Sanger sequencing. Our analysis showed that there is a subset of the adjacent CpG sites in human genome, with cytosine at one CpG site methylated and the other devoid of methyl group. These loci map to enhancers that are targeted by families of transcription factors involved in cell differentiation. Moreover, our results suggest that the methylation at these loci differ between alleles within a cell, what allows for remarkable level of heterogeneity of methylation patterns. However, different types of specialized cells acquire only one specific and stable pattern of methylation at each of these loci and that pattern is to a large extent lost during neoplastic transformation.ConclusionsWe identified a substantial number of adjacent CpG loci in human genome that display remarkably stable and cell type specific methylation pattern. The methylation pattern at these loci appears to reflect different methylation of alleles in cells. Furthermore, we showed that changes of methylation status at those loci are likely to be involved in regulation of the activity of enhancers and contribute to neoplastic transformation.

Intestinal Lactobacillus murinus-derived small RNAs target porcine polyamine metabolism

Gut microbiota plays a vital role in host metabolism; however, the influence of gut microbes on polyamine metabolism is unknown. Here, we found germ-free models possess elevated polyamine levels in the colon. Mechanistically, intestinal Lactobacillus murinus-derived small RNAs in extracellular vesicles down-regulate host polyamine metabolism by targeting the expression of enzymes in polyamine metabolism. In addition, Lactobacillus murinus delays recovery of dextran sodium sulfate-induced colitis by reducing polyamine levels in mice. Notably, a decline in the abundance of small RNAs was observed in the colon of mice with colorectal cancer (CRC) and human CRC specimens, accompanied by elevated polyamine levels. Collectively, our study identifies a specific underlying mechanism used by intestinal microbiota to modulate host polyamine metabolism, which provides potential intervention for the treatment of polyamine-associated diseases.

Correlation of programmed death-ligand 1 expression in tumour cells between diagnostic small biopsies performed by radial EBUS and surgical specimens of peripheral lung cancer

Background and objectiveExpression of programmed death-ligand 1 (PD-L1) in tumour cells (TCs) is predictive of immunotherapy efficacy in non-small cell lung cancer (NSCLC). Small biopsy samples collected by bronchoscopy are...

Visual pathology reports for communication of final margin status in laryngeal cancer surgery

BackgroundPositive margins are frequently observed in total laryngectomy (TL) specimens. Effective communication of margin sampling sites and final margin status between surgeons and pathologists is crucial. In this study, we evaluate the utility of multimedia visual pathology reports to facilitate interdisciplinary discussion of margin status in laryngeal cancer surgery. MethodsEx vivo laryngeal cancer surgical specimens were three-dimensional (3D) scanned before standard of care pathological analysis. Using computer-aided design software, the 3D model was annotated to reflect inking, sectioning, and margin sampling sites, generating a visual pathology report. These reports were distributed to head and neck surgeons and pathologists postoperatively. ResultsFifteen laryngeal cancer surgical specimens were 3D scanned and virtually annotated from January 2022 to December 2023. Most specimens (73.3%) were squamous cell carcinomas (SCCs). Among the cases, 26.7% had final positive surgical margins, whereas 13.3% had close margins, defined as <5 mm. The visual pathology report demonstrated sites of close or positive margins on the 3D specimens and was used to facilitate postoperative communication between surgeons and pathologists in 85.7% of these cases. Visual pathology reports were presented in multidisciplinary tumor board discussions (20%), email correspondences (13.3%), and teleconferences (6.7%), and were referenced in the final written pathology reports (26.7%). Conclusions3D scanning and virtual annotation of laryngeal cancer specimens for the creation of visual pathology reports is an innovative approach for postoperative pathology documentation, margin analysis, and surgeon–pathologist communication.

Rapid full-color serial sectioning tomography with speckle illumination and ultraviolet excitation

Three-dimensional (3D) high-resolution large-volume imaging has remained a challenge. Translational rapid ultraviolet-excited sectioning tomography (TRUST) achieves rapid and cost-effective whole-organ subcellular imaging through iterative optical scanning and mechanical sectioning. However, the axial resolution is limited by the mechanical sectioning thickness or the UV light penetration depth in tissue. Here, assisted with high-and-low-frequency (HiLo) microscopy (HiLoTRUST), the optical sectioning thickness has been reduced from tens of micrometers to ~5.8 µm. In addition, HiLoTRUST has attained a finer mechanical sectioning thickness (10–15 µm) compared to TRUST (50 µm). For high-content imaging as in TRUST, we employed two additional UV light-emitting diodes (LEDs) specifically for uniform illumination. The full-color imaging ability and improved axial resolution of HiLoTRUST have been validated by two-dimensional (2D)/3D imaging of various mouse organs and human lung cancer specimens. HiLoTRUST offers a cost-effective, full-color, and high-resolution 3D imaging approach, showing its great potential in 3D histology applications.

Digital mapping of resected cancer specimens: The visual pathology report

BackgroundThe current standard-of-care pathology report relies only on lengthy written text descriptions without a visual representation of the resected cancer specimen. This study demonstrates the feasibility of incorporating virtual, three-dimensional (3D) visual pathology reports to improve communication of final pathology reporting. Materials and methodsSurgical specimens are 3D scanned and virtually mapped alongside the pathology team to replicate grossing. The 3D specimen maps are incorporated into a hybrid visual pathology report which displays the resected specimen and sampled margins alongside gross measurements, tumor characteristics, and microscopic diagnoses. ResultsVisual pathology reports were created for 10 head and neck cancer cases. Each report concisely communicated information from the final pathology report in a single page and contained significantly fewer words (293.4 words) than standard written pathology reports (850.1 words, p < 0.01). ConclusionsWe establish the feasibility of a novel visual pathology report that includes an annotated visual model of the resected cancer specimen in place of lengthy written text of standard of care head and neck cancer pathology reports.

Utility of an Archival Dried Blood Spot (DBS) Collection from HIV-Infected Individuals with and without Cancer in a Resource-Limited Setting.

The frequency of virus-associated cancers is growing worldwide, especially in resource-limited settings. One of the biggest challenges in cancer research among people living with HIV (PLWH) has been understanding how infection with both HIV and Kaposi sarcoma-associated herpesvirus (KSHV) promotes the pathogenesis of Kaposi sarcoma (KS), the most common cancer among PLWH worldwide and a significant public health problem in regions with high prevalence of HIV such as Sub-Saharan Africa (SSA). The AIDS and Cancer Specimen Resource (ACSR) provides samples for research, including dried blood spots (DBS) that were collected from large clinical epidemiology studies of KSHV and KS in PLWH conducted more than a decade ago in SSA. Here, we validated the quality of DNA derived from DBS samples from SSA studies and provided evidence of quantitative recovery of inflammatory cytokines using these DBS samples through comparison with paired frozen plasma. Significant differences in DNA, protein yields, and inflammatory biomarker levels were also observed between PLWH with/without KS. Establishing the fitness of DBS samples for studies of KS pathogenesis extends the number of projects that can be supported by these ACSR special collections and provides evidence that DBS collection for future KS research is a practical option in resource-limited settings.