Colorectal Cancer Patient Samples Research Articles

AURKA inhibition shows promise as a therapeutic strategy for ARID1A-mutant colorectal cancer

PurposeMutations in ARID1A frequently occur in colorectal cancer (CRC) cells. However, there are currently no clinical treatment options specifically addressing this aberration. The preliminary in vitro experiments revealed a synthetic lethal interaction between ARID1A and Aurora kinase A (AURKA) in colorectal cancer (CRC) cells.MethodsWe collected samples from 80 CRC patients and evaluated the efficacy of AURKA inhibitor (AURKAi) using the ATP-tumor chemosensitivity assay (ATP-TCA) on untreated ARID1A-proficient (ARID1A +) and ARID1A-deficient (ARID1A-) CRC patient samples. In addition, we validated this result by a clonogenic assay. Additionally, we examined the effects of AURKA inhibitors on cell cycle progression and apoptosis in ARID1A + and ARID1A- CRC patient samples using flow cytometry.ResultsThe results showed that AURKAi selectively inhibited the growth of ARID1A- CRC cells. Furthermore, AURKA inhibitors significantly increased G2/M arrest and induced apoptosis in ARID1A- cells.ConclusionWe believe that AURKAi hold promise as potential therapeutics for ARID1A mutation colorectal cancer patients.

Gut bacterial type III secretion systems aggravate colitis in mice and serve as biomarkers of Crohn’s disease

Mesenteric adipose tissue (mAT) hyperplasia, known as creeping fat, is a pathologic characteristic of Crohn's disease (CD). In our previously reported cohort, we observed that Achromobacter pulmonis was the most abundant and prevalent bacteria cultivated from creeping fat. A whole genomic sequencing and identification of T3SS orthologs of mAT-derived A. pulmonis were used. A functional type III secretion system (T3SS) mediated the pathogenic potential of A. pulmonis invitro and in mouse colitis model. Furthermore, a T3SS Finder pipeline was introduced to evaluate gut bacterial T3SS orthologs in the feces of CD patients, ulcerative colitis and colorectal cancer patients. Here, we reveal that mAT-derived A. pulmonis possesses a functional T3SS, aggravates colitis in mice via T3SS, and exhibits T3SS-dependent cytotoxicity via a caspase-independent mechanism in macrophages and epithelial cells, which demonstrated the pathogenic potential of the T3SS-harboring A. pulmonis. Metagenomic analyses demonstrate an increased abundance of Achromobacter in the fecal of Crohn's disease patients compared to healthy controls. A comprehensive comparison of total microbial vT3SS abundance in various intestine diseases demonstrated that the specific enrichment of vT3SS genes was shown in fecal samples of CD, neither ulcerative colitis nor colorectal cancer patients, and ten T3SS gene-based biomarkers for CD were discovered and validated in a newly recruited CD cohort. Furthermore, treatment with exclusive enteral nutrition (EEN), an intervention that improves CD patient symptomatology, was found associated with a significant reduction in the prevalence of T3SS genes in fecal samples. These findings highlight the pathogenic significance of T3SSs in the context of CD and identify specific T3SS genes that could potentially function as biomarkers for diagnosing and monitoring the clinical status of CD patients. This work is supported by the National Key Research and Development Program of China (2020YFA0907800), the China Postdoctoral Science Foundation (2023M744089), the National Natural Science Foundation of China (32000096), the Shenzhen Science and Technology Programs (KQTD20200820145822023, RCIC20231211085944057, and ZDSYS20220606100803007), National Key Clinical Discipline, Guangdong Provincial Clinical Research Center for Digestive Diseases (2020B1111170004), Qingfeng Scientific Research Fund of the China Crohn's & Colitis Foundation (CCCF) (CCCF-QF-2022B71-1), and the Sixth Affiliated Hospital, Sun Yat-sen University Clinical Research 1010 Program 1010CG(2023)-08. These funding provided well support for this research work, which involved data collection, analysis, interpretation, patient recruitment and so on.

Detection of JC and BK polyomaviruses in patients with colorectal cancer (CRC) by PCR

ABSTRACT Background Overall, 20–30% of all cancers are estimated to be linked to infectious agents. Polyomaviruses are oncogenic cause in rodent models, readily transform their cells, and cause chromosomal instability in animal and human cells in-vitro. Some reports have indicated the presence of JCPyV and BKPyV in some human tumors. The JCPyV and BKPyV genome encodes some transforming proteins such as LT-Ag. Thus, these viruses could cause or promote some neoplasia, such as lymphomas, pancreatic, prostate, and colorectal cancers. Colorectal cancer (CRC) is the third most common cancer in the world. Risk factors for developing CRC are associated with personal features or habits, such as age, lifestyle, and gut microbiota. Materials and Methods In this study, we examined the prevalence of JCPyV and BKPyV in the 23 fecal samples of CRC patients and 24 healthy samples (control group). Virus DNA was extracted by a Favorgen DNA extraction kit. The large T antigen of JCPyV and VP1 of BKPyV were investigated by optimized multiplex PCR. Results One of the samples was positive for the JCPyV (4.3%), while in the samples of healthy individuals, the JCPyV was negative. Also, positive results for BKPyV PCR were obtained for five cases (21.7%) in the samples of the CRC group and one case (4.1%) in healthy individuals. Conclusion The result showed no direct correlation between tumorigenesis and polyomavirus infections in CRC development. However, the exact role of BKPyV and JCPyV is still controversial and needs further study with larger sample size.

MiR-29a expression negatively correlates with Bcl-2 levels in colorectal cancer and is correlated with better prognosis

MicroRNAs (miRNAs) are a class of small non-coding RNAs that act as important regulators of gene expression, involved in various biological pathways. Aberrant miRNAs expression is associated with the onset and progression of colorectal cancer (CRC). The aim of this study was to investigate the correlation between five miRNAs (miR-29a, miR-101, miR-125b, miR-146a, and miR-155), found to be deregulated in tissue samples of CRC patients, and clinicopathological characteristics and histological markers. Analysis of histological markers was performed by immunohistochemical staining of tumour tissues with Ki-67, p53, CD34, and Bcl-2. Our findings revealed a significant negative correlation between miR-29a expression and Bcl-2 levels. Furthermore, high miR-29a expression was associated with a lower incidence of distant metastasis in CRC patients. We observed negative correlations between miR-101 expression and the number of lymph nodes with metastasis, as well as the size of the largest metastasis; miR-125b expression and lymphovascular invasion; and miR-155 expression and mucus presence. Our survival analysis demonstrated that high miR-29a expression correlated with better progression-free survival of CRC patients, underscoring its potential as a prognostic marker. Our study unveiled intricate relationships between specific miRNA expressions and clinicopathological features in CRC, highlighting the potential utility of miR-29a as a valuable prognostic biomarker.

Ultra-sensitive detection of femtomolar lead ions using DNAzyme-mediated biosensing on tilted fiber Bragg grating plasmonic sensor

Ultra-trace lead ion detection has significant implications in various domains, notably in point-of-care testing, environmental monitoring, and cancer-targeted therapies and diagnostics. The demand for rapid and precise lead-ion detection in clinical settings necessitates innovative approaches. In this study, a lead-ion biosensor was designed using DNAzyme-based tilted fiber Bragg grating surface plasmon resonance (TFBG-SPR). The lead ions specifically cleave toward DNAzyme’s ribonucleotide adenosine (rA)-containing substrate strand, and a high sensitivity “on–off” sensing structure on the TFBG-SPR surface was established by using the DNA-conjugated AuNPs as a signal amplification element. This “on–off”-type lead ion biosensor has a competitive limit of detection of 3 fM and a wide dynamic measurement range up to ten orders, meeting stringent requirements for ultra-trace, label-free and online clinical detection. Owing to the unique catalytic effect of DNAzyme binding to lead ions, high selectivity was demonstrated. Moreover, to validate its practicality in clinical diagnosis, we successfully achieved spiked-recovery results with 100.39 % average recovery rate and a swift 17-minute analysis time within the colorectal cancer patient samples. By combining DNA biomolecular, TFBG-SPR probe and “on–off” AuNPs-DNA structure, the fM level detection of lead ion in fiber highlighted its potential in vivo and in vitro complex application scenarios.

Measure of minimal residual burden on circulating tumor cells with over-expression of programmed death-ligand 1 as a dynamic biomarker in patients with colorectal cancer.

e14553 Background: In stage III colorectal cancer (CRC) patients, the extent of oxaliplatin-combination as an adjuvant therapy is still undetermined. Approx. 25-50% Stage II-III CRC patients are known to develop recurrence and metastasis even after comprehensive treatment, attributed to occult disease and Minimal Residual Disease (MRD). Circulating Tumor Cells (CTCs) are bio-mechanistic extravasation source for micro-metastatic disease. CRC patients, with lower adjuvant therapy from 3 to 6 months are known to exhibit increased CTCs and positivity rate due to the emergence of resistant clones. Assays to detect CTCs and expression of Programmed Cell Death-Ligand 1 (PD-L1) as a dynamic biomarker simultaneously has wide clinical implications. Especially, when the tissue biopsy is not inadequate to detect molecular targets for immune checkpoint inhibitor (ICT) therapy. Methods: Retrospectively, 182 CRC cancer patients were analyzed for the presence of CTC and distribution at baseline and follow-ups (up to 0-4 follow ups). The peripheral blood 1.5 ml was analyzed using the OncoDiscover platform approved by CDSCO, India consisting multifunctional magneto-nanosystem mediated by anti-epithelial cellular adhesion molecule (EpCAM) antibody. CTCs were analyzed in patients with early stages- pre and post treatment, progressive disease, Disease Free Status (DFS) and in metastasis. The isolated cells were immune-stained to detect CK-18 +ve, CD45 -ve, DAPI +ve and PD-L1 +ve expression. PD-L1 expression in CTCs was validated by analyzing the linear intensity gradients of the fluorescence signals. CTCs were termed as PD-L1 -ve based on a weak or no detectable fluorescence signal and termed +ve based on a high fluorescence signal using automated image acquisition Zeiss microscope. Results: In a cohort of 182 CRC patient samples, n = 128 (70.3 %) showed the presence of CTCs. The fluorescence intensity for PD-L1 expression as a robust functional assay on CTCs for molecular characterization was developed. The distribution of CTCs ranged from 1-9. The mean fluorescence intensity value and cut-off for the expression of PD-L1 in CTCs was accounted to be ~1.02. Interestingly, in n = 54 (42.2 %) patients, CTCs showed positive expression of PD-L1. CTC +ve patients with PD-L1 expression were associated at all stages and even in early stage, progressive disease, and metastasis. Patients without any CTCs n = 54 (29.7%) either had clinically stable disease or were in DFS with no radio-graphical image. Conclusions: The presence of PD-L1 over-expression on CTCs is a dynamic biomarker in blood, showing the progression of disease even in patients with DFS status. CTC enumeration and assessing the PD-L1 expression on CTCs could offer highly individualized treatment plans in CRC patients.

NLRX1: a key regulator in mitochondrial respiration and colorectal cancer progression.

Colorectal cancer (CRC) is a prevalent and aggressive malignancy with high mortality rates and significant risks to human well-being. Population-wide screening for tumor suppressor genes and oncogenes shows promise for reducing the incidence and fatality of CRC. Recent studies have suggested that NLRX1, an innate immunity suppressor, may play a role in regulating chronic inflammation and tumorigenesis. However, further investigation is needed to understand the specific role of NLRX1 in CRC. To evaluate the impact of NLRX1 on migration, invasion, and metastasis, two human colon cancer cell lines were studied in vitro. Additionally, a knockout mouse tumor-bearing model was used to validate the inhibitory effect of NLRX1 on tumor emergence and progression. The Seahorse XF96 technology was employed to assess mitochondrial function and glycolysis in colorectal cancer cells overexpressing NLRX1. Moreover, public databases were consulted to analyze gene and protein expression levels of NLRX1. Finally, the results were validated using a series of CRC patient samples. Our findings demonstrate that downregulation of NLRX1 enhances proliferation, colony formation, and tumor-forming capacity in HCT116 and LoVo cells. Conversely, overexpression of NLRX1 negatively impacts basal respiration and mitochondrial ATP-linked respiration in both cell lines, resulting in a notable decrease in maximal respiration during the standard mitochondrial stress test. Furthermore, analysis of data from the TCGA database reveals a significant reduction in NLRX1 expression in colon and rectal cancer tissues compared to normal tissues. This result was validated using clinical samples, where immunohistochemistry staining and western blotting demonstrated a notable reduction in NLRX1 protein levels in CRC compared to adjacent normal tissues. The decreased expression of NLRX1 may serve as a significant prognostic indicator and diagnostic biomarker for CRC patients.

Isthmin-1 promotes growth and progression of colorectal cancer through the interaction with EGFR and YBX-1

While previous studies have indicated the involvement of Isthmin 1 (ISM1), a secreted protein, in cancer development, the precise mechanisms have remained elusive. In this study, we unveiled that ISM1 is significantly overexpressed in both the blood and tissue samples of colorectal cancer (CRC) patients, correlating with their poor prognosis. Functional experiments demonstrated that enforced ISM1 expression significantly enhances CRC proliferation, migration, invasion and tumor growth. Notably, our investigation reveals an interaction of ISM1 with epidermal growth factor receptor (EGFR), a member of the receptor tyrosine kinase (RTK) family of CRC cells. The binding of ISM1 triggered EGFR activation and initiate downstream signaling pathways. Meanwhile, intracellular ISM1 interacted with Y-box binding protein 1 (YBX1), enhancing its transcriptional regulation on EGFR. Furthermore, our research uncovered the regulation of ISM1 expression by the hypoxia-inducible transcription factor HIF-1α in CRC cells. Mechanistically, we identified HIF-1α as a direct regulator of ISM1, binding to a hypoxia response element on its promoter. This novel mechanism illuminated potential therapeutic targets, offering insights into restraining HIF-1α/ISM1/EGFR-driven CRC progression and metastasis.

Abstract 1507: Involvement of GABAergic signaling in enhanced tumor cell invasion in a mechanically dynamic tumor microenvironment

Abstract Metastasis is a major contributor to cancer morbidity and mortality. However, studying this complex, multi-step, multi-organ process is challenging. There is a pressing need to dissect the contributions of the tumor microenvironment (TME) on this process in a controlled and precise manner. Fortunately, the utilization of microfluidic “organs-on-chips” (OOC) in cancer research is facilitating such investigations. Moreover, by combining organoids and organs-on-chips we can enhance the progress of these studies in a patient specific manner. In this study, we have developed a cancer-on-chip model aimed at investigating early metastatic spread within the colon milieu. To achieve this, we employ colorectal cancer (CRC) cell lines as well as patient-derived CRC organoids chosen from our biorepository to encompass diverse representations across race/ethnicity, sex, and mutational profiles. The tumor cells are introduced into the upper chamber of the OOC model, while human microvascular endothelial cells (HIMECs) are introduced into the lower chamber to establish a tube-like structure resembling a blood vessel. These two chambers are separated by a porous membrane, and the chip is flanked by vacuum chambers to introduce stretch-like motions, simulating peristalsis in the gastrointestinal track. Creating a mechanically dynamic microenvironment facilitates the exploration of neurotransmitters and their impact on tumor cell behavior. Recent studies have suggested that tumor cells may exploit physiological processes, such as neurotransmitter signaling, to their benefit. By utilizing mass spectrometry-based metabolomics we detected dynamic and patient organoid-specific changes in neurotransmitter levels (i.e., serotonin, aspartate, glutamate, γ-aminobutyric acid (GABA)) in the effluent of our CRC-on-chip model. Coupled with live-cell imaging, we discovered tumor cell-derived GABA, a major inhibitory neurotransmitter, serves as an energy source for supporting tumor cell intravasation. This finding was most pronounced in KRAS-mutant tumor cells and further supported by analysis of CRC patient samples from The Cancer Genome Atlas (TCGA) database. We were able to reverse the GABA-mediated invasion effect by inhibiting 4-aminobutyrate aminotransferase (ABAT), the enzyme responsible for GABA catabolism. In summary, our cancer-on-chip model holds promise for exploring various aspects of the metastatic process and uncovering potential therapeutic targets, such as neurotransmitters. Citation Format: Carly Strelez, Rachel Perez, John S. Chlystek, Christopher Cherry, Bethany Haliday, Ah Young Yoon, Curran Shah, Ren X. Sun, Roy Lau, Aaron Schatz, Josh Neman, Heinz Josef-Lenz, Jonathan Katz, Shannon M. Mumenthaler. Involvement of GABAergic signaling in enhanced tumor cell invasion in a mechanically dynamic tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1507.

Molecular analysis to identify novel potential biomarkers as drug targets in colorectal cancer therapy: an integrated bioinformatics analysis

ABSTRACT Colorectal cancer (CRC) is a heterogeneous disease that requires new diagnostic and prognostic markers. Integrated bioinformatics approach to identify novel therapeutic targets associated with CRC. Using GEO2R identified DEGs in CRC, and Funrich software facilitated the visualization of DEGs through Venn diagrams. From a total of 114 enhanced DEGs, potential hub genes were further filtered based on their nodal strength and edges using STRING database. To gain insights into the functional roles of these hub genes, gene ontology and pathway enrichment were conducted thorough g: profiler web server. Subsequently, overall survival plots from GEPIA and oncogenic predictive functions like mRNA expressions for stages and nodal metastasis were employed to identify hub genes in CRC patient samples. Additionally, the cBioPortal and HPA databases also revealed genetic alterations and expression levels in these hub genes in CRC patients, further supporting their involvement in colorectal cancer. Gene expression by RT-PCR shows upregulation of hub genes in HT-29 cells. Finally, our integrated bioinformatic analysis revealed that ABCE1, AURKA, HSPD1, PHKA1, CDK4, and YWHAE as hub genes with potential oncogenic roles in CRC. These genes hold promise as diagnostic and prognostic markers for colorectal tumorigenesis, providing insights into targeted therapies for improved patient outcomes.

The multispecies microbial cluster of Fusobacterium, Parvimonas, Bacteroides and Faecalibacterium as a precision biomarker for colorectal cancer diagnosis.

The incidence of colorectal cancer (CRC) has increased worldwide, and early diagnosis is crucial to reduce mortality rates. Therefore, new noninvasive biomarkers for CRC are required. Recent studies have revealed an imbalance in the oral and gut microbiomes of patients with CRC, as well as impaired gut vascular barrier function. In the present study, the microbiomes of saliva, crevicular fluid, feces, and non-neoplastic and tumor intestinal tissue samples of 93 CRC patients and 30 healthy individuals without digestive disorders (non-CRC) were analyzed by 16S rRNA metabarcoding procedures. The data revealed that Parvimonas, Fusobacterium, and Bacteroides fragilis were significantly over-represented in stool samples of CRC patients, whereas Faecalibacterium and Blautia were significantly over-abundant in the non-CRC group. Moreover, the tumor samples were enriched in well-known periodontal anaerobes, including Fusobacterium, Parvimonas, Peptostreptococcus, Porphyromonas, and Prevotella. Co-occurrence patterns of these oral microorganisms were observed in the subgingival pocket and in the tumor tissues of CRC patients, where they also correlated with other gut microbes, such as Hungatella. This study provides new evidence that oral pathobionts, normally located in subgingival pockets, can migrate to the colon and probably aggregate with aerobic bacteria, forming synergistic consortia. Furthermore, we suggest that the group composed of Fusobacterium, Parvimonas, Bacteroides, and Faecalibacterium could be used to design an excellent noninvasive fecal test for the early diagnosis of CRC. The combination of these four genera would significantly improve the reliability of a discriminatory test with respect to others that use a single species as a unique CRC biomarker.

Oncogenic microRNA-1290 and SCAI Gene as Potential Biomarker for Colorectal Carcinoma.

Colorectal cancer (CRC) is the world's third most frequent cancer, with a significant mortality rate due to late detection. There is a need to search for biomarkers that can detect colorectal cancer at an early stage. MicroRNAs (miRNAs) regulate several targets that function as oncogenes and/or tumor suppressor genes, so any change in microRNA expression level can predict abnormality. The objective of the study was to evaluate the expression of miR-1290, and Suppressor of cancer cell invasion (SCAI) gene that may be used as biomarkers for early diagnosis of colorectal carcinoma. This study included 50 subjects consisting of newly diagnosed colorectal carcinoma patients (n = 25), and healthy controls (n = 25). After RNA isolation and reverse transcription, the expression level of miR-1290 and SCAI gene in the tissues and plasma samples of CRC patients were analyzed using real time PCR and compared with healthy individuals as normal controls. The 2-ΔΔCt formula was used to compute the fold-change, while using miR-16 and GAPDH as reference genes for normalization. We found that miR-1290 is upregulated, whereas SCAI gene is downregulated in both plasma and tissue samples of CRC patients. For miR-1290, the sensitivity was 96% and specificity was 100%, and for SCAI, 100% sensitivity and 88% specificity was calculated by ROC analysis. The expression of miR-1290 and SCAI gene may be utilized as biomarkers for diagnosis of colorectal carcinoma.

Comparative genomic analysis to identify a signature of sporadic colorectal cancer development in young adults.

208 Background: Young-onset sporadic CRC is an important yet understudied heterogeneous group of aggressive cancers with distinct clinical and histopathological features. There is a steady increase in the incidence of cancer in this group of patients and currently, there are no screening guidelines to identify these patients due to a lack of understanding of the molecular mechanisms driving cancer in this patient group. Introduction: Despite screening guidelines and recent advances in cancer treatment, colorectal cancer (CRC) remains the second most diagnosed cancer and the second and third leading cause of cancer-related mortality in Canadian men and women, respectively [Canadian Cancer Statistics 2017.]. More striking is the rise in incidence of CRC in young adults in the United States [Siegel, R.L., et al, Bailey, C.E., et al., Dozois, E.J., et al., Deen, K.I., et al.], and the expectation that by the year 2030, the incidence rate will increase by 90% in this patient population. Data from the Surveillance and Cancer registry at Cancer Care Ontario shows a similar trend with increased rates in younger adults (ages 30 to 49) by 5.2 per cent per year between 2005 and 2012 [Ontario, C.C., Cancer Fact.]. Moreover, these younger patient groups are often diagnosed with aggressive forms and advanced stages of the disease [Ontario, C.C., Cancer Fact.]. Methods: In this study, using a total of 30 colorectal cancer patient samples from Windsor Regional Hospital Cancer Program, we performed comprehensive targeted gene sequencing to identify single nucleotide variants, small insertions/deletions, copy number variants in over 500 genes that are implicated in cancer. Mean age of the patients in this study was 44 years and only patients without any personal or family history of colon cancer /other malignancies or IBD were enrolled in the study. Results: While identifying previously known colorectal cancer associated genetic variants, our preliminary data shows distinct missense mutations in several genes potentially contributing to the development and progression of cancer in these patients. In addition to showing pathogenic mutations in colorectal cancers associated genes, such as PIK3CA (H1047R, E545K, E545G, R93W, V344A), KRAS (G12V, G12D, A146T) and APC, our study showed recurring missense mutations in several genes including AXIN2, ALK, CDKN1A, MAP3K1, ROS1, EPCAM, KDM5A and AURKA in over 50% of our samples. Conclusions: The genomic profiling performed using biopsies from young colorectal cancer patients through this study provides a unique ability to identify the potential “genomic triggers” for the development and progression of cancer in young sporadic colorectal cancer patients. This information can not only be used to develop targeted treatment options for these patients but also to design new screening protocols as well as optimal surveillance strategies.

High-Abundance Protein-Guided Hybrid Spectral Library for Data-Independent Acquisition Metaproteomics.

Metaproteomics offers a direct avenue to identify microbial proteins in microbiota, enabling the compositional and functional characterization of microbiota. Due to the complexity and heterogeneity of microbial communities, in-depth and accurate metaproteomics faces tremendous limitations. One challenge in metaproteomics is the construction of a suitable protein sequence database to interpret the highly complex metaproteomic data, especially in the absence of metagenomic sequencing data. Herein, we present a high-abundance protein-guided hybrid spectral library strategy for in-depth data independent acquisition (DIA) metaproteomic analysis (HAPs-hyblibDIA). A dedicated high-abundance protein database of gut microbial species is constructed and used to mine the taxonomic information on microbiota samples. Then, a sample-specific protein sequence database is built based on the taxonomic information using Uniprot protein sequence for subsequent analysis of the DIA data using hybrid spectral library-based DIA analysis. We evaluated the accuracy and sensitivity of the method using synthetic microbial community samples and human gut microbiome samples. It was demonstrated that the strategy can successfully identify taxonomic compositions of microbiota samples and that the peptides identified by HAPs-hyblibDIA overlapped greatly with the peptides identified using a metagenomic sequencing-derived database. At the peptide and species level, our results can serve as a complement to the results obtained using a metagenomic sequencing-derived database. Furthermore, we validated the applicability of the HAPs-hyblibDIA strategy in a cohort of human gut microbiota samples of colorectal cancer patients and controls, highlighting its usability in biomedical research.

The correlation between bacteria and colorectal cancer

Colorectal cancer (CRC) is the third most commonly diagnosed cancer with a high mortality rate worldwide. The global burden of CRC imposes the need to understand the mechanism of CRC progression. Accumulating evidence reveals gut bacteria may contribute to the risk of CRC. The purpose of this project was to determine whether the bacterial composition is altered in stool samples of CRC patients. We hypothesized that patients with CRC would have a set of differentially abundant bacteria species in their stool samples compared to the control samples. Using 11 CRC datasets across 9 countries, consisting of 1395 samples from the curatedMetagenomicData database, we examined the bacterial composition and compared the prevalence and relative abundance of bacteria species across 701 CRC patients and 694 control samples. We found that CRC-associated bacteria species and their prevalence varied across different demographic regions. Combining 11 datasets, we performed differential abundance analysis to analyze the prevalence and compare the relative abundance of bacteria species between CRC samples and control samples, and we found a set of CRC-associated bacteria species that were significantly more abundant than those of control samples. Many of these species have previously been found to influence CRC development. Moreover, we identified a set of control-associated species that were important in maintaining a beneficial microbiome. This project provided insights that support further investigation into the role of CRC-associated bacteria in CRC tumorigenesis.

Combined DNA Analysis from Stool and Blood Samples Improves Tumor Tracking and Assessment of Clonal Heterogeneity in Localized Rectal Cancer Patients.

Objectives: In this study, stool samples were evaluated for tumor mutation analysis via a targeted next generation sequencing (NGS) approach in a small patient cohort suffering from localized rectal cancer. Introduction: Colorectal cancer (CRC) causes the second highest cancer-related death rate worldwide. Thus, improvements in disease assessment and monitoring that may facilitate treatment allocation and allow organ-sparing "watch-and-wait" treatment strategies are highly relevant for a significant number of CRC patients. Methods: Stool-based results were compared with mutation profiles derived from liquid biopsies and the gold standard procedure of tumor biopsy from the same patients. A workflow was established that enables the detection of de-novo tumor mutations in stool samples of CRC patients via ultra-sensitive cell-free tumor DNA target enrichment. Results: Notably, only a 19% overall concordance was found in mutational profiles across the compared sample specimens of stool, tumor, and liquid biopsies. Conclusion: Based on these results, the analysis of stool and liquid biopsy samples can provide important additional information on tumor heterogeneity and potentially on the assessment of minimal residual disease and clonal tumor evolution.

CD177 drives the transendothelial migration of Treg cells enriched in human colorectal cancer.

Regulatory T (Treg) cells regulate immunity in autoimmune diseases and cancers. However, immunotherapies that target tumor-infiltrating Treg cells often induce unwanted immune responses and tissue inflammation. Our research focussed on exploring the expression pattern of CD177 in tumor-infiltrating Treg cells with the aim of identifying a potential target that can enhance immunotherapy effectiveness. Single-cell RNA sequencing (scRNA-seq) data and survival data were obtained from public databases. Twenty-one colorectal cancer patient samples, including fresh tumor tissues, peritumoral tissues and peripheral blood mononuclear cells (PBMCs), were analysed using flow cytometry. The transendothelial activity of CD177+ Treg cells was substantiated using in vitro experiments. ScRNA-seq and flow cytometry results indicated that CD177 was exclusively expressed in intratumoral Treg cells. CD177+ Treg cells exhibited greater activation status and expressed elevated Treg cell canonical markers and immune checkpoint molecules than CD177- Treg cells. We further discovered that both intratumoral CD177+ Treg cells and CD177-overexpressing induced Treg (iTreg) cells had lower levels of PD-1 than their CD177- counterparts. Moreover, CD177 overexpression significantly enhanced the transendothelial migration of Treg cells in vitro. These results demonstrated that Treg cells with higher CD177 levels exhibited an enhanced activation status and transendothelial migration capacity. Our findings suggest that CD177 may serve as an immunotherapeutic target and that overexpression of CD177 may improve the efficacy of chimeric antigen receptor T (CAR-T) cell therapy.

Mối liên quan giữa mức độ sao chép gen KIAA1199 với một số đặc điểm lâm sàng, giải phẫu bệnh của người bệnh ung thư đại trực tràng tại Bệnh viện đa khoa Đức Giang năm 2022-2023

Background: Determine the level of KIAA1199 gene copy in FFPE tissue samples of colorectal cancer (CR) patients and evaluate of the relationship between KIAA1199 gene copy level and some clinical and pathological symptoms of CRC patients at Duc Giang General Hospital in year 2022-2023. Methods: A cross-sectional descriptive study on 40 FFPE samples and 40 corresponding medical records of CRC patients diagnosted and treated at Duc Giang General Hospital in year 2022-2023. Result: 26/40 FFPE tissue samples (65.0%) were processed to meet the requirements for RNA extraction quality to evaluate the KIAA1199 gene copy level. Furthermore, 20/26 samples (76.9%) had a higher level of KIAA1199 gene copy in tumor tissue than in normal tissue. There was a statistically significant association between increased KIAA1199 gene copy levels and level of tumor differentiations and types in CR patients (p<0.05); among them, CR patients with neoplasms have increased 11.3 times the KIAA1199 gen copy level higher than CR patients with other types of tumors (p<0.05). However, it was not possible to evaluate the statistically significant relationship between the KIAA1199 gene copy level and some histopathological characteristics such as tumor location, tumor number, histopathological type, level of serosal invasion, lymph node metastasis, and stages classified according to TNM (p>0.05). Conclusion: In this study, the KIAA1199 gene copy levels in tumor tissue increased more strongly than in normal tissue and a statistically significant relationship between the increased KIAA1199 gene copy levels and the tumor differentiations and types in CR patients (p<0.05).

ANP32B promotes colorectal cancer cell progression and reduces cell sensitivity to PRAP1 inhibitor through up-regulating HPF1

ANP32B, a member of the acidic leucine-rich nuclear phosphoprotein 32 family member B, is aberrantly expressed in various cancers, including colorectal cancer. However, the function and mechanism of action of ANP32B in colorectal cancer remain unclear. The present study therefore analyzed the expression of ANP32B and its activity in colorectal cancer patient samples and colorectal cancer cell lines. ANP32B expression was found to be significantly upregulated in colorectal cancer patient samples and cell lines. Upregulation of ANP32B enhanced colorectal cancer cell proliferation and migration, whereas downregulation of ANP32B suppressed colorectal cancer cell proliferation. RNA sequencing analysis of differentially expressed genes in ANP32B silenced colorectal cancer cells showed that histone PARylation factor 1 (HPF1), which protects against DNA damage by interacting with the anti-tumor target PARP1, was significantly downregulated. Luciferase promoter assays testing the regulatory association between ANP32B and HPF1 showed that ANP32B interacted with the HPF1 promoter. Analysis of colorectal cancer samples from The Cancer Genome Atlas showed that ANP32B and HPF1 expression were positively correlated, and recovery assays showed that ANP32B promoted colorectal cancer progression by up-regulating HPF1. Overexpression of ANP32B also reduced the sensitivity of colorectal cancer cells to PARP1 inhibitor, consistent with the oncogenic role of ANP32B. ANP32B may alter the sensitivity of colorectal cancer cells to PARP1 inhibitor via a mechanism associated with the HPF1 gene. In summary, these findings showed that ANP32B acted as a tumor promoter, potentiating both colorectal cancer malignancy and drug resistance. Targeting the ANP32B/HPF1 axis may have benefit for patients with colorectal cancer.

USP47 inhibits m6A-dependent c-Myc translation to maintain regulatory T cell metabolic and functional homeostasis.

The functional integrity of Tregs is interwoven with cellular metabolism; however, the mechanisms governing Treg metabolic programs remain elusive. Here, we identified that the deubiquitinase USP47 inhibited c-Myc translation mediated by the RNA N6-methyladenosine (m6A) reader YTHDF1 to maintain Treg metabolic and functional homeostasis. USP47 positively correlated with the tumor-infiltrating Treg signature in samples from patients with colorectal cancer and gastric cancer. USP47 ablation compromised Treg homeostasis and function in vivo, resulting in the development of inflammatory disorders, and boosted antitumor immune responses. USP47 deficiency in Tregs triggered the accumulation of the c-Myc protein and in turn exacerbated hyperglycolysis. Mechanistically, USP47 prevented YTHDF1 ubiquitination to attenuate the association of YTHDF1 with translation initiation machinery, thereby decreasing m6A-based c-Myc translation efficiency. Our findings reveal that USP47 directs m6A-dependent metabolic programs to orchestrate Treg homeostasis and suggest novel approaches for selective immune modulation in cancer and autoimmune diseases by targeting of USP47.