DNA Microsatellite Instability Research Articles

Quinazoline derivatives inhibit cell growth of prostate cancer as a WRN helicase dependent manner by regulating DNA damage repair and microsatellite instability

WRN helicase is a crucial target of synthetic death in cancer and has a unique advantage in the treatment of microsatellite unstable cancers. Our previous studies have found that quinazoline derivatives showed the WRN-dependent antiproliferative activity. In this study, a series of new quinazoline derivatives were designed and synthesized by optimizing the structure, and evaluating the targeting and sensitivity to WRN helicase. Cell growth inhibition experiments on WRN overexpressing PC3 cells (PC3-WRN) showed that the antiproliferative activity of some compounds was significantly dependent on WRN helicase. Moreover, the antitumor activity of 9in vivo was significantly decreased in the nude mouse model constructed with WRN knockdown PC3 cells (PC3-shWRN) compare (P < 0.01) to the control group. The molecular docking and CETSA results showed that 9 directly binds to WRN protein. Mechanism studies have confirmed that 9 targeted WRN, and may affect the binding between WRN and other key regulators, to destroy the repair function and regulate genomic stability. In addition, 9 also has suitable pharmacokinetic parameters and low toxicity in vivo. This result indicates that the quinazoline derivative 9 could be a novel WRN function inhibitor for the treatment of prostate cancer.

Investigation of the Relationship Between DNA Mismatch Repair Genes and Microsatellite Instability in Solid Tumors

Aim: In this study, we aimed to detect the MSI status and somatic mutations in MMR genes (MSH2, MSH6, MLH1, PMS2) of a total of 55 solid tumors diagnosed with colorectal, endometrium and ovarian cancer by NGS method and to reveal the relationship between them. Material and Method: DNA isolation was performed by taking 10-micron sections from paraffin-embedded tissue samples of 55 patients diagnosed with kolorektal, endometrium ve ovarian solid tümörlerinin and Kapa NGS DNA extraction kit was used for sequence analysis. The purity and concentration of the DNA obtained was measured by Qubit fluoremeter, and NadPrep DNA Universal Library Preparation Kit was used for high quality library preparation. Bioinformatics analyses were performed on the Genomize Seq platform. The MSI value was analysed by Roche Navify Mutation Caller software and percentage MSI values were determined using the MSIsensor2 pipeline for secondary analysis of NGS. Results: All ovarian tumors were in the MSI-Stable category. The average MSI value was 2.01. One sample had an MSI of zero. In addition, no mutations in the MSH2 and MLH1 genes were detected in any of the ovarian tumors. 3 of 4 endometrial tumors were in the MSI-Stable category, and 1 tumor was in the MSI-low (MSI value: 13.2) category. No variants were detected in the MSH2 and PMS2 genes in endometrial tumors. 2 of the 41 colorectal tumors (Case4, Case16) were in the MSI-High category. No variants were detected in the MMR genes in 19 tumors. Conclusion: Although frame-shift and stop-gain mutations were detected in 23 tumors that would cause protein deficiency in MMR genes, MSI-H was not detected, as expected, except for two colorectal tumors. Therefore, the results of our study emphasise the need to define new predictive biomarkers clinically within the framework of algorithms to predict response to immunotherapy and determine prognosis.

Fusobacterium Nucleatum Promotes Microsatellite Instability in Colorectal Carcinoma Through Up-regulation of miRNA-155-5p-Targeted Inhibition of MSH6 via the TLR4/NF-κB Signaling Pathway.

Fusobacterium nucleatum (Fn) is significantly associated with poor prognosis in colorectal carcinoma (CRC), however, mechanisms of Fn in DNA mismatch repair (MMR) and microsatellite instability (MSI) in CRC have not been fully elucidated. Clinical samples are collected to analyze the relationship between Fn abundance and microsatellite stability. Tumor cells are treated with Fn to detect the expression of proteins related to toll-like receptor 4 (TLR4), myeloid differentiation factor 88 (Myd88), mutS homolog 6 (MSH6), and nuclear factor-κB (NF-κB) signaling pathways, respectively. Combined with the prediction results from TargetScan, the regulatory role of microRNA upstream of MSH6 is demonstrated. The effect of this regulatory axis on CRC development is demonstrated using a nude mouse tumor model. Compared with microsatellite stability (MSS)-type CRC patients, MSI-type showed higher Fn abundance. Fn treatment of CRC cells activated TLR4/Myd88/NF-κB signaling pathway, transcriptionally activating miRNA-155-5p expression, thereby negatively regulating MSH6. Fn treatment accelerated the malignant progression of CRC in mice, and this process is inhibited by miRNA-155-5p antagomir. Fn in CRC upregulated miRNA-155-5p by activating TLR4/NF-κB signaling to inhibit MSH6, and this regulatory pathway may affect MSS of cancer cells.

Comprehensive analysis of EphA2 in pan-cancer: A prognostic biomarker associated with cancer immunity.

Several studies have reported a significant relationship between Ephrin receptor A2 (EphA2) and malignant progression in numerous cancers. However, there is a lack of comprehensive pan-cancer analysis on the prognostic value, mutation status, methylation landscape, and potential immunological function of EphA2. Using The Cancer Genome Atlas, Genotype Tissue Expression Database and GEO data, we analysed the differences in EphA2 expression between normal and tumour tissues and the effects of EphA2 on the prognosis of different tumours. Furthermore, using GSCALite, cBioPortal, TISDB, ULCLAN and TIMER 2.0 databases or platforms, we comprehensively analysed the potential oncogenic mechanisms or manifestations of EphA2 in 33 different tumour types, including tumour mutation status, DNA methylation status and immune cell infiltration. The correlation of EphA2 with immune checkpoints, tumour mutational burden, DNA microsatellite instability and DNA repair genes was also calculated. Finally, the effects of EphA2 inhibitors on the proliferation of human glioma and lung cancer cells were verified in cellular experiments. EphA2 is differentially expressed in different tumours, and patients with overexpression have poorer overall survival. In addition, gene mutations, gene copy number variation and DNA/RNA methylation of EphA2 have been identified in various tumours. Moreover, EphA2 is positively associated with immune infiltration involving macrophages and CD8+ T cells. Further, EphA2 mRNA expression is significantly associated with immune checkpoint in various cancers, especially programmed death-ligand 1. Finally, the EphA2 inhibitor ALW-II-41-27 shows potent anti-tumour activity. Our first pan-cancer study of EphA2 provides insight into the prognostic and immunological roles of EphA2 in different tumours, suggesting that EphA2 might be a potential biomarker for poor prognosis and immune infiltration in cancer.

Abstract 340: Validation of TSO500 NGS panel for comprehensive genomic profiling from FFPE tumor samples

Abstract Comprehensive genomic profiling (CGP) of tumor sample using large targeted NGS panels (e.g. MSK-IMPACT) has been shown to allow the detection of biomarkers from hundreds of cancer relevant genes involved in targeted and immunotherapy. Illumina TruSight Oncology 500 (TSO500), a commercial CGP assay, allows concurrent analysis of DNA and RNA to simultaneously detect multiple types of variants across 523 genes. The assay is intended to detect single nucleotide variants (SNV), insertions and deletions (indel), and multinucleotide variants (MNV), copy number gain (CNV), tumor mutational burden (TMB) and microsatellite instability (MSI) in DNA, and fusions and splicing variants (exon skipping) in RNA. Here we aimed to validate TSO500 assay for its analytical performance on FFPE tumor samples. The validation samples include commercial controls, cell lines, clinical FFPE from NSCLC, CRC, Uterus and GIST (tumor content ≥20%). Library preparation was performed from minimum of 40 ng DNA and 40ng RNA. The data analysis is performed using TruSight Oncology 500 Local App software (LRM v2.2). A custom script (v1.0) was used to add SNP annotation for small variants and combine data output into cumulative format. For SNV and indel detection QC, 61 of 64 DNA libraries (95%) passed the QC for library size (median insert size ≥70bp) and coverage (median exon coverage ≥150). The percentage of DNA libraries passing QC for CNV and MSI are 95% and 88%, respectively. All 64 RNA libraries passed QC. The analytical performance of TSO500 was summarized in the Table below. In summary, the results showed that all the acceptance criteria were met and the TSO500 assay can be utilized for genomic profiling of FFPE tumor samples. The study also identified a few limitations of the Illumina LRM software e.g. potential false positive SNV within a indel background, potential false negative of complex indel, and the challenge of long indel detection. Summary of analytical performance of TSO500 Sensitivity and specificity Assay LoD Accuracy by concordance Inter-run reproducibility SNV/Small indel Sensitivity for SNV and indel detection are 99.24% and 99.36%. The LoD for SNV is 3-5%, for DEL is 5-10% and for INS is 3-5%. PPA for SNV detections is 96.64% (115/119; 95% CI: 91.68%, 98.69%) and for small indel is 92.86% (13/14; 95% CI: 68.53%, 98.73%) between TSO500 and comparator assays. The positive call rate across all SNV and small indel variants is 98.7% (42842/43419). Specificity for SNV and small indel detection are 99.9998% and 100.00%, respectively. MSI Sensitivity and Specificity for MSI detection are both 100%. NA MSI status for all samples were detected with 100% of concordance by three assays; MSI concordance for MSI-H is 100% (95% CI: 60.97%, 100.0%) and for MSS is 100% (87.13%, 100.0%). PPA is 100% (95% CI: 51.01%, 100%) and NPA is 100% (95% CI: 34.24%, 100%). TMB NA NA TSO500 reported TMB is well correlated and comparable to exome determined TMB. The CV values for samples are acceptable. CNV NA NA All positive CNVs detected by the comparator assay were detected by the TSO500 assay with similar fold changes; The overall reproducible call rate is 91.5% (43/47). PPA between TSO500 and OCAV3 assays is 100% (95% CI: 51.01%, 100%). Fusion Sensitivity and specificity for fusion detection is 91.94% and 100%, respectively. NA All TSO500 assay detected fusions were confirmed by other assays;PPA is 100% (95% CI: 60.97%, 100%) and NPA is 100% (95% CI: 75.75%, 100%) The reproducibility of fusion call is 92.59% (25/27; 95% CI: 76.63%, 97.94%). Splicing Sensitivity and Specificity for splicing variant detection are 91.67% and 100.00%, respectively. NA The splicing variant detections were confirmed by OCAV3, OFA and Archer assays; The overall reproducibility of positive call is 100% with 95% CI (43.85%, 100%) and negative call reproducibility is 100% with 95% CI (87.13%, 100%). PPA is 100% (95%% CI: 20.65%, 100%) and NPA is 100% (95% CI: 83.18%, 100%) Citation Format: Jin Li, Zhenyu Yan, Weihua Liu, Lin Shi, Cynthia Spittle, Chad Galderisi. Validation of TSO500 NGS panel for comprehensive genomic profiling from FFPE tumor samples [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 340.

Pathogenic Insights into DNA Mismatch Repair (MMR) Genes-Proteins and Microsatellite Instability: Focus on Adrenocortical Carcinoma and Beyond.

DNA damage repair pathways, including mismatch repair (MMR) genes, are prone to carcinoma development in certain patients. The assessment of the MMR system is widely recognized as part of strategies concerning solid tumors (defective MMR cancers), especially MMR proteins (through immunohistochemistry), and molecular assays for microsatellite instability (MSI). We aim to highlight the status of MMR genes-proteins (including MSI) in the relationship with ACC (adrenocortical carcinoma) according to current knowledge. This is a narrative review. We included PubMed-accessed, full-length English papers published between January 2012 and March 2023. We searched studies on ACC patients for whom MMR status was assessed, respectively subjects harboring MMR germline mutations, namely Lynch syndrome (LS), who were diagnosed with ACC. MMR system assessments in ACCs involve a low level of statistical evidence. Generally, there are two main types of endocrine insights: 1. the role of MMR status as a prognostic marker in different endocrine malignancies (including ACC)-which is the topic of the present work, and 2. establishing the indication of immune checkpoint inhibitors (ICPIs) in selective, mostly highly aggressive, non-responsive to standard care forms upon MMR evaluation (which belongs to the larger chapter of immunotherapy in ACCs). Our one-decade, sample-case study (which, to our knowledge, it is the most comprehensive of its kind) identified 11 original articles (from 1 patient to 634 subjects per study diagnosed with either ACC or LS). We identified four studies published in 2013 and 2020 and two in 2021, three cohorts and two retrospective studies (the publication from 2013 includes a retrospective and a cohort distinct section). Among these four studies, patients already confirmed to have LS (N = 643, respective 135) were found to be associated with ACC (N = 3, respective 2), resulting in a prevalence of 0.0046%, with a respective of 1.4% being confirmed (despite not having a large amount of similar data outside these two studies). Studies on ACC patients (N = 364, respective 36 pediatric individuals, and 94 subjects with ACC) showed that 13.7% had different MMR gene anomalies, with a respective of 8.57% (non-germline mutations), while 3.2% had MMR germline mutations (N = 3/94 cases). Two case series included one family, with a respective four persons with LS, and each article introduced one case with LS-ACC. Another five case reports (between 2018 and 2021) revealed an additional five subjects (one case per paper) diagnosed with LS and ACC (female to male ratio of 4 to 1; aged between 44 and 68). Interesting genetic testing involved children with TP53-positive ACC and further MMR anomalies or an MSH2 gene-positive subject with LS with a concurrent germline RET mutation. The first report of LS-ACC referred for PD-1 blockade was published in 2018. Nevertheless, the use of ICPI in ACCs (as similarly seen in metastatic pheochromocytoma) is still limited. Pan-cancer and multi-omics analysis in adults with ACC, in order to classify the candidates for immunotherapy, had heterogeneous results, and integrating an MMR system in this larger and challenging picture is still an open issue. Whether individuals diagnosed with LS should undergo surveillance for ACC has not yet been proven. An assessment of tumor-related MMR/MSI status in ACC might be helpful. Further algorithms for diagnostics and therapy, also taking into consideration innovative biomarkers as MMR-MSI, are necessary.

Androgen receptor signaling mechanism in prostate cancer: resistance to antiandrogen therapy and association with DNA repair genes

Background. Metastatic castration-resistant prostate cancer remains a complex problem due to patients' previous treatments and limited selection of subsequent therapies. While 2nd generation antiandrogens are initially effective, resistance to them is not an exceptional event. Mechanisms depending on androgen receptor and independent of it have been described. A special focus is on mutations in DNA repair genes, particularly genes involved in homologous recombination repair (HRR) as a possible cause of somatic genetic abnormalities specifically in progressive metastatic disease. However, data on the effect of the HRR defect on the effectiveness of antiandrogen therapy for prostate cancer are very limited, which requires additional clinical studies.Aim. To evaluate the effect of clinical, morphological, molecular and genetic factors on the effectiveness of enzalutamide antiandrogen therapy in patients with prostate cancer and known mutations in DNA repair genes involved in HRR and mismatch repair.Materials and methods. The study was performed at the Clinical Oncological Dispensary No. 1 (Krasnodar). Retrospective analysis of clinical and morphological parameters of 54 patients with prostate cancer who received enzalutamide antiandrogen therapy and with known status of germ line and somatic mutations of HRR DNA repair genes (BRCA1, BRCA2, ATM, BARD, BRIP1, CDK12, CHEK1, CHEK2, PALB2, RAD51B, RAD51C, RAD54L, FANCL) and microsatellite instability in immunohistochemical determination of mismatch repair deficit was performed. Statistical analysis was performed using IBM SPSS Statistics v.22 software.Results and conclusion. In 17 of 54 patients, pathogenic germline and somatic mutations of HRR genes were detected: 7 mutations in BRCA2 gene, 4 - in CHEK2, 2 - in BRCA1, 2 - in CDK12, 1 - in BRIP1 and 1 - in ATM. It was shown that in the group of patients with metastatic castration-resistant prostate cancer, histological grade per the International Society of Urological Pathology (ISUP) G2 (total Gleason score 7 (3 + 4)) is significantly associated with the absence of HRR mutation, and grade G3 (total Gleason score 7 (4 + 3)) was associated with HRR mutations (р &lt;0.05). Increase in prostate-specific antigen (PSA) level/biochemical progression 12-16 weeks after enzalutamide therapy start was significantly associated with metastatic castration-resistant prostate cancer without HRR mutations (р &lt;0.05). In case of tumor response to enzalutamide therapy, decrease in PSA level did not depend on the age of disease onset, differentiation grade, primary advancement, previous docetaxel treatment, and presence of HRR mutation. Cox multivariate regression test showed that prescription of docetaxel before enzalutamide increased the risk of PSA-progression (hazard ratio (HR) 5.160; 95 % confidence interval (CI) 1.549-17.189; р = 0.008) and radiographic progression (HR 5.161; 95 % CI 1.550-17.187; р = 0.008). Progression risk decreased with increased level of PSA decrease 12-16 weeks after enzalutamide therapy start: for PSA decrease &gt;30 % HR 0.150; 95 % CI 0.040-0.570; р = 0.005; for PSA decrease &gt;50 % HR 0.039; 95 % CI 0.006-0.280; р = 0.001; for PSA decrease &gt;90 % HR 0.116; 95 % CI 0.036-0.375; р = 0.000. Presence of HRR mutation, age &lt;58 years, primary metastatic disease and poorly differentiated morphology did not affect duration without PSA-progression (p &gt;0.05). Kaplan-Meier curves showed a trend towards increased time to development of castration resistance in the group of primary early cancer (Breslow р = 0.06; Tarone-Ware р = 0.062). Subgroup analysis showed that in the cohort of patients with castration-resistant prostate cancer (n = 48), absence of HRR mutation in patients who previously received docetaxel therapy increases time to PSA-progression compared to patients with mutations (log-rank р &lt;0.05).

The role of immunotherapy in microsatellites stable metastatic colorectal cancer: state of the art and future perspectives.

Colorectal cancer (CRC) is the third leading cause of cancer-related deaths worldwide, despite several advances has been achieved in last decades. Few prognostic and predictive biomarkers guide therapeutic choice in metastatic CRC (mCRC), among which DNA mismatch repair deficiency and/or microsatellite instability (dMMR/MSI) holds a crucial role. Tumors characterized by dMMR/MSI benefit from immune checkpoint inhibitors. However, most of the mCRC patients (around 95%) are microsatellite stable (MSS), thereby intrinsically resistant to immunotherapy. This represents a clear unmet need for more effective treatments in this population of patients. In this review, we aim to analyze immune-resistance mechanisms and therapeutic strategies to overcome them, such as combinations of immunotherapy and chemotherapy, radiotherapy or target therapies specifically in MSS mCRC. We also explored both available and potential biomarkers that may better select MSS mCRC patients for immunotherapy. Lastly, we provide a brief overview on future perspectives in this field, such as the gut microbiome and its potential role as immunomodulator.

Regulation, genomics, and clinical characteristics of cuproptosis regulators in pan-cancer.

Cuproptosis, a copper-dependent controlled cell death, is a novel form of cell death that differs from known cell death mechanisms; however, its overall regulation in cancer remains elusive. Multiple open-source bioinformatic platforms were used to comprehensively elucidate the expression levels, prognostic efficiency, potential biological functions, genomic and epigenetic characteristics, immune microenvironment, and drug sensitivity of cuproptosis regulators (ATP7A, ATP7B, DLAT, DLD, FDX1, GLS, LIAS, LIPT1, MTF1, NLRP3, PDHA1, PDHB, and SLC31A1) in pan-cancer. Cuproptosis-related genes (CRGs) were upregulated in most cancers tested. In KIRC, KIRP, LGG, MESO, and PCPG, most highly expressed CRGs predicted a better prognosis but poorer prognosis in patients with ACC, LIHC, and UCEC. Pathway analysis confirmed that cuproptosis regulators were associated with the metabolism-related pathways. The expression of MTF1, NLRP3, and SLC31A1 was positively related with ImmuneScore, StromalScore, and ESTIMATEScore in almost all types of tumor, whereas ATP7B, DLAT, DLD, LIAS, PDHA1, and PDHB were significantly negatively correlated with the scores. In addition, CRGs were significantly correlated with RNA stemness score, DNA stemness score, microsatellite instability, and tumor mutational burden. The expression of ATP7A, ATP7B, LIAS, and DLAT was significantly positively correlated with the drug sensitivity of Docetaxel. ATP7A, LIAS, and FDX1 were significantly negatively correlated with the drug sensitivity of UNC0638, XMD13-2, YM201636, and KIN001-260. The altered genomic and clinical characteristics of cuproptosis regulators were comprehensively elucidated, providing a preliminary basis for understanding the functions of cuproptosis in pan-cancer.

Treatment of metastatic pancreatic cancer

Pancreatic cancer is the 4th most common cause of cancer death in Germany and continues to be associated with apoor prognosis. Aprerequisite for chemotherapy or radiotherapy is always the pathohistological (or cytological) confirmation of the tumor disease. Molecular diagnostics include analysis of DNA mismatch repair in the tumor and of the germline mutations in BRCA 1/2 (gBRCA mutation). Systemic chemotherapy remains the mainstay in the management of locally advanced and metastatic disease. If agBRCA mutation is detected, platinum-based therapy should be used. Patients with good performance status benefit from second-line therapy. Immunotherapy with checkpoint inhibitors (not yet approved) may be considered in pretreated patients with evidence of deficient DNA mismatch repair or microsatellite instability.

Fusobacterium nucleatum impairs DNA mismatch repair and stability in patients with squamous cell carcinoma of the head and neck.

Dysbiosis of the laryngeal microbiota has been demonstrated to the development of head and neck squamous cell carcinoma (HNSCC), but the association of Fusobacterium and Fusobacterium nucleatum (F. nucleatum) with DNA mismatch repair (MMR) and microsatellite instability (MSI) has not been investigated. The abundance of Fusobacterium and F. nucleatum, the status of deficient MMR (dMMR) and MSI, and MMR-related gene expression were analyzed in 171 HNSCC tissues, 61 paired para-tumor tissues, and 60 vocal cord polyp tissues. The molecular mechanism of F. nucleatum and MMR-related gene expression were investigated in two human HNSCC cell lines (Tu 686 and FD-LSC-1). Our results demonstrated that a high Fusobacterium abundance was detected in the HNSCC tissues and was exaggerated in the recurrent patients. We further found that a high Fusobacterium abundance was detected in the HNSCC tissues with dMMR and MSI. The Fusobacterium abundance was negatively correlated with the expression of MLH1, MSH2, and MSH6 in the HNSCC tissues. The Fusobacterium abundance was closely associated with the F. nucleatum abundance in the HNSCC tissues. F. nucleatum increased miR-205-5p expression to suppress MLH1, MSH2, and MSH6 expression via the TLR4- and MYD88-dependent innate immune signaling pathway, resulting in dMMR, DNA damage, and cell proliferation in HNSCC. F. nucleatum impacts HNSCC epigenetic changes in tissues with dMMR to promote DNA damage and cell proliferation by suppressing MMR-related gene expression via the TLR4/MYD88/miR-205-5p signaling pathway, which is valuable in the development of efficient strategies for HNSCC prevention and treatment. This study clearly indicates that Fusobacterium induced head and neck squamous cell carcinoma (HNSCC) aggressiveness to affect poor prognosis in HNSCC patients by epigenetic alteration of DNA mismatch repair (MMR) and microsatellite instability. Moreover, the research has shown that Fusobacterium nucleatum ( F. nucleatum ) impacts HNSCC epigenetic changes in tissues with deficient MMR to promote DNA damage and cell proliferation by suppressing MMRrelated gene expression via the TLR4/MYD88/miR-205-5p signaling pathway.

P1257: MOLECULAR CHARACTERIZATION AND CLONAL EVOLUTION OF MYCOSIS FUNGOIDES

Background: Mycosis fungoides (MF) is the most common primary cutaneous T-cell lymphoma with a frequency of over 50% of all cases. MF has an indolent progression over several years through different stages. Symptoms evolve from a non-aggressive “low-risk” (LR) clinical form to an aggressive and treatment-resistant “high-risk” (HR) form. Approximately 20% of patients with MF evolve to a HR MF with transformed cells (tMF), which is associated with a poor prognosis. Aims: At the molecular level, the genomic landscape of MF remains poorly studied. Furthermore, the mechanisms that determine the progression to HR and tMF are still unknown. Methods: We performed whole exome sequencing (WES) of 70 samples from 48 patients at the University Hospital Center (CHU) of Lille, France, between 2007 and 2018. Some patients have multiple sequential samples over several years, with or without progression from LR to HR. Sequencing was performed on the Illumina NovaSeq 6000 system at the Broad Institute (BI) Genomics Platform. The bioinformatics analysis was performed on the Terra platform (BI), which includes tools for the analysis of genomic data. Copy number variations (CNVs) are detected with ModelSegments software in Tumor-Only mode and common large and focal CNVs in the cohort are highlighted by GISTIC2.0. Single nucleotide variants (SNVs) were detected with the CGA WES Characterization Pipeline (Getz lab, BI). Significantly mutated genes were determined by MutSig2CV. The mutational signature was performed with SignatureAnalyzer software. Subsequently ABSOLUTE software is used to calculate the cancer cells fraction of each variant and CNVs in order to follow the clonal evolution of sequential samples. Results: Somatic mutation analysis at the time of diagnosis detected genes involved in T-cell oncogenesis, by order of frequency: the transcription factor JUNB, the MAP kinase member MAPK1, the JAK/STAT member STAT5A and the epigenetic regulators of DNA SUZ12 and TET2. Mutational signatures were represented by the COSMIC SBS1, SBS7, and SBS15, characterized by aging, ultraviolet (UV) exposure, and defective DNA mismatch repair and microsatellite instability, respectively, suggesting their role in the mutational process of MF oncogenesis. The analysis of the CNVs revealed focal deletions affecting genes involved in ER stress TMEM259 (cytoband 19p13.3), the tumor suppressor gene TP53 (17p13.1), the transcriptional repressor gene ZEB1 (10p11.22) which inhibits interleukin 2 IL-2 gene expression, the TNFAIP3 gene (6q16.3) which inhibits nuclear factor kappa B (NF-kB), and the CDKN2A and MTAP genes (9p21.3) which are frequently co-deleted in cancers. The single focal amplification identified a small cytoband in 10p15.1 that carries the genes encoding the interleukin 2 receptor alpha (IL2RA) and interleukin 15 receptor alpha (IL15RA) which have a central role in T cell survival and proliferation. Clonal evolution analysis established that del10p11.22, amp10p15.1 and triplication of chromosome 7 are present only in HR stage, suggesting their role in the tumor progression. Overall survival analysis shows that amp10p15.1 and del10p11.22 – both associated with IL2 pathway - are significantly associated with reduced survival. Summary/Conclusion: WES data from MF identified key CNVs events of oncogenesis and clonal evolution of MF that could serve as predictive markers in clinical practice. Our findings clarify MF genetics and provide novel insights into the disease progression.

Colorectal cancer metastatic dMMR immuno-therapy (COMMIT) study: A randomized phase III study of atezolizumab (atezo) monotherapy versus mFOLFOX6/bevacizumab/atezo in the first-line treatment of patients (pts) with deficient DNA mismatch repair (dMMR) or microsatellite instability high (MSI-H) metastatic colorectal cancer (mCRC)—NRG-GI004/SWOG-S1610.

TPS3647 Background: Despite the superiority in progression-free survival (PFS) of inhibition of programmed cell death-1 (PD-1) pathway in dMMR/MSI-H as compared to chemotherapy with either anti-vascular endothelial growth factor receptor (VEGFr) or anti-epithelial growth factor receptor (EGFr) antibodies in mCRC, more pts had progressive disease as the best response in the anti-PD1 monotherapy arm (29.4% v 12.3%) with mean PFS of 13.7 mos, with ̃45% of pts in the IO arm progressed at 12 mos ( N Engl J Med 2020; 383:2207). We hypothesize that the dMMR/MSI-H mCRC pts may be more effectively treated with the combination of PD-1 pathway blockade and mFOLFOX6/bevacizumab (bev) rather than with anti-PD-1 therapy (atezo) alone. Preclinical work demonstrated synergistic effects between anti-PD-1/anti-VEGF and between oxaliplatin/anti-PD-1 in murine CRC models and phase II data, which showed activity of anti-PD-1/anti-VEGF in chemotherapy refractory colon cancer. A recent randomized trial subgroup analyses of 8 pts with dMMR metastatic colon cancer treated with FOLFOXIRI+bev+atezo, with the first patient having progression ̃16 mos ( ESMO 2021, Abstt LBA20). Additionally, in other solid tumor malignancies, anti-PD1 plus anti-VEGFr (i.e., HCC and RCC) as well as anti-PD1 plus chemotherapy (i.e., gastric and esophageal cancers) combinations are standard first-line treatments. Methods: The redesigned COMMIT study was reactivated on 1/29/2021 as a two-arm prospective phase III open-label trial randomizing (1:1) mCRC dMMR/MSI-H to atezo monotherapy v mFOLFOX6/bev+atezo combination. Assuming our control arm, atezo monotherapy (48% PFS at 24 mos as assessed by site investigator), we have 80% power to detect a hazard ratio of 0.6 (equivalent to 64.4% PFS at 24 mos) with alpha 0.025 one-sided. Stratification factors include BRAFV600E status, metastatic site, and prior adjuvant CRC therapy. Secondary endpoints include OS, objective response rate, safety profile, disease control rate, and duration of response. Health-related quality of life is an exploratory objective. Archived tumor tissue and blood samples will be collected for correlative studies. Key inclusion criteria are: mCRC without prior chemotherapy for advanced disease; dMMR tumor determined by local CLIA-certified IHC assay (MLH1/MSH2/MSH6/PMS2) or MSI-H by local CLIA-certified PCR or NGS panel; and measurable disease per RECIST. Enrollment actively continues to the target accrual of 211 patients randomized between the two immunotherapy arms. Support: U10CA180868, -180822, -180888, UG1CA189867, U24CA196067. Clinical trial information: NCT02997228.

Modulation of Mismatch Repair and the SOCS1/p53 Axis by microRNA-155 in the Colon of Patients with Primary Sclerosing Cholangitis

Deficient mismatch repair (MMR) proteins may lead to DNA damage and microsatellite instability. Primary sclerosing cholangitis (PSC) is a risk factor for colitis-associated colon cancer. MiR-155 is suggested to act as a key regulating node, linking inflammation and tumorigenesis. However, its involvement in the chronic colitis of PSC-UC patients has not been examined. We investigated the involvement of miR-155 in the dysregulation of MMR genes and colitis in PSC patients. Colon tissue biopsies were obtained from patients with PSC, PSC with concomitant ulcerative colitis (PSC-UC), uncomplicated UC, and healthy controls (n = 10 per group). In the ascending colon of PSC and PSC-UC patients, upregulated miR-155 promoted high microsatellite instability and induced signal transducer and activator of transcription 3 (STAT-3) expression via the inhibition of suppressors of cytokine signalling 1 (SOCS1). In contrast, the absence of miR-155 overexpression in the sigmoid colon of PSC-UC patients activated the Il-6/S1PR1 signalling pathway and imbalanced the IL17/FOXP3 ratio, which reinforces chronic colitis. Functional studies on human intestinal epithelial cells (HT-29 and NCM460D) confirmed the role of miR-155 over-expression in the inhibition of MMR genes and the modulation of p53. Moreover, those cells produced more TNFα upon a lipopolysaccharide challenge, which led to the suppression of miR-155. Additionally, exposure to bile acids induced upregulation of miR-155 in Caco-2 cell lines. Thus, under different conditions, miR-155 is involved in either neoplastic transformation in the ascending colon or chronic colitis in the sigmoid colon of patients with PSC. New insight into local modulation of microRNAs, that may alter the course of the disease, could be used for further research on potential therapeutic applications.

FOXM1/lncRNA TYMSOS/miR-214-3p-Mediated High Expression of NCAPG Correlates With Poor Prognosis and Cell Proliferation in Non-Small Cell Lung Carcinoma.

Lung cancer is the most common cancer with high mortality. Increasing evidence has demonstrated that nonstructural maintenance of chromosomes condensin I complex subunit G (NCAPG) plays a crucial role in the progression of human cancers. However, the biological function and underlying mechanism of NCAPG in non–small cell lung cancer (NSCLC) are still unclear. Here, we utilized diverse public databases to analyze the expression of NCAPG in pan-cancer. We found that NCAPG was highly expressed in various human cancers, especially in NSCLC. NCAPG expression was significantly positively correlated with poor clinical-pathological features, poor prognosis, tumor mutational burden, DNA microsatellite instability, and immune cell infiltration in NSCLC. In addition, our results showed that depletion of NCAPG significantly inhibited NSCLC cell proliferation, migration, and self-renewal abilities, yet these could be reversed by adding microRNA (miRNA)-214-3p. Knockdown of long noncoding RNA (lncRNA) thymidylate synthetase opposite strand (TYMSOS) also inhibits the NSCLC cell proliferation, migration, and self-renewal abilities. In summary, our findings demonstrated that the crucial roles of the FOXM1/lncRNA-TYMSOS/miRNA-214-3p/NCAPG axis in NSCLC may shed light on how NCAPG may act as a therapeutic target for NSCLC.

Prognostic and Immunological Roles of MMP-9 in Pan-Cancer.

Background Matrix metalloproteinase-9 (MMP-9) can degrade the extracellular matrix and participate in tumor progression. The relationship between MMP-9 and immune cells has been reported in various malignant tumors. However, there is a lack of comprehensive pan-cancer studies on the relationship between MMP-9 and cancer prognosis and immune infiltration. Method We used data from TCGA and GTEx databases to comprehensively analyze the differential expression of MMP-9 in normal and cancerous tissues. Survival analysis was performed to understand the prognostic role of MMP-9 in different tumors. We then analyzed the expression of MMP-9 across different tumors and at different clinical stages. Based on the results, we assessed the correlation between MMP-9 expression and immune-associated genes and immunocytes. Finally, we calculated the tumor mutation burden (TMB) of 33 cancer types and analyzed the correlation between MMP-9 and TMB, DNA microsatellite instability, and DNA repair genes. Results MMP-9 significantly affected the prognosis and metastasis of various cancers. It was associated based on overall survival, disease-specific survival in five tumors, progression-free interval in seven tumors, and clinical stage in eight tumors, as well as with prognosis and metastasis in adrenocortical carcinoma and kidney renal clear cell carcinoma. It was also coexpressed with immune-related genes and DNA repair genes. The expression of MMP-9 was positively correlated with the markers of T cells, tumor-associated macrophages, Th1 cells, and T cell exhaustion. Furthermore, MMP-9 expression was highly correlated with macrophage M0 in 28 tumors. In addition, its expression was associated with TMB in eight cancer types and DNA microsatellite instability in six cancer types. Conclusion MMP-9 is related to immune infiltration in pan-cancer and can be used as a biomarker related to cancer prognosis and metastasis. Our findings provide prognostic molecular markers and new ideas for immunotherapy.

Systematic evaluation of the prognostic and immunological role of PDLIM2 across 33 cancer types

The protein PDLIM2 regulates the stability of various transcription factors and is required for polarized cell migration. However, the clinical relevance and immune infiltration of PDLIM2 in cancer are not well-understood. We utilized The Cancer Genome Atlas and Genotype-Tissue Expression database to characterize alterations in PDLIM2 in pan-cancer. TIMER was used to explore PDLIM2 expression and immune infiltration levels. We assessed the correlation between PDLIM2 expression and immune-associated gene expression, immune score, tumor mutation burden, and DNA microsatellite instability. PDLIM2 significantly affected the prognosis of various cancers. Increased expression of PDLIM2 was significantly correlated with the tumor grade in seven types of tumors. The expression level of PDLIM2 was positively correlated with immune infiltrates, including B cells, CD8+ T cells, CD4+ T cells, neutrophils, macrophages, and dendritic cells in bladder urothelial, kidney renal papillary cell, and colon adenocarcinoma. High expression levels of PDLIM2 tended to be associated with higher immune and stromal scores. PDLIM2 expression was associated with the tumor mutation burden in 12 cancer types and microsatellite instability in 5 cancer types. PDLIM2 levels were strongly correlated with diverse immune-related genes. PDLIM2 can act as a prognostic-related therapeutic target and is correlated with immune infiltrates in pan-cancer.

NRG-GI004/SWOG-S1610: Colorectal cancer metastatic dMMR immuno-therapy (COMMIT) study—A randomized phase III study of atezolizumab (atezo) monotherapy versus mFOLFOX6/bevacizumab/atezo in the first-line treatment of patients (pts) with deficient DNA mismatch repair (dMMR) or microsatellite instability high (MSI-H) metastatic colorectal cancer (mCRC).

TPS232 Background: Despite the superiority in progression-free survival (PFS) of inhibition of programmed cell death-1 (PD-1) pathway in dMMR/MSI-H as compared to chemotherapy with either anti-vascular endothelial growth factor receptor (VEGFr) or anti-epithelial growth factor receptor (EGFr) antibodies in mCRC, more pts had progressive disease as the best response in the anti-PD1 monotherapy arm (29.4% vs. 12.3%) with mean PFS of 13.7 months ( N Engl J Med 2020; 383:2207). We hypothesize that the dMMR/MSI-H mCRC pts may be more effectively treated by the combination of PD-1 pathway blockade and mFOLFOX6/bevacizumab (bev) rather than with anti-PD-1 therapy (atezo) alone. Preclinical work demonstrated synergistic effects between anti-PD-1/anti-VEGF and between oxaliplatin/anti-PD-1 in murine CRC models and phase II data showed activity of anti-PD-1/anti-VEGF in chemotherapy refractory colon cancer. Additionally, in other solid tumor malignancies, anti-PD1 plus anti-VEGFr (i.e., HCC and RCC) as well as anti-PD1 plus chemotherapy (i.e., gastric and esophageal cancers) combinations are standard first-line treatments. Methods: The redesigned COMMIT study was reactivated on 1/29/2021 as a two-arm prospective phase III open-label trial randomizing (1:1) mCRC dMMR/MSI-H (211 pts) to atezo monotherapy versus mFOLFOX6/bev+atezo combination. Assuming our control arm, atezo monotherapy, 48% PFS at 24 months, as assessed by site investigator, we have 80% power to detect a hazard ratio of 0.6 (equivalent to 64.4% PFS at 24 months) with alpha 0.025 one-sided. Stratification factors include BRAFV600E status, metastatic site, and prior adjuvant CRC therapy. Secondary endpoints include OS, objective response rate, safety profile, disease control rate, duration of response, and centrally-reviewed PFS. Health-related quality of life is an exploratory objective. Archived tumor tissue and blood samples will be collected for correlative studies. Key inclusion criteria are: mCRC without prior chemotherapy for advanced disease; dMMR tumor determined by local CLIA-certified IHC assay (MLH1/MSH2/MSH6/PMS2) or MSI-H by local CLIA-certified PCR or NGS panel; and measurable disease per RECIST. Enrollment actively continues to the target accrual of 211 patients randomized between the two immunotherapy arms. Support: U10CA180868, -180822, -180888, UG1CA189867, U24CA196067; Genentech, Inc. Clinical trial information: NCT02997228.

DNA mismatch repair and microsatellite instability in colorectal tumors: an observational study in the Veterans Affairs Health Care System.

Background: Challenges in identifying microsatellite instability (MSI)/mismatch repair (MMR)-tested colorectal carcinoma (CRC) patients in electronic health records have led to gaps in the understanding of MSI-high/deficient mismatch repair prevalence. Methods: An algorithm to identify MSI-/MMR-tested Veterans Affairs patients was developed and an observational study of adult CRC patients with MSI/MMR testing from 2010 to 2018 was undertaken. Results: An optimized model to identify MSI-/MMR-tested patients yielded high positive predictive value (89.0%) and specificity (97.8%). The authors observed MSI-high/deficient mismatch repair CRC in 54 of 291 patients (18.6%); highest frequencies were observed in stages II (25.9%) and III (22.6%) and lowest in stage IV (5.8%). Conclusions: In this real-world study, the authors proposed a novel method of identifying MSI-/MMR-tested patients. Further validation and refinement of this model, and study in a larger CRC cohort, is warranted.

Research highlights on contributions of mitochondrial DNA microsatellite instability in solid cancers - an overview.

Cancer has been broadly considered a genetic disease involving mutations in nuclear DNA and the mitochondrial genome (mtDNA). Mitochondria are essential bioenergetics and biosynthetic machinery found in most eukaryotic organisms. Thus, failure of their function is crucial for tumourigenesis, tumour cell growth, and metastasis. Mitochondrial dysregulation can occur as a consequence of molecular alterations in mtDNA, such as point mutations, deletions, inversions, microsatellite instability (MSI), and copy number variations. This review article aims to highlight the published research work on alterations in mtDNA, with a particular focus on mitochondrial MSI (mtMSI) in various types of solid cancers. Databases including PubMed, Scopus, and Google Scholar were searched for articles about mtMSI and its link to solid cancer published from 1990 till 2021. In this review, we briefly summarize the knowledge related to possible molecular mechanisms causing mtMSI formation and the available information on mtMSI frequency values in all main solid cancer types. Mutations in the mitochondrial genome are widely believed to have a broad impact across various cancers. Based on the available published data, mtMSI can act as a vital risk factor and a potential marker for cancer progression. Further research is required to unravel the role of mtMSI in tumourigenesis.