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Sequence alterations in microsatellites and an elevated mutational burden are observed in 20% of gastric cancers (GC) and associated with clinical response to anti-programmed death (PD)-1 antibodies. However, 50% of microsatellite instability-high (MSI-H) cancers are intrinsically resistant to PD-1 therapies. We conducted a phase II trial of pembrolizumab in advanced MSI-H GC patients and included serial and multi-region tissue samples in addition to serial peripheral blood analyses. The number of whole-exome sequencing (WES)-derived nonsynonymous mutations correlated with anti-tumor activity and prolonged progressionfree survival (PFS). Coupling WES to single-cell RNA sequencing, we identified dynamic tumor evolution with greater on treatment collapse of mutational architecture in responders. Diverse T-cell receptor repertoire was associated with longer PFS to pembrolizumab. Additionally, increase in PD-1 + CD8 + T cells correlated with durable clinical benefit. Our findings highlight the genomic, immunologic, and clinical outcome heterogeneity within MSI-H GC and may inform development of strategies to enhance responsiveness.Research.

Chemotherapy is ubiquitous in first-line treatment of advanced gastric cancer, yet responses are heterogeneous, and little is known about mediators of chemotherapy response. To move forward, an understanding of the effects of standard chemotherapy on the tumor–immune microenvironment (TME) is needed. Coupling whole-exome sequencing, bulk RNA and single-cell transcriptomics from paired pretreatment and on-treatment samples in treatment-naïve patients with HER2-positive and HER2-negative gastric cancer, we define features associated with response to platinum-based chemotherapy. Response was associated with on-treatment TME remodeling including natural killer (NK) cell recruitment, decreased tumor-associated macrophages, M1-macrophage repolarization, and increased effector T-cell infiltration. Among chemotherapy nonresponders, we observed low/absent PD-L1 expression or modulation, on-treatment increases in Wnt signaling, B-cell infiltration, and LAG3-expressing T cells coupled to an exodus of dendritic cells. We did not observe significant genomic changes in early on-treatment sampling. We provide a map of on-treatment TME modulation with standard chemotherapy and nominate candidate future approaches. Significance: Using paired pretreatment and on-treatment samples during standard first-line chemotherapy, we identify chemotherapy-induced NK-cell infiltration, macrophage repolarization, and increased antigen presentation among responders. Increased LAG3 expression and decreased dendritic cell abundance were seen in nonresponders, emphasizing remodeling of the TME during chemotherapy response and resistance. This article is highlighted in the In This Issue feature, p. 873

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Non-IBD control Crohn's disease Patient-derived Enteroid TNF-ɑ Necroptotic cell death ↑ Non-IBD control Crohn's disease Patient-derived Entero r r id TNF-ɑ Necroptotic cell death ↑ Damaged Enteroid

BackgroundNoninvasive prenatal testing (NIPT) using massively parallel sequencing of cell-free DNA (cfDNA) is increasingly being used to predict fetal chromosomal abnormalities. However, concerns over erroneous predictions which occur while performing NIPT still exist in pregnant women at high risk for fetal aneuploidy. We performed the largest-scale clinical NIPT study in Korea to date to assess the risk of false negatives and false positives using next-generation sequencing.MethodsA total of 447 pregnant women at high risk for fetal aneuploidy were enrolled at 12 hospitals in Korea. They underwent definitive diagnoses by full karyotyping by blind analysis and received aneuploidy screening at 11–22 weeks of gestation. Three steps were employed for cfDNA analyses. First, cfDNA was sequenced. Second, the effect of GC bias was corrected using normalization of samples as well as LOESS and linear regressions. Finally, statistical analysis was performed after selecting a set of reference samples optimally adapted to a test sample from the whole reference samples. We evaluated our approach by performing cfDNA testing to assess the risk of trisomies 13, 18, and 21 using the sets of extracted reference samples.ResultsThe adaptive selection algorithm presented here was used to choose a more optimized reference sample, which was evaluated by the coefficient of variation (CV), demonstrated a lower CV and higher sensitivity than standard approaches. Our adaptive approach also showed that fetal aneuploidies could be detected correctly by clearly splitting the z scores obtained for positive and negative samples.ConclusionsWe show that our adaptive reference selection algorithm for optimizing trisomy detection showed improved reliability and will further support practitioners in reducing both false negative and positive results.Electronic supplementary materialThe online version of this article (doi:10.1186/s12920-016-0222-5) contains supplementary material, which is available to authorized users.

Single-cell ribonucleic acid (RNA) sequencing (scRNA-seq) is an effective technique for estimating the cellular composition and transcriptional profiles of individual cells from fresh tissue. Single-nucleus RNA sequencing (snRNA-seq) is necessary to perform this type of analysis in frozen or difficult-to-dissociate tissues, which cannot be subjected to scRNA-seq. This difference in the state of tissues leads to variation in cell-type distributions among each platform. To identify the characteristics of these methods and their differences, scRNA-seq and snRNA-seq were performed in parallel for colon and liver tissues. The two platforms revealed similar diversity but different proportions of cell types in matched tissues. The proportions of epithelial cells in the colon and hepatocytes in the liver were relatively high in snRNA-seq and that of immune cells was relatively high in scRNA-seq. This difference could be explained by variations in the expression scores of adhesion genes due to the disruption of the cytoplasmic contents during scRNA-seq. The enrichment of epithelial cells in the colon resulted in a discrepancy in the differentiation of epithelial cells. This enrichment was also well matched with the images of hematoxylin and eosin staining and the estimated distribution of cell types in bulk RNA sequencing. These results showed that snRNA-seq could be used to analyze tissues that cannot be subjected to scRNA-seq and provides more information in specific cell type analysis.

e15542 Background: Colorectal cancer (CRC) is the third most common cancer and second leading cause of cancer-related death worldwide. What makes CRC treatment a challenge is synchronous or metachronous recurrence at distant organs; metastasis. Approximately half of CRC patients develop metastases in the course of the disease and the most prevalent metastatic site is liver, followed by lung and peritoneum. A 5-year survival rate metastatic CRC is much poorer than that of patients with regional and localized CRC. Methods: From 2019 to 2020, 9 metastatic CRC patients who had recurrence to lung oligo-metastases were enrolled. These patients were eligible for lung metastatectomy of curative intent. The surgically resected lung metastases were collected and whole exome sequencing/RNA sequencing,10x chromium single cell RNA sequencing analysis were performed. The purpose of this study was to uncover distinctive tumor microrenvironment (TME) of the lung metastases from CRC, we compared these results with those from public available primary CRC data. Results: We successfully analyzed all 9 metastatic lung samples. Compared to primary CRC, we found that lung metastasis had more immune-suppressive TMEs, represented by downregulation of TCR signaling, innate/adaptive immune system and antigen presentation. In addition, there were higher expression levels of immune checkpoint molecules, such as PD-1, LAG-3 and TIGIT in metastatic lung samples when compared to primary colon cancer public database. Macrophage polarization of lung metastases toward alternatively activated M2 subset, rather than classically activated M1 subset, resulting in low M1/M2 ratio, was also thought to attribute to immune suppressive environments of the lung metastases and successful colonization of primary tumors. Conclusions: This study identified different TMEs of lung metastasis specimens from primary CRCs. Our study underscores the importance of the tumor microenvironment and the anatomic location of the tumor cells for optimized immunotherapeutic strategies.