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Background: Human coronaviruses (HCoV) cause mild upper respiratory infections; however, in 2019, a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged, causing an acute respiratory disease pandemic. Coronaviruses exhibit marked epidemiological and clinical differences.Purpose: This study compared the clinical, laboratory, and radiographic findings of children infected with SARS-CoV-2 versus HCoV.Methods: SARS-CoV-2 data were obtained from the Korea Disease Control and Prevention Agency (KDCA) registry and 4 dedicated coronavirus disease 2019 (COVID-19) hospitals. Medical records of children admitted with a single HCoV infection from January 2015 to March 2020 were collected from 10 secondary/tertiary hospitals. Clinical data included age, sex, underlying disease, symptoms, test results, imaging findings, treatment, and length of hospital stay.Results: We compared the clinical characteristics of children infected with HCoV (n=475) to those of children infected with SARS-CoV-2 (272 from KDCA, 218 from COVID-19 hospitals). HCoV patients were younger than KDCA patients (older than 9 years:3.6% vs. 75.7%; P

Purpose Plasma circulating tumor DNA (ctDNA) could reflect the genetic alterations present in tumor tissues. However, there is little information about the clinical relevance of cell-free DNA genotyping in peripheral T-cell lymphoma (PTCL).Materials and Methods After targeted sequencing plasma cell-free DNA of patients with various subtypes of PTCL (n=94), we analyzed the mutation profiles of plasma ctDNA samples and their predictive value of dynamic ctDNA monitoring for treatment outcomes.Results Plasma ctDNA mutations were detected in 53 patients (56%, 53/94), and the detection rate of somatic mutations was highest in angioimmunoblastic T-cell lymphoma (24/31, 77%) and PTCL, not otherwise specified (18/29, 62.1%). Somatic mutations were detected in 51 of 66 genes that were sequenced, including the following top 10 ranked genes: RHOA, CREBBP, KMT2D, TP53, IDH2, ALK, MEF2B, SOCS1, CARD11, and KRAS. In the longitudinal assessment of ctDNA mutation, the difference in ctDNA mutation volume after treatment showed a significant correlation with disease relapse or progression. Thus, a ≥ 1.5-log decrease in genome equivalent (GE) between baseline and the end of treatment showed a significant association with better survival outcomes than a < 1.5-log decrease in GE.Conclusion Our results suggest the clinical relevance of plasma ctDNA analysis in patients with PTCL. However, our findings should be validated by a subsequent study with a larger study population and using a broader gene panel.

The chemokine CXCL13 is known to influence local anti-tumor immunity by recruiting immune cells and forming tertiary lymphoid structures (TLS). It has been hypothesized that TLS, led by the expression of CXCL13, could be a predictive or prognostic biomarker for immunotherapy. We investigated the predictive value of CXCL13 to immune checkpoint inhibitors (ICI) in lung adenocarcinoma.We constructed an exploratory dataset (n = 63) and a validation dataset (n = 57) in metastatic lung adenocarcinoma patients treated with ICI. Based on the clinical response, the difference in gene expression profile, including CXCL13, was evaluated.From the exploratory dataset, CXCL13 expression was significantly upregulated in the ICI responders (p = 0.002). Survival analysis using a cut-off value of the median expression value of CXCL13 showed prolonged progression-free survival (PFS) (p = 0.004) and overall survival (OS) (p = 0.007). CXCL13 expression was correlated with other immune response genes, such as GZMA, CD8A, IFNG, PRF1, TLS-related gene sets and its receptor, CXCR5. Notably, subgroup analyses based on CXCL13 expression and CD8A showed that CXCL13-upregulated patients demonstrated comparably prolonged survival regardless of CD8A expression. In the validation dataset, CXCL13 upregulation also demonstrated a significant prolongation of both PFS (p = 0.050) and OS (p = 0.026).We observed that CXCL13 upregulation is correlated to better ICI response in lung adenocarcinoma. Our results support that CXCL13 could be an important chemokine in shaping the immunoactive tumor microenvironment which affects the anti-tumor effect of ICI.

Despite substantial advances in disease genetics, studies to date have largely focused on individuals of European descent. This limits further discoveries of novel functional genetic variants in other ethnic groups. To alleviate the paucity of East Asian population genome resources, we established the Korean Variant Archive 2 (KOVA 2), which is composed of 1896 whole-genome sequences and 3409 whole-exome sequences from healthy individuals of Korean ethnicity. This is the largest genome database from the ethnic Korean population to date, surpassing the 1909 Korean individuals deposited in gnomAD. The variants in KOVA 2 displayed all the known genetic features of those from previous genome databases, and we compiled data from Korean-specific runs of homozygosity, positively selected intervals, and structural variants. In doing so, we found loci, such as the loci ofADH1A/1BandUHRF1BP1, that are strongly selected in the Korean population relative to other East Asian populations. Our analysis of allele ages revealed a correlation between variant functionality and evolutionary age. The data can be browsed and downloaded from a public website (https://www.kobic.re.kr/kova/). We anticipate that KOVA 2 will serve as a valuable resource for genetic studies involving East Asian populations.

Since late preterm neonates are physiologically less mature than term neonates, the use of antenatal corticosteroids in the late preterm period has been recommended. The use of tocolytics can also be considered to gain valuable time for using antenatal corticosteroids in the late preterm period. In this study, we examined the efficacy of tocolytics on prolonging pregnancy in the late preterm period, by comparing women who received tocolytics with those who received none.This retrospective cohort study included women who were admitted due to preterm labor after 34 weeks of gestation and delivered in the late preterm period. Primary outcome was time from admission to delivery (days). Secondary outcomes were the proportion of preterm births within 2 days, and within 7 days, completed cycles of antenatal corticosteroids, and the neonatal outcomes. Primary and secondary outcomes were compared according to the use of tocolytics. Propensity score matching was performed to create comparable groups. The maternal age, pre-pregnancy body mass index, nulliparity, history of preterm birth, hypertensive disease during pregnancy, gestational diabetes mellitus, history of preterm labor, gestational age at admission, cervical length, and the number of contractions were the baseline characteristics included in the propensity score.Of 275 women, 44 women received tocolytics (tocolytics group) and 231 women did not (no tocolytics group). We matched 44 women who received tocolytics and 44 women who didn't. The tocolytics group was shown to exhibit a longer time from admission to delivery than the no tocolytics group, with a hazard ratio for tocolytics of 0.4 (95 % confidence interval, 0.2-0.6). In addition, the proportion of preterm births occurring within 2 days and 7 days were lower in those receiving tocolytics compared to those that didn't.In this propensity score matched-study, the use of tocolytics had a significant effect on pregnancy prolongation, which allows more time for use of corticosteroids in women with preterm labor after 34 weeks of gestation.

In cases with a large recipient left atrium (LA), matching of the donor and recipient anastomoses can be challenging. In the presented case, this is addressed by reducing the circumference of the recipient LA cuff by extending the pulmonary veins. The inferior pulmonary veins were extended by making neopulmonary veins using the remnant recipient LA cuff; the circumference of the recipient LA cuff could then be reduced to easily make an anastomosis. This new technique could be an alternative method to resolve LA size discrepancies in orthotopic heart transplantation.

Purpose: Although programmed death 1/programmed death ligand 1 (PD-1/PD-L1) inhibitors are promising agents for recurrent or metastatic nasopharyngeal carcinoma (NPC), PD-1/PD-L1 inhibitor monotherapy has shown modest efficacy. This study evaluated the efficacy and safety of nivolumab plus gemcitabine in patients with NPC who failed prior platinum-based chemotherapy. Patients and Methods: This is a phase II, multicenter, open-label, single-arm study. Patients with recurrent or metastatic NPC received nivolumab 3 mg/kg and gemcitabine 1,250 mg/m2 every 2 weeks until disease progression or intolerable toxicity. The primary endpoint was progression-free survival (PFS). The secondary endpoints included objective response rate (ORR), overall survival (OS), and safety. To identify potential biomarkers, whole-exome sequencing, whole-transcriptome sequencing, and immune phenotype analysis based on Lunit SCOPE IO, an artificial intelligence–powered spatial tumor-infiltrating lymphocyte analyzer, were performed. Results: Thirty-six patients were enrolled between June 2018 and June 2019. The ORR was 36.1% and disease control rate was 97.2%. With median follow-up of 22.0 months, median PFS was 13.8 months [95% confidence interval (CI), 8.6–16.8 months]. Median OS was not reached, and OS rate at 6 months was 97.0% (95% CI, 80.4%–99.6%). The grade ≥3 treatment-related adverse events were hypertension (2.8%) and anemia (2.8%). In multivariate analysis of mutation of chromatin modifier gene, tumor mutational burden (≥ 2.1 mut/Mb), and somatic copy-number alteration (SCNA) level, the group with high SCNA (> 3 points; HR, 7.0; 95% CI, 1.3–37.9; P = 0.02) had independently associated with poor PFS. Immune phenotype analysis showed that tumors with high proportion of immune-excluded immune phenotype was significantly correlated with poor PFS (HR, 4.4; 95% CI, 1.2–16.2; P = 0.018). Conclusions: Nivolumab plus gemcitabine showed promising efficacy with favorable toxicity profiles in patients with advanced NPC in whom platinum-based combination chemotherapy failed.

Background/Aims: We evaluated the feasibility and long-term efficacy of the combination of cytarabine, idarubicin, and all-trans retinoic acid (ATRA) for treating patients with newly diagnosed acute promyelocytic leukemia (APL).Methods: We included 87 patients with newly diagnosed acute myeloid leukemia and a t(15;17) or promyelocytic leukemia/retinoic acid receptor alpha (PML-RARα) mutation. Patients received 12 mg/m2/day idarubicin intravenously for 3 days and 100 mg/m2/day cytarabine for 7 days, plus 45 mg/m2/day ATRA. Clinical outcomes included complete remission (CR), relapse-free survival (RFS), overall survival (OS), and the secondary malignancy incidence during a 20-year follow-up.Results: The CR, 10-year RFS, and 10-year OS rates were 89.7%, 94.1%, and 73.8%, respectively, for all patients. The 10-year OS rate was 100% for patients that achieved CR. Subjects were classified according to the white blood cell (WBC) count in peripheral blood at diagnosis (low-risk, WBC < 10,000/mm3; high-risk, WBC ≥ 10,000/mm3). The low-risk group had significantly higher RFS and OS rates than the high-risk group, but the outcomes were not superior to the current standard treatment (arsenic trioxide plus ATRA). Toxicities were similar to those observed with anthracycline plus ATRA, and higher than those observed with arsenic trioxide plus ATRA. The secondary malignancy incidence after APL treatment was 2.7%, among the 75 patients that achieved CR, and 5.0% among the 40 patients that survived more than 5 years after the APL diagnosis.Conclusions: Adding cytarabine to anthracycline plus ATRA was not inferior to anthracycline plus ATRA alone, but it was not comparable to arsenic trioxide plus ATRA. The probability of secondary malignancy was low.

Background and Objective From the past, several researchers have studied and measured the partial pressure of carbon dioxide during sleep in normal children to establish diagnostic criteria for hypoventilation in children. Here we tried to verify the existing definition of sleep-related hypoventilation in Asian by evaluating and analyzing the carbon dioxide partial pressure in pediatric subjects who underwent polysomnography.Methods We retrospectively analyzed clinical information of 196 children who underwent polysomnography at our hospital from Feb 2011 to Apr 2021. Among Asian pediatric subjects, those with serious chronic or genetic diseases, craniofacial deformities, and hypoventilation confirmed by polysomnography were excluded. We evaluated partial pressure of carbon dioxide in target group by end-tidal carbon dioxide (EtCO2) measured with a stream capnometer through nasal cannula. The target group was classified by apnea-hypopnea index and analyzed.Results The mean value of the time with EtCO2 ≥ 45 mm Hg in total sleep time was 47.00% which is higher than previous studies. The mean value of the time with EtCO2 ≥ 50 mm Hg in total sleep time was 2.77% which is similar to previous studies. Also, our subjects showed the highest mean EtCO2 value in non-rapid eye movement (NREM) stage and lowest mean EtCO2 value when wake.Conclusions In this study, the diagnostic criteria for sleep-related hypoventilation at the American Academy of Sleep Medicine (AASM) in 2017 established by measuring the EtCO2 in western children seems appropriate to apply to Asian children to define hypoventilation.

PurposeAnalysis of circulating tumor DNA (ctDNA) in blood could allow noninvasive genetic analysis of primary tumors. Although there have been unmet needs for noninvasive methods in patients with primary central nervous system lymphoma (PCNSL), it is still not determined whether plasma ctDNA analysis could be useful for patients with PCNSL. Materials and MethodsTargeted deep sequencing of 54 genes was performed in cell-free DNA isolated from plasma samples collected pretreatment, during treatment, and at the end of treatment in 42 consecutively diagnosed PCNSL patients between January 2017 and December 2018.ResultsTargeted sequencing of plasma cell-free DNA detected somatic mutations representing ctDNA in 11 cases (11/41, 27%). The detection of ctDNA was not related to the concentration of cell-free DNA or tumor volume. The mutation profiles of these 11 cases varied between patients. The most frequently mutated gene was PIM1 (4/11, 36.4%), whereas KMT2D, PIK3CA, and MYD88 were each observed in three patients (3/11, 27%). The mutations of 13 genes were concordantly found in primary tumor tissue and plasma ctDNA, giving a detection sensitivity of 45%. During the serial tracking of seven patients with complete response, the disappearance of ctDNA mutations was found in four patients, whereas three patients had detected ctDNA mutation at the end of treatment. ConclusionThe plasma ctDNA mutation analysis still has limited value for surveillance and predicting treatment outcomes of PCNSL because the detection efficiency was lower than other systemic lymphomas. Thus, analytical platforms should be improved to overcome anatomical hurdles associated with PCNSL.

Background: Palbociclib plus endocrine therapy (ET) demonstrated significant progression-free survival (PFS) benefit in Young Pearl, a randomized phase ll trial comparing palbociclib + ET versus capecitabine in premenopausal women with hormone receptor positive, HER2 negative metastatic breast cancer (MBC). This exploratory analysis investigated potential biomarkers of palbociclib plus ET on PFS. Patients and methods: Of 178 patients randomized (92 palbociclib plus ET; 86 capecitabine), we performed targeted sequencing (141 patients) and whole transcriptome sequencing (165 patients) using baseline tumor samples to examine genomic alteration in relation to drug response on PFS. Hazard ratios (HRs) were estimated using unstratified Cox proportional hazards models. Results: PIK3CA (41%) and TP53 (33%) mutations and CCND1 copy number variation (29%) were found most frequently in targeted sequencing of 141 patients. ESR1 mutations were found only in 3.5% of patients of this population. Luminal type showed better prognosis in palbociclib + ET arm but no impact on PFS difference in capecitabine arm. High TMB, TP53 mutation, PTEN loss of function mutation and RB1 pathway alteration showed worse prognosis in palbociclib plus ET arm. Patients with BRCA2 pathogenic mutations showed worse prognosis regardless of PAM50 subtypes. AURKA mutation/amplification, BRIP1/MYC/RAD51C amplification were significantly associated to the patients with short PFS

Cone-beam computed tomography (CBCT) is a promising imaging modality for sinonasal evaluation, with advantages of relatively low radiation dose, low cost, and quick outpatient imaging. Our study aimed to compare the diagnostic performance and image quality of CBCT with those of multi-detector computed tomography (MDCT) with different slice thickness.We retrospectively reviewed 60 consecutive patients who had undergone both CBCT and MDCT. MDCT images was reconstructed with 1 and 3 mm slice thickness. The quantitative image quality parameters (image noise, signal-to-noise ratio [SNR], and contrast-to noise ratio [CNR] were calculated and compared between the two imaging modalities. Two observers (ENT surgeon and neuroradiologist) evaluated the presence of seven sinonasal anatomic variations in each patient and interobserver agreements were analyzed. The diagnostic performance of CBCT (0.3 mm) and MDCT (3 mm) was assessed and compared with that of high resolution MDCT (1 mm), which is considered as the gold standard.The image noise was significantly higher and SNR and CNR values were lower in the CBCT (0.3 mm) group than in the MDCT groups (1 and 3 mm). The diagnostic performance of CBCT (0.3 mm) was similar to that of MDCT (1 mm) and superior to that of MDCT (3 mm). The highest interobserver agreement was for high resolution MDCT (1 mm), followed by CBCT (0.3 mm), and MDCT (3 mm).Considering its low radiation dose, low cost, and ease of clinical access, CBCT may be a useful imaging modality for as first line sinonasal evaluation and repeated follow up.Study design: Retrospective study in a tertiary referral university center.Level of evidence: NA.

Adding anti-PD1 antibodies to 5-FU/platinum chemotherapy improves survival in a subset of advanced gastroesophageal adenocarcinoma (GEA) patients. Beyond PD-L1 expression and mismatch repair status we have limited insight into molecular predictors of response, or the relative contribution of PD-1 blockade. We conducted an investigator sponsored phase II trial (n = 47) sequentially adding pembrolizumab to standard 5-FU/platinum in previously untreated advanced GEA (ClinicalTrials.gov: NCT04249739). With an overall response rate of 67% the activity paralleled phase III chemoimmunotherapy trials. To understand on-treatment tumor and immune adaptations patients underwent serial biopsy of the primary tumor, including baseline, after one cycle of 5-FU/platinum, and after the addition of pembrolizumab. We leveraged transcriptional profiling from 358,067 cells to identify multicellular networks of malignant, stromal, and immune cells after chemotherapy and concurrent chemoimmunotherapy. The relative usage of pro-tumor and anti-tumor interaction hubs differed between fast and slow progressing patients. Chemotherapy induced early on-treatment formation of hubs centered on tumor-reactive T-cell and M1-oriented macrophage interactions with pro-inflammatory cytokines in slow progressors. Faster progression was characterized by increased MUC5A and MSLN containing programs in tumor cells and M2-oriented macrophages with immunosuppressive stromal interactions. After adding pembrolizumab we observed increased CD8 T-cell infiltration by scRNAseq and multiplex immunofluorescence and development of an immunity hub involving co-variation of the tumor-reactive CXCL13 program and epithelial interferon-stimulated gene programs enriched in slow progressors. Together this data provides prospective evidence of differential early on-treatment evolution of the gastric immune microenvironment and nominates candidate cellular interactions for clinical targeting.

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

Supplementary Figure from Early Tumor–Immune Microenvironmental Remodeling and Response to First-Line Fluoropyrimidine and Platinum Chemotherapy in Advanced Gastric Cancer

Adding anti-PD1 antibodies to 5-FU/platinum chemotherapy improves survival in a subset of advanced gastroesophageal adenocarcinoma (GEA) patients. Beyond PD-L1 expression and mismatch repair status we have limited insight into molecular predictors of response or the relative contribution of PD-1 blockade. We conducted an investigator sponsored phase II trial (n = 47) sequentially adding pembrolizumab to standard 5-FU/platinum in previously untreated advanced GEA (ClinicalTrials.gov:NCT04249739). With an overall response rate of 67% the activity paralleled phase III chemoimmunotherapy trials. To understand on-treatment tumor and immune adaptations patients underwent serial biopsy of the primary tumor, including baseline, after one cycle of 5-FU/platinum, and after the addition of pembrolizumab. We leveraged transcriptional profiling from 358,067 cells to identify multicellular networks of malignant, stromal, and immune cells after chemotherapy and concurrent chemoimmunotherapy. The relative usage of pro-tumor and anti-tumor interaction hubs differed between fast and slow progressing patients. Chemotherapy induced early on-treatment formation of hubs centered on tumor-reactive T-cell and M1-oriented macrophage interactions with pro-inflammatory cytokines in slow progressors. Faster progression was characterized by increased MUC5A and MSLN containing programs in tumor cells and M2-oriented macrophages with immunosuppressive stromal interactions. After adding pembrolizumab we observed increased CD8 T-cell infiltration by scRNAseq and multiplex immunofluorescence and development of an immunity hub involving co-variation of the tumor-reactive CXCL13 program and epithelial interferon-stimulated gene programs enriched in slow progressors. Together this data provides prospective evidence of differential early on-treatment evolution of the gastric immune microenvironment and nominates candidate cellular interactions for clinical targeting.

Supplementary Table from Early Tumor–Immune Microenvironmental Remodeling and Response to First-Line Fluoropyrimidine and Platinum Chemotherapy in Advanced Gastric Cancer

Figure S8. Volcano plot of GSVA analyses showing the difference between (A) merged gBRCA1/2 mutation vs. wild type (WT), (B) gBRCA mutations vs. WT in triple negative patients, (C) gBRCA2 mutations vs. WT in estrogen receptor-positive patients.

Figure S4. Gene expression profile of pre-selected representative genes of interest based on concordance of immunohistochemistry (IHC) subtype and molecular subtype identified by PAM50. (IHC subtype > PAM50 subtype)

Figure S5. Heatmap plot of gene expression profile between samples from patients with gBRCA1 and gBRCA2 mutations showing the top 20 ranked genes.

Table S1. List of 381 genes from CancerSCANTM Table S2. gBRCA1/2 mutation profile of study population. Table S3. Raw data for differentially expressed genes found by comparing gBRCA1 and gBRCA2 mutants. Table S4. Raw GSVA data derived by comparing gBRCA1 and gBRCA2 mutants. Table S5. Raw data for differentially expressed genes found by comparing patients with mutated and wild-type gBRCA1/2. Table S6. Raw GSVA data derived by comparing patients with mutated and wild-type gBRCA1/2. Table S7. Raw data for differentially expressed genes found by comparing mutated and wild-type gBRCA1 in triple negative patients. Table S8. Raw GSVA data derived by comparing mutated and wild-type gBRCA1 in triple negative patients. Table S9. Raw data for differentially expressed genes found by comparing mutated and wild-type gBRCA2 in estrogen receptor-positive patients. Table S10. Raw GSVA data derived by comparing mutated and wild-type gBRCA2 in estrogen receptor-positive patients. Table S11. Loss of heterozygosity status and the allele frequency of samples available for the target sequencing.

Figure S1. (A) Statistics for deep target sequencing data (CancerSCANTM) from study patients (n = 45). (B) Quality control data for whole transcriptome sequencing from the study population (n = 34).

Figure S6. (A) Volcano plot of GSVA analyses showing the difference between samples with gBRCA1 and gBRCA2 mutations. (B) Gene sets enriched in either gBRCA1 mutants or gBRCA2 mutants.

Figure S2. Hazard ratio based on individual mutations in BRCA2 and survival curves from representative loci and ranges.

Figure S3. Mutation profile of genes with top 30 incidence rate in the study population and reference samples.

Figure S7. (A) Volcano plot of hallmark gene sets showing the difference between gBRCA1 and gBRCA2 mutant samples. (B) Hallmark gene sets enriched in either gBRCA1 mutants or gBRCA2 mutants and the list (C).

Purpose:Although programmed death 1/programmed death ligand 1 (PD-1/PD-L1) inhibitors are promising agents for recurrent or metastatic nasopharyngeal carcinoma (NPC), PD-1/PD-L1 inhibitor monotherapy has shown modest efficacy. This study evaluated the efficacy and safety of nivolumab plus gemcitabine in patients with NPC who failed prior platinum-based chemotherapy.Patients and Methods:This is a phase II, multicenter, open-label, single-arm study. Patients with recurrent or metastatic NPC received nivolumab 3 mg/kg and gemcitabine 1,250 mg/m2 every 2 weeks until disease progression or intolerable toxicity. The primary endpoint was progression-free survival (PFS). The secondary endpoints included objective response rate (ORR), overall survival (OS), and safety. To identify potential biomarkers, whole-exome sequencing, whole-transcriptome sequencing, and immune phenotype analysis based on Lunit SCOPE IO, an artificial intelligence–powered spatial tumor-infiltrating lymphocyte analyzer, were performed.Results:Thirty-six patients were enrolled between June 2018 and June 2019. The ORR was 36.1% and disease control rate was 97.2%. With median follow-up of 22.0 months, median PFS was 13.8 months [95% confidence interval (CI), 8.6–16.8 months]. Median OS was not reached, and OS rate at 6 months was 97.0% (95% CI, 80.4%–99.6%). The grade ≥3 treatment-related adverse events were hypertension (2.8%) and anemia (2.8%). In multivariate analysis of mutation of chromatin modifier gene, tumor mutational burden (≥ 2.1 mut/Mb), and somatic copy-number alteration (SCNA) level, the group with high SCNA (> 3 points; HR, 7.0; 95% CI, 1.3–37.9; P = 0.02) had independently associated with poor PFS. Immune phenotype analysis showed that tumors with high proportion of immune-excluded immune phenotype was significantly correlated with poor PFS (HR, 4.4; 95% CI, 1.2–16.2; P = 0.018).Conclusions:Nivolumab plus gemcitabine showed promising efficacy with favorable toxicity profiles in patients with advanced NPC in whom platinum-based combination chemotherapy failed.

Supplementary Data from A Phase II Study of Nivolumab plus Gemcitabine in Patients with Recurrent or Metastatic Nasopharyngeal Carcinoma (KCSG HN17–11)

Figure S1. Somatic mutations of each tumor. Missense, nonsense and splicing identified by whole-exome sequencing analysis

Supplementary Figure S1. Histopathology of NSCLC brain metastases and their corresponding PDXs. Histological subtype and differentiation status was indicated for each case. ADC = adenocarcinoma, LCC = large cell carcinoma, SQCC = squamous cell carcinoma.

Supplementary Table S1. Read mapping information of CRC samples

Supplementary Figure 1. Survival plot using Kaplan-Meier survival analysis between two patient groups with high- and low-heterogeneity.

Figure S4. The genomic and transcriptomic pattern of TH6 case. (A) The mutation heatmap. (B) The scatter plot shows the similarity of gene expression profiles between nodes (using 15,842 genes with at least > 5 reads) by measuring Pearson's correlation coefficient (r). (C) The density plot of cancer cell fraction (CCF) between the primary and the lymph node. (D) The gene expression pattern of genes belonging to SQCCs, PI(3)K/RTK/RAS signaling. Gene expression values in lymph nodes were mapped on the distribution of gene expression in TCGA SQCCs (n=495), represented by the boxplot. AKT2 and RASA1 show significant clinical outcome difference in the gene expression of TCGA SQCCs patients; *P < 0.05.

Supplementary Figure 2. Circle chart of the number of KRAS and TP53 mutation occurrences belonging to the four categories of CCFs. The four categories are based on CCF distribution (G1: 1st quantile, G2: 2nd quantile, G3: 3rd quantile, and G4: 4th quantile).

Visualization of immune cell landscape for multiple myeloma and healthy bone marrow.

Gene expression features of myeloma cells.

Purpose: Tumors continuously evolve to maintain growth; secondary mutations facilitate this process, resulting in high tumor heterogeneity. In this study, we compared mutations in paired primary and metastatic colorectal cancer tumor samples to determine whether tumor heterogeneity can predict tumor metastasis.Experimental Design: Somatic variations in 46 pairs of matched primary-liver metastatic tumors and 42 primary tumors without metastasis were analyzed by whole-exome sequencing. Tumor clonality was estimated from single-nucleotide and copy-number variations. The correlation between clinical parameters of patients and clonal heterogeneity in liver metastasis was evaluated.Results: Tumor heterogeneity across colorectal cancer samples was highly variable; however, a high degree of tumor heterogeneity was associated with a worse disease-free survival. Highly heterogeneous primary colorectal cancer was correlated with a higher rate of liver metastasis. Recurrent somatic mutations in APC, TP53, and KRAS were frequently detected in highly heterogeneous colorectal cancer. The variant allele frequency of these mutations was high, while somatic mutations in other genes such as PIK3CA and NOTCH1 were low. The number and distribution of primary colorectal cancer subclones were preserved in metastatic tumors.Conclusions: Heterogeneity of primary colorectal cancer tumors can predict the potential for liver metastasis and thus, clinical outcome of patients. Clin Cancer Res; 23(23); 7209–16. ©2017 AACR.

Table S5. Mapping statistics of sequencing reads of RNA sequencing

Supplementary table S3. Clinicopathological characteristics and in vivo tumorigenicity of primary NSCLC cases.

Figure S1, Figure S2, Figure S3, Figure S4, Figure S5

Multivariate analysis of overall survival

Cytotoxic immune cells in the peripheral blood of healthy donors and multiple myeloma patients.

Gene expression features of myeloma cells.

Immune cell type identification using DEGs and annotation package SingleR.