Introduction: Triple-negative breast cancer (TNBC) is group of heterogeneity caner. Despite majority of them had the unfavorable prognosis, a subset of patients who do not receive chemotherapy exhibit a good prognosis. Biomarkers are required to recognize these group of pateints and improve the current therapeutic strategies for them. Methods: A retrospective analysis of 997 patients with TNBC from three datasets including 188 case of Peking Union Medical College Hospital (PUMCH) and two TNBC datasets from published cohort studies(279 case of Affy-set, 530 case of GSE set) was conducted. Intrinsic subtypes (basal-like, immune-enhanced, human epidermal growth factor receptor-2 [HER2]-enriched and luminal A/B) and tumor environmental immunity were evaluated using expression profiles of a 72-gene panel. Association of intrinsic subtype and immunity score with distant metastasis-free survival (DMFS) and overall survival (OS) was analyzed. Results: Five intrinsic subtypes were identified in the patients with TNBC, comprising 64 % basal-like, 19 % immune-enhanced, 11 % HER2-enriched, 5 % luminal A, and 2 % luminal B. In the absence of adjuvant chemotherapy (ACT), Luminal A and immune-enhanced subtypes showed better DMFS than basal-like, HER2-enriched, and luminal B subtypes(P = 0.35). Significantly good OS was observed in luminal A and immune-enhanced subtypes compared to basal-like and HER2-enriched subtypes (P < 0.05). So two subtype groups were further classified as low-risk subtypes, including luminal A and immune-enhanced, and high-risk subtypes, including basal-like, HER2-enriched, and luminal B. Except for the immune-enhanced subtype, each subtype was further sorted and grouped according to immunity score, istrong and iweak. Significant improvements in both DMFS and OS were observed in patients with istrong compared with those with iweak(P = 0.01 and 0.0051 respectively). When combining intrinsic subtype and immunity status to predict the benefit from ACT, all high-risk subtype patients demonstrated improved DMFS(P = 0.075) and OS(P < 0.0001), with istrong patients exhibiting greater benefit; low-risk subtype plus iweak patients showed marginal benefit, whereas low-risk subtype plus istrong patients demonstrated least benefit from ACT. Conclusion: Intrinsic subtype and immunity score is good prognostic biomarkers for patients with TNBC in the absence of chemotherapy. Combined intrinsic subtype and immunity evaluation could identify patients with TNBC who do not benefit from chemotherapy.

Abstract Background Naturally occurring colorectal cancers (CRC) in rhesus macaques share many features with their human counterparts and are useful models for cancer immunotherapy; but mechanistic data are lacking regarding the comparative molecular pathogenesis of these cancers. Methods We conducted state-of-the-art imaging including CT and PET, clinical assessments, and pathological review of 24 rhesus macaques with naturally occurring CRC. Additionally, we molecularly characterized these tumors utilizing immunohistochemistry (IHC), microsatellite instability assays, DNAseq, transcriptomics, and developed a DNA methylation-specific qPCR assay for MLH1, CACNA1G, CDKN2A, CRABP1, and NEUROG1, human markers for CpG island methylator phenotype (CIMP). We furthermore employed Monte-Carlo simulations to in-silico model alterations in DNA topology in transcription-factor binding site-rich promoter regions upon experimentally demonstrated DNA methylation. Results Similar cancer histology, progression patterns, and co-morbidities could be observed in rhesus as reported for human CRC patients. IHC identified loss of MLH1 and PMS2 in all cases, with functional microsatellite instability. DNA sequencing revealed the close genetic relatedness to human CRCs, including a similar mutational signature, chromosomal instability, and functionally-relevant mutations affecting KRAS (G12D), TP53 (R175H, R273*), APC, AMER1, ALK, and ARID1A. Interestingly, MLH1 mutations were rarely identified on a somatic or germline level. Transcriptomics not only corroborated the similarities of rhesus and human CRCs, but also demonstrated the significant downregulation of MLH1 but not MSH2, MSH6, or PMS2 in rhesus CRCs. Methylation-specific qPCR suggested CIMP-positivity in 9/16 rhesus CRCs, but all 16/16 exhibited significant MLH1 promoter hypermethylation. DNA hypermethylation was modelled to affect DNA topology, particularly propeller twist and roll profiles. Modelling the DNA topology of a transcription factor binding motif (TFAP2A) in the MLH1 promoter that overlapped with a methylation-specific probe, we observed significant differences in DNA topology upon experimentally shown DNA methylation. This suggests a role of transcription factor binding interference in epigenetic silencing of MLH1 in rhesus CRCs. Conclusions These data indicate that epigenetic silencing suppresses MLH1 transcription, induces the loss of MLH1 protein, abrogates mismatch repair, and drives genomic instability in naturally occurring CRC in rhesus macaques. We consider this spontaneous, uninduced CRC in immunocompetent, treatment-naïve rhesus macaques to be a uniquely informative model for human CRC. Graphical abstract

Single cell RNA sequencing (scRNA-Seq) is useful to classify cell-specific gene expression profiles in kidney tissue. As viable cells are required, we report an optimized cell dissociation methodology and the necessity of screening tissue histology prior to scRNA-Seq. We demonstrate that glomerular injury can selectively reduce the appearance of groups of cells during analysis of cell clustering and we confirmed reductions in cell-specific markers among injured cells on kidney sections with fluorescence microscopy. Interpretation of scRNA-Seq results may be refined based upon these considerations.

Abstract Background While high-grade serous ovarian cancer (HGSC) has proven largely resistant to immunotherapy, sporadic incidents of partial and complete response have been observed in clinical trials and case reports. These observations suggest that a molecular basis for effective immunity may exist within a subpopulation of HGSC. Herein, we developed an algorithm, CONSTRU (Computing Prognostic Marker Dependencies by Successive Testing of Gene-Stratified Subgroups), to facilitate the discovery and characterization of molecular backgrounds of HGSC that confer resistance or susceptibility to protective anti-tumor immunity. Methods We used CONSTRU to identify genes from tumor expression profiles that influence the prognostic power of an established immune cytolytic activity signature (CYTscore). From the identified genes, we developed a stratification signature (STRATsig) that partitioned patient populations into tertiles that varied markedly by CYTscore prognostic power. The tertile groups were then analyzed for distinguishing biological, clinical and immunological properties using integrative bioinformatics approaches. Results Patient survival and molecular measures of immune suppression, evasion and dysfunction varied significantly across STRATsig tertiles in validation cohorts. Tumors comprising STRATsig tertile 1 (S-T1) showed no immune-survival benefit and displayed a hyper-immune suppressed state marked by activation of TGF-β, Wnt/β-catenin and adenosine-mediated immunosuppressive pathways, with concurrent T cell dysfunction, reduced potential for antigen presentation, and enrichment of cancer-associated fibroblasts. By contrast, S-T3 tumors exhibited diminished immunosuppressive signaling, heightened antigen presentation machinery, lowered T cell dysfunction, and a significant CYTscore-survival benefit that correlated with mutational burden in a manner consistent with anti-tumor immunoediting. These tumors also showed elevated activity of DNA damage/repair, cell cycle/proliferation and oxidative phosphorylation, and displayed greater proportions of Th1 CD4 + T cells. In these patients, but not those of S-T1 or S-T2, validated predictors of immunotherapy response were prognostic of longer patient survival. Further analyses showed that STRATsig tertile properties were not explained by known HGSC molecular or clinical subtypes or singular immune mechanisms. Conclusions STRATsig is a composite of parallel immunoregulatory pathways that mirrors tumor immunogenic potential. Approximately one-third of HGSC cases classify as S-T3 and display a hypo-immunosuppressed and antigenic molecular composition that favors immunologic tumor control. These patients may show heightened responsiveness to current immunotherapies.

Gene expression profile in the post-menarchal macaque breast by microarray. (A) Venn diagram showing number of genes that changed with time (i.e. between 7-12 months to 18-24 months after menarche) in the control (CL) and soy group (SOY), based on unadjusted P-values from a paired t-test in each diet group. (B) The list of top-10 genes that showed significant difference by dietary treatment using empirical Bayes statistics. (C) The top-10 significantly enriched KEGG pathways in CL and SOY groups across time. FC = fold-change; FDR=false discovery rate.

Supplementary Table S1 from Ataxia Telangiectasia-Mutated–Dependent DNA Damage Checkpoint Functions Regulate Gene Expression in Human Fibroblasts

Representative photomicrographs of ERα staining in a transitional duct from a prepubertal animal (A); ERα staining in post-pubertal, differentiated lobuloalveolar tissue (B); ERβ staining in prepubertal transitional duct (C ); and ERβ staining in mature lobuloalveolar tissue (D). Bar = 50 microns.

Obesity is a key risk factor for metabolic syndrome (MetS); however, >10% of lean individuals meet MetS criteria. Visceral adipose tissue (VAT) disproportionately contributes to inflammation and insulin resistance compared with subcutaneous fat depots. The primary aim of this study was to profile tissue microbiome components in VAT over a wide range of metabolic statuses in a highly clinically relevant model.

1A. Cynomolgus macaque and human primer probe sets used to generate custom Taqman-based assay for qRT-PCR 1B. Applied Biosystems (ABI) Taqman gene expression assays used in qRT-PCR.

ObjectiveTo define novel gene biomarkers for prognosis of head and neck squamous cell carcinoma (HNSCC) patients' survival. Study DesignRetrospective study. SettingThe Cancer Genome Atlas (TCGA) HNSCC RNA-Seq dataset. MethodsCoexpressed gene clusters were extracted from TCGA RNA-seq data using our previously published method (EPIG). Kaplan-Meier estimator was then used for overall survival-relevant analysis, with patients partitioned into 3 groups based on gene expression levels: female, male_low, and male_high. ResultsMale had better overall survival than female and male with higher expression level of Y-chromosome-linked (Y-linked) genes had significantly better survival than those with lower expression levels. In addition, male with a higher expression level of Y-linked genes showed even better survival when they have a higher level of coexpressed cluster of genes related to B or T cell immune response. Other clinical conditions related to immune responses also consistently showed favorable effects on the Y-linked genes for survival estimation. Male patients with higher expression level of Y-linked genes also have significantly higher tumor/normal tissue (T/N) ratio of those genes and higher level of several immune responses related clinical measurements (eg, lymphocyte and TCR related). Male patients with lower expression level of Y-linked genes benefited from radiation-only treatment. ConclusionsThe favorable role of a cluster of coexpressed Y-linked genes in HNSCC patients' survival is potentially associated with elevated level of immune responses. These Y-linked genes could serve as useful prognostic biomarkers for HNSCC patients' survival estimation and treatment.

Immunolocalization of Steroidogenic Enzymes in the Mammary Gland.

Supplementary Table S2 from Ataxia Telangiectasia-Mutated–Dependent DNA Damage Checkpoint Functions Regulate Gene Expression in Human Fibroblasts

Cynomolgus macaque primer sets (forward, F; reverse, R; and sequencing, S) for pyrosequencing assay.

Serum isoflavonoid concentrations across the pubertal transition. Levels of circulating total isoflavonoids (genistein + daidzein + equol) were significantly higher in soy-fed monkeys. Values represent LSMs for n=11-17 monkeys/group (bars = SEM). Significant main effects and interactions are indicated in the panel.

Supplementary Table S4 from Ataxia Telangiectasia-Mutated–Dependent DNA Damage Checkpoint Functions Regulate Gene Expression in Human Fibroblasts

Supplementary Table S7 from Ataxia Telangiectasia-Mutated–Dependent DNA Damage Checkpoint Functions Regulate Gene Expression in Human Fibroblasts

Supplementary Table S6 from Ataxia Telangiectasia-Mutated–Dependent DNA Damage Checkpoint Functions Regulate Gene Expression in Human Fibroblasts

Supplementary Table S3 from Ataxia Telangiectasia-Mutated–Dependent DNA Damage Checkpoint Functions Regulate Gene Expression in Human Fibroblasts

Figure S1. Dose escalation schema. Figure S2. Acetyl-CoA synthetase is expressed in OCI-AML3 and MFL2 cells. Figure S3 Acetate and methyl-succinate rescue of CPI-613 cytotoxicity. Figure S4. Treatment schema. Figure S5. Efficacy of HiDAC, mitoxantrone and CPI-613. Figure S6. Baseline bone marrow mononuclear cell gene expression profiles of responders (n=10) versus nonresponders (n=7). Figure S7. SOD2 expression levels are higher in non-responders Figure S8. SOD2 confers resistance to CPI-613. Figure S9. Mutational analysis from RNA sequence data of baseline marrow samples. Supplemental Table 1. Dose and Response by Patient Supplementary Table 2. Gene ontology enrichment analysis of genes overexpressed in responding patients