Oral PD-L1 inhibitor GS-4224 selectively engages PD-L1 high cells and elicits pharmacodynamic responses in patients with advanced solid tumors

BACKGROUND

Checkpoint inhibitors targeting the programmed cell death 1 (PD-1)/programmed cell death 1 ligand 1 (PD-L1) pathway are effective therapies in a range of immunogenic cancer types. Blocking this pathway with an oral therapy could benefit patients through greater convenience, particularly in combination regimens, and allow flexible management of immune-mediated toxicities.

METHODS

PD-L1 binding activity was assessed in engineered dimerization and primary cell target occupancy assays. Preclinical antitumor activity was evaluated in ex vivo and in vivo human PD-L1-expressing tumor models. Human safety, tolerability, pharmacokinetics, and biomarker activity were evaluated in an open-label, multicenter, sequential dose-escalation study in patients with advanced solid tumors. Biomarkers evaluated included target occupancy, flow cytometric immunophenotyping, plasma cytokine measurements, and T-cell receptor sequencing.

RESULTS

GS-4224 binding caused dimerization of PD-L1, blocking its interaction with PD-1 and leading to reversal of T-cell inhibition and increased tumor killing in vitro and in vivo. The potency of GS-4224 was dependent on the density of cell surface PD-L1, with binding being most potent on PD-L1-high cells. In a phase 1 dose-escalation study in patients with advanced solid tumors, treatment was well tolerated at doses of 400-1,500 mg once daily. Administration of GS-4224 was associated with a dose-dependent increase in plasma GS-4224 exposure and reduction in free PD-L1 on peripheral blood T cells, an increase in Ki67 among the PD-1-positive T-cell subsets, and elevated plasma cytokines and chemokines.

CONCLUSIONS

GS-4224 is a novel, orally bioavailable small molecule inhibitor of PD-L1. GS-4224 showed evidence of expected on-target biomarker activity, including engagement of PD-L1 and induction of immune-related pharmacodynamic responses consistent with PD-L1 blockade.

TRIAL REGISTRATION NUMBER

NCT04049617.

Final Results From the Randomized Phase III ASCENT Clinical Trial in Metastatic Triple-Negative Breast Cancer and Association of Outcomes by Human Epidermal Growth Factor Receptor 2 and Trophoblast Cell Surface Antigen 2 Expression

Clinical trials frequently include multiple end points that mature at different times. The initial report, typically based on the primary end point, may be published when key planned co-primary or secondary analyses are not yet available. Clinical Trial Updates provide an opportunity to disseminate additional results from studies, published in JCO or elsewhere, for which the primary end point has already been reported.Sacituzumab govitecan (SG), a first-in-class anti-trophoblast cell surface antigen 2 (Trop-2) antibody-drug conjugate, demonstrated superior efficacy over single-agent chemotherapy (treatment of physician's choice [TPC]) in patients with metastatic triple-negative breast cancer (mTNBC) in the international, multicenter, phase III ASCENT study.Patients were randomly assigned 1:1 to receive SG or TPC until unacceptable toxicity/progression. Final efficacy secondary end point analyses and post hoc analyses of outcomes stratified by Trop-2 expression and human epidermal growth factor receptor 2 status are reported. Updated safety analyses are provided.In this final analysis, SG (n = 267) improved median progression-free survival (PFS; 4.8 v 1.7 months; hazard ratio (HR), 0.41 [95% CI, 0.33 to 0.52]) and median overall survival (OS; 11.8 v 6.9 months; HR, 0.51 [95% CI, 0.42 to 0.63]) over TPC (n = 262). SG improved PFS over TPC in each Trop-2 expression quartile (n = 168); a trend was observed for improved OS across quartiles. Overall, SG had a manageable safety profile, with ≤5% of treatment-related discontinuations because of adverse events and no treatment-related deaths. The safety profile was consistent across all subgroups.These data confirm the clinical benefit of SG over chemotherapy, reinforcing SG as an effective treatment option in patients with mTNBC in the second line or later.

Pharmacodynamic effects of filgotinib treatment driving clinical improvement in patients with active psoriatic arthritis enrolled in the EQUATOR trial

OBJECTIVES

The goal of this study was to identify protein and transcriptional biomarkers and pathways associated with baseline disease state, the effect of filgotinib (FIL) treatment on these biomarkers, and to investigate the mechanism of action of FIL on clinical improvement in patients with active psoriatic arthritis (PsA).

METHODS

The phase II EQUATOR (NCT03101670) trial evaluated the efficacy of FIL, a Janus kinase 1-preferential inhibitor, in patients with PsA. Peripheral protein and gene expression levels in association with clinical state at baseline and post-treatment were assessed in 121 patients using linear mixed effects models for repeated measures analyses. Mediation analysis and structural equation modelling (SEM) were performed to investigate the mechanism of action of FIL at week 4 on downstream clinical improvement at week 16.

RESULTS

Baseline analyses showed that markers of inflammation were significantly associated with multiple PsA clinical metrics, except for Psoriasis Area and Severity Index (PASI), which corresponded to Th17 markers. FIL treatment resulted in sustained transcriptional inhibition of immune genes and pathways, a sustained increase in B-cell fraction and mature B-cells in circulation, and a transient effect on other cell fractions. Mediation analysis revealed that changes in B cells, systemic inflammatory cytokines and neutrophils at week 4 were associated with changes in clinical metrics at week 16. SEM suggested that FIL improved PASI through reduction of IL-23 p19 and IL-12 p40 proteins.

CONCLUSIONS

Our results revealed that FIL treatment rapidly downregulates inflammatory and immune pathways associated with PsA disease activity corresponding to clinical improvement in PsA.

TRIAL REGISTRATION NUMBER

NCT03101670.

RNA-seq RNAaccess identified as the preferred method for gene expression analysis of low quality FFPE samples

Clinical tumor tissues that are preserved as formalin-fixed paraffin-embedded (FFPE) samples result in extensive cross-linking, fragmentation, and chemical modification of RNA, posing significant challenges for RNA-seq-based gene expression profiling. This study sought to define an optimal RNA-seq protocol for FFPE samples. We employed a common RNA extraction method and then compared RNA-seq library preparation protocols including RNAaccess, RiboZero and PolyA in terms of sequencing quality and concordance of gene expression using FFPE and case-matched fresh-frozen (FF) triple-negative breast cancer (TNBC) tissues. We found that RNAaccess, a method based on exome capture, produced the most concordant results. Applying RNAaccess to FFPE gastric cancer tissues, we established a minimum RNA DV200 requirement of 10% and a RNA input amount of 10ng that generated highly reproducible gene expression data. Lastly, we demonstrated that RNAaccess and NanoString platforms produced highly concordant expression profiles from FFPE samples for shared genes; however, RNA-seq may be preferred for clinical biomarker discovery work because of the broader coverage of the transcriptome. Taken together, these results support the selection of RNA-seq RNAaccess method for gene expression profiling of FFPE samples. The minimum requirements for RNA quality and input established here may allow for inclusion of clinical FFPE samples of sub-optimal quality in gene expression analyses and ultimately increasing the statistical power of such analyses.

Overall survival with sacituzumab govitecan in hormone receptor-positive and human epidermal growth factor receptor 2-negative metastatic breast cancer (TROPiCS-02): a randomised, open-label, multicentre, phase 3 trial

BACKGROUND

Sacituzumab govitecan demonstrated significant progression-free survival benefit over chemotherapy in the phase 3 TROPiCS-02 trial in patients with pretreated, endocrine-resistant hormone receptor-positive, human epidermal growth factor receptor 2-negative (HR+ and HER2-) metastatic breast cancer with limited treatment options. Here, we report the protocol-specified final analysis of overall survival and endpoints by trophoblast cell-surface antigen 2 (Trop-2) expression and other variables.

METHODS

In this randomised, open-label, multicentre, phase 3 trial, which took place in 91 centres across North America (the USA and Canada) and Europe (Belgium, France, Germany, Italy, the Netherlands, Spain, and the UK), patients were randomly assigned (1:1) to receive sacituzumab govitecan or chemotherapy (eribulin, vinorelbine, capecitabine, or gemcitabine). Patients had confirmed HR+ and HER2- locally recurrent inoperable or metastatic breast cancer and had received at least one previous endocrine therapy, a taxane, and a CDK4/6 inhibitor in any setting and two to four previous chemotherapy regimens for metastatic disease. The primary endpoint was progression-free survival (previously reported and not included in this analysis), and secondary endpoints included overall survival, objective response rate (ORR), and patient-reported outcomes. Overall survival was assessed using stratified log-rank tests and Cox regression. Trop-2 expression was assessed in tumour tissue by immunohistochemistry. In the statistical testing hierarchy, ORR and patient-reported outcomes were tested sequentially if overall survival was significant. This study is registered with ClinicalTrials.gov, NCT03901339.

FINDINGS

At the data cutoff date of July 1, 2022, 543 of 776 screened patients were randomly assigned between May 30, 2019, and April 5, 2021, with 272 patients in the sacituzumab govitecan group and 271 patients in the chemotherapy group. With a 12·5-month (IQR 6·4-18·8) median follow-up, 390 deaths occurred among 543 patients. Overall survival was significantly improved with sacituzumab govitecan versus chemotherapy (median 14·4 months [95% CI 13·0-15·7] vs 11·2 months [10·1-12·7]; hazard ratio [HR] 0·79, 95% CI 0·65-0·96; p=0·020); survival benefit was consistent across Trop-2 expression-level subgroups. ORR was significantly improved with sacituzumab govitecan compared with chemotherapy (57 [21%] patients vs 38 [14%]; odds ratio 1·63 [95% CI 1·03-2·56]; p=0·035), as was time to deterioration of global health status and quality of life (median 4·3 months vs 3·0 months; HR 0·75 [0·61-0·92]; p=0·0059) and fatigue (median 2·2 months vs 1·4 months; HR 0·73 [0·60-0·89]; p=0·0021). The safety profile of sacituzumab govitecan was consistent with previous studies (including the TROPiCS-02 primary analysis and the ASCENT trial). One fatal adverse event (septic shock caused by neutropenic colitis) was determined to be related to sacituzumab govitecan treatment.

INTERPRETATION

Sacituzumab govitecan demonstrated statistically significant and clinically meaningful benefit over chemotherapy, with a 3·2-month median overall survival improvement and a manageable safety profile. These data support sacituzumab govitecan as a new treatment option for patients with pretreated, endocrine-resistant HR+ and HER2- metastatic breast cancer.

FUNDING

Gilead Sciences.

Impact of delayed PBMC processing on functional and genomic assays

Peripheral blood mononuclear cells (PBMCs) are commonly isolated from whole blood samples in clinical trials. Isolated PBMCs can be cryopreserved for use in downstream assays such as flow cytometry, single-cell RNA sequencing (scRNA-seq) and enzyme-linked immunosorbent spot (ELISpot) assays to aid understanding of disease biology and treatment effects, and biomarker identification. However, due to logistical practicalities, delays from blood collection to PBMC processing may exceed 24 h, which can potentially affect PBMC function and, ultimately, downstream assay results. Whole blood samples from 20 healthy adults were collected and incubated at 20-25 °C for 2-48 h before PBMC processing. PBMC viability was measured, and flow cytometry immunophenotyping, scRNA-seq and ELISpot were performed following increasing PBMC processing delays. The RosetteSep™ granulocyte depletion kit was used to evaluate the impact of granulocyte contamination following processing delay. Processed scRNA-seq reads were used to identify cell clusters based on marker genes. scRNA-seq data was further used to determine gene expression correlation and pathway activity score in major PBMC cell types (T cells, B cells, natural killer cells, monocytes and dendritic cells) between PBMC preparations subjected to shorter (2-4 h) and longer (8-48 h) processing delays. ELISpot assays evaluated the impact of processing delays on the number of interferon-γ (IFN-γ) secreting cells from ex vivo stimulated PBMCs. PBMC viability was reduced after a 48-h processing delay. Flow cytometry showed that granulocyte contamination of PBMCs increased after 24 h. Cluster analysis of scRNA-seq data identified 23 immune cell type gene expression clusters that were not significantly changed upon granulocyte depletion. Gene expression correlations across the major PBMC cell types were < 0.8 after 24 h of delay compared with 2 or 4 h of delay. Inflammatory, proliferation and signaling pathway activities increased, whereas IFN-γ and metabolic pathway activities decreased with increasing PBMC processing delays. The number of IFN-γ secreting cells trended towards a reduction as PBMC processing delays increased. PBMC processing delays should be minimised when designing clinical trials to reduce outcome variability in downstream assays. Ideally clinical trial sites should have on-site PBMC processing capabilities or be located close to such facilities.

Abstract 4392: Expression landscape of trophoblast cell surface antigen 2 (Trop-2) in breast cancer

Background: Antibody-drug conjugates (ADCs) are novel agents linking potent payloads to antibodies targeting antigen-expressing tumors. Sacituzumab govitecan (SG), a Trop-2-directed ADC, is approved for patients with metastatic triple-negative breast cancer (mTNBC) with ≥2 prior therapies (≥1 in metastatic setting). SG is also being investigated in other breast cancer subtypes, including hormone receptor-positive/human epidermal growth factor receptor 2-negative (HR+/HER2-) metastatic breast cancer and in earlier lines of treatment. To understand the landscape of Trop-2 expression and potential clinical actionability of Trop-2 and other antigens, we evaluated RNA expression data in breast cancer from The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC).

Methods: TCGA and METABRIC datasets were assessed for Trop-2, HER2, and programmed death ligand 1 (PD-L1) expression via processed RNA sequencing (RNA-seq) and microarray data of the corresponding genes TACSTD2, ERBB2, and CD274. Gene expression across clinical parameters was assessed via one-way ANOVA, t-test, or Spearman correlation. HER2 status was classified as HER2 immunohistochemistry (IHC) 0 or HER2-low (IHC1+, or IHC2+ and in situ hybridization-negative). Survival was estimated via Kaplan-Meier method. Neoadjuvant therapy datasets were assessed for effects of aromatase inhibitors on Trop-2 expression.

Results: RNA-Seq data was available from 1030 and 2136 breast cancer patients in TCGA and METABRIC datasets, respectively. Most patients (96%) had high TACSTD2 expression (&gt;100 transcripts per million [TPM]). TACSTD2 expression was comparable by breast cancer histology (median log2TPM 6.8-7.5), by disease stages I-IV (median log2TPM 7.0-7.5), or by subtypes (median log2TPM 7.1-7.3). TACSTD2 expression was not correlated with ERBB2 (Spearman rho=0.06) or CD274 (Spearman rho=-0.13) expression. No difference in TACSTD2 expression was noted between HER2 IHC0 or HER2-low subtypes. TACSTD2 expression was not associated with survival, though low tertile TACSTD2 groups had better prognosis in the basal subtype; treatments were heterogeneous. Changes in TACSTD2 gene expression were not observed post-aromatase inhibitors.

Conclusions: While SG is approved for use in mTNBC, TACSTD2 is stably expressed across all breast cancer stages and subtypes, including HER2 IHC0 and HER2-low, and across all ranges of PD-L1 expression, suggesting a broad patient population may benefit from Trop-2-directed ADCs.

Citation Format: Kai Song, Oh Kyu Yoon, Luting Zhuo, Emon Elboudwarej, Biao Li, Jillian Boice, Yang Pan, See Phan, Monica Motwani. Expression landscape of trophoblast cell surface antigen 2 (Trop-2) in breast cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4392.

Abstract GS1-11: Sacituzumab Govitecan (SG) vs Treatment of Physician’s Choice (TPC): Efficacy by Trop-2 Expression in the TROPiCS-02 Study of Patients (Pts) With HR+/HER2– Metastatic Breast Cancer (mBC)

Background: HR+/HER2– mBC, the most common subset of breast cancer, is treated with sequential endocrine therapy + targeted agents followed by sequential single-agent chemotherapy (CT), with increasingly shorter benefit duration with each subsequent treatment. High Trop-2 expression is observed in breast cancer regardless of subtype. SG is a Trop-2-directed antibody-drug conjugate approved for pre-treated metastatic triple-negative breast cancer. In the phase 3 TROPiCS-02 study, SG showed both significant progression-free survival (PFS) benefit (HR, 0.66; P&lt;0.001; median 5.5 vs 4.0 mo; JCO 2022) at the primary analysis and overall survival (OS) benefit (median 14.4 vs 11.2 mo; HR, 0.79; P=0.02; ESMO 2022) at the 2nd planned interim OS analysis vs TPC in pretreated HR+/HER2- mBC. Here we compare efficacy outcomes for SG and TPC by Trop-2 expression. Methods: Eligible pts had HR+/HER2- locally recurrent inoperable or mBC; received ≥1 prior taxane, endocrine therapy, a CDK4/6 inhibitor; and received 2-4 prior CT regimens for mBC. Pts were randomized 1:1 to receive SG (10 mg/kg IV on d 1 and 8, every 21 d) or TPC (eribulin, gemcitabine, capecitabine, or vinorelbine) until disease progression or unacceptable toxicity. The primary endpoint was PFS by independent review per RECIST v1.1; OS and objective response rate (ORR) were key secondary endpoints. ORR was assessed by blinded independent central review per RECIST v1.1. Membrane Trop-2 expression on archival tumor tissue was assessed by immunohistochemistry and expressed as a histochemical score (H-score; range, 0-300); efficacy outcomes were assessed in H-score &lt;100 and ≥100 groups. The H-score &lt;100 group was further divided into H-score ≤10 and &gt;10- &lt;100 subgroups to assess the activity of SG in pts with very low Trop-2 expression. Results: Data cut-off was January 3, 2022 for PFS (median follow-up, 10.2 mo) and July 1, 2022 for OS (median follow-up, 12.5 mo). In total, 543 pts were randomized to receive SG (n=272) vs TPC (n=271). Pts had a median of 3 prior CT regimens for mBC; 95% had visceral metastases. There were 238 (88%) vs 224 (83%) Trop-2-evaluable pts in the SG vs TPC groups, respectively; of these, 95% had tumors with Trop-2 H-score &gt;0. Of Trop-2-evaluable pts, 192 (42%) and 270 (58%) had H-scores &lt;100 and ≥100, respectively. Demographics and baseline characteristics were generally consistent across H-score groups. PFS and OS benefit was observed for SG vs TPC across both Trop-2 groups (Table). Median PFS was 5.3 vs 4.0 mo (HR, 0.77; 95% CI, 0.54-1.09) and 6.4 vs 4.1 mo (HR, 0.60; 95% CI, 0.44-0.81) in the H-score &lt;100 and ≥100 groups; median OS was 14.6 vs 11.3 mo (HR, 0.75; 95% CI, 0.54-1.04) and 14.4 vs 11.2 mo (HR, 0.83; 95% CI, 0.62-1.11), respectively. Disease response was observed in the 34 pts with H-score ≤10 who received SG. In pts who received SG, those with H-score ≤10, &gt;10- &lt;100, and ≥100 had ORRs of 24%, 18%, and 23%, respectively. The safety profile for SG by Trop-2 H-score was consistent with previous reports. Conclusions: In this TROPiCS-02 post-hoc analysis, improved efficacy with SG vs TPC was observed regardless of Trop-2 expression, and there was no clear level of Trop-2 expression at which a better treatment effect for SG was observed. These results support SG as an effective novel treatment option for patients with pretreated, endocrine-resistant HR+/HER2- mBC, and reinforce that Trop-2 testing is not required for SG treatment.

Table

Citation Format: Hope Rugo, Aditya Bardia, Frederik Marmé, Javier Cortés, Peter Schmid, Delphine Loirat, Olivier Trédan, Eva Ciruelos, Florence Dalenc, Patricia Gómez Pardo, Komal Jhaveri, Monica Motwani, Oh Kyu Yoon, Hao Wang, Wendy Verret, Sara Tolaney. Sacituzumab Govitecan (SG) vs Treatment of Physician’s Choice (TPC): Efficacy by Trop-2 Expression in the TROPiCS-02 Study of Patients (Pts) With HR+/HER2– Metastatic Breast Cancer (mBC) [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr GS1-11.

Effects of JAK1-Preferential Inhibitor Filgotinib on Circulating Biomarkers and Whole Blood Genes/Pathways of Patients With Moderately to Severely Active Crohn's Disease

BACKGROUND

Pro-inflammatory cytokines are dysregulated in Crohn's disease (CD) and could serve as surrogate markers to improve diagnostic and therapeutic approaches, potentially addressing an unmet need. We profiled circulating biomarkers and whole blood transcriptional pathway activity to identify those associated with CD using data from the phase 2 FITZROY study with filgotinib, an oral preferential janus kinase-1 inhibitor.

METHODS

Patients with serum and whole blood samples taken from the induction period were included. Serum cytokines were measured (ELISA), whole blood RNA sequenced, and stool samples taken to measure fecal calprotectin (FC). Spearman's Rank correlations were assessed between biomarkers and baseline disease activity; post-treatment endoscopic improvement was measured by the Simplified Endoscopy Score for CD (SES-CD), FC and the Crohn's Disease Activity Index. Effect of filgotinib on circulating biomarkers was also evaluated.

RESULTS

Serum biomarkers (n = 168) and whole blood RNA sequencing (n = 104) were assessed. Moderate correlation between serum analytes with SES-CD and FC was noted; most highly correlated were acute phase proteins CRP (rho = 0.35 [SES-CD] and 0.47 [FC]), serum amyloid A (rho = 0.40 and 0.39, respectively) and pro-inflammatory cytokines interleukin (IL)-6 (rho = 0.31 and 0.30, respectively), IL-22 (rho = 0.36 and 0.35, respectively), and oncostatin M (rho = 0.35 and 0.33, respectively). Filgotinib treatment was associated with reduction of many candidate biomarkers, particularly in patients with treatment response. Early changes in IL-6 and IL-10 may be prognostic for endoscopic response.

CONCLUSIONS

Several circulating factors with potential as CD activity biomarkers were identified. Larger studies are necessary to investigate the best utility of these markers for CD.

Mucosal p-STAT1/3 correlates with histologic disease activity in Crohn's disease and is responsive to filgotinib

The validity and relevance of histologic disease activity in Crohn's disease (CD) is unclear, owing to disconnects with endoscopic pathology. Here, we explore relationships between endoscopic, histologic, and molecular activity. This post hoc analysis of the Phase 2 FITZROY trial (NCT02048618) assessed baseline and week 10 (W10) inflammation across matched ileal and colonic segments in CD patients receiving filgotinib 200 mg (n = 42) vs placebo (n = 18). Macroscopic and microscopic disease were assessed by Simple Endoscopic Score for CD ulceration subscore (uSES-CD) and Global Histologic Activity Score activity subscore (aGHAS), respectively. Molecular activity was quantified by phosphorylated signal transducer and activator of transcription (pSTAT)1 and pSTAT3 in epithelium and nonepithelium. Segments were classified as "low" or "high" activity; correlations and concordance were calculated. Logistic regression identified W10 outcome predictors. Overall, 300 segments in 60 patients were assessed. Baseline uSES-CD and aGHAS correlations were 0.72 and 0.53 in colon and ileum, respectively. pSTAT levels had poor-to-moderate concordance with uSES-CD (κ range, 0.11-0.49) but moderate-to-good concordance with aGHAS (0.43-0.77). With filgotinib vs placebo, uSES-CD and aGHAS decreased in significantly more segments with high baseline uSES-CD and aGHAS, and significantly more segments with high baseline pSTAT improved at W10. pSTAT1 was more sensitive to change than uSES-CD and aGHAS. Low baseline pSTAT3 in colon nonepithelium predicted W10 low uSES-CD (P = .044). There was better concordance between histologic and molecular disease activity associated with higher sensitivity to change vs endoscopic severity in ileocolonic CD. Our results suggest histologic activity be included in the assessment of CD inflammatory burden.

Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling

BACKGROUND

Elucidation of immune populations with single-cell RNA-seq has greatly benefited the field of immunology by deepening the characterization of immune heterogeneity and leading to the discovery of new subtypes. However, single-cell methods inherently suffer from limitations in the recovery of complete transcriptomes due to the prevalence of cellular and transcriptional dropout events. This issue is often compounded by limited sample availability and limited prior knowledge of heterogeneity, which can confound data interpretation.

RESULTS

Here, we systematically benchmarked seven high-throughput single-cell RNA-seq methods. We prepared 21 libraries under identical conditions of a defined mixture of two human and two murine lymphocyte cell lines, simulating heterogeneity across immune-cell types and cell sizes. We evaluated methods by their cell recovery rate, library efficiency, sensitivity, and ability to recover expression signatures for each cell type. We observed higher mRNA detection sensitivity with the 10x Genomics 5' v1 and 3' v3 methods. We demonstrate that these methods have fewer dropout events, which facilitates the identification of differentially-expressed genes and improves the concordance of single-cell profiles to immune bulk RNA-seq signatures.

CONCLUSION

Overall, our characterization of immune cell mixtures provides useful metrics, which can guide selection of a high-throughput single-cell RNA-seq method for profiling more complex immune-cell heterogeneity usually found in vivo.

Genetics and regulatory impact of alternative polyadenylation in human B-lymphoblastoid cells

Gene expression varies widely between individuals of a population, and regulatory change can underlie phenotypes of evolutionary and biomedical relevance. A key question in the field is how DNA sequence variants impact gene expression, with most mechanistic studies to date focused on the effects of genetic change on regulatory regions upstream of protein-coding sequence. By contrast, the role of RNA 3'-end processing in regulatory variation remains largely unknown, owing in part to the challenge of identifying functional elements in 3' untranslated regions. In this work, we conducted a genomic survey of transcript ends in lymphoblastoid cells from genetically distinct human individuals. Our analysis mapped the cis-regulatory architecture of 3' gene ends, finding that transcript end positions did not fall randomly in untranslated regions, but rather preferentially flanked the locations of 3' regulatory elements, including miRNA sites. The usage of these transcript length forms and motifs varied across human individuals, and polymorphisms in polyadenylation signals and other 3' motifs were significant predictors of expression levels of the genes in which they lay. Independent single-gene experiments confirmed the effects of polyadenylation variants on steady-state expression of their respective genes, and validated the regulatory function of 3' cis-regulatory sequence elements that mediated expression of these distinct RNA length forms. Focusing on the immune regulator IRF5, we established the effect of natural variation in RNA 3'-end processing on regulatory response to antigen stimulation. Our results underscore the importance of two mechanisms at play in the genetics of 3'-end variation: the usage of distinct 3'-end processing signals and the effects of 3' sequence elements that determine transcript fate. Our findings suggest that the strategy of integrating observed 3'-end positions with inferred 3' regulatory motifs will prove to be a critical tool in continued efforts to interpret human genome variation.

Stopped-flow kinetic analysis using Hadamard transform time-of-flight mass spectrometry

A home-built stopped-flow apparatus is interfaced to a Hadamard transform time-of-flight mass spectrometer, which permits study of reaction kinetics with a time between reaction initiation and observation as short as about 100 ms and a sampling rate of chemical change that can approach 1 ms. This technique is applied to the trypsin-catalyzed hydrolysis of several peptides and is validated by comparing the results with literature values as well as to optical data obtained with the present stopped-flow apparatus. In addition, we report a kinetic study of the action of trypsin on a peptide having more than one cleavage site.

Noncanonical transcript forms in yeast and their regulation during environmental stress

Surveys of transcription in many organisms have observed widespread expression of RNAs with no known function, encoded within and between canonical coding genes. The search to distinguish functional RNAs from transcriptional noise represents one of the great challenges in genomic biology. Here we report a next-generation sequencing technique designed to facilitate the inference of function of uncharacterized transcript forms by improving their coverage in sequencing libraries, in parallel with the detection of canonical mRNAs. We piloted this protocol, which is based on the capture of 3' ends of polyadenylated RNAs, in budding yeast. Analysis of transcript ends in coding regions uncovered hundreds of alternative-length coding forms, which harbored a unique sequence motif and showed signatures of regulatory function in particular gene categories; independent single-gene measurements confirmed the differential regulation of short coding forms during heat shock. In addition, our 3'-end RNA-seq method applied to wild-type strains detected putative noncoding transcripts previously reported only in RNA surveillance mutants, and many such transcripts showed differential expression in yeast cultures grown under chemical stress. Our results underscore the power of the 3'-end protocol to improve detection of noncanonical transcript forms in a sequencing experiment of standard depth, and our findings strongly suggest that many unannotated, polyadenylated RNAs may have as yet uncharacterized regulatory functions.

Continuous time-of-flight ion imaging: application to fragmentation

We have designed and constructed a continuous imaging reflectron time-of-flight mass spectrometer (TOFMS) that provides a mass spectrum at every pixel of a two-dimensional image with a 100% duty cycle. The technique is based on pseudorandom ion beam modulation and three-dimensional ( x, y, t) ion imaging. We use a multichannel plate detector with a delay-line anode that provides x, y positions and flight times t of every ion arrival event. The precision of the peak heights in the 100% duty cycle mass spectra is shown to be enhanced even at short (10 ms) acquisition times, which should prove useful for the study of solution kinetics or fast chromatographic separations. As a demonstration of the system's capability, we have imaged the fragmented ions that underwent surface-induced dissociation inside the reflectron and the ions that fragmented spontaneously through postsource decay.

Computer-controlled, variable-frequency power supply for driving multipole ion guides

A high voltage, variable-frequency driver circuit for powering resonant multipole ion guides is presented. Two key features of this design are (1) the use of integrated circuits in the driver stage and (2) the use a stepper motor for tuning a large variable capacitor in the resonant stage. In the present configuration the available frequency range spans a factor of 2. The actual values of the minimum and maximum frequencies depend on the chosen inductor and the capacitance of the ion guide. Feedback allows for stabilized, computer-adjustable rf amplitudes over the range of 5-500 V. The rf power supply was characterized over the range of 350-750 kHz and evaluated by driving a quadrupole ion guide in an electrospray time-of-flight mass spectrometer.

Simple template-based method to produce Bradbury-Nielsen gates

A Bradbury-Nielsen gate (BNG) consists of two interleaved and electrically isolated sets of wires and can transmit or deflect charged particles by applying a varying voltage difference across the two wire sets. We present a simple template-based method to fabricate BNGs with wire spacings as small as 50 microm with minimal use of a microscope. The small wire spacing allows modulation rates at tens of megahertz. Using this method, we have fabricated four BNGs with wire spacings of 500, 200, 100, and 50 microm using 10 microm gold-coated tungsten wires. The performance of the four BNGs is characterized using an imaging detector and compared with theoretical predictions.

Duty cycle and modulation efficiency of two-channel Hadamard transform time-of-flight mass spectrometry

Hadamard transform time-of-flight mass spectrometry (HT-TOFMS) is based on the pseudorandom gating of ion packets into a time-of-flight mass-to-charge analyzer. In its typical implementation, the technique is able to monitor continuous ion sources with a 50% duty cycle, independent of all other figures of merit. Recently, we have demonstrated that the duty cycle can be extended to 100% using patterned, two-channel detection. Two-channel HT-TOFMS involves the simultaneous optimization of paired one-channel experiments and imposes more stringent conditions to achieve high-quality spectra. An ion modulation device, known as Bradbury-Nielson Gate (BNG), is central to HT-TOFMS. It is an ideal deflection plate, capable of transmitting or deflecting an ion beam according to a known binary sequence without changing the times-of-flight of the ions. Analytical equations are derived that accurately describe the ion modulation process of the BNG as confirmed by good agreement with SimIon simulations and ion beam imaging experiments. From these expressions, the duty cycle and ion modulation efficiency were calculated for various BNG parameters, ion beam characteristics, and detector dimensions, which permit the optimum conditions to be chosen for the two-channel experiment. We conclude that the outer detector should be three times the maximum deflection angle to detect all deflected ions (100% duty cycle) and that the difference between the modulated ion counts in the sequence elements 0 and 1 should be maximized to achieve high modulation efficiency. This condition is best achieved by tight focusing of the ion beam in the center of the inner detector. When both channels are optimized, the two-channel advantage can be exploited to achieve a further improvement over a single-channel experiment.

A soft on-column metal coating procedure for robust sheathless electrospray emitters used in capillary electrophoresis-mass spectrometry

An on-column metal coating procedure was developed for sheathless electrospray emitters, based on Justus von Liebig's electroless silver mirror reaction followed by electrochemical deposition of gold onto the silver layer. The coating procedure is straightforward, mild, inexpensive, and can be performed with standard laboratory equipment. A long-term (600 h) stability investigation of the conductive coating was carried out by continuous electrospray in the positive electrospray mode, and no degradation in performance was found. The simplicity of the coating procedure and the robustness of the spray tips makes the spray tips highly suitable to couple delicate wall-coated or monolithic capillary columns to mass spectrometry. Peptide mixtures were separated by capillary electrophoresis and injected into either a Hadamard-transform time-of-flight mass analyzer or a commercial quadrupole mass analyzer using the described sheathless electrospray emitters. The performance was judged to be excellent.

Internal energy content of n-butylbenzene, bromobenzene, iodobenzene and aniline molecular ions generated by two-photon ionization at 266 nm. A photodissociation study

A technique to investigate photodissociation kinetics on a nanosecond time scale has been devised for molecular ions generated by multiphoton ionization (MPI) using mass-analyzed ion kinetic energy spectrometry. The branching ratio or rate constant has been determined for the photodissociation of the n-butylbenzene, bromobenzene, iodobenzene, and aniline molecular ions generated by MPI at 266 nm. The ion internal energies have been estimated by comparing the measured kinetic data with the previous energy dependence data. The analysis has shown that only those molecular ions generated by two-photon ionization contribute to the photodissociation signals. Around half of the available energy has been found to remain as molecular ion internal energy in the two-photon ionization process. Copyright 1999 John Wiley & Sons, Ltd.