Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq

Pooled CRISPR screens coupled with single-cell RNA-sequencing have enabled systematic interrogation of gene function and regulatory networks. Here, we introduce Cas13 RNA Perturb-seq (CaRPool-seq), which leverages the RNA-targeting CRISPR-Cas13d system and enables efficient combinatorial perturbations alongside multimodal single-cell profiling. CaRPool-seq encodes multiple perturbations on a cleavable CRISPR array that is associated with a detectable barcode sequence, allowing for the simultaneous targeting of multiple genes. We compared CaRPool-seq to existing Cas9-based methods, highlighting its unique strength to efficiently profile combinatorially perturbed cells. Finally, we apply CaRPool-seq to perform multiplexed combinatorial perturbations of myeloid differentiation regulators in an acute myeloid leukemia (AML) model system and identify extensive interactions between different chromatin regulators that can enhance or suppress AML differentiation phenotypes.

Residual cognitive and psychosocial functional impairment in outpatients in Greece who responded to conventional antidepressant monotherapy treatments for major depressive disorder (MDD)

BACKGROUND

Patients with MDD may experience diverse residual symptoms after clinical response to antidepressant treatment. Among these symptoms, cognitive problems in executive functioning are prominent and make functional recovery largely an unmet need for MDD patients. In this study we assessed cognitive symptoms and functional impairment in patients with MDD responding to antidepressant treatment.

METHODS

This was a national, multi-site, non-interventional, cross-sectional study of depressive symptomatology, cognitive performance and psychosocial functioning in Greek outpatients with MDD who had clinically responded to antidepressant treatment. Both clinician- and patient- rated measures were employed. Symptom remission was assessed with the Montgomery Asberg Depression Rating Scale (MADRS) total score (≤12) and functional recovery was assessed with the Sheehan Disability Scale (SDS) score (<6).

RESULTS

335 MDD patients participated in the study. After antidepressant monotherapy approximately 60 % of responders and 40 % of remitted patients did not meet the functional recovery criterion. More than 60 % of responders had concentration difficulties as assessed by MADRS item. Patient reported cognitive symptoms were statistically significantly associated with functionality (β coefficient = 0.126, p-value = 0.027).

LIMITATIONS

Non-interventional study design and lack of a control group or active comparator/reference.

CONCLUSIONS

This study highlights the persistence of decreased cognitive performance, particularly in executive functioning in patients with MDD who have shown response and/or remission to antidepressant treatment. This appears to contribute to psychosocial functional impairment. Patient-reported cognitive and psychosocial functioning impairment should be included in routine clinical monitoring of outcomes in MDD treatments.

Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells

Recent technological advances have enabled massively parallel chromatin profiling with scATAC-seq (single-cell assay for transposase accessible chromatin by sequencing). Here we present ATAC with select antigen profiling by sequencing (ASAP-seq), a tool to simultaneously profile accessible chromatin and protein levels. Our approach pairs sparse scATAC-seq data with robust detection of hundreds of cell surface and intracellular protein markers and optional capture of mitochondrial DNA for clonal tracking, capturing three distinct modalities in single cells. ASAP-seq uses a bridging approach that repurposes antibody:oligonucleotide conjugates designed for existing technologies that pair protein measurements with single-cell RNA sequencing. Together with DOGMA-seq, an adaptation of CITE-seq (cellular indexing of transcriptomes and epitopes by sequencing) for measuring gene activity across the central dogma of gene regulation, we demonstrate the utility of systematic multi-omic profiling by revealing coordinated and distinct changes in chromatin, RNA and surface proteins during native hematopoietic differentiation and peripheral blood mononuclear cell stimulation and as a combinatorial decoder and reporter of multiplexed perturbations in primary T cells.

Improvements in mood symptoms, cognitive symptoms and functioning in outpatients with mdd in greece treated with vortioxetine: A patient-rated evaluation

Introduction

Functional recovery is the contemporary treatment goal in Major Depressive Disorder (MDD). Although consistency among physician and patient expectations may influence the therapeutic result (Demyttenaere K et al, 2011), patients’ perceptions are not always fully captured. Vortioxetine,a multimodal antidepressant, has shown encouraging data in achieving functional recovery, improving both mood and cognitive symptoms (Mahableshwarkar AR et al, 2015).

Objectives

The aim of the study was to assess the effectiveness of vortioxetine on mood symptoms, cognitive symptoms and functionality, assessed by patient-rated tools, in MDD outpatients in Greece.

Methods

In this non-interventional study, vortioxetine was administered as flexible dosing (5-20 mg/d). Mood symptoms, cognitive symptoms and functioning were assessed by the patient-rated scales PHQ-9, PDQ-D and SDS respectively, at baseline, 1 and 3 months. Repeated measures analysis of variance and t-test were used for the statistical analyses.

Results

336 patients participated in the study. PHQ-9 score ±SD decreased from 16.1±5.3, to 10.0±5.7 and 4.6±4.5, PDQ-D score ±SD decreased from 37.3±16.6 to 23.1±14.8 and 12.0±10.6, SDS Score ±SD decreased from 18.7±5.3 to 12.9±5.9 and to 7.8±6.5, at baseline, 1 and 3 months, respectively. The 3 SDS subscales: work/school life improved from 5.8±2.4 to 4.2±2.2 and 2.6±2.2, social life improved from 6.6±2.0 to 4.5±2.2 and 2.7±2.3 and family life improved from 6.3±2.0 to 4.3±2.1 and 2.6±2.3 -baseline, 1 and 3 months, respectively (p<0.001 for all paired comparisons).

Conclusions

MDD patients in Greece treated with vortioxetine significantly improved on mood symptoms, cognitive symptoms and functioning, enriching the already published efficacy data which is mostly based on clinician-rated scales.

Conflict of interest

A. Galanopoulos and E. Papalexi are full-time employees in Lundbeck Hellas.

Integrated analysis of multimodal single-cell data

The simultaneous measurement of multiple modalities represents an exciting frontier for single-cell genomics and necessitates computational methods that can define cellular states based on multimodal data. Here, we introduce "weighted-nearest neighbor" analysis, an unsupervised framework to learn the relative utility of each data type in each cell, enabling an integrative analysis of multiple modalities. We apply our procedure to a CITE-seq dataset of 211,000 human peripheral blood mononuclear cells (PBMCs) with panels extending to 228 antibodies to construct a multimodal reference atlas of the circulating immune system. Multimodal analysis substantially improves our ability to resolve cell states, allowing us to identify and validate previously unreported lymphoid subpopulations. Moreover, we demonstrate how to leverage this reference to rapidly map new datasets and to interpret immune responses to vaccination and coronavirus disease 2019 (COVID-19). Our approach represents a broadly applicable strategy to analyze single-cell multimodal datasets and to look beyond the transcriptome toward a unified and multimodal definition of cellular identity.

The impact of dose on the real-world effectiveness of vortioxetine in outpatients with mdd in greece

Introduction

The current treatment goal in Major Depressive Disorder (MDD) is functional recovery (Zimmerman M et al, 2012). However, finding the “right dose for the right patient” may be challenging and the dose-response relationship for antidepressant efficacy remains controversial (Hieronymus F et al, 2016). Efficacy evaluated by MADRS increases with higher vortioxetine doses, based on meta-analysis data (Thase ME et al, 2016).

Objectives

The aim of this exploratory analysis was to assess the impact of different doses on vortioxetine effectiveness in clinical practice in Greece.

Methods

In this non-interventional study, open-label vortioxetine was administered at a flexible dosage (5-20 mg/d). Patients receiving 5/10 mg vortioxetine (group A), at the end of the study, were compared to patients receiving 15/20mg vortioxetine (group B). At baseline, 1 and 3 months, depressive symptoms and functioning were assessed by MADRS and SDS. Multiple regression was used for the statistical analyses.

Results

The study included 336 MDD patients. At the end of the study, 64.3% (n=200) of patients were receiving 15/20 mg vortioxetine. Higher vortioxetine dose at month 3 was significantly correlated with higher MADRS total score at baseline (p<0.001). SDS total score change from baseline to month 3 was significantly associated with vortioxetine dose (p<0.001), with group A and group B showing improvements of -9.2±8.2 and -12.1±6.0, respectively- whereas such association was not observed for MADRS total score.

Conclusions

In conclusion, patients with more severe depressive symptoms were treated with higher antidepressant doses. However, beyond symptom improvement, vortioxetine effectiveness on patient functioning seems to increase with higher doses.

Conflict of interest

A. Galanopoulos and E. Papalexi are full-time employees in Lundbeck Hellas. A. Ettrup is a full-time employee in H. Lundbeck A/S.

Comprehensive Integration of Single-Cell Data

Single-cell transcriptomics has transformed our ability to characterize cell states, but deep biological understanding requires more than a taxonomic listing of clusters. As new methods arise to measure distinct cellular modalities, a key analytical challenge is to integrate these datasets to better understand cellular identity and function. Here, we develop a strategy to "anchor" diverse datasets together, enabling us to integrate single-cell measurements not only across scRNA-seq technologies, but also across different modalities. After demonstrating improvement over existing methods for integrating scRNA-seq data, we anchor scRNA-seq experiments with scATAC-seq to explore chromatin differences in closely related interneuron subsets and project protein expression measurements onto a bone marrow atlas to characterize lymphocyte populations. Lastly, we harmonize in situ gene expression and scRNA-seq datasets, allowing transcriptome-wide imputation of spatial gene expression patterns. Our work presents a strategy for the assembly of harmonized references and transfer of information across datasets.

Comprehensive Integration of Single-Cell Data

Single-cell transcriptomics has transformed our ability to characterize cell states, but deep biological understanding requires more than a taxonomic listing of clusters. As new methods arise to measure distinct cellular modalities, a key analytical challenge is to integrate these datasets to better understand cellular identity and function. Here, we develop a strategy to "anchor" diverse datasets together, enabling us to integrate single-cell measurements not only across scRNA-seq technologies, but also across different modalities. After demonstrating improvement over existing methods for integrating scRNA-seq data, we anchor scRNA-seq experiments with scATAC-seq to explore chromatin differences in closely related interneuron subsets and project protein expression measurements onto a bone marrow atlas to characterize lymphocyte populations. Lastly, we harmonize in situ gene expression and scRNA-seq datasets, allowing transcriptome-wide imputation of spatial gene expression patterns. Our work presents a strategy for the assembly of harmonized references and transfer of information across datasets.

Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells

Multimodal single-cell assays provide high-resolution snapshots of complex cell populations, but are mostly limited to transcriptome plus an additional modality. Here, we describe expanded CRISPR-compatible cellular indexing of transcriptomes and epitopes by sequencing (ECCITE-seq) for the high-throughput characterization of at least five modalities of information from each single cell. We demonstrate application of ECCITE-seq to multimodal CRISPR screens with robust direct single-guide RNA capture and to clonotype-aware multimodal phenotyping of cancer samples.

Kinetics of adult hematopoietic stem cell differentiation in vivo

The process whereby hematopoietic stem cells (HSCs) generate different blood cell types in the steady-state is poorly understood. Upadhaya et al. used inducible lineage tracing to characterize the earliest steps of adult HSC differentiation in vivo.

Adult hematopoiesis has been studied in terms of progenitor differentiation potentials, whereas its kinetics in vivo is poorly understood. We combined inducible lineage tracing of endogenous adult hematopoietic stem cells (HSCs) with flow cytometry and single-cell RNA sequencing to characterize early steps of hematopoietic differentiation in the steady-state. Labeled cells, comprising primarily long-term HSCs and some short-term HSCs, produced megakaryocytic lineage progeny within 1 wk in a process that required only two to three cell divisions. Erythroid and myeloid progeny emerged simultaneously by 2 wk and included a progenitor population with expression features of both lineages. Myeloid progenitors at this stage showed diversification into granulocytic, monocytic, and dendritic cell types, and rare intermediate cell states could be detected. In contrast, lymphoid differentiation was virtually absent within the first 3 wk of tracing. These results show that continuous differentiation of HSCs rapidly produces major hematopoietic lineages and cell types and reveal fundamental kinetic differences between megakaryocytic, erythroid, myeloid, and lymphoid differentiation.

Integrating single-cell transcriptomic data across different conditions, technologies, and species

Computational single-cell RNA-seq (scRNA-seq) methods have been successfully applied to experiments representing a single condition, technology, or species to discover and define cellular phenotypes. However, identifying subpopulations of cells that are present across multiple data sets remains challenging. Here, we introduce an analytical strategy for integrating scRNA-seq data sets based on common sources of variation, enabling the identification of shared populations across data sets and downstream comparative analysis. We apply this approach, implemented in our R toolkit Seurat (http://satijalab.org/seurat/), to align scRNA-seq data sets of peripheral blood mononuclear cells under resting and stimulated conditions, hematopoietic progenitors sequenced using two profiling technologies, and pancreatic cell 'atlases' generated from human and mouse islets. In each case, we learn distinct or transitional cell states jointly across data sets, while boosting statistical power through integrated analysis. Our approach facilitates general comparisons of scRNA-seq data sets, potentially deepening our understanding of how distinct cell states respond to perturbation, disease, and evolution.

Molecular transitions in early progenitors during human cord blood hematopoiesis

Hematopoietic stem cells (HSCs) give rise to diverse cell types in the blood system, yet our molecular understanding of the early trajectories that generate this enormous diversity in humans remains incomplete. Here, we leverage Drop-seq, a massively parallel single-cell RNA sequencing (scRNA-seq) approach, to individually profile 20,000 progenitor cells from human cord blood, without prior enrichment or depletion for individual lineages based on surface markers. Our data reveal a transcriptional compendium of progenitor states in human cord blood, representing four committed lineages downstream from HSC, alongside the transcriptional dynamics underlying fate commitment. We identify intermediate stages that simultaneously co-express "primed" programs for multiple downstream lineages, and also observe striking heterogeneity in the early molecular transitions between myeloid subsets. Integrating our data with a recently published scRNA-seq dataset from human bone marrow, we illustrate the molecular similarity between these two commonly used systems and further explore the chromatin dynamics of "primed" transcriptional programs based on ATAC-seq. Finally, we demonstrate that Drop-seq data can be utilized to identify new heterogeneous surface markers of cell state that correlate with functional output.

JAK2/IDH-mutant-driven myeloproliferative neoplasm is sensitive to combined targeted inhibition

Patients with myeloproliferative neoplasms (MPNs) frequently progress to bone marrow failure or acute myeloid leukemia (AML), and mutations in epigenetic regulators such as the metabolic enzyme isocitrate dehydrogenase (IDH) are associated with poor outcomes. Here, we showed that combined expression of Jak2V617F and mutant IDH1R132H or Idh2R140Q induces MPN progression, alters stem/progenitor cell function, and impairs differentiation in mice. Jak2V617F Idh2R140Q-mutant MPNs were sensitive to small-molecule inhibition of IDH. Combined inhibition of JAK2 and IDH2 normalized the stem and progenitor cell compartments in the murine model and reduced disease burden to a greater extent than was seen with JAK inhibition alone. In addition, combined JAK2 and IDH2 inhibitor treatment also reversed aberrant gene expression in MPN stem cells and reversed the metabolite perturbations induced by concurrent JAK2 and IDH2 mutations. Combined JAK2 and IDH2 inhibitor therapy also showed cooperative efficacy in cells from MPN patients with both JAK2mut and IDH2mut mutations. Taken together, these data suggest that combined JAK and IDH inhibition may offer a therapeutic advantage in this high-risk MPN subtype.

Dual Targeting of Oncogenic Activation and Inflammatory Signaling Increases Therapeutic Efficacy in Myeloproliferative Neoplasms

Genetic and functional studies underscore the central role of JAK/STAT signaling in myeloproliferative neoplasms (MPNs). However, the mechanisms that mediate transformation in MPNs are not fully delineated, and clinically utilized JAK inhibitors have limited ability to reduce disease burden or reverse myelofibrosis. Here we show that MPN progenitor cells are characterized by marked alterations in gene regulation through differential enhancer utilization, and identify nuclear factor κB (NF-κB) signaling as a key pathway activated in malignant and non-malignant cells in MPN. Inhibition of BET bromodomain proteins attenuated NF-κB signaling and reduced cytokine production in vivo. Most importantly, combined JAK/BET inhibition resulted in a marked reduction in the serum levels of inflammatory cytokines, reduced disease burden, and reversed bone marrow fibrosis in vivo.

Dose-dependent role of the cohesin complex in normal and malignant hematopoiesis

Cohesin complex members have recently been identified as putative tumor suppressors in hematologic and epithelial malignancies. The cohesin complex guides chromosome segregation; however, cohesin mutant leukemias do not show genomic instability. We hypothesized that reduced cohesin function alters chromatin structure and disrupts cis-regulatory architecture of hematopoietic progenitors. We investigated the consequences of Smc3 deletion in normal and malignant hematopoiesis. Biallelic Smc3 loss induced bone marrow aplasia with premature sister chromatid separation and revealed an absolute requirement for cohesin in hematopoietic stem cell (HSC) function. In contrast, Smc3 haploinsufficiency increased self-renewal in vitro and in vivo, including competitive transplantation. Smc3 haploinsufficiency reduced coordinated transcriptional output, including reduced expression of transcription factors and other genes associated with lineage commitment. Smc3 haploinsufficiency cooperated with Flt3-ITD to induce acute leukemia in vivo, with potentiated Stat5 signaling and altered nucleolar topology. These data establish a dose dependency for cohesin in regulating chromatin structure and HSC function.

JAK-STAT pathway activation in malignant and nonmalignant cells contributes to MPN pathogenesis and therapeutic response

The identification of JAK2/MPL mutations in patients with myeloproliferative neoplasms (MPN) has led to the clinical development of JAK kinase inhibitors, including ruxolitinib. Ruxolitinib reduces splenomegaly and systemic symptoms in myelofibrosis and improves overall survival; however, the mechanism by which JAK inhibitors achieve efficacy has not been delineated. Patients with MPN present with increased levels of circulating proinflammatory cytokines, which are mitigated by JAK inhibitor therapy. We sought to elucidate mechanisms by which JAK inhibitors attenuate cytokine-mediated pathophysiology. Single-cell profiling demonstrated that hematopoietic cells from myelofibrosis models and patient samples aberrantly secrete inflammatory cytokines. Pan-hematopoietic Stat3 deletion reduced disease severity and attenuated cytokine secretion, with similar efficacy as observed with ruxolitinib therapy. In contrast, Stat3 deletion restricted to MPN cells did not reduce disease severity or cytokine production. Consistent with these observations, we found that malignant and nonmalignant cells aberrantly secrete cytokines and JAK inhibition reduces cytokine production from both populations.

SIGNIFICANCE

Our results demonstrate that JAK-STAT3-mediated cytokine production from malignant and nonmalignant cells contributes to MPN pathogenesis and that JAK inhibition in both populations is required for therapeutic efficacy. These findings provide novel insight into the mechanisms by which JAK kinase inhibition achieves therapeutic efficacy in MPNs.

The impact of escitalopram on sleep problems of depressive patients in real-life clinical practice in greece

Introduction

There is a bidirectional relationship between depression and insomnia, the latter being both a risk factor for the development of depression and a consequence of depression itself. Since depressive patients with residual symptoms of insomnia are at higher risk for disease recurrence, dealing successfully with sleep disorders during antidepressive treatment is of great importance.

Objectives

The aim of the current study was to evaluate the effectiveness and tolerability of escitalopram on both depressive symptoms and sleep problems of depressive patients.

Methods

An observational, open-label, 3-month study was conducted in Greece.

Effectiveness was assessed using the CGI-S and AIS (Athens Insomnia Scale) scales. Tolerability was evaluated by spontaneously reported adverse events and treatment discontinuation rates.

Results

The study included 2,103 patients (mean age 51 ± 15 years, 64.0% women).

Patients showed significant improvement during the treatment period for both depressive symptoms and sleep problems. Mean CGI-S scores decreased from 4.2 ± 0.8 to 2.2 ± 1.0 and total AIS score decreased from 13.6 ± 4.9 to 3.5 ± 3.8 (repeated measures analysis of variance Hotelling's test, p < 0.001). The positive effect of escitalopram treatment was significant both on “night sleep” and “behaviour on the following days”. Moreover, the percentage of patients suffering from insomnia (AIS score >=6) decreased from 89.1% to 22.1% (Cochran's Q test p < 0.001). Escitalopram was also well tolerated, as 1909 (90.8%) patients successfully completed the study and 39 patients (1.85%) discontinued due to adverse events.

Conclusions

Escitalopram combines significant effectiveness on both depressive symptoms and sleep problems with good tolerability.

An open-label, multicenter observational study for patients with Alzheimer's disease treated with memantine in the clinical practice

Background/Aims

In this post-marketing observational study, the safety and effectiveness of memantine were evaluated in patients with Alzheimer's disease (AD).

Methods

In a 6-month, observational, open-label study at 202 specialist sites in Greece, the effectiveness of memantine was evaluated using the Mini-Mental State Examination (MMSE) and the Instrumental Activities of Daily Living (IADL) scale at baseline, and after 3 and 6 months. Discontinuation rates and adverse drug reactions (ADRs) were also recorded to evaluate the safety profile of memantine.

Results

2,570 patients participated in the study. Three and 6 months after baseline, MMSE and IADL scores were significantly improved compared to baseline. At the end of the study, 67% of the patients had improved their MMSE score; 7.1% of the patients reported ≥1 ADRs, and treatment was discontinued due to ADR in 0.7%.

Conclusion

Memantine was well tolerated and had a positive effect on the patient's cognitive and functional ability in real-life clinical practice, in agreement with randomized, controlled trials.

Early impact of a fat-enriched diet on behavioral responses of male and female rats

Prolonged high-fat diets have been shown to affect an organism's stress responsiveness at the neuroendocrine level. In the present study, the authors used a 7-day protocol of fat administration in adult rats of both sexes to investigate the early behavioral impact of a moderately fat (20%) diet, often used by Western societies, on rats' reaction to acute stress and novelty. Their results show that this diet can reduce the rats' active behavioral responses to subsequent stressors and influence their corticosterone secretion. Fat-fed male rats adopted a less active behavior to cope with forced swimming stress, whereas their exploratory behavior in the open field environment was rather increased compared with chow-fed males. Fat-fed female rats exhibited a less active behavioral response to both stress paradigms compared with their chow-fed counterparts. Fat diet abolished facilitation in corticosterone secretion following a subsequent stressor in both sexes. However, only in males did fat diet exaggerate corticosterone response to novelty, irrespective of the previous stress history of the rat. These data indicate that a short-term metabolic stress can modify the rats' stress coping strategy in interaction with the gender.

Sex differences in behavioral, neurochemical and neuroendocrine effects induced by the forced swim test in rats

The forced swim test (FST) has been considered as a pharmacologically valid test of the depressive syndrome in rodents. However, few studies have focused on neurochemical and behavioral responses during FST in both male and female rats. Thus, we investigated certain behavioral and neuroendocrine responses as well as the serotonergic activity after the application of FST in both sexes. Our data show that the duration of immobility was increased in both male and female rats during the 2nd session of the FST. Sex differences are observed in some behavioral responses, such as head swinging that is mostly present in male rats. In female rats FST induced a decrease in serotonergic activity in hippocampus and hypothalamus while in male rats it induced an increase in serotonergic activity in hypothalamus. Corticosterone serum levels were elevated in both sexes. However, hippocampal GR mRNA levels tended to be increased in males and females respectively. Moreover, hypothalamic serotonin (5-HT)1A mRNA levels were decreased in female rats while in male rats hippocampal 5-HT1A mRNA levels were increased. These data have shown that FST induces "depressive like symptoms" in both sexes and provide evidence that sex differences characterize certain behavioral aspects in the FST. Notably, hippocampal and hypothalamic serotonergic activity has been differentially modified in male rats compared with female rats and these neurochemical findings could be relevant to the differentiated expression of 5-HT1A receptor. Hypothalamic-pituitary-adrenal axis activity was also affected by FST application in a sex specific manner. The present results support that FST induced behavioral, neurochemical and neurobiological alterations, which are sex dependent.