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Comparing functional and genomic-based precision medicine in blood cancer patients
Get PDFTumor-agnostic precision medicine (PM) strategies promise to support treatment decisions in relapsed/refractory blood cancer patients. Genomic-based PM (gPM) and drug screening-based functional PM (fPM) currently represent the most prominent PM methodologies. In this study, we report the feasibility analysis of the first 55 patients enrolled in the multicentric, randomized controlled EXALT-2 trial (NCT04470947) comparing treatment recommendations of gPM, fPM, and physicians' choice (PC) head to head. In 54 patients (98%), the diagnostic workflow was successfully implemented, resulting in treatment recommendations for 42 patients (76%), of whom 29 (69%) received the suggested individualized treatments. Actionable targets were identified in 65% by gPM and 80% by fPM (64% microscopy-based, 86% flow cytometry-based fPM). The median time to report was shorter for fPM than for gPM testing. The two strategies revealed overlapping drug targets in 60% of cases. Both, gPM and fPM can efficiently be integrated into the clinical routine to guide therapy decisions for the majority of patients
PET imaging and key radiotracers for evaluating response to locoregional therapy in hepatocellular carcinoma
No full textT cell receptors specific for an imatinib-induced mutation in BCR-ABL for adoptive T cell therapy
Get PDFBCR-ABL kinase is the major oncogenic driver of chronic myeloid leukemia (CML). Tyrosine kinase inhibitors (TKIs), which are highly potent in targeting BCR-ABL, are currently used as first-line treatment. Although TKIs are effective, drug resistance caused by the emergence of drug-selected secondary mutations in BCR-ABL remains a major problem for relapse, especially in patients with compound mutations. In this study, we aimed to investigate potential neoepitopes derived from mutated BCR-ABL and to generate neoepitope-specific TCRs for adoptive T cell therapy. Two candidate peptides derived from the E255V and the T315I mutation (designated ABL-E255V and ABL-T315I) were selected for study based on their in silico predicted binding affinity to HLA-A2. By immunizing transgenic mice that express a diverse human T cell receptor (TCR) repertoire restricted to HLA-A2, we detected CD8+ T cell responses against the ABL-E255V, but not the ABL-T315I peptide. From immune responding mice, two E255V-specific TCRs were isolated. Human CD8+ T cells were engineered to express the specific TCRs for characterization, in which one TCR was identified as a therapeutic candidate due to its superior avidity and lack of detectable off-target reactivity. Importantly, we demonstrated that the ABL-E255V neoepitope was naturally processed and presented. In summary, our results demonstrate that HLA-A2+ CML cells harboring the E255V mutation can be targeted by specific TCRs, which may benefit patients who are highly resistant to available TKIs due to compound mutations
LINNAEUS: simultaneous single-cell lineage tracing and cell type identification
No full textA key goal of biology is to understand the origin of the many cell types that can be observed during diverse processes such as development, regeneration, and disease. Single-cell RNA-sequencing (scRNA-seq) is commonly used to identify cell types in a tissue or organ. However, organizing the resulting taxonomy of cell types into lineage trees to understand the origins of cell states and relationships between cells remains challenging. Here we present LINNAEUS (Spanjaard et al, Nat Biotechnol 36:469–473. https://doi.org/10.1038/nbt.4124, 2018; Hu et al, Nat Genet 54:1227–1237. https://doi.org/10.1038/s41588-022-01129-5, 2022) (LINeage tracing by Nuclease-Activated Editing of Ubiquitous Sequences)—a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA-seq with computational analysis of lineage barcodes, generated by genome editing of transgenic reporter genes, LINNAEUS can be used to reconstruct organism-wide single-cell lineage trees. LINNAEUS provides a systematic approach for tracing the origin of novel cell types, or known cell types under different conditions
Early-life adversity predicts markers of aging-related neuroinflammation, neurodegeneration, and cognitive impairment in women
Get PDFOBJECTIVE: Despite the overwhelming evidence for profound and longstanding effects of early-life stress (ELS) on inflammation, brain structure, and molecular aging, its impact on human brain aging and risk for neurodegenerative disease is poorly understood. We examined the impact of ELS severity in interaction with age on blood-based markers of neuroinflammation and neurodegeneration, brain volumes, and cognitive function in middle-aged women. METHODS: We recruited 179 women (aged 30-60 years) with and without ELS exposure before the onset of puberty. Using Simoa technology, we assessed blood-based markers of neuroinflammation and neurodegeneration, including serum concentrations of glial fibrillary acidic protein (GFAP) and neurofilament light chain (NfL). We further obtained T1-weighted and T2-weighted magnetic resonance images to assess brain volumes and we assessed cognitive performance sensitive to early impairments associated with the development of dementia, using the Cambridge Neuropsychological Automated Test Battery. We used generalized additive models to examine nonlinear interaction effects of ELS severity and age on these outcomes. RESULTS: Analyses revealed significant nonlinear interaction effects of ELS severity and age on NfL and GFAP serum concentrations, total and subcortical gray matter volume loss, increased third ventricular volume, and cognitive impairment. INTERPRETATION: These findings suggest that ELS profoundly exacerbates peripheral, neurostructural, and cognitive markers of brain aging. Our results are critical for the development of novel early prevention strategies that target the impact of developmental stress on the brain to mitigate aging-related neurological diseases
Sequential visual stimuli increase high frequency power in the visual cortex
Get PDFToday, 40 Hz flickering full-field visual stimulation is used to entrain neuronal oscillations for a variety of therapeutic purposes. We here propose spatially organized sequential visual flickering stimulation as a newer tool to entrain the visual system. We show that sequential visual flickering can evoke increased power in high frequencies (100 to 190 Hz) in the visual cortex of mice. Consequently, sequential sensory stimulation should be regarded as a putative new way leading to power increases in high frequency domains
Hippo signaling regulates high-NaCl-induced increase of RORγt+ pro-inflammatory lymphocytes
Get PDFArterial hypertension is a major health challenge worldwide. Lifestyle factors including dietary NaCl increase the risk of hypertension. Pathophysiologically, the activation of the renin–angiotensin–aldosterone system and vascular remodeling, as well as the increase in Th17 lymphocytes, contribute to increased blood pressure and end-organ damage. To date, it is unknown whether NaCl, changed osmolarity, and/or angiotensin II directly induce Th17 differentiation, and, if so, which molecular pathways are involved. One major transcription factor inducing Th17 differentiation is RORγt. RORγt+ immune-cell subtypes increased in a mouse model of hypertension. In primary splenocytes, NaCl and mannitol but not angiotensin II increased the frequency of RORγt+ lymphocytes and IL-17 and IL-22 expression. NaCl and angiotensin II induced angiotensin II receptor expression. NaCl led to the inactivation of the Hippo pathway in lymphocytes and decreased phosphorylation of the transcription factor TAZ, leading to increased functionality as a transcriptional coregulator. Inhibition of TAZ by verteporfin blocked the NaCl-induced increase in RORγt+ lymphocytes. Taken together, we found that NaCl induced pro-inflammatory lymphocytes via the regulation of Hippo signaling. The results suggest the possible involvement of Hippo signaling in the pathophysiology of salt-sensitive hypertension, with the potential for therapeutic targeting by small-molecule approaches
Reduced monocytic IL10 expression in PD1 inhibitor-treated patients is a harbinger of severe immune-related adverse events
Get PDFBACKGROUND: Despite remarkable clinical efficacy, little is known about the system-wide immunological alterations provoked by PD1 blockade. Dynamics of quantitative immune composition and functional repertoire during PD1 blockade could delineate cohort-specific patterns of treatment response and therapy-induced toxicity. METHODS: We longitudinally assessed therapy-induced effects on the immune system in fresh whole blood using flow cytometry-based cell quantifications, accompanied by analyses of effector properties of all major immune populations upon cell-type specific stimulations. 43 cancer patients undergoing PD1 blockade were recruited with assessments performed pre-treatment and before cycles 2/4/6, which resulted in the collection of more than 30,000 cytometric data values. RESULTS: We observed no intrinsic immune pattern correlating with clinical outcome before PD1 blockade initiation, but cohort-specific immune alterations emerged during therapy. The most striking evolving changes in therapy responders were an increase in activated T and NK cell subsets, which showed high IFNγ and TNFα expression upon ex vivo stimulation. Patients affected by severe immune-related adverse events (s-irAE) presented with an analogously increased number of activated CD4(+) and CD8(+) T cells compared to patients with no/mild irAE, but lacked the functional divergences observed between responders versus non-responders. Instead, their monocytes showed discriminatory functional deficits with less IL10 production upon stimulation, which led to an abrogated inhibition of T cell proliferation in vitro and thus may account for the observed T cell expansion in patients with s-irAE. CONCLUSION: Our holistic explorative approach allowed the delineation of clinically relevant cohorts by treatment-triggered immune changes, potentially enabling better patient stratification and further revealed new mechanistic insights into the pathogenesis of s-irAE
The lncRNA landscape of cardiac resident macrophages and identification of Schlafenlnc as a regulator of macrophage migratory function
No full textCardiac resident macrophages (crMPs) were recently shown to exert pivotal functions in cardiac homeostasis and disease, but the underlying molecular mechanisms are largely unclear. Long non-coding RNAs (lncRNAs) are increasingly recognized as important regulatory molecules in a number of cell types, but neither the identity nor the molecular mechanisms of lncRNAs in crMPs are known. Here, we have employed deep RNA-seq and single cell RNA sequencing to resolve the crMP lncRNA landscape from healthy and diseased murine myocardium. CrMPs express previously unknown and highly cell type-specific lncRNAs, among which one lncRNA, termed Schlafenlnc, was particularly abundant and enriched in crMPs. We found Schlafenlnc to be necessary for migration-associated gene expression in macrophages in vitro and in vivo and essential for their adhesion and migration. Collectively, our data provide a basis to the systematic characterization of lncRNAs in crMPs and establish Schlafenlnc as a critical regulator of macrophage migratory functions
Early time window for memory ensemble allocation specifically depending on activity in Syt2+ early-born parvalbumin interneurons
Get PDFIn learning and memory, the encoding of experience is converted into memory ensembles, affecting future behavior. The mechanisms underlying such memory formation are poorly understood, but parvalbumin-expressing (PV) interneurons might be important due to their roles in shaping offline network activity. Here, we addressed the roles of early- and late-born PV neuron subpopulations in memory formation and consolidation in mice. Subpopulation-specific silencing of early-born Syt2+ hippocampal PV neurons during an early 15-min time window upon learning prevented allocation of cFos expression to the correct learning-related principal neuron (PN) subpopulation and memory formation. Conversely, late-born Syt2 PV neurons were specifically required for subsequent memory consolidation and recall, but not PN allocation. During memory formation, the recruitment of one PN subpopulation prevented the subsequent recruitment of the alternative subpopulation. Therefore, memory ensemble allocation to the correct PN subpopulation is a critical early step in memory formation, specifically depending on the activity of Syt2+ early-born PV neurons