Transcriptional programs mediating neuronal toxicity and altered glial-neuronal signaling in a Drosophila knock-in tauopathy model

Missense mutations in the gene encoding the microtubule-associated protein tau cause autosomal dominant forms of frontotemporal dementia. Multiple models of frontotemporal dementia based on transgenic expression of human tau in experimental model organisms, including Drosophila, have been described. These models replicate key features of the human disease, but do not faithfully recreate the genetic context of the human disorder. Here we use CRISPR-Cas mediated gene editing to model frontotemporal dementia caused by the tau P301L mutation by creating the orthologous mutation, P251L, in the endogenous Drosophila tau gene. Flies heterozygous or homozygous for tau P251L display age-dependent neurodegeneration, metabolic defects, and accumulate DNA damage in affected neurons. To understand the molecular events promoting neuronal dysfunction and death in knock-in flies we performed single-cell RNA sequencing on approximately 130,000 cells from brains of tau P251L mutant and control flies. We found that expression of disease-associated mutant tau altered gene expression cell autonomously in all neuronal cell types identified. Gene expression was also altered in glial cells, suggestive of non-cell autonomous regulation. Cell signaling pathways, including glial-neuronal signaling, were broadly dysregulated as were brain region and cell type-specific protein interaction networks and gene regulatory programs. In summary, we present here a genetic model of tauopathy, which faithfully recapitulates the genetic context and phenotypic features of the human disease and use the results of comprehensive single cell sequencing analysis to outline pathways of neurotoxicity and highlight the potential role of non-cell autonomous changes in glia.

A systems-biology approach connects aging mechanisms with Alzheimer's disease pathogenesis

Age is the strongest risk factor for developing Alzheimer's disease, the most common neurodegenerative disorder. However, the mechanisms connecting advancing age to neurodegeneration in Alzheimer's disease are incompletely understood. We conducted an unbiased, genome-scale, forward genetic screen for age-associated neurodegeneration in Drosophila to identify the underlying biological processes required for maintenance of aging neurons. To connect genetic screen hits to Alzheimer's disease pathways, we measured proteomics, phosphoproteomics, and metabolomics in Drosophila models of Alzheimer's disease. We further identified Alzheimer's disease human genetic variants that modify expression in disease-vulnerable neurons. Through multi-omic, multi-species network integration of these data, we identified relationships between screen hits and tau-mediated neurotoxicity. Furthermore, we computationally and experimentally identified relationships between screen hits and DNA damage in Drosophila and human iPSC-derived neural progenitor cells. Our work identifies candidate pathways that could be targeted to attenuate the effects of age on neurodegeneration and Alzheimer's disease.

Transcriptional programs mediating neuronal toxicity and altered glial-neuronal signaling in a Drosophila knock-in tauopathy model

Missense mutations in the gene encoding the microtubule-associated protein tau cause autosomal dominant forms of frontotemporal dementia. Multiple models of frontotemporal dementia based on transgenic expression of human tau in experimental model organisms, including Drosophila, have been described. These models replicate key features of the human disease, but do not faithfully recreate the genetic context of the human disorder. Here we use CRISPR-Cas mediated gene editing to model frontotemporal dementia caused by the tau P301L mutation by creating the orthologous mutation, P251L, in the endogenous Drosophila tau gene. Flies heterozygous or homozygous for tau P251L display age-dependent neurodegeneration, metabolic defects and accumulate DNA damage in affected neurons. To understand the molecular events promoting neuronal dysfunction and death in knock-in flies we performed single-cell RNA sequencing on approximately 130,000 cells from brains of tau P251L mutant and control flies. We found that expression of disease-associated mutant tau altered gene expression cell autonomously in all neuronal cell types identified and non-cell autonomously in glial cells. Cell signaling pathways, including glial-neuronal signaling, were broadly dysregulated as were brain region and cell-type specific protein interaction networks and gene regulatory programs. In summary, we present here a genetic model of tauopathy, which faithfully recapitulates the genetic context and phenotypic features of the human disease and use the results of comprehensive single cell sequencing analysis to outline pathways of neurotoxicity and highlight the role of non-cell autonomous changes in glia.

Integrative analysis reveals a conserved role for the amyloid precursor protein in proteostasis during aging

Aβ peptides derived from the amyloid precursor protein (APP) have been strongly implicated in the pathogenesis of Alzheimer's disease. However, the normal function of APP and the importance of that role in neurodegenerative disease is less clear. We recover the Drosophila ortholog of APP, Appl, in an unbiased forward genetic screen for neurodegeneration mutants. We perform comprehensive single cell transcriptional and proteomic studies of Appl mutant flies to investigate Appl function in the aging brain. We find an unexpected role for Appl in control of multiple cellular pathways, including translation, mitochondrial function, nucleic acid and lipid metabolism, cellular signaling and proteostasis. We mechanistically define a role for Appl in regulating autophagy through TGFβ signaling and document the broader relevance of our findings using mouse genetic, human iPSC and in vivo tauopathy models. Our results demonstrate a conserved role for APP in controlling age-dependent proteostasis with plausible relevance to Alzheimer's disease.

Calreticulin mutant myeloproliferative neoplasms induce MHC-I skewing, which can be overcome by an optimized peptide cancer vaccine

The majority of JAK2V617F-negative myeloproliferative neoplasms (MPNs) have disease-initiating frameshift mutations in calreticulin (CALR), resulting in a common carboxyl-terminal mutant fragment (CALRMUT), representing an attractive source of neoantigens for cancer vaccines. However, studies have shown that CALRMUT-specific T cells are rare in patients with CALRMUT MPN for unknown reasons. We examined class I major histocompatibility complex (MHC-I) allele frequencies in patients with CALRMUT MPN from two independent cohorts. We observed that MHC-I alleles that present CALRMUT neoepitopes with high affinity are underrepresented in patients with CALRMUT MPN. We speculated that this was due to an increased chance of immune-mediated tumor rejection by individuals expressing one of these MHC-I alleles such that the disease never clinically manifested. As a consequence of this MHC-I allele restriction, we reasoned that patients with CALRMUT MPN would not efficiently respond to a CALRMUT fragment cancer vaccine but would when immunized with a modified CALRMUT heteroclitic peptide vaccine approach. We found that heteroclitic CALRMUT peptides specifically designed for the MHC-I alleles of patients with CALRMUT MPN efficiently elicited a CALRMUT cross-reactive CD8+ T cell response in human peripheral blood samples but not to the matched weakly immunogenic CALRMUT native peptides. We corroborated this effect in vivo in mice and observed that C57BL/6J mice can mount a CD8+ T cell response to the CALRMUT fragment upon immunization with a CALRMUT heteroclitic, but not native, peptide. Together, our data emphasize the therapeutic potential of heteroclitic peptide-based cancer vaccines in patients with CALRMUT MPN.

Inherited causes of clonal haematopoiesis in 97,691 whole genomes

Age is the dominant risk factor for most chronic human diseases; yet the mechanisms by which aging confers this risk are largely unknown.¹ Recently, the age-related acquisition of somatic mutations in regenerating hematopoietic stem cell populations leading to clonal expansion was associated with both hematologic cancer ^2–4 and coronary heart disease⁵, a phenomenon termed ‘Clonal Hematopoiesis of Indeterminate Potential’ (CHIP).⁶ Simultaneous germline and somatic whole genome sequence analysis now provides the opportunity to identify root causes of CHIP. Here, we analyze high-coverage whole genome sequences from 97,691 participants of diverse ancestries in the NHLBI TOPMed program and identify 4,229 individuals with CHIP. We identify associations with blood cell, lipid, and inflammatory traits specific to different CHIP genes. Association of a genome-wide set of germline genetic variants identified three genetic loci associated with CHIP status, including one locus at TET2 that was African ancestry specific. In silico-informed in vitro evaluation of the TET2 germline locus identified a causal variant that disrupts a TET2 distal enhancer resulting in increased hematopoietic stem cell self-renewal. Overall, we observe that germline genetic variation shapes hematopoietic stem cell function leading to CHIP through mechanisms that are both specific to clonal hematopoiesis and shared mechanisms leading to somatic mutations across tissues.

Long-term survival and functional capacity in cardiac surgery patients after prolonged intensive care

OBJECTIVE

To determine whether hospital discharge alone represents a good outcome for patients who had prolonged intensive care after cardiac surgery by studying their postdischarge survival and functional outcome. The secondary objective is to estimate the proportion of intensive care unit (ICU) resources used by the long-stay (> or = 10 initial consecutive ICU days) patients and to identify preoperative patient characteristics that are associated with a prolonged ICU stay and hospital and long-term survival.

DESIGN

Inception cohort study.

SETTING

The Cleveland Clinic Foundation, a tertiary care, academic teaching institution.

PATIENTS

Cardiac surgery patients with an initial ICU stay of 10 or more consecutive days.

INTERVENTIONS

Data were collected daily during hospitalization on every adult who underwent coronary artery bypass graft and/or valve surgery at one institution in 1993. Discharged patients who spent >10 initial consecutive days in the ICU after surgery were contacted by telephone to determine vital status and functional capacity using the Duke Activity Status Index. Total ICU and total hospital direct costs were obtained for each patient.

MEASUREMENTS AND MAIN RESULTS

The primary outcome measurements were ICU length of stay, hospital mortality, after-surgery and postdischarge mortality and functional capacity, and relative resource utilization. Of the 2,618 cardiac surgery patients who met the inclusion criteria, 142 (5.4%) had an initial ICU length of stay of 10 or more consecutive days. Of these, 47 (33.1%) died in the hospital. Ninety-four of the 95 discharged patients were followed up (median follow-up, 30.6 months), and 44 of the 94 (46.8%) died during the follow-up period. The median Duke Activity Status Index for the 50 survivors was 26 out of a possible 58.2. The 142 long-stay patients used 50% of the total ICU days and 48% of the total ICU direct cost for all 2,618 patients.

CONCLUSIONS

Many survivors of prolonged intensive care die soon after hospital discharge and many longer term survivors have a poor functional state. Therefore, hospital discharge is an incomplete measure of outcome for these patients, and longer follow-up is more appropriate. The relatively small number of patients who require prolonged intensive care consumes a disproportionate amount of the total ICU and total hospital direct cost.

Association between postoperative hypothermia and adverse outcome after coronary artery bypass surgery

BACKGROUND

We examined the effect on outcome of mild hypothermia (< 36 degrees C) upon intensive care unit (ICU) admission on patient outcome after coronary artery bypass grafting (CABG) with cardiopulmonary bypass (CPB).

METHODS

We performed a retrospective database analysis of 5,701 isolated CABG patients requiring CPB, operated upon from January 1995 to June 1997. Patients were classified as either hypo- (< 36 degrees C) or normothermic (> or = 36 degrees C) upon ICU admission. ICU admission bladder core temperature (BCT) versus outcome was evaluated. Outcome measures included mortality, resource utilization (mechanical ventilation time, ICU and hospital length of stay, and postoperative packed red blood cell transfusion), and major morbidity (cardiac, renal, neurologic, or major infection).

RESULTS

Overall, patients admitted to the ICU with BCT < 36 degrees C had a significantly greater mortality (p = 0.02), prolonged mechanical ventilation (p = 0.007), packed red blood cell transfusion (p = 0.001), ICU (p = 0.01), and hospital (p = 0.005) length of stay.

CONCLUSIONS

BCT of less than 36 degrees C, upon ICU admission, has a significant association with adverse outcome after CABG with CPB. M An __ Tl QA_7_t-0