Cell secretome: basic insights and therapeutic opportunities for CNS disorders

Transplantation of stem cells, in particular mesenchymal stem cells (MSCs), stands as a promising therapy for trauma, stroke or neurodegenerative conditions such as spinal cord or traumatic brain injuries (SCI or TBI), ischemic stroke (IS), or Parkinson’s disease (PD). Over the last few years, cell transplantation-based approaches have started to focus on the use of cell byproducts, with a strong emphasis on cell secretome. Having this in mind, the present review discusses the current state of the art of secretome-based therapy applications in different central nervous system (CNS) pathologies. For this purpose, the following topics are discussed: (1) What are the main cell secretome sources, composition, and associated collection techniques; (2) Possible differences of the therapeutic potential of the protein and vesicular fraction of the secretome; and (3) Impact of the cell secretome on CNS-related problems such as SCI, TBI, IS, and PD. With this, we aim to clarify some of the main questions that currently exist in the field of secretome-based therapies and consequently gain new knowledge that may help in the clinical application of secretome in CNS disorders.This research was funded by Prémios Santa Casa Neurociências—Prize Melo e Castro for Spinal Cord Injury Research, grant number MC-04/17 and the Portuguese Foundation for Science and Technology (FCT) through the Scientific Employment Stimulus to N. Silva and S. Monteiro (CEECIND/04794/2017 and CEECIND/01902/2017). This work was also funded by FEDER, through the Competitiveness Internalization Operational Programme (POCI), and by National funds, through the Foundation for Sciences and Technology (FCT), under the scope of the projects POCI-01-0145-FEDER-007038, TUBITAK/0007/2014, POCI-01-0145-FEDER-029206, POCI-01-0145-FEDER-029751, and NORTE-01-0145-FEDER-029968. This work was also developed under the scope of the projects NORTE-01-0145-FEDER-000013 and NORTE-01-0145-FEDER-000023, supported by the Northern Portugal Regional Operational Programme (NORTE 2020), under the Portugal 2020 Partnership Agreement, through the European Regional Development Fund (FEDER)

Repeatability and temporal consistency of lower limb biomechanical variables expressing interlimb coordination during the double-support phase in people with and without stroke sequelae

Reliable biomechanical methods to assess interlimb coordination during the double-support phase in post-stroke subjects are needed for assessing movement dysfunction and related variability. The data obtained could provide a significant contribution for designing rehabilitation programs and for their monitorisation. The present study aimed to determine the minimum number of gait cycles needed to obtain adequate values of repeatability and temporal consistency of lower limb kinematic, kinetic, and electromyographic parameters during the double support of walking in people with and without stroke sequelae. Eleven post-stroke and thirteen healthy participants performed 20 gait trials at self-selected speed in two separate moments with an interval between 72 h and 7 days. The joint position, the external mechanical work on the centre of mass, and the surface electromyographic activity of the tibialis anterior, soleus, gastrocnemius medialis, rectus femoris, vastus medialis, biceps femoris, and gluteus maximus muscles were extracted for analysis. Both the contralesional and ipsilesional and dominant and non-dominant limbs of participants with and without stroke sequelae, respectively, were evaluated either in trailing or leading positions. The intraclass correlation coefficient was used for assessing intra-session and inter-session consistency analysis. For most of the kinematic and the kinetic variables studied in each session, two to three trials were required for both groups, limbs, and positions. The electromyographic variables presented higher variability, requiring, therefore, a number of trials ranging from 2 to >10. Globally, the number of trials required inter-session ranged from 1 to >10 for kinematic, from 1 to 9 for kinetic, and 1 to >10 for electromyographic variables. Thus, for the double support analysis, three gait trials were required in order to assess the kinematic and kinetic variables in cross-sectional studies, while for longitudinal studies, a higher number of trials (>10) were required for kinematic, kinetic, and electromyographic variables.info:eu-repo/semantics/publishedVersio

Methodological considerations in assessing interlimb coordination on poststroke gait: a scoping review of biomechanical approaches and outcomes

To identify and summarize biomechanical assessment approaches in interlimb coordination on poststroke gait. Interlimb coordination involves complex neurophysiological mechanisms that can be expressed through the biomechanical output. The deepening of this concept would have a significant contribution in gait rehabilitation in patients with an asymmetric neurological impairment as poststroke adults. Poststroke adults (>19 years old), with assessment of interlimb coordination during gait, in an open context, according to the Population, Concept, Context framework. A literature search was performed in PubMed, Web of Science™, Scopus, and gray literature in Google Scholar™, according to the PRISMA-ScR recommendations. Studies written in Portuguese or English language and published between database inception and 14 November 2021 were included. Qualitative studies, conference proceedings, letters, and editorials were excluded. The main conceptual categories were “author/year”, “study design”, “participant’s characteristics”, “walking conditions”, “instruments” and “outcomes”. The search identified 827 potentially relevant studies, with a remaining seven fulfilling the established criteria. Interlimb coordination was assessed during walking in treadmill (n = 3), overground (n = 3) and both (n = 1). The instruments used monitored electromyography (n = 2), kinetics (n = 2), and kinematics (n = 4) to assess spatiotemporal parameters (n = 4), joint kinematics (n = 2), anteroposterior ground reaction forces (n = 2), and electromyography root mean square (n = 2) outcomes. These outcomes were mostly used to analyze symmetry indices or ratios, to calculate propulsive impulse and external mechanical power produced on the CoM, as well as antagonist coactivation. Assessment of interlimb coordination during gait is important for consideration of natural auto-selected overground walking, using kinematic, kinetic, and EMG instruments. These allow for the collection of the main biomechanical outcomes that could contribute to improve better knowledge of interlimb coordination assessment in poststroke patients.info:eu-repo/semantics/publishedVersio

Spinal cord RNA-seq data after a baclofen treatment in mice with a spinal cord injury

Spinal cord injury (SCI) leads to severe functional deficits. Currently, there are no available pharmacological treatments to promote neurological recovery in SCI patients. Recent work from our group has shown that a baclofen treatment can promote functional recovery after a compression SCI in mice [1]. Here, we provide transcriptomic (RNA-seq) data from adult mouse spinal cords collected 7 days after a compression SCI and baclofen (vs vehicle) administration. The Illumina NovaSeq 6000 platform was used to generate the raw transcriptomic data. In addition, we also present bioinformatic analyses including differential gene expression analysis, enrichment analyses for various functional annotations (gene ontology, KEGG and BioCarta pathways or InterPro domains) and transcription factor targets. The raw RNA-seq data has been uploaded to the NCBI Sequence Read Archive (SRA) database (Bioproject ID PRJNA886048). The data generated from the bioinformatic analyses is contained within the articleThis work was supported by the Wings for Life Spinal Cord Research Foundation (grant reference WFL-ES-03/19), the Portuguese Foundation for Science and Technology (FCT) EXPL/MED-FAR/1529/2021 to N. de Sousa and through the Scientific Employment Stimulus to N. Silva and S. Monteiro (CEECIND/04794/2017 and CEECIND/01902/2017) and Grant PID2020-115121GB-I00 funded by MCIN/AEI/10.13039/501100011033 to A. Barreiro-IglesiasS

Quinone oxidoreductase from Staphylococcus aureus

Funding Information: Helena Gaspar is acknowledged for the HPLC analyses and Bruno Victor for advice on modelling. F.M.S. and M.S.S. are recipients of fellowships by Fundação para a Ciência e a Tecnologia (PD/BD/128213/2016 and PD/BD/128202/2016, respectively, both within the scope of the PhD program Molecular Biosciences PD/00133/2012). A.B. is recipient of a fellowship by Fundação para a Ciência e a Tecnologia UI/BD/153052/2022. The work was funded by Fundação para a Ciência e a Tecnologia ( PTDC/BIA-BQM/2599/2021 to M.M.P). The project was further supported by UIDB/04046/2020 and UIDP/04046/2020 Centre grants from FCT , Portugal (to BioISI), by LISBOA-01-0145-FEDER-007660 cofunded by FEDER through COMPETE2020-POCI and by Fundação para a Ciência e a Tecnologia and by UIDB/04612/2020 and UIDP/04612/2020 research unit grants from FCT (to Mostmicro). The NMR spectrometers are part of the National NMR Network (PTNMR) and are supported by Infrastructure Project N° 022161 (co-financed by FEDER through COMPETE 2020, POCI, and PORL and FCT through PIDDAC). Funding Information: Helena Gaspar is acknowledged for the HPLC analyses and Bruno Victor for advice on modelling. F.M.S. and M.S.S. are recipients of fellowships by Fundação para a Ciência e a Tecnologia (PD/BD/128213/2016 and PD/BD/128202/2016, respectively, both within the scope of the PhD program Molecular Biosciences PD/00133/2012). A.B. is recipient of a fellowship by Fundação para a Ciência e a Tecnologia UI/BD/153052/2022. The work was funded by Fundação para a Ciência e a Tecnologia (PTDC/BIA-BQM/2599/2021 to M.M.P). The project was further supported by UIDB/04046/2020 and UIDP/04046/2020 Centre grants from FCT, Portugal (to BioISI), by LISBOA-01-0145-FEDER-007660 cofunded by FEDER through COMPETE2020-POCI and by Fundação para a Ciência e a Tecnologia and by UIDB/04612/2020 and UIDP/04612/2020 research unit grants from FCT (to Mostmicro). The NMR spectrometers are part of the National NMR Network (PTNMR) and are supported by Infrastructure Project N° 022161 (co-financed by FEDER through COMPETE 2020, POCI, and PORL and FCT through PIDDAC). Publisher Copyright: © 2022 The Author(s)Staphylococcus aureus is an opportunistic pathogen and one of the most frequent causes for community acquired and nosocomial bacterial infections. Even so, its energy metabolism is still under explored and its respiratory enzymes have been vastly overlooked. In this work, we unveil the dihydroorotate:quinone oxidoreductase (DHOQO) from S. aureus, the first example of a DHOQO from a Gram-positive organism. This protein was shown to be a FMN containing menaquinone reducing enzyme, presenting a Michaelis-Menten behaviour towards the two substrates, which was inhibited by Brequinar, Leflunomide, Lapachol, HQNO, Atovaquone and TFFA with different degrees of effectiveness. Deletion of the DHOQO coding gene (Δdhoqo) led to lower bacterial growth rates, and effected in cell morphology and metabolism, most importantly in the pyrimidine biosynthesis, here systematized for S. aureus MW2 for the first time. This work unveils the existence of a functional DHOQO in the respiratory chain of the pathogenic bacterium S. aureus, enlarging the understanding of its energy metabolism.publishersversionpublishe

Identification of unique neoantigen qualities in long-term survivors of pancreatic cancer

Pancreatic ductal adenocarcinoma is a lethal cancer with fewer than 7% of patients surviving past 5 years. T-cell immunity has been linked to the exceptional outcome of the few long-term survivors1,2, yet the relevant antigens remain unknown. Here we use genetic, immunohistochemical and transcriptional immunoprofiling, computational biophysics, and functional assays to identify T-cell antigens in long-term survivors of pancreatic cancer. Using whole-exome sequencing and in silico neoantigen prediction, we found that tumours with both the highest neoantigen number and the most abundant CD8+ T-cell infiltrates, but neither alone, stratified patients with the longest survival. Investigating the specific neoantigen qualities promoting T-cell activation in long-term survivors, we discovered that these individuals were enriched in neoantigen qualities defined by a fitness model, and neoantigens in the tumour antigen MUC16 (also known as CA125). A neoantigen quality fitness model conferring greater immunogenicity to neoantigens with differential presentation and homology to infectious disease-derived peptides identified long-term survivors in two independent datasets, whereas a neoantigen quantity model ascribing greater immunogenicity to increasing neoantigen number alone did not. We detected intratumoural and lasting circulating T-cell reactivity to both high-quality and MUC16 neoantigens in long-term survivors of pancreatic cancer, including clones with specificity to both high-quality neoantigens and predicted cross-reactive microbial epitopes, consistent with neoantigen molecular mimicry. Notably, we observed selective loss of high-quality and MUC16 neoantigenic clones on metastatic progression, suggesting neoantigen immunoediting. Our results identify neoantigens with unique qualities as T-cell targets in pancreatic ductal adenocarcinoma. More broadly, we identify neoantigen quality as a biomarker for immunogenic tumours that may guide the application of immunotherapies

Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer

Background and aims: Continuing recalcitrance to therapy cements pancreatic cancer (PC) as the most lethal malignancy, which is set to become the second leading cause of cancer death in our society. The study aim was to investigate the association between DNA damage response (DDR), replication stress and novel therapeutic response in PC to develop a biomarker driven therapeutic strategy targeting DDR and replication stress in PC. Methods: We interrogated the transcriptome, genome, proteome and functional characteristics of 61 novel PC patient-derived cell lines to define novel therapeutic strategies targeting DDR and replication stress. Validation was done in patient derived xenografts and human PC organoids. Results: Patient-derived cell lines faithfully recapitulate the epithelial component of pancreatic tumors including previously described molecular subtypes. Biomarkers of DDR deficiency, including a novel signature of homologous recombination deficiency, co-segregates with response to platinum (P < 0.001) and PARP inhibitor therapy (P < 0.001) in vitro and in vivo. We generated a novel signature of replication stress with which predicts response to ATR (P < 0.018) and WEE1 inhibitor (P < 0.029) treatment in both cell lines and human PC organoids. Replication stress was enriched in the squamous subtype of PC (P < 0.001) but not associated with DDR deficiency. Conclusions: Replication stress and DDR deficiency are independent of each other, creating opportunities for therapy in DDR proficient PC, and post-platinum therapy

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts