Biology subjects

Lehtonen, S.

Publications and source records attributed to Lehtonen, S..

15 recordsLinked to original sources

bioRxiv2026

The role of reticulate evolution in biodiversity formation: the case of neotropical Adiantum ferns

Hybridization and introgression are thought to play key roles in the formation of biodiversity. However, detecting gene flow between species and understanding reticulation patterns remain challenging, especially in species-rich lineages with complex evolutionary histories. Adiantum is a large fern genus, and ecological studies in Amazonia have found that species identification is often difficult due to morphological similarity and overlapping characteristics among species. Although several hybrids have been described in tropical America, comprehensive studies investigating genetic exchanges in this genus are still lacking. We used chloroplast and nuclear phylogenomic data to examine evolutionary relationships among tropical American Adiantum species. By combining traditional phylogenetic analyses with advanced bioinformatic methods such as HybSeq-based target capture, reference-guided phasing (HybPhaser), and network-based analyses, we found widespread reticulate evolution involving both recent and ancient hybridization events. These were especially common among those species that have been difficult to delineate morphologically. Our findings indicate that reticulate evolution has played an important role in shaping the diversity of neotropical Adiantum, especially within the tetraphyllum lineage. Such widespread hybridization has no doubt contributed to morphological ambiguity and taxonomic challenges. Our integrated analytical approach provides a first attempt at untangling the reticulate evolutionary history in this group, and future studies with additional sampling can be expected to clarify the evolutionary processes further.

evolutionary biology↗

bioRxiv2025

A schizophrenia-associated radial glia cell state perturbs early human brain development

Multidisciplinary evidence support a neurodevelopmental origin for schizophrenia, yet the mechanistic translation of known risk factors remains poorly understood. In this study, we leverage multi-lineage, forebrain-patterned organoids derived from monozygotic twins discordant for schizophrenia, integrating single-cell transcriptomic and epigenomic profiling to uncover disease-associated gene expression and chromatin accessibility topics. By constructing fate probability maps, we identify an accelerated developmental trajectory emerging from a distinct, schizophrenia-associated radial glia cell state, and reveal unique interactions among schizophrenia risk genes through unbiased multimodal analyses. Further, we confirm that schizophrenia-enriched states persist in differentiated lineages and disrupt synaptic programs, accompanied by molecular and cellular phenotypes mimicking observed disease pathology. Collectively, our findings delineate an early disruption in forebrain development, providing novel mechanistic insights into the origins of schizophrenia risk.

neuroscience↗

bioRxiv2025

Long-chain polyphosphates induce glomerular microthrombi and exacerbate LPS-induced acute kidney injury in mouse

Polyphosphates are evolutionarily conserved anionic polymers mediating pleiotropic functions in eukaryotes and prokaryotes, depending on their chain-length. Bacteria typically synthetize long-chains, while human platelets harbour exclusively medium-chains. Polyphosphate-mediated lung and liver-injury have been reported in experimental mouse models but their effects on the kidney remain undefined. Here we assessed kidney histopathology and cytokine levels following intravenous administration of medium-chain (P100) and long-chain (P700) polyphosphates and their synergistic effects with lipopolysaccharides (LPS) in mice. We found that P700 induced albuminuria, renal Kim-1 and Lcn2 transcription, focal renal damage with glomerular microthrombi, tubular degeneration, granular phenotype of slit diaphragm components nephrin and ZO1, and enlarged electron dense vesicles in podocyte cytoplasm indicating lysosome swelling. P700 combined with LPS induced marked multifocal acute tubular necrosis in the cortex, and augmented LPS-induced proinflammatory cytokine levels. No notable effects were seen with P100, indicating that PolyP-mediated kidney injury development is dependent on chain-length. We conclude that long-chain polyphosphates may play a procoagulant role behind kidney injury, by inducing microthrombi characteristic of thrombotic microangiopathy and augmenting cytokine levels under inflammatory conditions.

pathology↗

bioRxiv2025

Parsing glomerular and tubular structure variability in high-throughput kidney organoid culture

High variability in stem cell research is a well-known limiting phenomenon, with technical variation across experiments and laboratories often surpassing variation caused by genotypic effects of induced pluripotent stem cell (iPSC) lines. Evaluation of kidney organoid protocols and culture conditions across laboratories remains scarce in the literature. We used the original air-medium interface protocol to evaluate kidney organoid success rate and reproducibility with several human iPSC lines, including a novel patient-derived GRACILE syndrome iPSC line. Organoid morphology was assessed with light microscopy and immunofluorescence-stained maturing glomerular and tubular structures. The protocol was further adapted to four microplate-based high-throughput approaches utilizing spheroid culture steps. Quantitative high-content screening analysis of the nephrin-positive podocytes and ECAD-positive tubular cells revealed that the choice of approach and culture conditions were significantly associated with structure development. The culture approach, iPSC line, experimental replication, and initial cell number explained 35-77% of the variability in the logit-transformed proportion of nephrin and ECAD-positive area, when fitted into multiple linear models. Our study highlights the benefits of high-throughput culture and multivariate techniques to better distinguishing sources of technical and biological variation in morphological analysis of organoids. Our microplate-based high-throughput approach is easily adaptable for other laboratories to combat organoid size variability.

developmental biology↗

bioRxiv2024

C9orf72 repeat expansion-carrying iPSC-microglia from FTD patients show increased phagocytic activity concomitantly with decreased number of autophagosomal-lysosomal vesicles

C9orf72 hexanucleotide repeat expansion (HRE) is a major genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia. The role of microglia in these C9orf72 HRE-associated diseases is understudied. To elucidate effects of C9orf72 HRE on microglia, we have characterized human induced pluripotent stem cell-derived microglia (iMG) from behavioral variant frontotemporal dementia (bvFTD) patients carrying the C9orf72 HRE. C9orf72 HRE iMG were compared to iMG from healthy controls and sporadic bvFTD patients. The phenotypes of iMG were analyzed using bulk RNA sequencing, biochemical and immunofluorescence analyses, and live cell imaging. C9orf72 HRE-carrying iMG showed nuclear RNA foci and poly-GP dipeptide repeat proteins but no decreased C9orf72 mRNA or protein expression. TDP-43 pathology was absent from all bvFTD iMG. As compared to healthy control iMG, quantitative immunofluorescence analyses indicated that all bvFTD iMG had reduced number, size, and intensity of LAMP2-A-positive vesicles. C9orf72 HRE-carrying iMG additionally showed decreased number, size, and intensity of p62/SQSTM1-positive vesicles. These changes were accompanied by increased phagocytic activity of the C9orf72 HRE-carrying iMG. Serum starvation increased phagocytic activity also in the iMG of sporadic bvFTD patients. RNA sequencing revealed that iMG of C9orf72 HRE-carrying bvFTD patients as compared to the iMG of sporadic bvFTD patients showed differential gene expression in pathways related to RNA and protein regulation and mitochondrial metabolism. Our data suggest potential alterations in the autophagosomal/lysosomal pathways in bvFTD patient iMG, which are further reinforced by the C9orf72 HRE and functionally manifest as increased phagocytic activity.

neuroscience↗

bioRxiv2024

Human iPSC-derived pericyte-like cells carrying APP Swedish mutation overproduce beta-amyloid and induce cerebral amyloid angiopathy-like changes

Alzheimers disease (AD) patients often exhibit cerebral amyloid angiopathy (CAA), i.e beta-amyloid (A{beta}) accumulation within cerebral blood vessels causing cerebrovascular dysfunction. Pericytes wrap around vascular capillaries, thus regulating cerebral blood flow, angiogenesis, and vessel stability. Vascular dysfunction can promote the development and progression of neurodegenerative diseases, yet the specific contribution of pericytes to AD pathology remains unclear. Here we show that human induced pluripotent stem cell (iPSC)-derived pericyte-like cells (iPLCs) can generate A{beta} peptides, and that the cells carrying Swedish mutation in amyloid precursor protein (APPswe) secrete 10 times more A{beta}1-42 than the control cells. Additionally, APPswe iPLCs have an impaired capacity to support angiogenesis and barrier integrity, exhibit a prolonged contractile response, and produce increased levels of pro-inflammatory cytokines upon inflammatory stimulation. These functional alterations in APPswe iPLCs are accompanied by transcriptional upregulation of actin cytoskeleton and extracellular matrix organization-related genes. Therefore, the APPswe mutation in iPLCs recapitulates several features of CAA pathology in vitro. Our iPSC-based vascular cell model may thus serve as a platform for drug discovery targeting vascular dysfunction in AD.

cell biology↗

bioRxiv2023

Astrocytes regulate neuronal network burst frequency through NMDA receptors species- anddonor-specifically

BackgroundDevelopment of synaptic activity is a neuronal key characteristic that relies largely on interactions between neurons and astrocytes. Although astrocytes have known roles in regulating synaptic function and malfunction, the use of human or donor-specific astrocytes in disease models is still rare. Rodent astrocytes are routinely used to enhance neuronal activity in cell cultures, but less is known how human astrocytes influence neuronal activity. MethodsWe established human induced pluripotent stem cell (hiPSC)-derived neuron-astrocyte co-cultures and studied their functional development on microelectrode array (MEA). We used cell lines from 5 neurotypical control individuals and 3 pairs of monozygotic twins discordant for schizophrenia. A method combining Ngn2 overexpression and dual SMAD inhibition was used for neuronal differentiation. The neurons were co-cultured with hiPSC-derived astrocytes differentiated from 6-month-old astrospheres or rat astrocytes. ResultsWe found that the hiPSC-derived co-cultures develop complex network bursting activity similarly to neuronal co-cultures with rat astrocytes. However, the effect of NMDA receptors on neuronal network burst frequency (NBF) differed between co-cultures containing human or rat astrocytes. By using co-cultures derived from patients with schizophrenia and unaffected individuals, we found lowered NBF in the affected cells. We continued to demonstrate how astrocytes from an unaffected individual rescue the lowered NBF in the affected neurons by increasing NMDA receptor activity. ConclusionsOur results indicate that astrocytes participate in the regulation of neuronal NBF through a mechanism involving NMDA receptors. These findings shed light on the importance of using human and donor-specific astrocytes in disease modeling.

neuroscience↗

bioRxiv2023

Kynurenic acid promotes activity-dependent synaptic pruning in schizophrenia

Schizophrenia is a neurodevelopmental disorder characterized by an excessive loss of synapses. Recent data suggest that this is due to increased microglia-mediated synaptic pruning. Here, we utilize human induced pluripotent stem cell-derived models to show that kynurenic acid (KYNA), an endogenous NMDA-receptor antagonist observed to be increased in the brains of individuals with schizophrenia, reduces neuronal activity and promote microglial uptake of synapses. In a human brain organoid model, we confirm reduced microglia-mediated synaptic pruning upon inhibiting the endogenous KYNA production. To verify our experimental data in a clinical context, we integrate large-scale transcriptomic and genetic datasets and show that KYNA-producing kynurenine aminotransferases (KATs) enrich for genes governing synaptic activity and genetic risk variants for schizophrenia. Together, these results link genetic risk variants for schizophrenia to elevated production of KYNA and excessive activity-dependent synaptic pruning, while implicating pharmacological inhibition of KATs as a strategy to avoid synapse loss in schizophrenia.

neuroscience↗

bioRxiv2023

Air-liquid interface culture of midbrain organoids improves neuronal functionality and integration of microglia

Midbrain organoids derived from human induced pluripotent stem cells have emerged as a promising in vitro model for studying the molecular and cellular mechanisms in Parkinsons disease. However, the absence of microglia and the development of a necrotic core in mature organoids have remained key limitations on their utility as functional models of the human midbrain. Here we propose a novel methodology for extended cultivation of midbrain organoid slices, which involves the incorporation of microglia and utilizes an air-liquid culture system. Compared to conventional whole organoids, we found that our model increased the efficacy and consistency of the integration of microglia progenitors. Using single-cell RNA sequencing, we showed that organoid slices maturated in ALI give rise to astrocytes and oligodendrocyte progenitors. Furthermore, the cultivation in air-liquid interface greatly improved neuronal functionality in response to stimulation by NMDA. This stimulation consistently induced robust and stable network activity evaluated by microelectrode array recording. Our newly developed midbrain organoid model with its improved cell type composition and neuronal functionality has potential applications in basic research of Parkinsons disease and in the development of therapeutics. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/561672v1_ufig1.gif" ALT="Figure 1"> View larger version (99K): org.highwire.dtl.DTLVardef@4c8672org.highwire.dtl.DTLVardef@ed3a8org.highwire.dtl.DTLVardef@169bebaorg.highwire.dtl.DTLVardef@168a81c_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2023

Species-specific metabolic reprogramming in human and mouse microglia during inflammatory pathway induction

Metabolic reprogramming is a hallmark of the immune cells in response to inflammatory stimuli. This metabolic process involves a switch from oxidative phosphorylation (OXPHOS) to glycolysis, or alterations in other metabolic pathways. However, most of the experimental findings have been acquired in murine immune cells and little is known about the metabolic reprogramming of human microglia. In this study, we investigated the transcriptomic and metabolic profiles of mouse and iPSC-derived human microglia challenged with the TLR4 agonist LPS. We found that both species displayed a metabolic shift and an overall increased glycolytic gene signature in response to LPS treatment. The metabolic reprogramming was characterized by the upregulation of hexokinases in mouse microglia and phosphofructokinases in human microglia. This study provides the first direct comparison of energy metabolism between mouse and human microglia, highlighting the species-specific pathways involved in immunometabolism and the importance of considering these differences in translational research.

cell biology↗

bioRxiv2022

SARS-CoV-2 infection of human neurons requires endosomal cell entry and can be blocked by inhibitors of host phosphoinositol-5 kinase

COVID-19 is a disease caused by coronavirus SARS-CoV-2. In addition to respiratory illness, COVID-19 patients exhibit neurological symptoms that can last from weeks to months (long COVID). It is unclear whether these neurological manifestations are due to infection of brain cells. We found that a small fraction of cortical neurons, but not astrocytes, were naturally susceptible to SARS-CoV-2. Based on the inhibitory effect of blocking antibodies, the infection seemed to depend on the receptor angiotensin-converting enzyme 2 (ACE2), which was expressed at very low levels. Although only a limited number of neurons was infectable, the infection was productive, as demonstrated by the presence of double-stranded RNA in the cytoplasm (the hallmark of viral replication), abundant synthesis of viral late genes localized throughout the neuronal cell, and an increase in viral RNA in the culture medium within the first 48 h of infection (viral release). The productive entry of SARS-CoV-2 requires the fusion of the viral and cellular membranes, which results in the delivery of viral genome into the cytoplasm of the target cell. The fusion is triggered by proteolytic cleavage of the viral surface protein spike, which can occur at the plasma membrane or from endo/lysosomes. Using specific combinations of small-molecule inhibitors, we found that SARS-CoV-2 infection of human neurons was insensitive to nafamostat and camostat, which inhibit cellular serine proteases found on the cell surface, including TMPRSS2. In contrast, the infection was blocked by apilimod, an inhibitor of phosphatidyl-inositol 5 kinase (PIK5K) that regulates endosomal maturation. ImportanceCOVID-19 is a disease caused by coronavirus SARS-CoV-2. Millions of patients display neurological symptoms, including headache, impairment of memory, seizures and encephalopathy, as well as anatomical abnormalities such as changes in brain morphology. Whether these symptoms are linked to brain infection is not clear. The mechanism of the virus entry into neurons has also not been characterized. Here we investigated SARS-CoV-2 infection using a human iPSC-derived neural cell model and found that a small fraction of cortical neurons was naturally susceptible to infection. The infection depended on the ACE2 receptor and was productive. We also found that the virus used the late endosomal/lysosomal pathway for cell entry and that the infection could be blocked by apilimod, an inhibitor of the cellular phosphatidyl-inositol 5 kinase.

neuroscience↗

bioRxiv2022

Microglial amyloid beta clearance is driven by PIEZO1 channels

BackgroundMicroglia are the endogenous immune cells of the brain and act as sensors of pathology to maintain brain homeostasis and eliminate potential threats. In Alzheimers disease (AD), toxic amyloid beta (A{beta}) accumulates in the brain and forms stiff plaques. In late-onset AD accounting for 95% of all cases, this is thought to be due to reduced clearance of A{beta}. Human genome-wide association studies and animal models suggest that reduced clearance results from aberrant function of microglia. While the impact of neurochemical pathways on microglia have been broadly studied, mechanical receptors regulating microglial functions remain largely unexplored. MethodsHere we showed that a mechanotransduction ion channel, PIEZO1, is expressed and functional in human and mouse microglia. We used a small molecule agonist, Yoda1, to study how activation of PIEZO1 affects AD-related functions in human induced pluripotent stem cell (iPSC) -derived microglia-like cells (iMGL) under controlled laboratory experiments. Cell survival, metabolism, phagocytosis and lysosomal activity were assessed using real-time functional assays. To evaluate the effect of activation of PIEZO1 in vivo, 5-month-old 5xFAD male mice were infused daily with Yoda1 for two weeks through intracranial cannulas. Microglial Iba1 expression and A{beta} pathology were quantified with immunohistochemistry and confocal microscopy. Published human and mouse AD datasets were used for in-depth analysis of PIEZO1 gene expression and related pathways in microglial subpopulations. ResultsWe show that PIEZO1 orchestrates A{beta} clearance by enhancing microglial survival, phagocytosis, and lysosomal activity. A{beta} inhibited PIEZO1-mediated calcium transients, whereas activation of PIEZO1 with a selective agonist, Yoda1, improved microglial phagocytosis resulting in A{beta} clearance both in human and mouse models of AD. Moreover, PIEZO1 expression was associated with a unique microglial transcriptional phenotype in AD as indicated by assessment of cellular metabolism, and human and mouse single cell datasets. ConclusionThese results indicate that the compromised function of microglia in AD could be improved by controlled activation of PIEZO1 channels resulting in alleviated A{beta} burden. Pharmacological regulation of these mechanoreceptors in microglia could represent a novel therapeutic paradigm for AD. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=176 HEIGHT=200 SRC="FIGDIR/small/484831v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@832eadorg.highwire.dtl.DTLVardef@6d8719org.highwire.dtl.DTLVardef@c09740org.highwire.dtl.DTLVardef@9fa85_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2020

Microglia orchestrate neuronal activity in brain organoids

Human stem cell-derived brain organoids provide a physiologically relevant in vitro 3D brain model for studies of neurological development that are unique to the human nervous system. Prior studies have reported protocols that support the maturation of microglia from mesodermal progenitors leading to innately developing microglia within the organoids. However, although microglia are known to support neuronal development in rodents, none of the previous studies have reported what is the impact of microglia on neuronal growth and maturation in human brain organoids. Here we show that incorporating microglial progenitors into the developing organoid supports neuronal maturation, the emergence of neurons capable of firing repetitive action potentials and the appearance of synaptic and neuronal bursting activity. Immunocompetent organoids enable experimental strategies for interrogating fundamental questions on microglial and neuronal diversity and function during human brain development.

neuroscience↗

bioRxiv2020

Patient iPSC-astrocytes show transcriptional and functional dysregulation in schizophrenia

Human astrocytes are multifunctional brain cells and may contribute to the pathophysiology of schizophrenia (SCZ). We differentiated astrocytes from induced pluripotent stem cells of monozygotic twins discordant for SCZ, and found sex-specific gene expression and signaling pathway alterations related particularly to inflammation and synaptic functions. While Ingenuity Pathway Analysis identified SCZ disease and synaptic transmission pathway changes in SCZ astrocytes, the most consistent findings were related to collagen and cell adhesion associated pathways. Neuronal responses to glutamate and GABA differed between astrocytes from control persons, affected twins, and their unaffected co-twins, and were normalized by clozapine treatment. SCZ astrocyte cell transplantation to the mouse forebrain caused gene expression changes in demyelination, synaptic dysfunction and inflammation pathways of mouse brain cells and resulted in behavioral changes in cognitive and olfactory functions. Altogether, our results show that astrocytes contribute to both familial risk and clinical manifestation of SCZ in a sex-specific manner.

neuroscience↗

bioRxiv2020

Molecular signaling pathways underlying schizophrenia

The molecular pathophysiological mechanisms underlying schizophrenia have remained unknown, and no treatment exists for primary prevention. Studies using stem cell-derived neurons have investigated differentially expressed genes (DEGs) and GO and KEGG pathways between patients and controls, but not analyzed data-driven causal molecular pathways involved. We used Ingenuity Pathway Analysis (IPA) to analyze canonical and causal pathways in two different datasets, including patients from Finland and USA. The most significant findings in canonical pathway analysis were observed for glutamate receptor signaling, hepatic fibrosis, and glycoprotein 6 (GP6) pathways in the Finnish dataset, and GP6 and hepatic fibrosis pathways in the US dataset. In data-driven causal pathways, ADCYAP1, ADAMTS, and CACNA genes were involved in the majority of the top 10 pathways differentiating patients and controls in both Finnish and US datasets. In contrast, no dopamine-specific genes were consistently involved. Results from a Finnish nation-wide database showed that the risk of schizophrenia relapse was 41% lower among first-episode patients during the use of losartan, the master regulator of an ADCYAP1, ADAMTS, and CACNA -related pathway, compared to those time periods when the same individual did not use the drug. This association was not attributable to general adherence to drug treatments. The results from the two independent datasets suggest that the GP6 signaling pathway, and the ADCYAP1, ADAMTS, and CACNA -related purine, oxidative stress, and glutamatergic signaling pathways are primary pathophysiological alterations in schizophrenia among patients with European ancestry. While no reproducible dopaminergic alterations were observed, the results imply that agents such as losartan, and ADCYAP1/PACAP -deficit alleviators, such as metabotropic glutamate 2/3 agonist MGS0028 and 5-HT7 antagonists - which have shown beneficial effects in an experimental Adcyap1-/- mouse model for schizophrenia - could be potential treatments before the full manifestation of illness involving dopaminergic abnormalities.

neuroscience↗