Biology subjects

Schwab, M.

Publications and source records attributed to Schwab, M..

15 recordsLinked to original sources

bioRxiv2024

Focal persistence and phylodynamics of Heartland virus in Georgia

Heartland virus (HRTV) is an emerging tick-bone virus associated with severe illness in the U.S. There are large gaps in knowledge of HRTV diversity, evolution, and transmission due to a paucity of HRTV-positive samples and genome sequences. We identified a focal site of HRTV- positive Amblyomma americanum ticks in central Georgia and developed a novel multiplex- amplicon sequencing assay to generate full HRTV genome sequences. By screening over 21,000 field-collected ticks from 2021-2023, we identified six positive pools. Five were collected from the site in central Georgia where our group first detected HRTV-positive ticks in 2019, and one from a site in western Georgia approximately 175 km away. The HRTV genome sequences from Georgia were highly related, even across this distance and over five years. Reference HRTV genome sequences from across the U.S. were also geographically clustered. Time-scaled phylogenetic analysis suggested recent spread of HRTV in the U.S., with all available sequences sharing a common ancestor within the last 300 years, and sequences from Georgia sharing a common ancestor within the last 40 years. Our observed spatial clustering of HRTV and the high degree of genetic conservation in our persistent focus suggest the importance of small spatial dynamics in HRTV transmission ecology. Author SummaryHeartland virus (HRTV) was first discovered in humans in 2009 and has since caused over 60 cases of severe and fatal disease in the United States. HRTV is transmitted by the lone star tick, Amblyomma americanum, across the Southeast, East coast, and Midwest. Little information is known about how this virus circulates and changes across time and space due to a lack of genetic data. Here, we created a new procedure to generate more genetic sequence data for HRTV and collected over 21,000 ticks to screen for HRTV across three years in Georgia. We generated 6 new HRTV sequences and compared them to existing sequences from our group in Georgia, and across the country, finding evidence of regional clustering of HRTV and highly related HRTV across time in Georgia. Our analyses additionally found that this virus was likely introduced to the U.S. in the last 300 years. Our study provides new context and information in understanding the landscape and transmission of HRTV in the U.S.

genomics↗

bioRxiv2024

Onco-fetal protein Nogo-A restricts human and mouse glioma vascularization and growth via VEGF-Notch-hippo-metabolic signaling

Glioblastoma is one of the most deadly human cancers characterized by high degrees of vascularization, but targeting its vasculature has resulted in very limited success so far. Angiogenesis, the growth of new blood vessels, is highly dynamic during brain development, enters a mostly quiescent state in the adult homeostatic brain, and is reactivated in vascular-dependent CNS diseases including brain tumors. In consequence, a better understanding of the relevance of the onco-fetal axis - describing the reactivation of fetal signaling programs in tumors - in endothelial- and perivascular cells of the human brain tumor vasculature harbors great translational potential, yet remains poorly defined. In development, neurovascular link (NVL) molecules guide both neuronal growth cones as well as capillary endothelial tip cells. Nogo-A is an NVL molecule known to inhibit axonal growth in the developing and adult CNS and to restrict angiogenesis during brain development, but its role in the mouse and human brain tumor vasculature along the onco-fetal axis remains unknown. Here, we characterize Nogo-A as an onco-fetal protein expressed in the neurovascular unit (NVU) in human fetal brains and human gliomas in vivo that negatively regulates sprouting angiogenesis and endothelial tip cells in glioma vascularization. The Nogo-A-specific Delta 20 domain restricts angiogenic sprouting and branching and promotes vascular normalization while inhibiting glioma growth in experimental gliomas. Moreover, Nogo-A expression in tumor cells negatively correlate/s with glioma malignancy in vivo. In vitro, Nogo-A Delta 20 reduced human brain- and brain tumor endothelial cell (HBMVEC, HBTMVEC) and human umbilical vein endothelial cell (HUVEC) spreading, migration, and sprouting, in a dose-dependent manner and inhibited filopodia extension glucose metabolism. Mechanistically, RNA sequencing of Nogo-A Delta 20-treated HBMVECs and HBTMVECs revealed Nogo-A Delta 20-induced positive regulation of the angiogenesis-inhibiting Dll4-Notch-pathway and inhibition of the angiogenesis-promoting VEGF-VEGFR and Hippo-YAP-TAZ pathways, whereas metabolomics and functional metabolic assays revealed Nogo-A Delta 20-induced negative regulation of endothelial glycolysis in HBMVECs and HBTMVECs. These findings characterize Nogo-A as an onco-fetal protein in the human glial brain tumor vasculature and identify Nogo-A Delta 20 signaling as an important negative regulator of human glioma vascularization and growth. Enhancing Nogo-A signaling may be an attractive alternative or combinatorial anti-angiogenic therapy to restrict human glioma/glioblastoma vascularization and growth.

neuroscience↗

bioRxiv2023

mitoBKCa is functionally expressed in murine and human breast cancer cells and promotes metabolic reprogramming

Alterations in the function of K+ channels such as the voltage- and Ca2+ activated K+ channel of large conductance (BKCa) reportedly promote breast cancer (BC) development and progression. Underlying molecular mechanisms remain, however, elusive. Here, we provide electrophysiological evidence for a BKCa splice variant localized to the inner mitochondrial membrane of murine and human BC cells (mitoBKCa). Through a combination of genetic knockdown and knockout along with cell permeable BKCa channel blocker, we show that mitoBKCa modulates overall cellular and mitochondrial energy production and mediates the metabolic rewiring referred to as the "Warburg effect", thereby promoting BC cell proliferation in the presence and absence of oxygen. Additionally, we detect mitoBKCa and BKCa transcripts in low or high abundance, respectively, in clinical BC specimens. Together, our results emphasize, that targeting mitoBKCa could represent a treatment strategy for selected BC patients in future.

cancer biology↗

bioRxiv2023

Development of an optimized, non-stem cell line for intranasal delivery of therapeutic cargo to the central nervous system

Neural stem cells (NSC) are considered to be valuable candidates for delivering a variety of anti-cancer agents to brain tumors, including oncolytic viruses. However, owing to the previously reported tumorigenic potential of NSC cell line after intranasal administration (INA), here we identified the human hepatic stellate cell line (LX-2) as a cell type capable of longer resistance to replication of oncolytic adenoviruses (OAV) as therapeutic cargo, and being non-tumorigenic after INA. Our data show that LX-2 cells can longer withstand the OAV XVir-N-31 replication and oncolysis than NSCs. By selecting the highly migratory cell population out of LX-2, an offspring cell line with a higher and more stable capability to migrate was generated. Additionally, as a safety backup, we applied genomic HSV-TK integration into LX-2 leading to the high vulnerability to Ganciclovir. Histopathological analyses confirmed the absence of neoplasia in the respiratory tracts and brains of immuno-compromised mice 3 months after INA of LX-2 cells. Our data suggest that LX-2 is a novel robust and safe cell line for delivering anti-cancer and other therapeutic agents to the brain.

molecular biology↗

bioRxiv2023

Dnmt3a1 regulates hippocampus-dependent memory via the downstream target Nrp1

Epigenetic factors are well established players in memory formation. Specifically, DNA methylation is necessary for the formation of long-term memory in multiple brain regions including the hippocampus. Despite the demonstrated role for DNA methyltransferases (Dnmts) in memory formation, it is unclear whether individual Dnmts have unique or redundant functions in long-term memory formation. Furthermore, the downstream processes controlled by Dnmts during memory consolidation have not been investigated. In this study, we demonstrated that Dnmt3a1, the predominant Dnmt in the adult brain, is required for long-term spatial object recognition and contextual fear memory. Using RNA-sequencing, we identified an activity-regulated Dnmt3a1-dependent genomic program in which several genes were associated with functional and structural plasticity. Furthermore, we found that some of the identified genes are selectively dependent on Dnmt3a1, but not its isoform Dnmt3a2. Specifically, we identified Neuropilin 1 (Nrp1) as a downstream target of Dnmt3a1 and further demonstrated the involvement of Nrp1 in hippocampus-dependent memory formation. Importantly, we found that Dnmt3a1 regulates hippocampus-dependent memory via Nrp1. In contrast, Nrp1 overexpression did not rescue memory impairments triggered by reduced Dnmt3a2 levels. Taken together, our study uncovered a Dnmt3a-isoform-specific mechanism in memory formation, identified a novel regulator of memory, and further highlighted the complex and highly regulated functions of distinct epigenetic regulators in brain function.

neuroscience↗

bioRxiv2021

Molecular atlas of the human brain vasculature at the single-cell level

A broad range of brain pathologies critically relies on the vasculature, and cerebrovascular disease is a leading cause of death worldwide. However, the cellular and molecular architecture of the human brain vasculature remains poorly understood. Here, we performed single-cell RNA sequencing of 599,215 freshly isolated endothelial, perivascular and other tissue-derived cells from 47 fetuses and adult patients to construct a molecular atlas of the developing fetal, adult control and diseased human brain vasculature. We uncover extensive molecular heterogeneity of healthy fetal and adult human brains and across eight vascular-dependent CNS pathologies including brain tumors and brain vascular malformations. We identify alteration of arteriovenous differentiation and reactivated fetal as well as conserved dysregulated pathways in the diseased vasculature. Pathological endothelial cells display a loss of CNS-specific properties and reveal an upregulation of MHC class II molecules, indicating atypical features of CNS endothelial cells. Cell-cell interaction analyses predict numerous endothelial-to-perivascular cell ligand-receptor crosstalk including immune-related and angiogenic pathways, thereby unraveling a central role for the endothelium within brain neurovascular unit signaling networks. Our single-cell brain atlas provides insight into the molecular architecture and heterogeneity of the developing, adult/control and diseased human brain vasculature and serves as a powerful reference for future studies.

neuroscience↗

bioRxiv2020

Nucleolin is expressed in human fetal brain development and reactivated in human glial brain tumors regulating angiogenesis and vascular metabolism

Glioblastoma (GBM) is amongst the deadliest human cancers and is characterized by high levels of vascularisation. Angiogenesis is highly dynamic during brain development and almost quiescent in the adult brain, but is reactivated in vascular-dependent CNS pathologies such as brain tumors. Nucleolin (NCL) is a known regulator of cell proliferation and angiogenesis, but its roles on physiological and pathological brain vasculature remain unknown. Here, we studied the expression of Nucleolin in the neurovascular unit (NVU) in human fetal brains and human gliomas in vivo as well as its effects on sprouting angiogenesis and endothelial metabolism in vitro. Nucleolin is highly expressed in endothelial- and perivascular cells during brain development, downregulated in the adult brain, and upregulated in glioma. Moreover, Nucleolin expression in tumor- and blood vessel cells correlated with glioma malignancy in vivo. In culture, siRNA-mediated NCL knockdown reduced human umbilical vein endothelial cell (HUVEC) sprouting angiogenesis, proliferation and filopodia extension, and reduced glucose metabolism. Mechanistically, RNA sequencing of Nucleolin knockdown in HUVECs revealed a putative p53-TIGAR-HK2 regulation of endothelial glycolysis. These findings identify Nucleolin as a neurodevelopmental factor reactivated in glioma that positively regulates sprouting angiogenesis and endothelial metabolism. Our findings have important implications in therapeutic targeting of glioma.

neuroscience↗

bioRxiv2020

A mosaic renal myeloid subtype with T-cell inhibitory and protumoral features is linked to immune escape and survival in clear cell renal cell cancer

Mononuclear phagocytes moderate tissue repair, immune activation and tolerance. In the renal tubulo-interstitium specialized dendritic cells help maintain homeostasis and protect tubuli from immune injury. Human renal cell carcinoma (RCC) is immunogenic; yet immunotherapies that target T-cell dysfunction show limited clinical efficacy suggesting additional mechanisms of immunoinhibiton. We previously described "enriched-in-renal cell carcinoma" (erc)DCs that are often found in tight contact with T cells which are dysfunctional. Here we describe that ercDCs exhibit a distinct polarization state imparted by tissue-specific signals characteristic for RCC and renal tissue homeostasis. The resulting mosaic transcript signature includes features associated with host defense activity, angiogenesis/invasion and T-cell inhibition. An ercDC-specific profile was predictive for patient survival and suggests potential therapeutic targets for improved immunotherapy. SignificanceImmunotherapies, which re-invigorate T-cell activity, achieve clinical responses in subsets of patients only revealing additional layers of T-cell inhibition. Mononuclear phagocytes can be immunoinhibitory. But, they are highly plastic and repolarization may be possible if key programming molecules can be identified, potentially enabling antitumor responses in tumors refractory to checkpoint blockade. We describe a myeloid cell type with mosaic feature including tumor-promotion and immunoinhibition in human clear cell renal cell carcinoma. Observed tight contacts with T cells may translate into T-cell dysfunction. A high ercDC score in tumor tissue correlates with poor patient survival suggesting ercDCs as targets for therapeutic intervention. Targeting molecules that are identified in the ercDC profile may expand the range of patients effectively treated by immunotherapy. HighlightsBullet points: O_LIRenal cell carcinoma (ccRCC) harbors polarized mosaic myeloid cells (ercDCs) C_LIO_LIercDCs are found in contact with dysfunctional T cells in ccRCC C_LIO_LIercDCs express novel immunoinhibitory proteins C_LIO_LIHigh ercDC z-score in ccRCC tissue correlates with poor patient survival C_LI

immunology↗

bioRxiv2020

Fine-scale genomic analyses of admixed individuals reveal unrecognized genetic ancestry components in Argentina

Similarly to other populations across the Americas, Argentinean populations trace back their genetic ancestry into African, European and Native American ancestors, reflecting a complex demographic history with multiple migration and admixture events in pre- and post-colonial times. However, little is known about the sub-continental origins of these three main ancestries. We present new high-throughput genotyping data for 87 admixed individuals across Argentina. This data was combined to previously published data for admixed individuals in the region and then compared to different reference panels specifically built to perform population structure analyses at a sub-continental level. Concerning the Native American ancestry, we could identify four Native American components segregating in modern Argentinean populations. Three of them are also found in modern South American populations and are specifically represented in Central Andes, Central Chile/Patagonia, and Subtropical and Tropical Forests geographic areas. The fourth component might be specific to the Central Western region of Argentina, and it is not well represented in any genomic data from the literature. As for the European and African ancestries, we confirmed previous results about origins from Southern Europe, Western and Central Western Africa, and we provide evidences for the presence of Northern European and Eastern African ancestries. Author SummaryThe human genetic diversity in Argentina reflects demographic processes during which the European colonists invaded a territory where Native American populations were settled. During the colonial period, the slave trade also prompted many African people to move to Argentina. Little is known about the origins of these three continental ancestry components in Argentinean populations nowadays. Genotyping data for 87 admixed individuals throughout Argentina was generated and data from the literature was re-analyzed to shed light on this question. We confirmed that most of the European genetic ancestry comes from the South, although several individuals are related to Northern Europeans. We confirmed that the African origins in Argentina mainly trace back from Western and Central/Western regions, and we document some proportion of Eastern African origins poorly described before. As for the Native American ancestry, we identified that it can be divided into four main components that correspond to Central Chile/Patagonia, Subtropical and Tropical Forests, Central Andes and Central Western region of Argentina. In order to understand the specificity of the genetic diversity in Argentina, more effort is required to generate specific massive genomic knowledge at the local level.

genetics↗

bioRxiv2019

Interaction of YAP with the Myb-MuvB (MMB) complex defines a transcriptional program to promote the proliferation of cardiomyocytes

The Hippo signalling pathway and its central effector YAP regulate proliferation of cardiomyocytes and growth of the heart. Using genetic models in mice we show that the increased proliferation of cardiomyocytes due to loss of the Hippo-signaling component SAV1 depends on the Myb-MuvB (MMB) complex. Similarly, proliferation of postnatal cardiomyocytes induced by constitutive active YAP requires MMB. Genome studies revealed that YAP and MMB regulate an overlapping set of cell cycle genes in cardiomyocytes. We find that YAP binds directly to B-MYB, a subunit of MMB, in a manner dependent on the YAP WW domains and a PPXY motif in B-MYB. Disruption of the interaction by overexpression of the YAP binding domain of B-MYB strongly inhibits the proliferation of cardiomyocytes. Our results point to MMB as a critical downstream effector of YAP in the control of cardiomyocyte proliferation.

molecular biology↗

bioRxiv2019

Short-term oxaliplatin exposure according to established hyperthermic intraperitoneal chemotherapy (HIPEC) protocols lacks effectiveness in vitro and ex vivo

Cytotoxicity of oxaliplatin-containing solutions (OCS), sampled during patient treatment with hyperthermic intraperitoneal chemotherapy (HIPEC), was assessed by well-established continuous impedance-based real-time cell analysis (RTCA) ex vivo. HIPEC treatment was replicated by exposing OAW-42 cancer cells to OCS for 30 or 60 minutes at 42 {degrees}C. In contrast to previous observations with continuous exposure, where cytotoxicity was proven, identical OCS obtained during HIPEC did not induce cell death reproducibly and showed strongly attenuated effects after only 30 minutes of application. Based on these unexpected findings, spike-ins of oxaliplatin (OX) into peritoneal dialysis solution (PDS) or dextrose 5 % in water (D5W) were used to replicate HIPEC conditions, as used in either our own protocols or the recently presented randomized controlled PRODIGE 7 trial, where OX HIPEC for 30 minutes failed to produce survival benefits in colorectal carcinoma patients. With OX-spiked into D5W or PDS at identical concentrations as used for PRODIGE 7 or conforming with own HIPEC protocols, we did not observe the expectable cytotoxic effects in RTCA, after replicating OX HIPEC for 30 minutes. These results were corroborated for both solvents at relevant drug concentrations by classical end-point assays for cytotoxicity in two cancer cell lines. Further results suggest that penetration depth, drug dosage, exposure time and drug solvents may constitute critical factors for HIPEC effectiveness. Accordingly, we witnessed substantial cell shrinkage with both PDS and D5W, potentially contributing to reduced drug effects. Based on these results, intensified pharmacological research seems warranted to establish effective HIPEC protocols.\n\nKey PointsO_LIOxaliplatin (OX)-containing solutions obtained during patient treatment with Hyperthermic intraperitoneal chemotherapy (HIPEC) unexpectedly showed low cytotoxicity in an impedance-based ex vivo cytotoxicity cell assay.\nC_LIO_LIOX cytotoxicity under HIPEC conditions could be enhanced by extending drug exposure to one hour by an impedance-based ex vivo cytotoxicity cell assay.\nC_LIO_LIHIPEC failed to show survival benefits in the randomized controlled PRODIGE 7 trial and was questioned in the aftermath.\nC_LIO_LIClinically relevant OX concentrations applied in conjunction with hyperthermia (42 {degrees}C) for 30 minutes, as used either at our own medical center or according to the PRODIGE 7 trial, proved predominantly ineffective, when used according to HIPEC routines in an impedance-based in vitro cytotoxicity cell assay.\nC_LIO_LIRespective findings were corroborated in two different cell lines and by two established end-point assays, showing that 50 % cell death could not be reached by the same HIPEC treatment with OX, in contrast to continuous drug exposure.\nC_LIO_LIAs potentially relevant factor, the thickness of the exposed cell layer was identified, requiring at least ~100 {micro}m penetration depth for our model to indicate effectiveness.\nC_LIO_LIAdditionally, we show relevant cell shrinkage by two drug diluents used either at our own medical center or according to the PRODIGE 7 trial, potentially associated with fluid shifts out of the cell and impaired drug effects.\nC_LIO_LIOur own as well as recent findings by Ubink et al. (Br J Surg. 2019. doi: 10.1002/bjs.11206) support the notion that lacking effectiveness of OX HIPEC may explain the negative PRODIGE 7 trial results.\nC_LI

pharmacology and toxicology↗

bioRxiv2018

Higher transcriptome stability during aging in long-lived giant mole-rats compared to short-lived rats

Many aging-associated physiological changes are known to come up in short- and long-lived species with a different trajectory and emerging evidence suggests that large parts of life history trait differences between species are based on inter-species variation in gene expression. Little information is yet available, however, about transcriptome changes during aging when comparing mammals with different lifespans. For this reason, we studied the transcriptomes of five tissues and two age cohorts in two similar sized rodent species with very different lifespans: rat (Rattus norvegicus) and giant mole-rat (Fukomys mechowii) with maximum lifespans of 3.8 and >20 years, respectively. Our results show that giant mole-rats exhibit higher transcriptome stability during aging than the rat. While well-known aging signatures (e.g. up-regulation of pro-inflammatory genes) were detected in all rat tissues, they showed up only in one giant mole-rat tissue. Furthermore, many differentially expressed genes that were found in both species, were regulated in opposite directions during aging. This suggests that expression changes that cause aging in short-lived species are counteracted in long-lived species. Taken together, transcriptome stability may be one key causal factor of the long life- and healthspan of giant mole-rats and maybe of African mole-rats in general.

systems biology↗

bioRxiv2017

Long-lived rodents reveal signatures of positive selection in genes associated with lifespan and eusociality

The genetic mechanisms that determine lifespan are poorly understood. Most research has been done on short lived animals and it is unclear if these insights can be transferred to long-lived mammals like humans. Some African mole-rats (Bathyergidae) have life expectancies that are multiple times higher than similar sized and phylogenetically closely related rodents. We obtained genomic and transcriptomic data from 17 rodent species and systematically scanned eleven lineages associated with the evolution of longevity and eusociality for positively selected genes (PSGs). The set of 319 PSGs contains regulators of mTOR and is enriched in functional terms associated with (i) processes that are regulated by the mTOR pathway, e.g. translation, autophagy and mitochondrial biogenesis, (ii) the immune system and (iii) antioxidant defense. Analyzing gene expression of PSGs during aging in the long-lived naked mole-rat and up-regulation in the short-lived rat, we found a pattern fitting the antagonistic pleiotropy theory of aging.

evolutionary biology↗

bioRxiv2017

Effects of Prenatal Stress on Structural Brain Development and Aging in Humans

Healthy brain aging is a major determinant of quality of life, allowing integration into society at all ages. Human epidemiological and animal studies indicate that in addition to lifestyle and genetic factors, environmental influences in prenatal life have a major impact on brain aging and age-associated brain disorders. The aim of this review is to summarize the existing literature on the consequences of maternal anxiety, stress, and malnutrition for structural brain aging and predisposition for age-associated brain diseases, focusing on studies with human samples. In conclusion, the results underscore the importance of a healthy mother-child relationship, starting in pregnancy, and the need for early interventions if this relationship is compromised.

neuroscience↗

bioRxiv2017

Genetic variation in human drug-related genes

Variability in drug efficacy and adverse effects are observed in clinical practice. While the extent of genetic variability in classical pharmacokinetic genes is rather well understood, the role of genetic variation in drug targets is typically less studied. Based on 60,706 human exomes from the ExAC dataset, we performed an in-depth computational analysis of the prevalence of functional-variants in in 806 drug-related genes, including 628 known drug targets. We find that most genetic variants in these genes are very rare (f < 0.1%) and thus likely not observed in clinical trials. Overall, however, four in five patients are likely to carry a functional-variant in a target for commonly prescribed drugs and many of these might alter drug efficacy. We further computed the likelihood of 1,236 FDA approved drugs to be affected by functional-variants in their targets and show that the patient-risk varies for many drugs with respect to geographic ancestry. A focused analysis of oncological drug targets indicates that the probability of a patient carrying germline variants in oncological drug targets is with 44% high enough to suggest that not only somatic alterations, but also germline variants carried over into the tumor genome should be included in therapeutic decision-making.

bioinformatics↗