Biology subjects

Anders, R.

Publications and source records attributed to Anders, R..

7 recordsLinked to original sources

bioRxiv2026

Deep phenotyping and multi-omics analyses reveal systems-wide metabolic dysregulation in a refined trisomy mouse model of Down syndrome

Trisomy 21 or Down syndrome (DS) affects multi-organ systems across the lifespan. The presence of an extra chromosome, along with genome dosage imbalance due to triplicated genes, contributes to the DS phenotypes. Of the DS mouse models, few are aneuploid with a freely segregating extra chromosome. We previously showed that the aneuploid Ts65Dn mice exhibit metabolic deficits consistent with the metabolic profile of DS. However, the genotype-phenotype relationships in Ts65Dn mice are complicated by the presence of triplicated genes unrelated to human chromosome 21 (Hsa21). To address this issue, we leveraged a refined model, Ts66Yah, where the extra triplicated genes in Ts65Dn have been removed. Deep phenotyping and multi-omics analyses showed that Ts66Yah mice develop pronounced and widespread metabolic disturbances. Despite sexual dimorphism in weight gain, body temperature, lipid and lipoprotein profiles, hepatic injury and adipose fibrosis, both male and female Ts66Yah mice share a common phenotype of pronounced glucose intolerance and insulin resistance, reduced mitochondrial respiratory capacity in visceral fat, altered serum inflammatory cytokine profile, and dysregulated serum and liver metabolomes. Pan-tissue transcriptomes also reveal signatures of immune activation, disrupted metabolic processes and cellular respiration, altered cytokine signaling, enhanced oxidative stress, and extracellular matrix remodeling. These combined changes across tissues disrupt metabolic homeostasis more severely in Ts66Yah than in Ts65Dn mice. Several phenotypes, including glucose intolerance, insulin resistance, tissue fibrosis, and oxidative stress were further exacerbated by an obesogenic diet. This foundational data establishes Ts66Yah as a valuable reference model for the mechanistic and comparative study of metabolic dysfunction in DS.

physiology↗

bioRxiv2024

The interplay between executive functions and updating predictive representations

Modifying habits, particularly unwanted behaviors, is often challenging. Cognitive research has focused on understanding the mechanisms underlying habit formation and how habits can be rewired. A key mechanism is statistical learning, the continuous, implicit extraction of probabilistic patterns from the environment, which forms the basis of predictive processing. However, the interplay between executive functions (EF) and the rewiring - or updating - of these probabilistic representations remains largely unexplored. To address this gap, we conducted an experiment consisting of four sessions: 1) Learning Phase - acquisition of probabilistic representations, 2) Rewiring Phase - updating these probabilistic representations, 3) Retrieval Phase - accessing learned representations, and 4) EF assessment, targeting five key aspects: attentional control, inhibition, working memory, flexibility, and verbal fluency. We focused on the relationship between these EF measures and the updating of previously acquired knowledge using an interindividual differences approach. Our results revealed a positive relationship between rewiring and inhibition, suggesting that better inhibitory control may facilitate the adaptive restructuring of probabilistic predictive representations. Conversely, a negative relationship was identified between rewiring and semantic fluency, implying that certain underlying aspects of verbal fluency tasks, such as access to long-term memory representations, may hinder the updating process. We interpret this relationship through the lens of competitive memory network models. Our findings indicate that the rewiring of implicit probabilistic representations is a multifaceted cognitive process requiring both the suppression of proactive interference from prior knowledge through cognitive inhibition and a strong reliance on model-free functioning.

neuroscience↗

bioRxiv2023

Immune landscape of tertiary lymphoid structures in hepatocellular carcinoma (HCC) treated with neoadjuvant immune checkpoint blockade

Neoadjuvant immunotherapy is thought to produce long-term remissions through induction of antitumor immune responses before removal of the primary tumor. Tertiary lymphoid structures (TLS), germinal center-like structures that can arise within tumors, may contribute to the establishment of immunological memory in this setting, but understanding of their role remains limited. Here, we investigated the contribution of TLS to antitumor immunity in hepatocellular carcinoma (HCC) treated with neoadjuvant immunotherapy. We found that neoadjuvant immunotherapy induced the formation of TLS, which were associated with superior pathologic response, improved relapse free survival, and expansion of the intratumoral T and B cell repertoire. While TLS in viable tumor displayed a highly active mature morphology, in areas of tumor regression we identified an involuted TLS morphology, which was characterized by dispersion of the B cell follicle and persistence of a T cell zone enriched for ongoing antigen presentation and T cell-mature dendritic cell interactions. Involuted TLS showed increased expression of T cell memory markers and expansion of CD8+ cytotoxic and tissue resident memory clonotypes. Collectively, these data reveal the circumstances of TLS dissolution and suggest a functional role for late-stage TLS as sites of T cell memory formation after elimination of viable tumor. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=128 SRC="FIGDIR/small/562104v2_fig0.gif" ALT="Figure 0"> View larger version (30K): org.highwire.dtl.DTLVardef@859572org.highwire.dtl.DTLVardef@169ed2org.highwire.dtl.DTLVardef@11510f0org.highwire.dtl.DTLVardef@b39a4_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LSTHighlightsC_LSTO_LIIn patients with hepatocellular carcinoma (HCC), tertiary lymphoid structures (TLS) are induced by neoadjuvant immunotherapy and are associated with favorable clinical outcomes. C_LIO_LITLS within the same tumor demonstrate extensive sharing of expanded granzyme K and granzyme B-expressing CD8+ T effector memory clonotypes, but the B cell repertoires of individual TLS are almost wholly distinct, consistent with independent germinal center reactions. C_LIO_LIWithin areas of viable tumor, mature TLS are characterized by high expression of CD21 and CD23, BCL6+ germinal center B cells, and close interactions between DCLAMP+ mature dendritic cells and CXCR5-CXCR3+ CD4 T peripheral helper cells within a T cell zone adjacent to the B cell follicle. C_LIO_LIWithin areas of tumor regression, an involuted TLS morphology is identified that is notable for dissolution of the B cell germinal center, retention of the T cell zone, and increased T cell memory. C_LI

immunology↗

bioRxiv2023

Discovery and characterization of cross-reactive intrahepatic antibodies in severe alcoholic hepatitis

The pathogenesis of antibodies in severe alcoholic hepatitis (SAH) remains unknown. We sought to determine if there was antibody deposition in SAH livers and whether antibodies extracted from SAH livers were cross-reactive against both bacterial antigens and human proteins. We analyzed immunoglobulins (Ig) in explanted livers from SAH patients (n=45) undergoing liver transplantation and tissue from corresponding healthy donors (HD, n=10) and found massive deposition of IgG and IgA isotype antibodies associated with complement fragment C3d and C4d staining in ballooned hepatocytes in SAH livers. Ig extracted from SAH livers, but not patient serum exhibited hepatocyte killing efficacy in an antibody-dependent cell-mediated cytotoxicity (ADCC) assay. Employing human proteome arrays, we profiled the antibodies extracted from explanted SAH, alcoholic cirrhosis (AC), nonalcoholic steatohepatitis (NASH), primary biliary cholangitis (PBC), autoimmune hepatitis (AIH), hepatitis B virus (HBV), hepatitis C virus (HCV) and HD livers and found that antibodies of IgG and IgA isotypes were highly accumulated in SAH and recognized a unique set of human proteins as autoantigens. The use of an E. coli K12 proteome array revealed the presence of unique anti-E. coli antibodies in SAH, AC or PBC livers. Further, both Ig and E. coli captured Ig from SAH livers recognized common autoantigens enriched in several cellular components including cytosol and cytoplasm (IgG and IgA), nucleus, mitochondrion and focal adhesion (IgG). Except IgM from PBC livers, no common autoantigen was recognized by Ig and E. coli captured Ig from AC, HBV, HCV, NASH or AIH suggesting no cross-reacting anti-E. coli autoantibodies. The presence of cross-reacting anti-bacterial IgG and IgA autoantibodies in the liver may participate in the pathogenesis of SAH.

pathology↗

bioRxiv2023

Evidence for a competitive relationship between executive functions and statistical learning

The ability of the brain to extract patterns from the environment and predict future events, known as statistical learning, has been proposed to interact in a competitive manner with prefrontal lobe related networks and their characteristic cognitive or executive functions. However, it remains unclear whether these cognitive functions also show competitive relationship with implicit statistical learning across individuals and at the level of latent executive function components. In order to address this currently unknown aspect, we investigated, in two independent experiments (NStudy1 = 186, NStudy2 = 157), the relationship between implicit statistical learning, measured by the Alternating Serial Reaction Time task, and executive functions, measured by multiple neuropsychological tests. In both studies, a modest, but consistent negative correlation between implicit statistical learning and most executive function measures was observed. Factor analysis further revealed that a factor representing the verbal fluency and complex working memory seemed to drive these negative correlations. Thus, an antagonism between implicit statistical learning and executive functions might specifically be mediated by updating component of executive functions or/and long-term memory access.

animal behavior and cognition↗

bioRxiv2022

Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces

Recent advances in spatial transcriptomics (ST) enable gene expression measurements from a tissue sample while retaining its spatial context. This technology enables unprecedented in situ resolution of the regulatory pathways that underlie the heterogeneity in the tumor and its microenvironment (TME). The direct characterization of cellular co-localization with spatial technologies facilities quantification of the molecular changes resulting from direct cell-cell interaction, as occurs in tumor-immune interactions. We present SpaceMarkers, a novel bioinformatics algorithm to infer molecular changes from cell-cell interaction from latent space analysis of ST data. We apply this approach to infer molecular changes from tumor-immune interactions in Visium spatial transcriptomics data of metastasis, invasive and precursor lesions, and immunotherapy treatment. Further transfer learning in matched scRNA-seq data enabled further quantification of the specific cell types in which SpaceMarkers are enriched. Altogether, SpaceMarkers can identify the location and context-specific molecular interactions within the TME from ST data.

bioinformatics↗

bioRxiv2017

Harnessing the adaptive potential of mechanoresponsive proteins to overwhelm pancreatic cancer dissemination and invasion

Metastatic disease is often characterized by altered cellular contractility and deformability, lending cells and groups of cells the flexibility to navigate through different microenvironments. This ability to change cell shape is driven in large part by the structural elements of the mechanobiome, which includes cytoskeletal proteins that sense and respond to mechanical stimuli. Here, we demonstrate that key mechanoresponsive proteins (those which accumulate in response to mechanical stress), specifically nonmuscle myosin IIA and IIC, -actinin 4, and filamin B, are highly upregulated in pancreatic ductal adenocarcinoma cancer (PDAC) and in patient-derived pancreatic cancer cell lines. Their less responsive sister paralogs (myosin IIB, -actinin 1, and filamin A) show a smaller dynamic range or disappear with PDAC progression. We demonstrate that these mechanoresponsive proteins directly impact cell mechanics using knock-down and overexpression cell lines. We further quantify the nonmuscle myosin II family members in patient-derived cell lines and identify a role for myosin IIC in the formation of transverse actin arcs in single cells and cortical actin belts in tissue spheroids. We harness the upregulation of myosin IIC and its impact of cytoskeletal architecture through the use of the mechanical modulator 4-hydroxyacetophenone (4-HAP), which increases myosin IIC assembly and stiffens cells. Here, 4-HAP decreases dissemination, induces cortical actin belts, and slows retrograde actin flow in spheroids. Finally, mice having undergone hemi-splenectomies with PDAC cells and then treated with 4-HAP have a reduction in liver metastases. Thus, increasing the activity of these mechanoresponsive proteins (in this case, by increasing myosin IIC assembly) to overwhelm the ability of cells to polarize and invade may be an effective strategy to improve the five-year survival rate of pancreatic cancer patients, currently hovering around 6%.

cancer biology↗