Biology subjects

Marttinen, M.

Publications and source records attributed to Marttinen, M..

10 recordsLinked to original sources

bioRxiv2026

AR suppression rewires a SOX4 regulatory program to promote enzalutamide resistance in prostate cancer

Treatment resistance in prostate cancer remains a major clinical challenge. While single-cell transcriptomics enables mapping of cellular composition and resistance-associated states, the gene regulatory programs driving these state transitions remain poorly defined. Here, we integrate single-cell chromatin accessibility and transcriptome sequencing data from an in vitro model to resolve the regulatory program architecture underlying anti-androgen resistance. We identify coordinated remodeling of androgen signaling- and stress response-associated regulatory programs, together with a pronounced gain of a SOX4-driven regulatory program in resistant cells. Analysis of clinical datasets reveals that SOX4 activity is both context-dependent and lineage-specific. In primary tumors, SOX4 cis-regulatory activity is elevated in PTEN-loss tumors, consistent with a PTEN-PI3K/AKT/mTOR-SOX4 axis that primes AR-independent epithelial lineages for subsequent activation of a more extensive SOX4 trans-regulatory program. This program is further amplified following AR-targeted therapy, indicating therapy-induced reinforcement of SOX4-linked regulatory adaptation. TF footprinting additionally implicates Nuclear Factor I family transcription factors as upstream regulators of SOX4, supporting a role in promoting SOX4 activation following AR inhibition. Together, these findings demonstrate that AR inhibition reshapes the gene regulatory landscape to promote engagement of the SOX4 program, facilitating prostate cancer progression under anti-androgen therapy.

cancer biology↗

bioRxiv2026

Hypoxia and Associated Acidosis Generate Cell-Type Specific Myeloid Responses in Glioblastoma

Hypoxia is a defining feature of glioblastoma (GBM), yet how it cooperates with hypoxia-associated acidosis to shape microglia and infiltrating monocyte-derived macrophages (MDM) remains poorly understood. We integrated cyclic immunohistochemistry, single-cell RNA sequencing, spatial transcriptomics, in vitro cell cultures, and DNA methylation profiling to outline hypoxia-driven responses in up to 136 GBMs. These hypoxic niches were selectively enriched for MDMs that activated carbonic anhydrase (CA) mediated pH buffering and other metabolic adaptation programs, enabling survival in acidic hypoxia, increasingly interacted with cancer cells, and show polarization toward immunosuppressive myeloid-derived suppressor cell (MDSC)-like states. In contrast, microglia were depleted in hypoxic areas, lacked compensatory CA isoenzymes, and developed TNF-linked stress responses and loss of homeostatic identity in acidic hypoxia. These findings identify metabolic adaptation to hypoxia-associated microenvironmental stress as a key determinant of GBM immune architecture, driving myeloid cell fates, spatial TME reorganization and the emergence of immunosuppressive tumor ecosystems.

cancer biology↗

bioRxiv2025

High-throughput single-cell CRISPRi screens stratify neurodevelopmental functions of schizophrenia-associated genes

Schizophrenia is a complex neuropsychiatric disorder with strong genetic underpinnings, yet the molecular mechanisms linking genetic risk to disrupted brain development remain poorly understood. Transcription factors (TFs) and chromatin regulators (CRs) are increasingly implicated in neuropsychiatric disorders, where their dysregulation may disrupt neurodevelopmental programs. Despite this, systematic functional interrogation in human models has been limited. Here, we combine pooled CRISPR interference (CRISPRi) screens with high- throughput single-cell multiomic profiling in hiPSC-derived neural progenitors and neurons to functionally assess 65 schizophrenia-associated genes. Based on public datasets and literature review, we selected 55 TFs and CRs, along with ten additional risk genes whose loss-of-function has been linked to schizophrenia. Our single-cell CRISPRi readouts revealed that perturbations in TFs and CRs converge on disrupting neurodevelopmental timing. CRISPRi of several factors delayed neural differentiation, whereas others, such as the knockdown of MCRS1, drove precocious neural commitment. Validation screens combined with cell cycle and metabolic indicators confirmed the differentiation-restricting or -promoting roles of these TFs and CRs. Multimodal trajectory analysis uncovered discrete transcriptional and epigenomic states representing delayed and accelerated neurodevelopment, enriched for schizophrenia GWAS loci and disease-relevant pathways. Gene regulatory network (GRN) inference identified TCF4 and ZEB1 as critical mediators opposing the neural differentiation trajectory. Functional overexpression of these TFs followed by chromatin profiling demonstrated that TCF4 restrains, while ZEB1 promotes, neural differentiation in a stage-specific and competitive manner. Furthermore, we show that MCRS1 represses ZEB1 expression, positioning MCRS1 as a key brake on premature neurodevelopment. Together, our study establishes a scalable framework that integrates genetic perturbation, single- cell multiomics, and GRN modeling to functionally annotate disease-linked genes. We reveal convergent regulatory axes that underlie altered neurodevelopmental timing in schizophrenia, offering mechanistic insights into how chromatin misregulation contributes to disease pathogenesis.

neuroscience↗

bioRxiv2024

Androgen deprivation therapy-resistant club cells are linked to myeloid cell-driven immunosuppression in the prostate tumor microenvironment

Prostate cancer treatment resistance is a significant challenge facing the field. Genomic and transcriptomic profiling have partially elucidated the mechanisms through which cancer cells escape treatment, but their relation toward the tumor microenvironment (TME) remains elusive. Here we present a comprehensive transcriptomic landscape of the prostate TME at multiple points in the standard treatment timeline employing single-cell RNA-sequencing and spatial transcriptomics data from 110 patients. We identify club-like cells as a key epithelial cell subtype that acts as an interface between the prostate and the immune system. Tissue areas enriched with club-like cells have depleted androgen signaling and upregulated expression of luminal progenitor cell markers. Club-like cells display a senescence-associated secretory phenotype and their presence is linked to increased polymorphonuclear myeloid-derived suppressor cell (PMN-MDSC) activity. Our results indicate that club-like cells partake in inducing myeloid inflammation previously associated with androgen deprivation therapy resistance, providing a rationale for their therapeutic targeting.

cancer biology↗

bioRxiv2023

Scalable ultra-high-throughput single-cell chromatin and RNA sequencing reveals gene regulatory dynamics linking macrophage polarization to autoimmune disease

Enhancers and transcription factors (TFs) are crucial in regulating cellular processes, including disease-associated cell states. Current multiomic technologies to study these elements in gene regulatory mechanisms lack multiplexing capability and scalability. Here, we present SUM-seq, a cost-effective, scalable Single-cell Ultra-high-throughput Multiomic sequencing method for co-assaying chromatin accessibility and gene expression in single nuclei. SUM-seq enables profiling hundreds of samples at the million cell scale and outperforms current high-throughput single-cell methods. We applied SUM-seq to dissect the gene regulatory mechanisms governing macrophage polarization and explored their link to traits from genome-wide association studies (GWAS). Our analyses confirmed known TFs orchestrating M1 and M2 macrophage programs, unveiled key regulators, and demonstrated extensive enhancer rewiring. Integration with GWAS data further pinpointed the impact of specific TFs on a set of immune traits. Notably, inferred enhancers regulated by the STAT1/STAT2/IRF9 (ISGF3) complex were enriched for genetic variants associated with Crohns disease, ulcerative colitis and multiple sclerosis, and their target genes included known drug targets. This highlights the potential of SUM-seq for dissecting molecular disease mechanisms. SUM-seq offers a cost-effective, scalable solution for ultra-high-throughput single-cell multiomic sequencing, excelling in unraveling complex gene regulatory networks in cell differentiation, responses to perturbations, and disease studies.

genomics↗

bioRxiv2023

HIPSD&R-seq enables scalable genomic copy number and transcriptome profiling

Single-cell DNA-sequencing (scDNA-seq) enables decoding somatic cancer variation. Existing methods are hampered by low throughput or cannot be combined with transcriptome sequencing in the same cell. We propose HIPSD&R-seq (HIgh-throughPut Single-cell Dna and Rna-seq), a scalable yet simple assay to profile low-coverage DNA and RNA in thousands of cells in parallel. Our approach builds on an accessible modification of the 10X Genomics platform for scATAC and multiome profiling. In applications to human cell models and primary tissue, we demonstrate the feasibility to detect rare clones and we combine the assay with combinatorial indexing to profile over 16,000 cells.

cancer biology↗

bioRxiv2020

The Alzheimer's disease-associated protective Plcγ2-P522R variant promotes beneficial microglial functions

BackgroundMicroglia-specific genetic variants are enriched in several neurodegenerative diseases, including Alzheimers disease (AD), implicating a central role for alterations of the innate immune system in the disease etiology. A rare coding variant in the PLCG2 gene (rs72824905, p.P522R) selectively expressed in microglia and macrophages was recently identified and shown to reduce the risk for AD. MethodsTo assess the role of this variant in the context of immune cell functions, we generated a Plc{gamma}2-P522R knock-in (KI) mouse model using CRISPR/Cas9 gene editing. ResultsFunctional analyses of macrophages derived from homozygous KI mice and wild type (WT) littermates revealed that the P522R variant potentiates the primary function of Plc{gamma}2 as a Pip2-metabolizing enzyme. This was associated with improved survival, enhanced phagocytic activity, and increased acute inflammatory response of the KI cells. Enhanced phagocytosis was also observed in mouse BV2 microglia-like cells overexpressing human PLC{gamma}2-P522R, but not in PLC{gamma}2-WT expressing cells. Furthermore, the brain mRNA signature together with microglia-specific PET imaging indicated microglia activation in Plc{gamma}2-P522R KI mice. ConclusionThus, we have delineated cellular mechanisms of the protective Plc{gamma}2-P522R variant, which provide further support for the emerging idea that activated microglia exert protective functions in AD.

neuroscience↗

bioRxiv2020

Diabetic phenotype in mouse and humans with β-amyloid pathology reduces the number of microglia around β-amyloid plaques

Type 2 diabetes (T2D) increases the risk of Alzheimers disease (AD). Even though these two diseases share common molecular pathways, the mechanisms remain elusive. To shed light into these mechanisms, mice with different AD- and/or tauopathy-linked genetic backgrounds were utilized; APPswe/PS1dE9 (A+Tw), Tau P301L (AwT+), and APPswe/PS1dE9/Tau P301L (A+T+). Feeding these mice with typical Western diet (TWD) led to obesity and diabetic phenotype as compared to respective mice with a standard diet. TWD also exacerbated memory and learning impairment in A+Tw and AwT+, but not in A+T+ mice. Furthermore, RNA sequencing of mouse hippocampal samples revealed altered responses to AD-related pathologies in A+Tw and A+T+ mice upon TWD, pointing specifically towards aberrant microglial functionality and PI3K-Akt signaling. Accordingly, fewer microglia alongside an increased number of dystrophic neurites around {beta}-amyloid plaques, and impaired PI3K-Akt signaling, were discovered in the hippocampus of TWD mice. Mechanistic elucidation revealed that disruption of the PI3K-Akt signaling pathway by pharmacological or genetic approaches significantly decreased the phagocytic uptake and proinflammatory response as well as increased the activity of Syk-kinase upon ligand-induced activation of Trem2/Dap12 signaling in mouse microglia. Finally, characterization of microglial pathology in cortical biopsies of idiopathic normal pressure hydrocephalus (iNPH) patients harboring {beta}-amyloid plaques revealed a significant decrease in the number of microglia per {beta}-amyloid plaque in obese iNPH patients with T2D as compared to both normal weight and obese iNPH patients without T2D. Collectively, these results suggest that the peripheral diabetic phenotype in mice and humans associates with reduced microglial response to {beta}-amyloid pathology.

neuroscience↗

bioRxiv2019

Alzheimer’s genetic risk factor FERMT2 (Kindlin-2) is regulated by risk allele-binding of miR-4504 and leads to synaptic dysfunction in an APP-dependent manner

Although APP metabolism is being intensively investigated, a large fraction of its modulators are yet to be characterized. In this context, we combined two genome-wide high-content screenings to assess the functional impact of miRNAs and genes on APP metabolism and the signaling pathways involved. This approach highlighted the involvement of FERMT2 (or Kindlin-2), a genetic risk factor of Alzheimers disease (AD), as a potential key modulator of axon guidance; a neuronal process that depends on the regulation of APP metabolism. We found that FERMT2 directly interacts with APP to modulate its metabolism and that FERMT2 under-expression impacts axonal growth, synaptic connectivity and long-term potentiation in an APP-dependent manner. Lastly, the rs7143400-T allele, which is associated with an increased AD risk and localized within the 3UTR of FERMT2, induced a down-regulation of FERMT2 expression through binding of miR-4504 among others. This miRNA is mainly expressed in neurons and significantly overexpressed in AD brains compared to controls. Altogether, our data provide strong evidence for a detrimental effect of FERMT2 under-expression in neurons and insight on how this may influence AD pathogenesis.

pathology↗

bioRxiv2018

BIN1 recovers tauopathy-induced long-term memory deficits in mice and interacts with Tau through Thr348 phosphorylation

The bridging integrator 1 gene (BIN1) is a major genetic risk factor for Alzheimers disease (AD). In this report, we investigated how BIN1-dependent pathophysiological processes might be associated with Tau. We first generated a cohort of control and transgenic mice either overexpressing human MAPT (TgMAPT) or both human MAPT and BIN1 (TgMAPT;TgBIN1), which we followed-up from 3 to 15 months. In TgMAPT;TgBIN1 mice short-term memory deficits appeared earlier than in TgMAPT mice; however - unlike TgMAPT mice - TgMAPT;TgBIN1 mice did not exhibit any long-term or spatial memory deficits for at least 15 months. After sacrifice of the cohort at 18 months, immunohistochemistry revealed that BIN1 overexpression prevents both Tau mislocalization and somatic inclusion in the hippocampus, where an increase in BIN1-Tau interaction was also observed. We then sought mechanisms controlling the BIN1-Tau interaction. We developed a high-content screening approach to characterize modulators of the BIN1-Tau interaction in an agnostic way (1,126 compounds targeting multiple pathways), and we identified - among others - an inhibitor of Calcineurin, a Ser/Thr phosphatase. We determined that Calcineurin dephosphorylates BIN1 on a Cyclin-dependent kinase phosphorylation site at T348, promoting the open conformation of the neuronal BIN1 isoform. Phosphorylation of this site increases the availability of the BIN1 SH3 domain for Tau interaction, as demonstrated by nuclear magnetic resonance experiments and in primary neurons. Finally, we observed that the levels of the neuronal BIN1 isoform were decreased in AD brains, whereas phospho-BIN1(T348):BIN1 ratio was increased, suggesting a compensatory mechanism. In conclusion, our data support the idea that BIN1 modulates the AD risk through an intricate regulation of its interaction with Tau. Alteration in BIN1 expression or activity may disrupt this regulatory balance with Tau and have direct effects on learning and memory.

neuroscience↗