Biology subjects

McCord, R. P.

Publications and source records attributed to McCord, R. P..

At least 19 recordsLinked to original sources

bioRxiv2026

Abnormal nuclear organization impairs adipogenic lineage commitment and terminal maturation in Hutchinson-Gilford progeria syndrome (HGPS)

Hutchinson-Gilford progeria syndrome (HGPS) is a fatal premature aging disorder driven by progerin, a truncated Lamin A protein that destabilizes nuclear architecture and disproportionately affects mesenchymal-lineage tissues. One notable mesenchymal lineage defect in Progeria patients is early and severe subcutaneous lipodystrophy. We hypothesized that disorganized chromatin architecture underlies the failure of mesenchymal stem cell (MSC) lineage commitment and adipogenesis in HGPS. To test this while preserving donor age, epigenetic history, and tissue context, we induced adipogenesis in age-matched healthy and HGPS patient-derived dermal fibroblasts and profiled cells using imaging, bulk RNA-seq, and Hi-C across the differentiation time course. We found that HGPS fibroblasts commit to the adipogenic lineage at rates comparable to healthy controls but diverge downstream: induced cells display aberrant lipid-droplet morphology, mount a disorganized and delayed transcriptional response, and retain priming for alternative mesenchymal lineages (osteochondrogenic, vascular) alongside stalled adipogenic maturation. Hi-C revealed that HGPS fibroblasts exhibit some baseline spatial compartment differences from healthy cells, but more notably show differences in how they reorganize compartments during adipogenic induction. Compartment-transcription coupling was strong during adipogenesis for lipid-metabolic genes in healthy cells but was more dysregulated in HGPS. These results indicate that HGPS disrupts lineage consolidation rather than initiation, associated with disease-specific failures in chromatin reorganization during differentiation.

cell biology↗

bioRxiv2026

Cancer stem cell transcriptomic signatures reveal patient-to-patient heterogeneity emphasizing the need for patient-specific ovarian cancer targets

Background/Objectives: In high-grade serous ovarian cancer (HGSOC), the abilities of tumor cells to resist cytotoxic treatment and relapse are largely driven by ovarian cancer stem cells (CSCs). CSCs are a population of cells within a tumor that maintain stem-like qualities and have the capacity to produce metastasis and drive drug resistance. Based on the complexity of CSC signaling and emerging evidence of differential isoform usage in development, we hypothesize that CSCs possess a patient-specific, heterogeneous landscape which exploits isoform diversity to sustain stemness, metastasis and drug resistance. Methods: RNA-seq was generated from 3 patient-derived HGSOC (PD-HGSOC) to investigate stemness and differentiation status comparing standard culture and CSCs. The data was analyzed at both gene- and isoform-levels to identify patient-specific CSC features and define mechanisms of cancer-related stemness and plasticity. Results: CSCs exhibited higher stemness characteristics and identified differentially expressed gene sets across PD-HGSOCs. We noted that each patient had a distinct subset of genes regulating stemness phenotypes which suggested multiple mechanisms of CSC development and maintenance. Additionally, a large proportion of gene-level expression changes were driven by the differential expression of a single predominant isoform. Importantly, our isoform-level analysis enabled the identification of differential isoform usage that would not be detected with gene level expression analysis. Conclusions: CSC phenotypes such as chemoresistance, metastasis and self-renewal are conserved across patients, but arise from largely patient-specific gene and isoform programs. This CSC heterogeneity is reflective of the heterogeneity seen in patients and should be further evaluated in deriving precision-medicine approaches for HGSOC.

cancer biology↗

bioRxiv2026

H3K27me3 Drives Constricted Migration Induced 3D Genome Rewiring in Melanoma

Repeated exposure of neoplastic cells to mechanical stresses during metastasis can drive stable morphological and physiological changes. We previously showed that A375 human melanoma cells subjected to 10 rounds of constricted migration ("Bottom-10 cells") became significantly more migratory and exhibited H3K9me3 relocalization, transcriptional remodeling, and chromatin compartment changes relative to naive parental A375 cells. Because these phenotypes persist across cell divisions, we hypothesized they are driven and maintained by specific epigenetic mechanisms. Here, we profiled candidate histone modifications by CUT&RUN and applied a computational model to identify marks that explain compartment switches. In parental cells, H3K9me3 and H3K4me1 strongly predict locus stability in the B and A compartments, respectively. In contrast, changes in H3K27me3 dynamically predict A-to-B compartment switching after constricted migration. Consistently, altered H3K27me3 enrichment correlates with both differentially regulated genes and chromatin compartment changes between Bottom-10 and parental populations. We therefore tested whether inhibiting H3K27me3 deposition alters migratory potential and/or the "memory" of the increased migratory phenotype. Inhibiting EZH1/2 reduced migration efficiency overall, with a stronger effect on constricted than unconstricted migration. This reduction was accompanied by decreased genomic H3K27me3 enrichment and reversal of some compartment changes in Bottom-10 cells. However, acute treatment did not durably reverse the highly migratory Bottom-10 phenotype; cells returned to their initial state after drug removal. Chronic inhibition across many sequential rounds of constricted migration dramatically reduced the fraction of cells able to migrate. Notably, cells that migrated despite chronic EZH inhibition appeared to escape treatment, acquiring many typical Bottom-10 H3K27me3 and compartment changes even though acute inhibition tends to prevent them. Overall, these results highlight H3K27me3 as a key contributor to establishing and maintaining constricted migration-induced 3D genome changes.

genomics↗

bioRxiv2026

Distinct principles of genome compartmentalization in Drosophila and humans revealed by osmotic stress

The three-dimensional organization of eukaryotic genomes into compartments, topologically associating domains, and loops is mediated by architectural proteins whose organizational principles vary across species. In Drosophila, insulator proteins including Su(Hw) and the histone variant {gamma}H2Av form liquid-liquid phase separation (LLPS) condensates, yet how this phase separation capacity relates to genome compartmentalization has remained unclear. Here we use hyperosmotic stress to simultaneously displace architectural proteins from chromatin in both Drosophila and human cells, enabling a comparative dissection of genome organization principles across species. We find that although human CTCF shares predicted LLPS properties with Drosophila insulator proteins, it does not form condensates upon osmotic stress, while Drosophila insulator proteins do. Hi-C analysis reveals that osmotic stress causes loss of compartments, TAD boundary strength, and loops in both organisms, but genome recovery after stress is rapid and near-complete in human cells while remaining substantially incomplete in Drosophila after one hour. Analysis of this recovery asymmetry reveals a fundamental difference in compartment organization: whereas human A and B compartments engage in robust homotypic long-range interactions, Drosophila B compartments rarely participate in long-range B-to-B contacts, indicating that the Drosophila genome does not replicate canonical A/B compartment organization. Instead, Drosophila genome architecture is dominated by A-to-A interactions, and A compartments are specifically enriched in {gamma}H2Av and Su(Hw), with moderate enrichment of cohesin subunits. Furthermore, loops in Drosophila are mechanistically independent from compartments and TADs, recovering before compartment structure is restored, and are anchored by Su(Hw) and cohesin rather than by dCTCF. Together, these findings suggest that the LLPS properties of {gamma}H2Av and Su(Hw) underlie A compartment formation in Drosophila through a mechanism distinct from the heterochromatin-driven B compartment interactions that predominate in vertebrates, revealing fundamentally different organizational principles between fly and human genomes.

genomics↗

bioRxiv2026

Visualizing Interchromosomal Interactions at Sub-Megabase Resolution Using Network Clustering Coefficients

Specific interchromosomal interactions involve communication between non-homologous chromosomes, enabling coordinated genomic activities such as gene regulation. However, because these communications are often embedded within a nonspecific and noisy background of contact interactions, it is essential to annotate these interaction patterns at the resolution of genomic positions. Such annotation facilitates clean visualization and comparison with linear genomic features to reveal underlying biological functions. We developed and validated a set of network-based metrics as cross-chromosomal interaction descriptors that bridge complex 3D genome structures and 1D functional genomics. By utilizing graph-theoretic representations, these network-based features succinctly summarize complex inter-chromosomal relationships. We constructed a graph representation of contact interactions derived from Hi-C data and implemented three annotations that capture the distinct "many-body" nature of the interactions. Among these, we demonstrate that {Delta}C4 (a cis-contact-mediated 4-cycle interaction metric) is superior to both {Delta}C3 (a cis-contact-mediated 3-cycle metric) and C4E (a direct 4-cycle metric of trans contacts) at filtering noise and providing the most straightforward interpretation. Applying these metrics to chromosomes 17, 19, and 22 of the GM12878 cell line, we found clear evidence that different chromosomes rely on a shared set of interaction hot spots to communicate. Overall, this network-based framework reveals distinct chromosomal regulation patches and provides insight into how chromosomes associate with each other and organize relative to the nuclear envelope.

genomics↗

bioRxiv2026

Reversibility of Nuclear and 3D Genomic Changes in Non-Cancerous Fibroblasts After Constricted Migration

Metastatic cancer cells and healthy fibroblasts must traverse constrictive spaces to reach secondary sites. After passing through multiple constrictions, cancer cells often experience stable changes to their nucleus morphology, 3D genome structure, and migratory phenotype. Here, we investigate whether fibroblasts (BJ-5ta), which are non-cancerous and have an inherent ability to migrate to fulfill roles in wound repair, likewise experience nuclear and 3D genomic changes with constricted migration. We find that BJ-5ta cells do not get progressively better at migrating with sequential attempts but do experience nuclear deformations and 3D genome alterations at the compartment level after constricted migration. Transient compartment shifts spatially rearranged genes associated with preparation for and response to migration. Unlike the stable changes associated with long term phenotype changes in cancer cells, however, the nucleus deformations recovered back to unmigrated levels following proliferation and cell movement. Some compartment changes persist and might influence responses to future stimuli, but most 3D genome changes revert to the unmigrated state after cell proliferation. Our study shows that non-cancerous migratory cells are not more robust against alterations caused by constricted migration but can recover from the ones that do arise more readily than cancer cells. Significance StatementO_LICancer cells experience stable phenotype shifts and 3D genome changes after constricted migration, but it is unknown whether these changes would occur in innately migratory non-cancerous fibroblasts. C_LIO_LIFibroblasts (BJ-5ta) show reversible nuclear morphology and 3D genome alterations after constricted migration. C_LIO_LIOur results reveal the connection between basic nucleus mechanobiology and genome structure in fibroblasts, showing how these cells adapt and respond to the forces of constriction during processes such as wound healing. C_LI

cell biology↗

bioRxiv2025

Spatial genome reorganization is associated with chromosomal breakage regions and karyotype changes induced by programmed DNA elimination

Programmed DNA elimination (PDE) is a notable exception to genome integrity, characterized by significant DNA loss during development. In many nematodes, PDE is initiated by DNA double-strand breaks (DSBs), which lead to chromosome fragmentation and subsequent DNA loss. However, the mechanism of nematode programmed DNA breakage remains largely unclear. Interestingly, in the human and pig parasitic nematode Ascaris, no conserved motif or sequence structures are present at chromosomal breakage regions (CBRs), suggesting the recognition of CBRs may be sequence-independent. Using Hi-C, we revealed that Ascaris CBRs engage in three-dimensional (3D) interactions before PDE, indicating that physical contacts between break regions may contribute to the PDE process. The 3D interactions are established in both Ascaris male and female germlines, demonstrating inherent genome organization associated with the CBRs and to-be-eliminated sequences. In contrast, in the unichromosomal horse parasite Parascaris univalens, transient pairwise interactions between neighboring CBRs that will form the ends of future somatic chromosomes were observed only during PDE. Intriguingly, we found that Ascaris PDE, which converts 24 germline chromosomes into 36 somatic ones, induces specific compartmentalization changes. Remarkably, Parascaris PDE generates the same set of 36 somatic chromosomes, and the 3D compartment changes following PDE are consistent between the two species. Overall, our findings suggest that CBRs spatially demarcate the retained and eliminated DNA and may contribute to their spatial organization during Ascaris PDE. We also demonstrated that the 3D genome reorganization of the somatic chromosomes in these nematodes following PDE is evolutionary and developmentally conserved.

genomics↗

bioRxiv2025

The multiscale distribution of radiation-induced DNA damage and its impact on local genome structure

The three-dimensional genome structure is critical for the regulation of gene expression and repair of DNA damage. While previous work has characterized genome-wide sites of DNA damage caused by etoposide or nucleases, the distribution of double-strand breaks (DSBs) caused by external radiation and how these interact with the 3D genome organization is less well understood. Here, we measure the genomic landscape of radiation-induced DNA damage using END-seq in fibroblasts and lymphoblasts after exposure to 5 Gy X-rays. We identify frequently broken regions and investigate the 3D genome properties around these breaks with Hi-C data. We observe that the distribution of robust breaks correlates with transcriptional and chromatin features of the genome. Transcriptionally active and decondensed regions, such as chromosome 19, the A compartment, and topologically associating domain (TAD) boundaries, show pronounced break probability. We also find evidence of DSB-induced loop formation in the vicinity of frequent radiation-induced breaks. Our data reveal that pre-existing 3D genome architecture influences the distribution of radiation-induced DSBs and that these breaks reshape local chromatin landscapes.

genomics↗

bioRxiv2025

Transient chromatin decompaction by histone deacetylation inhibition preferentially radiosensitizes cancerous breast epithelial cells at lower radiation doses

Radiation therapy plays a prominent role in breast cancer treatment, but the high doses of radiation damage both healthy and cancerous cells. Therefore, additional research is needed into combination therapies that could preferentially radiosensitize cancer cells compared to surrounding healthy tissue without causing deleterious side effects. Histone deacetylase inhibitor drugs (HDACis) have been tested as radiosensitizers in both basic research and clinical trials, but the long exposure time typically used in these treatments and the lack of matched healthy cell controls often leave aspects of their mechanism of action unclear. Here, we show that transient (2 hour) trichostatin A (TSA) treatment of cancerous and non-tumorigenic breast epithelial cell lines increases immediate DNA damage and decreases long term cell viability in both cell types at high radiation doses. Transient TSA treatment also causes an increase in DNA damage signals after 5 Gy in other cancer and healthy cell types: A375 melanoma cells and BJ5-ta fibroblasts. This suggests that chromatin decompaction acts to increase cellular vulnerability to initial DNA damage from high doses of radiation DNA damage in a cell type independent manner that does not rely on changes to DNA repair pathways caused by longer TSA treatment. However, responses to lower doses of radiation and long term survival are more cell type specific: only MCF7 cells experience an effect of TSA on DNA damage after 1 Gy radiation while MCF10a cells experience somewhat more evident cell viability effects of combined TSA and radiation treatment long term. Scope statementThis manuscript covers several topics that are core to the mission of Frontiers in Cell and Developmental Biology, including cancer cell biology as compared to non-cancerous cell function, cell death vs. survival, and epigenetics and chromosome structure. While some of the implications of this work touch on cancer therapeutics, the study itself focuses on the basics of the interplay between genome architecture and DNA damage and cellular survival / response. We noted several recent articles on related topics in this journal, including the effects of combination treatments on cancer cells (doi 10.3389/fcell.2025.1636288), radiotherapy effects on cells (doi 10.3389/fcell.2025.1568634), and DNA damage (doi 10.3389/fcell.2025.1575483). Our work is well suited for a Brief Research Report as it provides key but focused data on comparisons of radiosensitivity in response to transient chromatin decompaction in cancer vs. healthy cells.

cancer biology↗

bioRxiv2024

Polymer Model Integrates Super-Resolution Imaging and Epigenomic Sequencing to Elucidate the Role of Epigenetic Reactions in Shaping 4D Chromatin Organization

Chromatin, with its complex spatial and temporal organization, plays a crucial role in regulating gene expression. Recent advancements in super-resolution microscopy have revealed that nanoscale domains of heterochromatin (repressed segments) embedded within a euchromatin (active segments) background are fundamental units of 3D chromatin organization. In tissue-resident cells, the size of these heterochromatin domains varies with the microenvironment, particularly its stiffness, and chromatin organization is also influenced by pharmacological and epigenetic drugs. However, the mechanisms governing heterochromatin domain size under various conditions and their impact on gene expression remain unclear. To address this knowledge gap, we have developed a dynamic, next-generation sequencing informed chromatin copolymer model. Our model simulates the spatiotemporal evolution of chromatin, driven by passive diffusion and active epigenetic reactions, which interconvert euchromatin and heterochromatin. By integrating chromatin-chromatin interaction energetics and diffusion-reaction dynamics, we predict the formation of nanoscale heterochromatin-rich domains and establish a scaling relationship between their size and the modulation of epigenetic reaction rates. Additionally, our model predicts that epigenetic and chromatin compaction changes in response to changes in global reaction rates occur predominantly at domain boundaries. We validated these predictions via Hi-C contact map analysis and super-resolution imaging of hyperacetylated melanoma cells. Subsequent RNA-seq analysis suggested a pivotal role of these epigenetic shifts in influencing the metastatic potential of these cells. We further validated our mesoscale findings against chromatin rearrangement in hMSCs, which exhibit sensitivity of epigenetic reaction rates to changes in microenvironmental stiffness. Finally, we evaluated the effects of cycling of epigenetic reaction rates in silico, mimicking the cellular transition to different extracellular conditions, and back again. This finding reveals a cell-type invariant mechanism driven by domain boundaries, whereby chromatin organization guides epigenetic memory formation. Our findings show that chromatin reorganization in response to changes in epigenetic reaction rates resulting from alterations in the microenvironment, drug exposure and disease progression impacts both immediate cellular responses and long-term epigenetic memory.

biophysics↗

bioRxiv2024

Rearrangement of 3D genome organization in breast cancer epithelial - mesenchymal transition and metastasis organotropism

Breast cancer cells exhibit organotropism during metastasis, showing preferential homing to certain organs such as bone, lung, liver, and brain. One potential explanation for this organotropic behavior is that cancer cells gain properties that enable thriving in certain microenvironments. Such specific metastatic traits may arise from gene regulation at the primary tumor site. Spatial genome organization plays a crucial role in oncogenic transformation and progression, but the extent to which chromosome architecture contributes to organ-specific metastatic traits is unclear. This work characterizes chromosome architecture changes associated with organotropic metastatic traits. By comparing a collection of genomic data from different subtypes of localized and lung metastatic breast cancer cells with both normal and cancerous lung cells, we find important trends of genomic reorganization. The most striking differences in 3D genome compartments segregate cell types according to their epithelial vs. mesenchymal status. This EMT compartment signature occurs at genomic regions distinct from transcription-defined EMT signatures, suggesting a separate layer of regulation. Specifically querying organotropism, we find 3D genome changes consistent with adaptations needed to survive in a new microenvironment, with lung metastatic breast cells exhibiting compartment switch signatures that shift the genome architecture to a lung cell-like conformation and brain metastatic prostate cancer cells showing compartment shifts toward a brain-like state. TCGA patient data reveals gene expression changes concordant with these organ-permissive compartment changes. These results suggest that genome architecture provides an additional level of cell fate specification informing organotropism and enabling survival at the metastatic site. SIGNIFICANCEComputational analysis of a cohort of cancer cell lines reveals some 3D genome spatial compartment changes are associated with transitions in cancer cell state that relate to metastasis (EMT) and others reflect the characteristics of the metastatic organ context.

cancer biology↗

bioRxiv2024

Deciphering Pre-existing and Induced 3D Genome Architecture Changes involved in Constricted Melanoma Migration

Metastatic cancer cells traverse constricted spaces that exert forces on their nucleus and the genomic contents within. Cancerous tumors are highly heterogeneous and not all cells within them can achieve such a feat. Here, we investigated what initial genome architecture characteristics favor the constricted migratory ability of cancer cells and which arise only after passage through multiple constrictions. We identified a cell surface protein (ITGB4) whose expression correlates with increased initial constricted migration ability in human melanoma A375 cells. Sorting out this subpopulation allowed us to identify cellular and nuclear features that pre-exist and favor migration, as well as alterations that only appear after cells have passed through constrictions. We identified specific genomic regions that experienced altered genome spatial compartment profiles only after constricted migration. Our study reveals 3D genome structure contributions to both selection and induction mechanisms of cell fate change during cancer metastasis.

cell biology↗

bioRxiv2024

Integrating Chromosome Conformation and DNA Repair in a Computational Framework to Assess Cell Radiosensitivity

ObjectiveThe arrangement of chromosomes in the cell nucleus has implications for cell radiosensitivity. The development of new tools to utilize Hi-C chromosome conformation data in nanoscale radiation track structure simulations allows for in silico investigation of this phenomenon. We have developed a framework employing Hi-C-based cell nucleus models in Monte Carlo radiation simulations, in conjunction with mechanistic models of DNA repair, to predict not only the initial radiation-induced DNA damage, but also the repair outcomes resulting from this damage, allowing us to investigate the role chromosome conformation plays in the biological outcome of radiation exposure. ApproachIn this study, we used this framework to generate cell nucleus models based on Hi-C data from fibroblast and lymphoblastoid cells and explore the effects of cell type-specific chromosome structure on radiation response. The models were used to simulate external beam irradiation including DNA damage and subsequent DNA repair. The kinetics of the simulated DNA repair were compared with previous results. Main ResultsWe found that the fibroblast models resulted in a higher rate of inter-chromosome misrepair than the lymphoblastoid model, despite having similar amounts of initial DNA damage and total misrepairs for each irradiation scenario. SignificanceThis framework represents a step forward in radiobiological modeling and simulation allowing for more realistic investigation of radiosensitivity in different types of cells.

biophysics↗

bioRxiv2023

Node Features of Chromosome Structure Network and Their Connections to Genome Annotation

The 3D conformations of chromosomes can encode biological significance, and its implication is being increasingly appreciated recently. Certain chromosome structural features, such as A/B compartmentalization, are frequently extracted from pairwise contact information (physical association between different regions of the genome) and compared with linear annotations of the genome, such as histone modifications and lamina association. Here, we investigate how additional properties of chromosome structure can be deduced using the abstract graph representation of the contact heatmap, and how network properties can have a better connection with some of these biological annotations. We constructed chromosome structure networks (CSNs) from bulk Hi-C data and calculated a set of site-resolved (node-based) network properties of these CSNs. We found these network properties are useful for characterizing chromosome structure features. We examined the ability of network properties in differentiating several scenarios, such as haploid vs diploid cells, partially inverted nuclei vs conventional architecture, and structural changes during cell development. We also examined the connection between network properties and a series of other linear annotations, such as histone modifications and chromatin states including poised promoter and enhancer labels. We found that semi-local network properties are more capable of characterizing genome annotations than diffusive or ultra-local node features. For example, local square clustering coefficient can be a strong classifier of lamina-associated domains (LADs), whereas a path-based network property, closeness centrality, does not vary concordantly with LAD status. We demonstrated that network properties can be useful for discerning large-scale chromosome structures that emerge in different biological situations. TOC Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC="FIGDIR/small/573476v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@45df0forg.highwire.dtl.DTLVardef@13776daorg.highwire.dtl.DTLVardef@5c1519org.highwire.dtl.DTLVardef@16d447f_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2023

Amorphous calcium phosphate-coated surfaces as a model for bone microenvironment in prostate cancer

Bone metastasis remains one of the biggest challenges in the treatment of prostate cancer, and other solid tumors such as breast, lung, and colon. Modeling a complex microenvironment in-vitro, such as the bone niche, requires interrogation of cell-cell interactions, specific extracellular matrix proteins and a high calcium environment. Here, we present a fast and cost-effective system in which commercially available, non-adhesive, cell culture vessels are coated with amorphous calcium phosphate (ACP) as a surrogate for bone matrix. We further present modified protocols for subculturing cells, as well as nucleic acid and protein collection in high calcium samples. We find that prostate epithelial cell lines show increased adhesion and proliferation when cultured in these surfaces, as well as independence from androgen starvation. We observe gene expression changes on ACP surfaces in early adenocarcinoma cell lines which may reflect alterations relevant to prostate cancer progression. Summary statementTo model the role of calcium in the microenvironment of the metastatic bone niche, we developed a cost-effective way to coat cell culture vessels in bioavailable calcium, and show that it has an effect on prostate cancer cell survival

cancer biology↗

bioRxiv2022

Differential contributions of nuclear lamina association and genome compartmentalization to gene regulation

Interactions of chromatin with the nuclear lamina play a significant role in properly organizing the genome in 3D space and in regulating gene expression. Genome wide studies have inferred the global association between the lamina, heterochromatin, gene repression and the B genomic compartment, and repositioning genes to the lamina can result in their repression. However, there are scenarios in which these features are discordant and, in those cases, the relative contribution to gene regulation of genomic compartment, chromatin, and lamin association status can be examined. Here we compared datasets from cell lines representing different states of differentiation across different cell type lineages to examine the relationships between changes in genomic compartmentalization, lamin association, and gene expression. With these data, we could examine, for example, what gene expression changes occur when a B compartment region is moved from the nuclear interior to the nuclear lamina and what differences exist between lamin associated and internal A compartment regions. In general, we observed an additive rather than redundant effect in which lamin association and compartment status both contribute to gene expression state. However, we found that cell type lineages differed in whether compartment status or lamin association had a dominant influence on gene expression. Finally, we identified conserved trends of how compartment and lamin association status influence the likelihood that gene expression will be induced or repressed in response to a physiochemical treatment.

genomics↗

bioRxiv2022

Transcriptional profiling of Hutchinson-Gilford Progeria syndrome fibroblasts reveals deficits in mesenchymal stem cell commitment to differentiation related to early events in endochondral ossification.

Hutchinson-Gilford Progeria Syndrome results from a mutation in Lamin A, and it is characterized by the incorporation of progerin into the nuclear lamina. Progerin expression leads to alterations in genome architecture, nuclear morphology, and epigenetic states, which in turn cause altered phenotypes in all cells of the mesenchymal lineage. Here, we report a comprehensive analysis of the transcriptional status of patient derived HGPS fibroblasts, including nine cell lines not previously reported. We observe that these fibroblasts carry abnormal transcriptional signatures, centering around five main functional hubs: DNA maintenance and epigenetics, bone development and homeostasis, blood vessel maturation and development, fat deposition and lipid management, and processes related to muscle growth. Stratification of patients by age revealed that a cohort of genes related to endochondral ossification and chondrogenic commitment show altered expression patterns in children aged four to seven years old, where this differentiation program starts in earnest, related to the growth of long bones. We further report changes in lamin associated domains and 3D genome organization around a cohort of genes of interest, identified in this study.

genomics↗

bioRxiv2022

Fast model-free standardization and integration of single-cell transcriptomics data

Single-cell transcriptomics datasets from the same anatomical sites generated by different research labs are becoming mainstream. However, fast, and computationally inexpensive tools for standardization of cell-type annotation and data integration are still needed to increase research inclusivity. To standardize cell-type annotation and integrate single-cell transcriptomics datasets, we have built a fast, model-free integration method called MASI (Marker-Assisted Standardization and Integration). MASI can run integrative annotation on a personal laptop for approximately one million cells, providing a cheap computational alternative for the single-cell data analysis community. MASI has an average macro F1/overall accuracy of 0.79/0.89 over the 4 benchmark datasets. We demonstrate that MASI outperforms other methods based on speed, and its performance for the tasks of data integration and cell-type annotation is comparable or even superior to other existing methods. We apply MASI for integrative lineage analysis and show that it preserves the underlying biological signal in datasets tested. Finally, to harness knowledge from single-cell atlases, we demonstrate three case studies that cover integration across research groups, biological conditions, and surveyed participants, respectively.

bioinformatics↗