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1.
ACS Synth Biol ; 2024 Sep 14.
Article in English | MEDLINE | ID: mdl-39276360

ABSTRACT

Enhancers are central for the regulation of metazoan transcription but have proven difficult to study, primarily due to a myriad of interdependent variables shaping their activity. Consequently, synthetic biology has emerged as the main approach for dissecting mechanisms of enhancer function. We start by reviewing simple but highly parallel reporter assays, which have been successful in quantifying the complexity of the activator/coactivator mechanisms at enhancers. We then describe studies that examine how enhancers function in the genomic context and in combination with other enhancers, revealing that they activate genes through a variety of different mechanisms, working together as a system. Here, we primarily focus on synthetic reporter genes that can quantify the dynamics of enhancer biology through time. We end by considering the consequences of having many genes and enhancers within a 'local environment', which we believe leads to correlated gene expression and likely reports on the general principles of enhancer biology.

2.
Sci Adv ; 10(32): eadl4893, 2024 Aug 09.
Article in English | MEDLINE | ID: mdl-39121214

ABSTRACT

Discontinuous transcription is evolutionarily conserved and a fundamental feature of gene regulation; yet, the exact mechanisms underlying transcriptional bursting are unresolved. Analyses of bursting transcriptome-wide have focused on the role of cis-regulatory elements, but other factors that regulate this process remain elusive. We applied mathematical modeling to single-cell RNA sequencing data to infer bursting dynamics transcriptome-wide under multiple conditions to identify possible molecular mechanisms. We found that Mediator complex subunit 26 (MED26) primarily regulates frequency, MYC regulates burst size, while cohesin and Bromodomain-containing protein 4 (BRD4) can modulate both. Despite comparable effects on RNA levels among these perturbations, acute depletion of MED26 had the most profound impact on the entire gene regulatory network, acting downstream of chromatin spatial architecture and without affecting TATA box-binding protein (TBP) recruitment. These results indicate that later steps in the initiation of transcriptional bursts are primary nodes for integrating gene networks in single cells.


Subject(s)
Cell Cycle Proteins , Chromatin , Gene Regulatory Networks , Transcription Factors , Transcription, Genetic , Chromatin/metabolism , Chromatin/genetics , Transcription Factors/metabolism , Transcription Factors/genetics , Cell Cycle Proteins/metabolism , Cell Cycle Proteins/genetics , Humans , Gene Expression Regulation , Mediator Complex/metabolism , Mediator Complex/genetics , Single-Cell Analysis , Transcriptome , Cohesins , Bromodomain Containing Proteins
3.
Sci Rep ; 14(1): 18426, 2024 08 08.
Article in English | MEDLINE | ID: mdl-39117696

ABSTRACT

High-throughput imaging (HTI) generates complex imaging datasets from a large number of experimental perturbations. Commercial HTI software programs for image analysis workflows typically do not allow full customization and adoption of new image processing algorithms in the analysis modules. While open-source HTI analysis platforms provide individual modules in the workflow, like nuclei segmentation, spot detection, or cell tracking, they are often limited in integrating novel analysis modules or algorithms. Here, we introduce the High-Throughput Image Processing Software (HiTIPS) to expand the range and customization of existing HTI analysis capabilities. HiTIPS incorporates advanced image processing and machine learning algorithms for automated cell and nuclei segmentation, spot signal detection, nucleus tracking, nucleus registration, spot tracking, and quantification of spot signal intensity. Furthermore, HiTIPS features a graphical user interface that is open to integration of new analysis modules for existing analysis pipelines and to adding new analysis modules. To demonstrate the utility of HiTIPS, we present three examples of image analysis workflows for high-throughput DNA FISH, immunofluorescence (IF), and live-cell imaging of transcription in single cells. Altogether, we demonstrate that HiTIPS is a user-friendly, flexible, and open-source HTI software platform for a variety of cell biology applications.


Subject(s)
Cell Nucleus , Image Processing, Computer-Assisted , Software , Cell Nucleus/genetics , Cell Nucleus/metabolism , Image Processing, Computer-Assisted/methods , Humans , Algorithms , In Situ Hybridization, Fluorescence/methods , Gene Expression , Machine Learning
4.
Hum Pathol ; 151: 105628, 2024 Sep.
Article in English | MEDLINE | ID: mdl-39029535

ABSTRACT

Salivary gland amyloidosis is an uncommon diagnosis. Most studies have focused on minor salivary gland biopsies as a surrogate site for diagnosing systemic amyloidosis, while only few studies have investigated major salivary gland amyloidosis. We retrospectively identified 57 major and minor salivary gland amyloidosis cases typed using a proteomics-based method between 2010 and 2022. Frequency of amyloid types, clinicopathologic features, and distribution patterns of amyloid deposits were assessed. The indication for salivary gland biopsy/resection (known in 34 cases) included suspected amyloidosis (N = 14; 41.2%), lesion/mass (N = 12; 35.3%), swelling/enlargement (N = 5; 14.7%), and rule out Sjogren syndrome (N = 3; 8.8%). Concurrent pathology was reported in 16 cases, and included chronic sialadenitis (N = 11), extranodal marginal zone lymphoma (N = 3), plasma cell neoplasm (N = 1), and pleomorphic adenoma (N = 1). We identified 3 types of amyloidosis: immunoglobulin light chain/AL (N = 47; 82.5%); immunoglobulin heavy chain/AH (N = 1; 1.8%), and transthyretin/ATTR (N = 9; 15.8%). The patterns of amyloid deposits (assessed in 35 cases) included: 1) Perivascular and/or periductal distribution (N = 18; 51.4%); 2) Mass formation (N = 9; 25.7%); 3) Stromal micronodule formation (N = 7; 20.0%); and 4) Diffuse interstitial involvement (N = 1; 2.9%). We also identified one case of AL amyloidosis localized to the major salivary gland, where only 6 other cases with adequate staging workup to exclude systemic amyloidosis were previously reported. In conclusion, salivary gland amyloidosis is an uncommon diagnosis but may be underrecognized due to low index of suspicion. Most cases of salivary gland amyloidosis are AL type, but a minority are ATTR. Therefore, proteomics-based typing remains essential for treatment and prognosis.


Subject(s)
Amyloidosis , Proteomics , Humans , Female , Male , Middle Aged , Amyloidosis/pathology , Amyloidosis/diagnosis , Aged , Retrospective Studies , Adult , Aged, 80 and over , Salivary Gland Diseases/pathology , Salivary Gland Diseases/diagnosis , Amyloid/metabolism , Amyloid/analysis , Salivary Glands/pathology , Biopsy
5.
Nat Commun ; 15(1): 6226, 2024 Jul 23.
Article in English | MEDLINE | ID: mdl-39043639

ABSTRACT

Fluctuations in the initiation rate of transcription, the first step in gene expression, ensue from the stochastic behavior of the molecular process that controls transcription. In steady state, the regulatory process is often assumed to operate reversibly, i.e., in equilibrium. However, reversibility imposes fundamental limits to information processing. For instance, the assumption of equilibrium is difficult to square with the precision with which the regulatory process executes its task in eukaryotes. Here we provide evidence - from microscopic analyses of the transcription dynamics at a single gene copy of yeast - that the regulatory process for transcription is cyclic and irreversible (out of equilibrium). The necessary coupling to reservoirs of free energy occurs via sequence-specific transcriptional activators and the recruitment, in part, of ATP-dependent chromatin remodelers. Our findings may help explain how eukaryotic cells reconcile the dual but opposing requirements for fast regulatory kinetics and high regulatory specificity.


Subject(s)
Gene Expression Regulation, Fungal , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae , Transcription, Genetic , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae Proteins/genetics , Chromatin Assembly and Disassembly , Transcription Factors/metabolism , Transcription Factors/genetics , Kinetics , Adenosine Triphosphate/metabolism
6.
bioRxiv ; 2024 Jun 08.
Article in English | MEDLINE | ID: mdl-38903099

ABSTRACT

Stochastic transcriptional bursting is a universal property of active genes. While different genes exhibit distinct bursting patterns, the molecular mechanisms for gene-specific stochastic bursting are largely unknown. We have developed and applied a high-throughput-imaging based screening strategy to identify cellular factors and molecular mechanisms that determine the bursting behavior of human genes. Focusing on epigenetic regulators, we find that protein acetylation is a strong acute modulator of burst frequency, burst size and heterogeneity of bursting. Acetylation globally affects the Off-time of genes but has gene-specific effects on the On-time. Yet, these effects are not strongly linked to promoter acetylation, which do not correlate with bursting properties, and forced promoter acetylation has variable effects on bursting. Instead, we demonstrate acetylation of the Integrator complex as a key determinant of gene bursting. Specifically, we find that elevated Integrator acetylation decreases bursting frequency. Taken together our results suggest a prominent role of non-histone proteins in determining gene bursting properties, and they identify histone-independent acetylation of a transcription cofactor as an allosteric modulator of bursting via a far-downstream bursting checkpoint.

7.
Arch Pathol Lab Med ; 2024 Jun 05.
Article in English | MEDLINE | ID: mdl-38838342

ABSTRACT

CONTEXT.­: The joint College of American Pathologists/American College of Medical Genetics and Genomics Cytogenetics Committee works to ensure competency and proficiency of clinical cytogenetics testing laboratories through proficiency testing programs for various clinical tests offered by such laboratories, including the evaluation of constitutional abnormalities. OBJECTIVE.­: To review and analyze 20 years of constitutional chromosome analysis proficiency testing results (2003-2022), primarily utilizing G-banded karyograms. DESIGN.­: A retrospective review of results from 2003 through 2022 was performed, identifying challenges addressing constitutional disorders. The chromosomal abnormalities and overall performance were evaluated. RESULTS.­: A total of 184 cases from 161 proficiency testing challenges were administered from 2003 through 2022. Challenges consisted of metaphase images and accompanying clinical history for evaluation of numerical and/or structural abnormalities. Of the 184 cases, only 2 (1%) failed to reach an 80% grading consensus for recognition of the abnormality. Both cases illustrated the limitations of correctly characterizing some chromosomal abnormalities, including recombinant chromosomal abnormalities and isochromosome identification. In addition, 2 cases failed to reach a consensus for nomenclature reporting: 1 with an isochromosome and another with a duplication. CONCLUSIONS.­: This 20-year review illustrates the high rate of competency and proficiency of cytogenetic laboratories in the correct identification of constitutional chromosome abnormalities.

8.
Nat Biomed Eng ; 8(4): 443-460, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38561490

ABSTRACT

Allogeneic mesenchymal stromal cells (MSCs) are a safe treatment option for many disorders of the immune system. However, clinical trials using MSCs have shown inconsistent therapeutic efficacy, mostly owing to MSCs providing insufficient immunosuppression in target tissues. Here we show that antigen-specific immunosuppression can be enhanced by genetically modifying MSCs with chimaeric antigen receptors (CARs), as we show for E-cadherin-targeted CAR-MSCs for the treatment of graft-versus-host disease in mice. CAR-MSCs led to superior T-cell suppression and localization to E-cadherin+ colonic cells, ameliorating the animals' symptoms and survival rates. On antigen-specific stimulation, CAR-MSCs upregulated the expression of immunosuppressive genes and receptors for T-cell inhibition as well as the production of immunosuppressive cytokines while maintaining their stem cell phenotype and safety profile in the animal models. CAR-MSCs may represent a widely applicable therapeutic technology for enhancing immunosuppression.


Subject(s)
Graft vs Host Disease , Immunosuppression Therapy , Mesenchymal Stem Cells , Receptors, Chimeric Antigen , Animals , Mesenchymal Stem Cells/immunology , Mesenchymal Stem Cells/cytology , Mesenchymal Stem Cells/metabolism , Mice , Immunosuppression Therapy/methods , Receptors, Chimeric Antigen/metabolism , Receptors, Chimeric Antigen/immunology , Receptors, Chimeric Antigen/genetics , Graft vs Host Disease/immunology , Humans , Mesenchymal Stem Cell Transplantation/methods , T-Lymphocytes/immunology , Cadherins/metabolism , Mice, Inbred C57BL , Cytokines/metabolism
9.
Int J Exerc Sci ; 17(1): 220-234, 2024.
Article in English | MEDLINE | ID: mdl-38665161

ABSTRACT

Electroencephalography (EEG) allows for the evaluation of real time changes in brain (electrocortical) activity during exercise. A few studies have examined changes in electrocortical activity using stationary cycling, but the findings have been mixed. Some of these studies have found increases in brain activity following exercise, while others have found decreases in brain activity following exercise. Hence, it is of importance to identify post-exercise changes in brain activity. Sixteen healthy, untrained subjects (8 males; 8 females) participated in the study. All 16 participants performed a graded exercise test (GXT) to volitional exhaustion on an upright cycle ergometer. Continuous EEG recordings were sampled before (PRE) and immediately following (IP) the GXT. Regions of interest were primarily the dorsolateral prefrontal cortex (DLPFC), ventrolateral prefrontal cortex (VLPFC), and left and right motor cortex (MC). In the DLPFC, a frontal asymmetry index was also identified. There was a statistically significant increase in theta power in the DLPFC, VLPFC, and left and right MC from PRE to IP (all p < 0.05). There was also a shift towards right hemisphere asymmetry at the IP time point in the DLPFC (p < 0.05). Finally, there was an increase in alpha power from PRE to IP in the right MC (p < 0.05). EEG could prove to be an important way to measure the effects of central fatigue on brain activity before and immediately following exercise.

10.
Psychol Aging ; 39(5): 551-564, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38421758

ABSTRACT

Appearance is an indicator of age and life stage, which are linked to socially salient stereotypes and prejudices. Older adults' appearance-related perceptions and behaviors may affect their experiences of aging within broader society, which may in turn influence health. This study examined associations between two measures related to aging appearance-assessment of one's aging appearance relative to same-age peers and investing time or effort to look younger-positive and negative experiences of aging, and health using multivariable regression. Cross-sectional data were from a nationally representative sample of 2006 U.S. adults ages 50-80 (Mage = 63, 52% women, 71% White) who completed Wave 6 of the National Poll on Healthy Aging in 2019. The majority (59%) reported appearing relatively younger than peers, while fewer reported appearing the same age (35%) or older (6%). About a third (35%) reported investing in looking younger. Appearing relatively younger was associated with more positive (p < .001) and less negative experiences of aging (p = .019). Appearing relatively older showed the opposite relationships (p values < .001). Investing in looking younger was associated with more positive and more negative experiences of aging (p values < .001). Few sociodemographic variations were detected. More positive and less negative experiences of aging were associated with better physical and mental health (p values < .001). While aging appearance is often the basis for jokes, it may affect the quality of older adults' experiences of aging and associated health outcomes. Nuanced findings caution against framing youthful biases in aging appearance and investments in looking younger as solely negative (or positive). (PsycInfo Database Record (c) 2024 APA, all rights reserved).


Subject(s)
Aging , Humans , Aged , Female , Male , Middle Aged , Aged, 80 and over , Aging/psychology , Aging/physiology , United States , Cross-Sectional Studies , Self Concept , Health Status
11.
Gait Posture ; 107: 194-198, 2024 01.
Article in English | MEDLINE | ID: mdl-37833200

ABSTRACT

BACKGROUND: Multiple sclerosis (MS) is a neurological disease characterized by demyelination disrupting the central nervous system. Persons with MS may exhibit symptomatic strength asymmetry (SA) that impacts motor gait and ankle mobility. The purpose of the present study was to investigate ankle dorsiflexion SA in people with MS and its relationship to functional performance. RESEARCH QUESTION: Is their a difference in dorsiflexion SA in MS participants compared to healthy individuals and does it impact functional performance? METHODS: 13 MS participants (EDSS 3.5 + 1.8) and 13 age matched NON-MS participants underwent maximal isometric (MVC) dynamometry testing for ankle dorsiflexion in both limbs to determine SA. Participants performed three functional tasks of walking performance. RESULTS: There was a significant intra-limb MVC difference in the MS group, and significantly greater isometric SA (p < 0.007) and isokinetic SA (p < 0.04) in the MS group compared to healthy individuals. The MS group exhibited significant correlations between outcomes of functional walking performance with isokinetic but not isometric SA. There was no significant correlation between disability status and functional task performance. SIGNIFICANCE: Ankle dorsiflexion SA is negatively correlated with functional performance in MS participants. MS disability status was not a predictor of functional task performance, and symptom testing may be appropriate to assess walking ability in persons with MS.


Subject(s)
Multiple Sclerosis , Humans , Multiple Sclerosis/complications , Ankle , Walking/physiology , Gait/physiology , Ankle Joint
12.
bioRxiv ; 2023 Nov 05.
Article in English | MEDLINE | ID: mdl-38076967

ABSTRACT

High-throughput imaging (HTI) generates complex imaging datasets from a large number of experimental perturbations. Commercial HTI software for image analysis workflows does not allow full customization and adoption of new image processing algorithms in the analysis modules. While open-source HTI analysis platforms provide individual modules in the workflow, like nuclei segmentation, spot detection, or cell tracking, they are often limited in integrating novel analysis modules or algorithms. Here, we introduce the High-Throughput Image Processing Software (HiTIPS) to expand the range and customization of existing HTI analysis capabilities. HiTIPS incorporates advanced image processing and machine learning algorithms for automated cell and nuclei segmentation, spot signal detection, nucleus tracking, spot tracking, and quantification of spot signal intensity. Furthermore, HiTIPS features a graphical user interface that is open to integration of new algorithms for existing analysis pipelines and to adding new analysis pipelines through separate plugins. To demonstrate the utility of HiTIPS, we present three examples of image analysis workflows for high-throughput DNA FISH, immunofluorescence (IF), and live-cell imaging of transcription in single cells. Altogether, we demonstrate that HiTIPS is a user-friendly, flexible, and open-source HTI analysis platform for a variety of cell biology applications.

13.
Nano Lett ; 23(22): 10334-10341, 2023 Nov 22.
Article in English | MEDLINE | ID: mdl-37955966

ABSTRACT

Intercalation reactions modify the charge density in van der Waals (vdW) materials through coupled electronic-ionic charge accumulation and are susceptible to modulation by interlayer hybridization in vdW heterostructures. Here, we demonstrate that charge transfer between graphene and α-RuCl3, which hole-dopes the graphene, greatly favors the intercalation of lithium ions into graphene-based vdW heterostructures. We systematically tune this effect on Li+ ion intercalation, modulating the intercalation potential, by using varying thicknesses of hexagonal boron nitride (hBN) as spacer layers between graphene and α-RuCl3. Confocal Raman spectroscopy and electronic transport measurements are used to monitor electrochemical intercalation, and density functional theory computations help quantify charge transfer to both α-RuCl3 and graphene upon Li intercalation. This work demonstrates a versatile approach for systematically modulating the electrochemical intercalation behavior of two-dimensional layers akin to electron donating/withdrawing substituent effects used to tune molecular redox potentials.

14.
Blood Cancer J ; 13(1): 124, 2023 08 18.
Article in English | MEDLINE | ID: mdl-37591873

ABSTRACT

T-lymphocytes are prevalent in the tumor microenvironment of follicular lymphoma (FL). However, the phenotype of T-cells may vary, and the prevalence of certain T-cell subsets may influence tumor biology and patient survival. We therefore analyzed a cohort of 82 FL patients using CyTOF to determine whether specific T-cell phenotypes were associated with distinct tumor microenvironments and patient outcome. We identified four immune subgroups with differing T-cell phenotypes and the prevalence of certain T-cell subsets was associated with patient survival. Patients with increased T cells with early differentiation stage tended to have a significantly better survival than patients with increased T-cells of late differentiation stage. Specifically, CD57+ TFH cells, with a late-stage differentiation phenotype, were significantly more abundant in FL patients who had early disease progression and therefore correlated with an inferior survival. Single cell analysis (CITE-seq) revealed that CD57+ TFH cells exhibited a substantially different transcriptome from CD57- TFH cells with upregulation of inflammatory pathways, evidence of immune exhaustion and susceptibility to apoptosis. Taken together, our results show that different tumor microenvironments among FL patients are associated with variable T-cell phenotypes and an increased prevalence of CD57+ TFH cells is associated with poor patient survival.


Subject(s)
Lymphoma, Follicular , T Follicular Helper Cells , Humans , Tumor Microenvironment , Cell Differentiation , Phenotype
15.
Physiol Rep ; 11(11): e15735, 2023 06.
Article in English | MEDLINE | ID: mdl-37287070

ABSTRACT

A monoexponential model characterizing cerebral blood velocity dynamics at the onset of exercise may mask dynamic responses by the cerebrovasculature countering large fluctuations of middle cerebral artery blood velocity (MCAv) and cerebral perfusion pressure (CPP) oscillations. Therefore, the purpose of this study was to determine whether the use of a monoexponential model attributes initial fluctuations of MCAv at the start of exercise as a time delay (TD). Twenty-three adults (10 women, 23.9 ± 3.3 yrs; 23.7 ± 2.4 kg/m2 ) completed 2 min of rest followed by 3 mins of recumbent cycling at 50 W. MCAv, CPP, and Cerebrovascular Conductance index (CVCi), calculated as CVCi = MCAv/MAP × 100 mmHg, were collected, a lowpass filter (0.2 Hz) was applied, and averaged into 3-second bins. MCAv data were then fit to a monoexponential model [ΔMCAv(t) = Amp(1 - e-(t-TD)/τ )]. TD, tau (τ), and mean response time (MRT = TD + τ) were obtained from the model. Subjects exhibited a TD of 20.2 ± 18.1 s. TD was directly correlated with MCAv nadir (MCAvN ), r = -0.560, p = 0.007, which occurred at similar times (16.5 ± 15.3 vs. 20.2 ± 18.1 s, p = 0.967). Regressions indicated CPP as the strongest predictor of MCAvN ( R a 2 $$ {R}_a^2 $$ = 0.36). Fluctuations in MCAv were masked using a monoexponential model. To adequately understand cerebrovascular mechanisms during the transition from rest to exercise, CPP and CVCi must also be analyzed. A concurrent drop in cerebral perfusion pressure and middle cerebral artery blood velocity at the start of exercise forces the cerebrovasculature to respond to maintain cerebral blood flow. The use of a monoexponential model characterizes this initial phase as a time delay and masks this large important response.


Subject(s)
Cerebrovascular Circulation , Exercise , Adult , Humans , Female , Blood Flow Velocity/physiology , Exercise/physiology , Cerebrovascular Circulation/physiology , Middle Cerebral Artery/physiology , Rest , Blood Pressure/physiology
16.
Curr Hematol Malig Rep ; 18(5): 144-157, 2023 10.
Article in English | MEDLINE | ID: mdl-37294394

ABSTRACT

PURPOSE OF REVIEW: The treatment paradigm of chronic lymphocytic leukemia (CLL) has dramatically changed with the advent of novel targeted agents over the past decade. Richter transformation (RT), or the development of an aggressive lymphoma from a background of CLL, is a well-recognized complication of CLL and carries significantly poor clinical outcomes. Here, we provide an update on current diagnostics, prognostication, and contemporary treatment of RT. RECENT FINDINGS: Several genetic, biologic, and laboratory markers have been proposed as candidate risk factors for the development of RT. Although a diagnosis of RT is typically suspected based on clinical and laboratory findings, tissue biopsy is essential for histopathologic confirmation of diagnosis. The standard of care for RT treatment at this time remains chemoimmunotherapy with the goal of proceeding to allogeneic stem cell transplantation in eligible patients. Several newer treatment modalities are being studied for use in the management of RT, including small molecules, immunotherapy, bispecific antibodies, and chimeric antigen receptor T-cell (CAR-T) therapy. The management of patients with RT remains a challenge. Ongoing trials show enormous promise for newer classes of therapy in RT, with the hope being that these agents can synergize, and perhaps supersede, the current standard of care in the near future.


Subject(s)
Leukemia, Lymphocytic, Chronic, B-Cell , Lymphoma, Large B-Cell, Diffuse , Humans , Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis , Leukemia, Lymphocytic, Chronic, B-Cell/etiology , Leukemia, Lymphocytic, Chronic, B-Cell/therapy , Lymphoma, Large B-Cell, Diffuse/pathology , Immunotherapy , Biopsy , Cell Transformation, Neoplastic/genetics
17.
Leukemia ; 37(7): 1485-1498, 2023 07.
Article in English | MEDLINE | ID: mdl-37117318

ABSTRACT

The role of the tumor microenvironment (TME) and intratumoral T cells in splenic marginal zone lymphoma (sMZL) is largely unknown. In the present study, we evaluated 36 sMZL spleen specimens by single cell analysis to gain a better understanding of the TME in sMZL. Using mass cytometry (CyTOF), we observed that the TME in sMZL is distinct from that of control non-malignant reactive spleen (rSP). We found that the number of TFH cells varied greatly in sMZL, ICOS+ TFH cells were more abundant in sMZL than rSP, and TFH cells positively correlated with increased numbers of memory B cells. Treg cell analysis revealed that TIGIT+ Treg cells are enriched in sMZL and correlate with suppression of TH17 and TH22 cells. Intratumoral CD8+ T cells were comprised of subsets of short-lived, exhausted and late-stage differentiated cells, thereby functionally impaired. We observed that T-cell exhaustion was present in sMZL and TIM-3 expression on PD-1low cells identified cells with severe immune dysfunction. Gene expression profiling by CITE-seq analysis validated this finding. Taken together, our data suggest that the TME as a whole, and T-cell population specifically, are heterogenous in sMZL and immune exhaustion is one of the major factors impairing T-cell function.


Subject(s)
Leukemia, Lymphocytic, Chronic, B-Cell , Lymphoma, B-Cell, Marginal Zone , Lymphoma , Splenic Neoplasms , Humans , Tumor Microenvironment , CD8-Positive T-Lymphocytes/metabolism , Splenic Neoplasms/genetics , Splenic Neoplasms/metabolism , Splenic Neoplasms/pathology , Lymphoma, B-Cell, Marginal Zone/genetics
18.
EMBO J ; 42(7): e112358, 2023 04 03.
Article in English | MEDLINE | ID: mdl-36762421

ABSTRACT

The recognition of polyadenylation signals (PAS) in eukaryotic pre-mRNAs is usually coupled to transcription termination, occurring while pre-mRNA is chromatin-bound. However, for some pre-mRNAs, this 3'-end processing occurs post-transcriptionally, i.e., through a co-transcriptional cleavage (CoTC) event downstream of the PAS, leading to chromatin release and subsequent PAS cleavage in the nucleoplasm. While DNA-damaging agents trigger the shutdown of co-transcriptional chromatin-associated 3'-end processing, specific compensatory mechanisms exist to ensure efficient 3'-end processing for certain pre-mRNAs, including those that encode proteins involved in the DNA damage response, such as the tumor suppressor p53. We show that cleavage at the p53 polyadenylation site occurs in part post-transcriptionally following a co-transcriptional cleavage event. Cells with an engineered deletion of the p53 CoTC site exhibit impaired p53 3'-end processing, decreased mRNA and protein levels of p53 and its transcriptional target p21, and altered cell cycle progression upon UV-induced DNA damage. Using a transcriptome-wide analysis of PAS cleavage, we identify additional pre-mRNAs whose PAS cleavage is maintained in response to UV irradiation and occurring post-transcriptionally. These findings indicate that CoTC-type cleavage of pre-mRNAs, followed by PAS cleavage in the nucleoplasm, allows certain pre-mRNAs to escape 3'-end processing inhibition in response to UV-induced DNA damage.


Subject(s)
Polyadenylation , Tumor Suppressor Protein p53 , Tumor Suppressor Protein p53/genetics , Tumor Suppressor Protein p53/metabolism , DNA Damage , RNA Precursors/genetics , RNA Precursors/metabolism , Chromatin
19.
Elife ; 122023 02 15.
Article in English | MEDLINE | ID: mdl-36790144

ABSTRACT

The role of the spatial organization of chromosomes in directing transcription remains an outstanding question in gene regulation. Here, we analyze two recent single-cell imaging methodologies applied across hundreds of genes to systematically analyze the contribution of chromosome conformation to transcriptional regulation. Those methodologies are (1) single-cell chromatin tracing with super-resolution imaging in fixed cells; and (2) high-throughput labeling and imaging of nascent RNA in living cells. Specifically, we determine the contribution of physical distance to the coordination of transcriptional bursts. We find that individual genes adopt a constrained conformation and reposition toward the centroid of the surrounding chromatin upon activation. Leveraging the variability in distance inherent in single-cell imaging, we show that physical distance - but not genomic distance - between genes on individual chromosomes is the major factor driving co-bursting. By combining this analysis with live-cell imaging, we arrive at a corrected transcriptional correlation of [Formula: see text] for genes separated by < 400 nm. We propose that this surprisingly large correlation represents a physical property of human chromosomes and establishes a benchmark for future experimental studies.


Subject(s)
Chromatin , Chromosomes , Humans , Chromosomes, Human , Gene Expression Regulation , Genome , Diagnostic Imaging
20.
Open J Blood Dis ; 13(4): 121-132, 2023 Dec.
Article in English | MEDLINE | ID: mdl-38361601

ABSTRACT

Adult intussusception is rare, highly associated with a malignant lead point, and often requires emergent surgical management. We report the case of a 44-year-old male who presented with generalized abdominal pain and was found to have early ileocolic intussusception secondary to a large ileocecal mass. Biopsies of the mass and an enlarged cardiophrenic lymph node, as well as pleural fluid cytology were all consistent with Burkitt lymphoma (BL). Curiously, the patient's abdominal exam was reassuring, and the intussusception and malignant bowel obstruction resolved over 36 hours with conservative management alone. With a Burkitt lymphoma international prognostic index (BL-IPI) score of 2, the patient proceeded to treatment with combination chemoimmunotherapy and attained a complete response after four cycles. There was no bowel perforation or recurrent intussusception throughout treatment. Thus, this report marks the first reported case of adult BL-associated intussusception to resolve with non-invasive management and establishes a precedent for conservative management in select patients.

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