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1.
Clin J Pain ; 2024 Sep 12.
Artigo em Inglês | MEDLINE | ID: mdl-39263907

RESUMO

OBJECTIVE: This study compares clinical pain outcomes between patients in a pain treatment program that was conducted in-person, compared to a virtual program. METHODS: In-Person (N=127) and Virtual (N=101) pain treatment programs were compared based on patient-reported, practitioner-collected, and medical record data. The patients were measured at baseline and post treatment (week 12 for In-Person and week 8 for Virtual patients). We employed last observation carried forward (LOCF) to handle missing data. RESULTS: Both the In-Person and Virtual groups were similar in regard to all baseline outcomes, except the In-Person group having significantly more co-morbidities at baseline, with particularly more cases of mental, behavioral, or neurodevelopmental diseases. Both groups demonstrated significant improvements in the pain-related measurements of pain interference and pain catastrophizing thoughts, but neither group displayed a change in average pain across treatment. Further, both groups improved significantly on emotional well-being scores, but not on physical functioning scores. No significant differences existed between groups on outcomes, except for pain catastrophizing, which was higher in the Virtual group at both time points. The Virtual group had lower rates of dropouts compared to In-Person, while the In-Person group had a larger proportion reach a clinically meaningful change in pain-related outcomes, defined as a >30% improvement. DISCUSSION: While some changes were unique to the In-Person program, overall, patients in the Virtual program achieved similar treatment outcomes, suggesting that it can successfully treat Veterans seeking pain management, with less need for in-person facilities for both patients and clinicians.

2.
bioRxiv ; 2024 Aug 27.
Artigo em Inglês | MEDLINE | ID: mdl-39253426

RESUMO

Epigenetic mechanisms govern the transcriptional activity of lineage-specifying enhancers; but recent work challenges the dogma that joint chromatin accessibility and DNA demethylation are prerequisites for transcription. To understand this paradox, we established a highly-resolved timeline of DNA demethylation, chromatin accessibility, and transcription factor occupancy during neural progenitor cell differentiation. We show thousands of enhancers undergo rapid, transient accessibility changes associated with distinct periods of transcription factor expression. However, most DNA methylation changes are unidirectional and delayed relative to chromatin dynamics, creating transiently discordant epigenetic states. Genome-wide detection of 5-hydroxymethylcytosine further revealed active demethylation begins ahead of chromatin and transcription factor activity, while enhancer hypomethylation persists long after these activities have dissipated. We demonstrate that these timepoint specific methylation states predict past, present and future chromatin accessibility using machine learning models. Thus, chromatin and DNA methylation collaborate on different timescales to mediate short and long-term enhancer regulation during cell fate specification.

3.
Nat Commun ; 15(1): 7204, 2024 Aug 22.
Artigo em Inglês | MEDLINE | ID: mdl-39169060

RESUMO

Crohn's disease (CD) is a complex chronic inflammatory disorder with both gastrointestinal and extra-intestinal manifestations associated immune dysregulation. Analyzing 202,359 cells from 170 specimens across 83 patients, we identify a distinct epithelial cell type in both terminal ileum and ascending colon (hereon as 'LND') with high expression of LCN2, NOS2, and DUOX2 and genes related to antimicrobial response and immunoregulation. LND cells, confirmed by in-situ RNA and protein imaging, are rare in non-IBD controls but expand in active CD, and actively interact with immune cells and specifically express IBD/CD susceptibility genes, suggesting a possible function in CD immunopathogenesis. Furthermore, we discover early and late LND subpopulations with different origins and developmental potential. A higher ratio of late-to-early LND cells correlates with better response to anti-TNF treatment. Our findings thus suggest a potential pathogenic role for LND cells in both Crohn's ileitis and colitis.


Assuntos
Colo , Doença de Crohn , Oxidases Duais , Células Epiteliais , Íleo , Lipocalina-2 , Doença de Crohn/patologia , Doença de Crohn/genética , Doença de Crohn/imunologia , Humanos , Células Epiteliais/metabolismo , Células Epiteliais/patologia , Colo/patologia , Íleo/patologia , Lipocalina-2/metabolismo , Lipocalina-2/genética , Oxidases Duais/genética , Oxidases Duais/metabolismo , Masculino , Óxido Nítrico Sintase Tipo II/metabolismo , Óxido Nítrico Sintase Tipo II/genética , Feminino , Adulto , Fator de Necrose Tumoral alfa/metabolismo , Mucosa Intestinal/patologia , Mucosa Intestinal/metabolismo , Pessoa de Meia-Idade
4.
Cell Death Differ ; 31(9): 1170-1183, 2024 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-39048708

RESUMO

Undifferentiated intestinal stem cells (ISCs) are crucial for maintaining homeostasis and resolving injury. Lgr5+ cells in the crypt base constantly divide, pushing daughter cells upward along the crypt axis where they differentiate into specialized cell types. Coordinated execution of complex transcriptional programs is necessary to allow for the maintenance of undifferentiated stem cells while permitting differentiation of the wide array of intestinal cells necessary for homeostasis. Previously, members of the myeloid translocation gene (MTG) family have been identified as transcriptional co-repressors that regulate stem cell maintenance and differentiation programs in multiple organ systems, including the intestine. One MTG family member, myeloid translocation gene related 1 (MTGR1), has been recognized as a crucial regulator of secretory cell differentiation and response to injury. However, whether MTGR1 contributes to the function of ISCs has not yet been examined. Here, using Mtgr1-/- mice, we have assessed the effects of MTGR1 loss specifically in ISC biology. Interestingly, loss of MTGR1 increased the total number of cells expressing Lgr5, the canonical marker of cycling ISCs, suggesting higher overall stem cell numbers. However, expanded transcriptomic and functional analyses revealed deficiencies in Mtgr1-null ISCs, including deregulated ISC-associated transcriptional programs. Ex vivo, intestinal organoids established from Mtgr1-null mice were unable to survive and expand due to aberrant differentiation and loss of stem and proliferative cells. Together, these results indicate that the role of MTGR1 in intestinal differentiation is likely stem cell intrinsic and identify a novel role for MTGR1 in maintaining ISC function.


Assuntos
Diferenciação Celular , Intestino Delgado , Células-Tronco , Animais , Camundongos , Células-Tronco/metabolismo , Células-Tronco/citologia , Intestino Delgado/citologia , Intestino Delgado/metabolismo , Camundongos Knockout , Receptores Acoplados a Proteínas G/metabolismo , Receptores Acoplados a Proteínas G/genética , Camundongos Endogâmicos C57BL , Organoides/metabolismo , Organoides/citologia , Proteínas Repressoras/metabolismo , Proteínas Repressoras/genética
5.
J Psychiatr Res ; 177: 97-101, 2024 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-39002532

RESUMO

Anhedonia, a transdiagnostic symptom present in many neuropsychiatric disorders, differs in males and females. Parietal EEG alpha asymmetry is associated with reduced arousal and low positive emotionality, and is, therefore, a promising neurophysiologic biomarker of anhedonia. To date, however, no prior studies have determined whether this measure captures sex differences in anhedonic expression. This preliminary study (N = 36) investigated whether anhedonia severity is associated with EEG resting-state parietal alpha asymmetry in adults and whether sex moderates this relationship. Results showed that there was a significant moderating effect of sex such that, only for females, higher levels of anhedonia were associated with increased parietal alpha asymmetry. These findings suggest that parietal alpha asymmetry is a promising biomarker of anhedonia severity in female adults and reinforces the need to account for sex differences in future research.


Assuntos
Ritmo alfa , Anedonia , Lobo Parietal , Caracteres Sexuais , Humanos , Feminino , Anedonia/fisiologia , Masculino , Ritmo alfa/fisiologia , Adulto , Lobo Parietal/fisiopatologia , Lobo Parietal/diagnóstico por imagem , Adulto Jovem , Eletroencefalografia , Adolescente , Escalas de Graduação Psiquiátrica , Lateralidade Funcional/fisiologia
6.
bioRxiv ; 2024 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-39005465

RESUMO

Glucolipotoxicity, caused by combined hyperglycemia and hyperlipidemia, results in ß-cell failure and type 2 diabetes (T2D) via cellular stress-related mechanisms. Activating transcription factor 4 (Atf4) is an essential effector of stress response. We show here that Atf4 expression in ß-cells is dispensable for glucose homeostasis in young mice, but it is required for ß-cell function during aging and under obesity-related metabolic stress. Henceforth, aged Atf4- deficient ß-cells display compromised secretory function under acute hyperglycemia. In contrast, they are resistant to acute free fatty acid-induced loss-of identity and dysfunction. At molecular level, Atf4 -deficient ß-cells down-regulate genes involved in protein translation, reducing ß-cell identity gene products under high glucose. They also upregulate several genes involved in lipid metabolism or signaling, likely contributing to their resistance to free fatty acid-induced dysfunction. These results suggest that Atf4 activation is required for ß-cell identity and function under high glucose, but this paradoxically induces ß-cell failure in the presence of high levels of free fatty acids. Different branches of Atf4 activity could be manipulated for protecting ß-cells from metabolic stress-induced failure. Highlights: Atf4 is dispensable in ß-cells in young miceAtf4 protects ß-cells under high glucoseAtf4 exacerbate fatty acid-induced ß-cell defectsAtf4 activates translation but depresses lipid-metabolism.

7.
Commun Biol ; 7(1): 893, 2024 Jul 29.
Artigo em Inglês | MEDLINE | ID: mdl-39075164

RESUMO

Maintenance of autonomic homeostasis is continuously calibrated by sensory fibers of the vagus nerve and sympathetic chain that convey compound action potentials (CAPs) to the central nervous system. Lipopolysaccharide (LPS) intravenous challenge reliably elicits a robust inflammatory response that can resemble systemic inflammation and acute endotoxemia. Here, we administered LPS intravenously in nine healthy subjects while recording ventral cervical magnetoneurography (vcMNG)-derived CAPs at the rostral Right Nodose Ganglion (RNG) and the caudal Right Carotid Artery (RCA) with optically pumped magnetometers (OPM). We observed vcMNG RNG and RCA neural firing rates that tracked changes in TNF-α levels in the systemic circulation. Further, endotype subgroups based on high and low IL-6 responders segregate RNG CAP frequency (at 30-120 min) and based on high and low IL-10 response discriminate RCA CAP frequency (at 0-30 min). These vcMNG tools may enhance understanding and management of the neuroimmune axis that can guide personalized treatment based on an individual's distinct endophenotype.


Assuntos
Inflamação , Lipopolissacarídeos , Humanos , Masculino , Feminino , Inflamação/induzido quimicamente , Adulto , Potenciais de Ação/efeitos dos fármacos , Adulto Jovem , Artérias Carótidas , Magnetometria/métodos
8.
Neurosci Biobehav Rev ; 163: 105750, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-38849067

RESUMO

Posttraumatic Stress Disorder (PTSD) is highly co-morbid with chronic pain conditions. When present, PTSD significantly worsens chronic pain outcomes. Likewise, pain contributes to a more severe PTSD as evidenced by greater disability, more frequent use of harmful opioid analgesics and increased pain severity. The biomechanism behind this comorbidity is incompletely understood, however recent work strongly supports the widely-accepted role of expectation, in the entanglement of chronic pain and trauma symptoms. This work has shown that those with trauma have a maladaptive brain response while expecting stress and pain, whereas those with chronic pain may have a notable impairment in brain response while expecting pain relief. This dynamical expectation model of the interaction between neural systems underlying expectation of pain onset (traumatic stress) and pain offset (chronic pain) is biologically viable and may provide a biomechanistic insight into pain-trauma comorbidity. These predictive mechanisms work through interoceptive pathways in the brain critically the insula cortex. Here we highlight how the neural expectation-related mechanisms augment the existing models of pain and trauma to better understand the dynamics of pain and trauma comorbidity. These ideas will point to targeted complementary clinical approaches, based on mechanistically separable neural biophenotypes for the entanglement of chronic pain and trauma symptoms.


Assuntos
Dor Crônica , Comorbidade , Transtornos de Estresse Pós-Traumáticos , Humanos , Dor Crônica/fisiopatologia , Transtornos de Estresse Pós-Traumáticos/fisiopatologia , Encéfalo/fisiopatologia , Antecipação Psicológica/fisiologia
9.
Cell Mol Gastroenterol Hepatol ; 18(3): 101366, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38815928

RESUMO

BACKGROUND & AIMS: Type 2 innate lymphoid cells (ILC2s) and interleukin-13 (IL-13) promote the onset of spasmolytic polypeptide-expressing metaplasia (SPEM) cells. However, little is known about molecular effects of IL-13 in SPEM cells. We now sought to establish a reliable organoid model, Meta1 gastroids, to model SPEM cells in vitro. We evaluated cellular and molecular effects of ILC2s and IL-13 on maturation and proliferation of SPEM cells. METHODS: We performed single-cell RNA sequencing to characterize Meta1 gastroids, which were derived from stomachs of Mist1-Kras transgenic mice that displayed pyloric metaplasia. Cell sorting was used to isolate activated ILC2s from stomachs of IL-13-tdTomato reporter mice treated with L635. Three-dimensional co-culture was used to determine the effects of ILC2s on Meta1 gastroids. Mouse normal or metaplastic (Meta1) and human metaplastic gastroids were cultured with IL-13 to evaluate cell responses. Air-Liquid Interface culture was performed to test long-term culture effects of IL-13. In silico analysis determined possible STAT6-binding sites in gene promoter regions. STAT6 inhibition was performed to corroborate STAT6 role in SPEM cells maturation. RESULTS: Meta1 gastroids showed the characteristics of SPEM cell lineages in vitro even after several passages. We demonstrated that co-culture with ILC2s or IL-13 treatment can induce phosphorylation of STAT6 in Meta1 and normal gastroids and promote the maturation and proliferation of SPEM cell lineages. IL-13 up-regulated expression of mucin-related proteins in human metaplastic gastroids. Inhibition of STAT6 blocked SPEM-related gene expression in Meta1 gastroids and maturation of SPEM in both normal and Meta1 gastroids. CONCLUSIONS: IL-13 promotes the maturation and proliferation of SPEM cells consistent with gastric mucosal regeneration.


Assuntos
Proliferação de Células , Interleucina-13 , Metaplasia , Camundongos Transgênicos , Fator de Transcrição STAT6 , Interleucina-13/metabolismo , Interleucina-13/farmacologia , Animais , Camundongos , Proliferação de Células/efeitos dos fármacos , Humanos , Fator de Transcrição STAT6/metabolismo , Mucosa Gástrica/imunologia , Mucosa Gástrica/citologia , Mucosa Gástrica/patologia , Mucosa Gástrica/metabolismo , Organoides/metabolismo , Linfócitos/metabolismo , Linfócitos/imunologia , Linfócitos/efeitos dos fármacos , Imunidade Inata , Estômago/patologia , Estômago/citologia , Análise de Célula Única , Peptídeos e Proteínas de Sinalização Intercelular
10.
Artigo em Inglês | MEDLINE | ID: mdl-38705463

RESUMO

BACKGROUND: Repetitive negative thinking (RNT) symptoms, which are characterized by pervasive, uncontrollable negative thoughts, are common in individuals with mood, anxiety, and traumatic stress disorders. Inability to regulate the contents of working memory is a hypothesized etiological factor in RNT, which suggests that training to improve working memory may be beneficial. This study examined the effects of working memory training on resting-state functional connectivity (rsFC) in individuals with elevated RNT and whether such changes would be associated with clinical improvement. METHODS: We conducted a secondary analysis of pre-post resting-state data collected as part of a randomized controlled trial (NCT04912089) of working memory training interventions (n = 42) compared with a waitlist control group (n = 23). We hypothesized that individuals who completed training would show increased rsFC between the 2 key intrinsic connectivity networks-the default mode network (posterior cingulate cortex) and the frontoparietal network (dorsolateral prefrontal cortex). We explored whether the magnitude of rsFC change was associated with change in RNT symptom severity. RESULTS: rsFC increased between the posterior cingulate cortex and regions including the frontal and parietal cortex in the training group compared with the waitlist group. Increased connectivity between the posterior cingulate cortex and superior frontal cortex was associated with RNT symptom reduction. CONCLUSIONS: These data provide evidence that working memory training can modulate neural circuitry at rest in individuals with RNT. Results are consistent with accounts of working memory training effects on large-scale neurocircuitry changes and suggest that these changes may contribute to clinical promise of this type of intervention on transdiagnostic RNT symptoms.

11.
J Patient Rep Outcomes ; 8(1): 42, 2024 Apr 09.
Artigo em Inglês | MEDLINE | ID: mdl-38592366

RESUMO

OBJECTIVE: This study compares clinical pain outcomes between patients in a pain treatment program that received a Fitbit, to patients that did not. We also explored: (1) cognitive, emotional, and psychological factors that may have impacted the decision to opt in to receiving a Fitbit; and (2) whether the choice to receive a Fitbit impacted changes in cognitive, emotional, and psychological factors following treatment. METHODS: Among 58 patients in a multidisciplinary pain treatment program at a Veterans Affairs Healthcare System hospital, 31 patients opted to receive a Fitbit as adjunct treatment, while 27 did not. This study utilized patient-reported and practitioner-collected data from the pain treatment program. RESULTS: Compared to the non-Fitbit group, the Fitbit group displayed a significant decrease in average pain intensity, however showed no correlation between Fitbit activity and average pain intensity. Additionally, treatment satisfaction was the only predictor of treatment group, when modeling pre- and post-treatment outcomes changes. CONCLUSION: The implementation of a Fitbit may lead to improved pain intensity. Initial evidence suggests that opting to receive a Fitbit during a pain treatment program indicates treatment engagement leading to greater treatment satisfaction. Future work is needed to verify and expand upon this potential mechanism.


Assuntos
Motivação , Veteranos , Humanos , Manejo da Dor , Resultado do Tratamento , Dor
12.
Front Hum Neurosci ; 18: 1357868, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38628969

RESUMO

Alterations in attention to cues signaling the need for inhibitory control play a significant role in a wide range of psychopathology. However, the degree to which motivational and attentional factors shape the neurocomputations of proactive inhibitory control remains poorly understood. The present study investigated how variation in monetary incentive valence and stake modulate the neurocomputational signatures of proactive inhibitory control. Adults (N = 46) completed a Stop-Signal Task (SST) with concurrent EEG recording under four conditions associated with stop performance feedback: low and high punishment (following unsuccessful stops) and low and high reward (following successful stops). A Bayesian learning model was used to infer individual's probabilistic expectations of the need to stop on each trial: P(stop). Linear mixed effects models were used to examine whether interactions between motivational valence, stake, and P(stop) parameters predicted P1 and N1 attention-related event-related potentials (ERPs) time-locked to the go-onset stimulus. We found that P1 amplitudes increased at higher levels of P(stop) in punished but not rewarded conditions, although P1 amplitude differences between punished and rewarded blocks were maximal on trials when the need to inhibit was least expected. N1 amplitudes were positively related to P(stop) in the high punishment condition (low N1 amplitude), but negatively related to P(stop) in the high reward condition (high N1 amplitude). Critically, high P(stop)-related N1 amplitude to the go-stimulus predicted behavioral stop success during the high reward block, providing evidence for the role of motivationally relevant context and inhibitory control expectations in modulating the proactive allocation of attentional resources that affect inhibitory control. These findings provide novel insights into the neurocomputational mechanisms underlying proactive inhibitory control under valence-dependent motivational contexts, setting the stage for developing motivation-based interventions that boost inhibitory control.

13.
Pain ; 165(8): 1735-1747, 2024 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-38501988

RESUMO

ABSTRACT: Pain anticipation during conditions of uncertainty can unveil intrinsic biases, and understanding these biases can guide pain treatment interventions. This study used machine learning and functional magnetic resonance imaging to predict anticipatory responses in a pain anticipation experiment. One hundred forty-seven participants that included healthy controls (n = 57) and individuals with current and/or past mental health diagnosis (n = 90) received cues indicating upcoming pain stimuli: 2 cues predicted high and low temperatures, while a third cue introduced uncertainty. Accurate differentiation of neural patterns associated with specific anticipatory conditions was observed, involving activation in the anterior short gyrus of the insula and the nucleus accumbens. Three distinct response profiles emerged: subjects with a negative bias towards high pain anticipation, those with a positive bias towards low pain anticipation, and individuals whose predictions during uncertainty were unbiased. These profiles remained stable over one year, were consistent across diagnosed psychopathologies, and correlated with cognitive coping styles and underlying insula anatomy. The findings suggest that individualized and stable pain anticipation occurs in uncertain conditions.


Assuntos
Antecipação Psicológica , Imageamento por Ressonância Magnética , Dor , Humanos , Incerteza , Masculino , Feminino , Adulto , Antecipação Psicológica/fisiologia , Dor/psicologia , Dor/fisiopatologia , Dor/diagnóstico por imagem , Adulto Jovem , Pessoa de Meia-Idade , Aprendizado de Máquina , Mapeamento Encefálico , Sinais (Psicologia) , Medição da Dor/métodos
14.
Res Sq ; 2024 Mar 07.
Artigo em Inglês | MEDLINE | ID: mdl-38496675

RESUMO

Endocrine islet b cells comprise heterogenous cell subsets. Yet when/how these subsets are produced and how stable they are remain unknown. Addressing these questions is important for preventing/curing diabetes, because lower numbers of b cells with better secretory function is a high risk of this disease. Using combinatorial cell lineage tracing, scRNA-seq, and DNA methylation analysis, we show here that embryonic islet progenitors with distinct gene expression and DNA methylation produce b-cell subtypes of different function and viability in adult mice. The subtype with better function is enriched for genes involved in vesicular production/trafficking, stress response, and Ca2+-secretion coupling, which further correspond to differential DNA methylation in putative enhancers of these genes. Maternal overnutrition, a major diabetes risk factor, reduces the proportion of endocrine progenitors of the b-cell subtype with better-function via deregulating DNA methyl transferase 3a. Intriguingly, the gene signature that defines mouse b-cell subtypes can reliably divide human cells into two sub-populations while the proportion of b cells with better-function is reduced in diabetic donors. The implication of these results is that modulating DNA methylation in islet progenitors using maternal food supplements can be explored to improve b-cell function in the prevention and therapy of diabetes.

16.
Biol Psychiatry ; 95(5): 434-443, 2024 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-37607657

RESUMO

BACKGROUND: Social disconnection is common and causes significant impairment in anxiety and depressive disorders, and it does not respond sufficiently to available treatments. The positive valence system supports social bond formation and maintenance but is often hyporesponsive in people with anxiety or depression. We conducted an experimental therapeutics trial to test the hypothesis that targeting positive valence processes through cognitive and behavioral strategies would enhance responsivity to social rewards, a core mechanism underlying social connectedness. METHODS: Sixty-eight adults who endorsed clinically elevated anxiety and/or depression with social impairment were randomized 1:1:1 to 5 (n = 23) or 10 (n = 22) sessions of amplification of positivity (AMP) treatment or waitlist (n = 23). Pre- to posttreatment change in striatal activity (primary outcome) during social reward anticipation was measured using functional magnetic resonance imaging, and reactivity to a social affiliation task (secondary) and self-reported social connectedness (exploratory) were examined. Primary analyses compared AMP (doses combined) versus waitlist. A second aim was to compare the effects of different doses. RESULTS: AMP engaged the hypothesized treatment target, leading to greater striatal activation during anticipation of social rewards versus waitlist (d = 1.01 [95% CI = 0.42-1.61]; largest striatal volume). AMP yielded larger improvements in positive affect and approach behavior during the affiliation task (but not other outcomes) and social connectedness. Larger striatal and social connectedness increases were observed for 5-session versus 10-session AMP (d range = 0.08-1.03). CONCLUSIONS: Teaching people with anxiety or depression strategies to increase positive thoughts, behaviors, and emotions enhances activity in brain regions that govern social reward processing and promotes social connectedness. Social reward sensitivity may be a transdiagnostic target for remediating social disconnection.


Assuntos
Transtornos de Ansiedade , Depressão , Humanos , Adulto , Depressão/terapia , Ansiedade , Encéfalo/diagnóstico por imagem , Recompensa
17.
Cell ; 186(25): 5620-5637.e16, 2023 12 07.
Artigo em Inglês | MEDLINE | ID: mdl-38065082

RESUMO

Colorectal cancer exhibits dynamic cellular and genetic heterogeneity during progression from precursor lesions toward malignancy. Analysis of spatial multi-omic data from 31 human colorectal specimens enabled phylogeographic mapping of tumor evolution that revealed individualized progression trajectories and accompanying microenvironmental and clonal alterations. Phylogeographic mapping ordered genetic events, classified tumors by their evolutionary dynamics, and placed clonal regions along global pseudotemporal progression trajectories encompassing the chromosomal instability (CIN+) and hypermutated (HM) pathways. Integrated single-cell and spatial transcriptomic data revealed recurring epithelial programs and infiltrating immune states along progression pseudotime. We discovered an immune exclusion signature (IEX), consisting of extracellular matrix regulators DDR1, TGFBI, PAK4, and DPEP1, that charts with CIN+ tumor progression, is associated with reduced cytotoxic cell infiltration, and shows prognostic value in independent cohorts. This spatial multi-omic atlas provides insights into colorectal tumor-microenvironment co-evolution, serving as a resource for stratification and targeted treatments.


Assuntos
Neoplasias Colorretais , Instabilidade de Microssatélites , Microambiente Tumoral , Humanos , Instabilidade Cromossômica/genética , Neoplasias Colorretais/patologia , Perfilação da Expressão Gênica , Quinases Ativadas por p21/genética , Filogenia , Mutação , Progressão da Doença , Prognóstico
18.
bioRxiv ; 2023 Oct 02.
Artigo em Inglês | MEDLINE | ID: mdl-37873404

RESUMO

Crohn's disease (CD) is a complex chronic inflammatory disorder that may affect any part of gastrointestinal tract with extra-intestinal manifestations and associated immune dysregulation. To characterize heterogeneity in CD, we profiled single-cell transcriptomics of 170 samples from 65 CD patients and 18 non-inflammatory bowel disease (IBD) controls in both the terminal ileum (TI) and ascending colon (AC). Analysis of 202,359 cells identified a novel epithelial cell type in both TI and AC, featuring high expression of LCN2, NOS2, and DUOX2, and thus is named LND. LND cells, confirmed by high-resolution in-situ RNA imaging, were rarely found in non-IBD controls, but expanded significantly in active CD. Compared to other epithelial cells, genes defining LND cells were enriched in antimicrobial response and immunoregulation. Moreover, multiplexed protein imaging demonstrated that LND cell abundance was associated with immune infiltration. Cross-talk between LND and immune cells was explored by ligand-receptor interactions and further evidenced by their spatial colocalization. LND cells showed significant enrichment of expression specificity of IBD/CD susceptibility genes, revealing its role in immunopathogenesis of CD. Investigating lineage relationships of epithelial cells detected two LND cell subpopulations with different origins and developmental potential, early and late LND. The ratio of the late to early LND cells was related to anti-TNF response. These findings emphasize the pathogenic role of the specialized LND cell type in both Crohn's ileitis and Crohn's colitis and identify novel biomarkers associated with disease activity and treatment response.

19.
iScience ; 26(7): 107242, 2023 Jul 21.
Artigo em Inglês | MEDLINE | ID: mdl-37496679

RESUMO

Droplet-based single-cell RNA-seq (scRNA-seq) data are plagued by ambient contaminations caused by nucleic acid material released by dead and dying cells. This material is mixed into the buffer and is co-encapsulated with cells, leading to a lower signal-to-noise ratio. Although there exist computational methods to remove ambient contaminations post-hoc, the reliability of algorithms in generating high-quality data from low-quality sources remains uncertain. Here, we assess data quality before data filtering by a set of quantitative, contamination-based metrics that assess data quality more effectively than standard metrics. Through a series of controlled experiments, we report improvements that can minimize ambient contamination outside of tissue dissociation, via cell fixation, improved cell loading, microfluidic dilution, and nuclei versus cell preparation; many of these parameters are inaccessible on commercial platforms. We provide end-users with insights on factors that can guide their decision-making regarding optimizations that minimize ambient contamination, and metrics to assess data quality.

20.
Sci Rep ; 13(1): 7581, 2023 05 10.
Artigo em Inglês | MEDLINE | ID: mdl-37164996

RESUMO

Chronic pain is not a singular disorder and presents in various forms and phenotypes. Here we show data from a cohort of patients seeking treatment in a transdisciplinary pain clinic. Patients completed a multidimensional patient-reported battery as part of routine initial evaluation at baseline and at each of the four subsequent visits over 1-year follow-up (0, 1, 3, 6, 12 months). The goal of this work was to use unsupervised modeling approach to identify whether patients with chronic pain undergoing transdisciplinary intensive rehabilitation treatment: (1) can be derived based upon self-reported outcome measures at baseline (or before treatment initiation), (2) are clinically validated based on their clinical diagnosis and medication use, and (3) differ in treatment trajectories over 1 year of transdisciplinary treatment. We applied unsupervised clustering on baseline outcomes using nine patient-reported symptoms and examined treatment trajectories. The three-cluster solution was internally validated. Psychiatric diagnosis, chronic back pain-related disability and symptoms severity determined cluster assignment and treatment prognosis. Conversely, clinical pain severity had lesser effect. Furthermore, clusters showed stability over time despite symptoms improvement. The accurate and meaningful subgrouping of the underlying chronic pain phenotypes would greatly enhance treatment and provide personalized and effective pain management.


Assuntos
Dor Crônica , Dor Lombar , Humanos , Prognóstico , Dor Crônica/diagnóstico , Dor Crônica/terapia , Aprendizado de Máquina não Supervisionado , Dor Lombar/terapia , Avaliação de Resultados em Cuidados de Saúde , Resultado do Tratamento
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