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1.
Science ; 385(6705): eadl6173, 2024 Jul 12.
Article in English | MEDLINE | ID: mdl-38991060

ABSTRACT

Isocitrate dehydrogenase 1 (IDH1) is the most commonly mutated metabolic gene across human cancers. Mutant IDH1 (mIDH1) generates the oncometabolite (R)-2-hydroxyglutarate, disrupting enzymes involved in epigenetics and other processes. A hallmark of IDH1-mutant solid tumors is T cell exclusion, whereas mIDH1 inhibition in preclinical models restores antitumor immunity. Here, we define a cell-autonomous mechanism of mIDH1-driven immune evasion. IDH1-mutant solid tumors show selective hypermethylation and silencing of the cytoplasmic double-stranded DNA (dsDNA) sensor CGAS, compromising innate immune signaling. mIDH1 inhibition restores DNA demethylation, derepressing CGAS and transposable element (TE) subclasses. dsDNA produced by TE-reverse transcriptase (TE-RT) activates cGAS, triggering viral mimicry and stimulating antitumor immunity. In summary, we demonstrate that mIDH1 epigenetically suppresses innate immunity and link endogenous RT activity to the mechanism of action of a US Food and Drug Administration-approved oncology drug.


Subject(s)
Immune Evasion , Immunity, Innate , Isocitrate Dehydrogenase , Neoplasms , Animals , Humans , Mice , Cell Line, Tumor , DNA/metabolism , DNA Demethylation , DNA Methylation , DNA Transposable Elements , Epigenesis, Genetic , Glutarates/metabolism , Immunity, Innate/genetics , Isocitrate Dehydrogenase/genetics , Isocitrate Dehydrogenase/metabolism , Mutation , Neoplasms/immunology , Neoplasms/genetics , Nucleotidyltransferases/genetics , Tumor Escape , Immune Evasion/genetics
2.
Curr Oncol ; 31(6): 3329-3341, 2024 Jun 13.
Article in English | MEDLINE | ID: mdl-38920736

ABSTRACT

Early integrated palliative care (EIPC) for patients with advanced cancers requires the involvement of family doctors (FDs) and oncologists. We compared attitudes between patients and their providers regarding the delivery of EIPC. Patients with newly diagnosed incurable gastrointestinal (GI) cancer at a tertiary cancer centre in Ontario, Canada, were surveyed using a study-specific instrument regarding the importance of and preferences for accessing support across eight domains of palliative care. Physicians within the circle of care completed a parallel survey for each patient. The concordance between patient and physician responses was analyzed. A total of 66 patients were surveyed (median age 69, 35% female). All had an oncologist, 12% had a specialist palliative care provider (SPC), and 97% had an FD, but only 41% listed the FD as part of the care team. In total, 95 providers responded (oncologist = 68, FD = 21, SPC = 6; response rate 92%; 1-3 physician responses per patient). Disease management and physical concerns were most important to patients. Patients preferred to access care in these domains from oncologists or SPCs. For all other domains, most patients attributed primary responsibility to self or family rather than any healthcare provider. Thus, concordance was poor between patient and physician responses. Across most domains of palliative care, we found low agreement between cancer patients and their physicians regarding responsibilities for care, with FDs appearing to have limited involvement at this stage.


Subject(s)
Gastrointestinal Neoplasms , Palliative Care , Humans , Palliative Care/methods , Female , Male , Gastrointestinal Neoplasms/therapy , Gastrointestinal Neoplasms/psychology , Aged , Middle Aged , Prospective Studies , Surveys and Questionnaires , Patient Preference , Attitude of Health Personnel , Aged, 80 and over , Adult , Ontario
3.
Psychooncology ; 33(6): e6365, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38898595

ABSTRACT

BACKGROUND: Cancer in a loved one can have negative effects on child health and development. Child Life Specialists (CLSs) specialize in assisting children understand and cope with difficult medical scenarios but are generally not available in adult care facilities to support the needs of patient-families with minor children. We conducted a mixed-methods study of the implementation of a pilot CLS program at a tertiary oncology centre. METHODS: We collected administrative and clinical data on referred families; encounter data; and patient-reported questionnaire data before and 2 months after engagement with the program. RESULTS: Over the initial 10 months, 98 families were referred, 91 of whom engaged through a total of 257 clinical encounters. The cancer patient in the family was most commonly a woman with a mean age of 45 years and in the role of mother. Breast cancer was the most common diagnosis (24%) and 78% of patients had stage IV disease. Most families had >1 child at home, and children were most commonly school-aged (5-14y). Phone and Hospital/Clinic visits accounted for the largest portion of CLS time. Interventions ranged from diagnosis education through to bereavement support. Most cancer patients indicated that the program was helpful to them and their families. There were trends of moderate improvements on patient reported outcomes. CONCLUSION: Our study was able to provide an understanding of the initial CLS program operations to guide program development and future study. Such a program holds promise as an important aspect of adult oncology family-centered care.


Subject(s)
Feasibility Studies , Neoplasms , Humans , Female , Male , Adult , Middle Aged , Child , Neoplasms/psychology , Adolescent , Child, Preschool , Family/psychology , Surveys and Questionnaires , Medical Oncology , Pilot Projects , Young Adult , Adaptation, Psychological , Aged , Social Support
4.
Cancer Res ; 84(14): 2364-2376, 2024 Jul 15.
Article in English | MEDLINE | ID: mdl-38695869

ABSTRACT

Oncogenesis and progression of pancreatic ductal adenocarcinoma (PDAC) are driven by complex interactions between the neoplastic component and the tumor microenvironment, which includes immune, stromal, and parenchymal cells. In particular, most PDACs are characterized by a hypovascular and hypoxic environment that alters tumor cell behavior and limits the efficacy of chemotherapy and immunotherapy. Characterization of the spatial features of the vascular niche could advance our understanding of inter- and intratumoral heterogeneity in PDAC. In this study, we investigated the vascular microenvironment of PDAC by applying imaging mass cytometry using a 26-antibody panel on 35 regions of interest across 9 patients, capturing more than 140,000 single cells. The approach distinguished major cell types, including multiple populations of lymphoid and myeloid cells, endocrine cells, ductal cells, stromal cells, and endothelial cells. Evaluation of cellular neighborhoods identified 10 distinct spatial domains, including multiple immune and tumor-enriched environments as well as the vascular niche. Focused analysis revealed differential interactions between immune populations and the vasculature and identified distinct spatial domains wherein tumor cell proliferation occurs. Importantly, the vascular niche was closely associated with a population of CD44-expressing macrophages enriched for a proangiogenic gene signature. Taken together, this study provides insights into the spatial heterogeneity of PDAC and suggests a role for CD44-expressing macrophages in shaping the vascular niche. Significance: Imaging mass cytometry revealed that pancreatic ductal cancers are composed of 10 distinct cellular neighborhoods, including a vascular niche enriched for macrophages expressing high levels of CD44 and a proangiogenic gene signature.


Subject(s)
Carcinoma, Pancreatic Ductal , Image Cytometry , Pancreatic Neoplasms , Tumor Microenvironment , Humans , Pancreatic Neoplasms/pathology , Pancreatic Neoplasms/blood supply , Pancreatic Neoplasms/metabolism , Carcinoma, Pancreatic Ductal/pathology , Carcinoma, Pancreatic Ductal/blood supply , Image Cytometry/methods , Neovascularization, Pathologic/pathology , Neovascularization, Pathologic/metabolism , Hyaluronan Receptors/metabolism , Hyaluronan Receptors/analysis
5.
Cleft Palate Craniofac J ; : 10556656241257101, 2024 May 22.
Article in English | MEDLINE | ID: mdl-38778755

ABSTRACT

OBJECTIVE: This study aimed to (1) assess layperson preferences for how surgical information is presented; (2) evaluate how the format of visual information relates to layperson comfort with undergoing surgery, perceptions of surgeon character traits, and beliefs about artistic skill impacting plastic surgery practice; and (3) identify sociodemographic characteristics associated with these outcomes. DESIGN: A survey was developed in which one of five standardized sets of information depicting a unilateral cleft lip repair was presented as (1) text alone, (2) quick sketches, (3) simple drawings, (4) detailed illustrations, or (5) photographs. SETTING: Online crowdsourcing platform. PARTICIPANTS: Raters aged 18 years and older from the United States. INTERVENTIONS: None. MAIN OUTCOME MEASURE(S): After viewing the surgical information, participants answered three sets of Likert scale questions. Ratings were averaged to produce three composite scores assessing (1) comfort with undergoing surgery (2) perceptions of surgeon character traits, and (3) beliefs about plastic surgery and artistry. RESULTS: Four hundred seventy-nine participants were included. Surgeon character traits score was highest among participants who viewed detailed illustrations at 4.46 ± 0.59, followed by photographs at 4.43 ± 0.54, text alone at 4.28 ± 0.59, simple drawings at 4.17 ± 0.67, and quick sketches at 4.17 ± 0.71 (p = 0.0014). Participants who viewed detailed illustrations rated surgical comfort score and plastic surgery and artistry score highest, although differences did not achieve statistical significance. CONCLUSIONS: Viewing detailed cleft lip repair illustrations was significantly associated with positive perceptions of surgeon character traits. Our data help to contextualize methods of communication and education valued by the public when seeking cleft care.

6.
J Craniofac Surg ; 2024 May 07.
Article in English | MEDLINE | ID: mdl-38710067

ABSTRACT

BACKGROUND: This study assesses nasal airway volumes in skeletally mature patients with CLP and healthy controls and examines the relationship among nasal volumes, cleft laterality, and facial asymmetry. METHODS: Computed tomography images from patients with CLP and controls were analyzed using Mimics Version 23.0 (Materialise, Leuven, Belgium). Relationships among nasal airway volume, cleft laterality, and facial asymmetry were compared. RESULTS: The 89 patients in this study included 66 (74%) CLP and 23 (17%) controls. Nasal airway volumes in CLP were more asymmetric than controls (26.8±17.5% vs. 17.2±14.4%; P=0.015). In UCLP, the smaller nasal airway was on the cleft side 81% of the time (P<0.001). Maximum airway stenosis was on the cleft side 79% of the time (P<0.001), and maximum stenosis was on the same side as the smaller airway 89% of the time (P<0.001). There was a mild linear relationship between nasal airway asymmetry and maximum stenosis (r=0.247, P=0.023). On 3-dimensional image reconstruction, the septum often bowed convexly into the cleft-sided nasal airway with a caudal deviation towards the noncleft side. Nasal airway asymmetry was not associated with facial midline asymmetry (P>0.05). CONCLUSION: The nasal airway is more asymmetric in patients with cleft lip and palate compared with the general population, with the area of maximum stenosis usually occurring on the cleft-sided airway. In patients with unilateral cleft lip and palate, the septum often bows into the cleft side, reducing the size of that nasal airway. Nasal airway asymmetry did not correlate with facial asymmetry.

7.
J Oncol Pharm Pract ; : 10781552241252627, 2024 May 05.
Article in English | MEDLINE | ID: mdl-38706192

ABSTRACT

BACKGROUND: Immune checkpoint inhibitor (ICI)-associated acute interstitial nephritis (AIN) is a recognized complication of immunotherapy (IO), but literature on its management and outcomes is limited. METHODS: We retrospectively reviewed patients who received ICIs and developed biopsy-proven or clinically-suspected ICI-associated AIN at the University of Virginia Comprehensive Cancer Center from 2012-2023. We analyzed baseline characteristics and clinical outcomes, including treatment interruption and rechallenge rates. Acute kidney injury (AKI) was defined as a ≥ 1.5-fold increase in baseline creatinine under seven days, a two-fold increase above the upper limit of normal, or an increase by ≥0.3 mg/dL. Kidney function returning to within 0.3 mg/dL or less than twice baseline was considered complete (CRc) and partial (PRc) recovery, respectively. RESULTS: We identified 12 cases of ICI-AIN: four by biopsy (33%) and eight (67%) by clinical suspicion. Two patients received anti-CTLA-4 and anti-PD1, six received anti-PD1 alone, and four received chemo-immunotherapy. The majority (58%) of patients developed AIN within the first 5 cycles. Eight patients developed ≥ Grade 3 AKI, and six developed multiple irAEs. ICI was permanently discontinued in seven patients (58%) and temporarily interrupted in four (30%). The CRc and PRc rates were 67% and 8%, respectively. Upon AIN onset, the best disease response was stable disease in five patients, partial response in three, and progressive disease in three. Median overall survival was 4.87 years, and progression-free survival was 1.5 years. CONCLUSIONS: Rechallenge with IO after kidney irAE may be possible in some patients but requires careful evaluation on an individual basis.

8.
Cancer Invest ; 42(5): 400-407, 2024 May.
Article in English | MEDLINE | ID: mdl-38773947

ABSTRACT

The CNS is a common site for distant metastasis and treatment failure in melanoma patients. This study aimed to evaluate the inclusion rate of patients with melanoma brain metastases (MBM) in prospective clinical trials. 69.3% of trials excluded MBM patients based on their CNS disease. In univariate analysis, trials not employing immunotherapy (p = 0.0174), inclusion of leptomeningeal disease (p < 0.0001) and non-pharmaceutical sponsor trials (p = 0.0461) were more likely to enroll patients with MBM. Thoughtful reconsideration of clinical trial designs is needed to give patients with MBMs access to promising investigational agents and improve outcomes for patients with MBM.


Subject(s)
Brain Neoplasms , Clinical Trials as Topic , Melanoma , Patient Selection , Humans , Melanoma/therapy , Melanoma/pathology , Melanoma/secondary , Brain Neoplasms/secondary , Brain Neoplasms/therapy , Male , Female , Prospective Studies , Middle Aged , Immunotherapy/methods
9.
Cell ; 187(12): 3120-3140.e29, 2024 Jun 06.
Article in English | MEDLINE | ID: mdl-38714197

ABSTRACT

Non-hematopoietic cells are essential contributors to hematopoiesis. However, heterogeneity and spatial organization of these cells in human bone marrow remain largely uncharacterized. We used single-cell RNA sequencing (scRNA-seq) to profile 29,325 non-hematopoietic cells and discovered nine transcriptionally distinct subtypes. We simultaneously profiled 53,417 hematopoietic cells and predicted their interactions with non-hematopoietic subsets. We employed co-detection by indexing (CODEX) to spatially profile over 1.2 million cells. We integrated scRNA-seq and CODEX data to link predicted cellular signaling with spatial proximity. Our analysis revealed a hyperoxygenated arterio-endosteal neighborhood for early myelopoiesis, and an adipocytic localization for early hematopoietic stem and progenitor cells (HSPCs). We used our CODEX atlas to annotate new images and uncovered mesenchymal stromal cell (MSC) expansion and spatial neighborhoods co-enriched for leukemic blasts and MSCs in acute myeloid leukemia (AML) patient samples. This spatially resolved, multiomic atlas of human bone marrow provides a reference for investigation of cellular interactions that drive hematopoiesis.


Subject(s)
Bone Marrow , Hematopoietic Stem Cells , Mesenchymal Stem Cells , Proteomics , Single-Cell Analysis , Transcriptome , Humans , Single-Cell Analysis/methods , Bone Marrow/metabolism , Hematopoietic Stem Cells/metabolism , Mesenchymal Stem Cells/metabolism , Mesenchymal Stem Cells/cytology , Proteomics/methods , Leukemia, Myeloid, Acute/metabolism , Leukemia, Myeloid, Acute/genetics , Leukemia, Myeloid, Acute/pathology , Hematopoiesis , Stem Cell Niche , Bone Marrow Cells/metabolism , Bone Marrow Cells/cytology
10.
bioRxiv ; 2024 Apr 13.
Article in English | MEDLINE | ID: mdl-38645178

ABSTRACT

Diffuse gliomas are epigenetically dysregulated, immunologically cold, and fatal tumors characterized by mutations in isocitrate dehydrogenase (IDH). Although IDH mutations yield a uniquely immunosuppressive tumor microenvironment, the regulatory mechanisms that drive the immune landscape of IDH mutant (IDHm) gliomas remain unknown. Here, we reveal that transcriptional repression of retinoic acid (RA) pathway signaling impairs both innate and adaptive immune surveillance in IDHm glioma through epigenetic silencing of retinol binding protein 1 (RBP1) and induces a profound anti-inflammatory landscape marked by loss of inflammatory cell states and infiltration of suppressive myeloid phenotypes. Restorative retinoic acid therapy in murine glioma models promotes clonal CD4 + T cell expansion and induces tumor regression in IDHm, but not IDH wildtype (IDHwt), gliomas. Our findings provide a mechanistic rationale for RA immunotherapy in IDHm glioma and is the basis for an ongoing investigator-initiated, single-center clinical trial investigating all-trans retinoic acid (ATRA) in recurrent IDHm human subjects.

11.
bioRxiv ; 2024 Mar 16.
Article in English | MEDLINE | ID: mdl-38559168

ABSTRACT

The bone marrow is the organ responsible for blood production. Diverse non-hematopoietic cells contribute essentially to hematopoiesis. However, these cells and their spatial organization remain largely uncharacterized as they have been technically challenging to study in humans. Here, we used fresh femoral head samples and performed single-cell RNA sequencing (scRNA-Seq) to profile 29,325 enriched non-hematopoietic bone marrow cells and discover nine transcriptionally distinct subtypes. We next employed CO-detection by inDEXing (CODEX) multiplexed imaging of 18 individuals, including both healthy and acute myeloid leukemia (AML) samples, to spatially profile over one million single cells with a novel 53-antibody panel. We discovered a relatively hyperoxygenated arterio-endosteal niche for early myelopoiesis, and an adipocytic, but not endosteal or perivascular, niche for early hematopoietic stem and progenitor cells. We used our atlas to predict cell type labels in new bone marrow images and used these predictions to uncover mesenchymal stromal cell (MSC) expansion and leukemic blast/MSC-enriched spatial neighborhoods in AML patient samples. Our work represents the first comprehensive, spatially-resolved multiomic atlas of human bone marrow and will serve as a reference for future investigation of cellular interactions that drive hematopoiesis.

12.
Ther Innov Regul Sci ; 58(4): 614-621, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38622455

ABSTRACT

The classification of medical devices by the Food and Drug Administration (FDA) involves rigorous scrutiny from specialized panels that designate devices as Class I, II, or III depending on their levels of relative risk to patient health. Posterior rigid pedicle screw systems were first classified by the FDA in 1984 and have since revolutionized the treatment of many spine pathologies. Despite this early classification by the FDA, posterior cervical pedicle and lateral mass screws were not reclassified from unclassified to Class III and then to Class II until 2019, nearly 35 years after their initial classification. This reclassification process involved a decades-long interplay between the FDA, formal panels, manufacturers, academic leaders, practicing physicians, and patients. It was delayed by lawsuits and a paucity of data demonstrating the ability to improve outcomes for cervical spinal pathologies. The off-label use of thoracolumbar pedicle screw rigid fixation systems by early adopters assisted manufacturers and professional organizations in providing the necessary data for the reclassification process. This case study highlights the collaboration between physicians and professional organizations in facilitating FDA reclassification and underscores changes to the current classification process that could avoid the prolonged dichotomy between common medical practice and FDA guidelines.


Subject(s)
Cervical Vertebrae , Pedicle Screws , United States Food and Drug Administration , United States , Humans , Cervical Vertebrae/surgery , Device Approval/legislation & jurisprudence , History, 21st Century , History, 20th Century
13.
Cancer Med ; 13(4): e6948, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38466233

ABSTRACT

BACKGROUND: The purpose of this study was to investigate associations between self-reported distress (anxiety/depression) and satisfaction with and desire for virtual follow-up (VFU) care among cancer patients during and beyond the COVID-19 pandemic. METHODS: Breast and prostate cancer patients receiving VFU at an urban cancer centre in Toronto, Canada completed an online survey on their sociodemographic, clinical, and technology, characteristics and experience with and views on VFU. EQ5D-5 L was used to assess distress. Statistical models adjusted for age, gender, education, income and Internet confidence. RESULTS: Of 352 participants, average age was 65 years, 48% were women,79% were within 5 years of treatment completion, 84% had college/university education and 74% were confident Internet users. Nearly, all (98%) had a virtual visit via phone and 22% had a virtual visit via video. The majority of patients (86%) were satisfied with VFU and 70% agreed that they would like VFU options after the COVID-19 pandemic. Participants who reported distress and who were not confident using the Internet for health purposes were significantly less likely to be satisfied with VFU (OR = 0.4; 95% CI: 0.2-0.8 and OR = 0.19; 95% CI: 0.09-0.38, respectively) and were less likely to desire VFU option after the COVID-19 pandemic (OR = 0.49; 95% CI: 0.30-0.82 and OR = 0.41; 95% CI: 0.23-0.70, respectively). CONCLUSIONS: The majority of respondents were satisfied with VFU and would like VFU options after the COVID-19 pandemic. Future research should determine how to optimize VFU options for cancer patients who are distressed and who are less confident using virtual care technology.


Subject(s)
COVID-19 , Prostatic Neoplasms , Male , Humans , Aged , COVID-19/epidemiology , Aftercare , Pandemics , Prostatic Neoplasms/epidemiology , Prostatic Neoplasms/therapy , Breast
14.
bioRxiv ; 2024 Mar 08.
Article in English | MEDLINE | ID: mdl-38496580

ABSTRACT

Pediatric high-grade glioma (pHGG) is an incurable central nervous system malignancy that is a leading cause of pediatric cancer death. While pHGG shares many similarities to adult glioma, it is increasingly recognized as a molecularly distinct, yet highly heterogeneous disease. In this study, we longitudinally profiled a molecularly diverse cohort of 16 pHGG patients before and after standard therapy through single-nucleus RNA and ATAC sequencing, whole-genome sequencing, and CODEX spatial proteomics to capture the evolution of the tumor microenvironment during progression following treatment. We found that the canonical neoplastic cell phenotypes of adult glioblastoma are insufficient to capture the range of tumor cell states in a pediatric cohort and observed differential tumor-myeloid interactions between malignant cell states. We identified key transcriptional regulators of pHGG cell states and did not observe the marked proneural to mesenchymal shift characteristic of adult glioblastoma. We showed that essential neuromodulators and the interferon response are upregulated post-therapy along with an increase in non-neoplastic oligodendrocytes. Through in vitro pharmacological perturbation, we demonstrated novel malignant cell-intrinsic targets. This multiomic atlas of longitudinal pHGG captures the key features of therapy response that support distinction from its adult counterpart and suggests therapeutic strategies which are targeted to pediatric gliomas.

15.
Nat Commun ; 15(1): 1761, 2024 Feb 26.
Article in English | MEDLINE | ID: mdl-38409161

ABSTRACT

Tissue damage elicits cell fate switching through a process called metaplasia, but how the starting cell fate is silenced and the new cell fate is activated has not been investigated in animals. In cell culture, pioneer transcription factors mediate "reprogramming" by opening new chromatin sites for expression that can attract transcription factors from the starting cell's enhancers. Here we report that SOX4 is sufficient to initiate hepatobiliary metaplasia in the adult mouse liver, closely mimicking metaplasia initiated by toxic damage to the liver. In lineage-traced cells, we assessed the timing of SOX4-mediated opening of enhancer chromatin versus enhancer decommissioning. Initially, SOX4 directly binds to and closes hepatocyte regulatory sequences via an overlapping motif with HNF4A, a hepatocyte master regulatory transcription factor. Subsequently, SOX4 exerts pioneer factor activity to open biliary regulatory sequences. The results delineate a hierarchy by which gene networks become reprogrammed under physiological conditions, providing deeper insight into the basis for cell fate transitions in animals.


Subject(s)
Cellular Reprogramming , Chromatin , Animals , Mice , Cell Differentiation/genetics , Cellular Reprogramming/genetics , Metaplasia , Transcription Factors/metabolism
16.
Blood Adv ; 8(6): 1449-1463, 2024 Mar 26.
Article in English | MEDLINE | ID: mdl-38290102

ABSTRACT

ABSTRACT: During development, erythroid cells are produced through at least 2 distinct hematopoietic waves (primitive and definitive), generating erythroblasts with different functional characteristics. Human induced pluripotent stem cells (iPSCs) can be used as a model platform to study the development of red blood cells (RBCs) with many of the differentiation protocols after the primitive wave of hematopoiesis. Recent advances have established that definitive hematopoietic progenitors can be generated from iPSCs, creating a unique situation for comparing primitive and definitive erythrocytes derived from cell sources of identical genetic background. We generated iPSCs from healthy fetal liver (FL) cells and produced isogenic primitive or definitive RBCs which were compared directly to the FL-derived RBCs. Functional assays confirmed differences between the 2 programs, with primitive RBCs showing a reduced proliferation potential, larger cell size, lack of Duffy RBC antigen expression, and higher expression of embryonic globins. Transcriptome profiling by scRNA-seq demonstrated high similarity between FL- and iPSC-derived definitive RBCs along with very different gene expression and regulatory network patterns for primitive RBCs. In addition, iPSC lines harboring a known pathogenic mutation in the erythroid master regulator KLF1 demonstrated phenotypic changes specific to definitive RBCs. Our studies provide new insights into differences between primitive and definitive erythropoiesis and highlight the importance of ontology when using iPSCs to model genetic hematologic diseases. Beyond disease modeling, the similarity between FL- and iPSC-derived definitive RBCs expands potential applications of definitive RBCs for diagnostic and transfusion products.


Subject(s)
Induced Pluripotent Stem Cells , Humans , Erythropoiesis/genetics , Erythrocytes , Cell Differentiation/genetics , Erythroblasts/metabolism
18.
Cancer Epidemiol ; 88: 102511, 2024 02.
Article in English | MEDLINE | ID: mdl-38071872

ABSTRACT

To evaluate the performance accuracy and workload savings of artificial intelligence (AI)-based automation tools in comparison with human reviewers in medical literature screening for systematic reviews (SR) of primary studies in cancer research in order to gain insights on improving the efficiency of producing SRs. Medline, Embase, the Cochrane Library, and PROSPERO databases were searched from inception to November 30, 2022. Then, forward and backward literature searches were completed, and the experts in this field including the authors of the articles included were contacted for a thorough grey literature search. This SR was registered on PROSPERO (CRD 42023384772). Among the 3947 studies obtained from search, five studies met the preplanned study selection criteria. These five studies evaluated four AI tools: Abstrackr (four studies), RobotAnalyst (one), EPPI-Reviewer (one), and DistillerSR (one). Without missing final included citations, Abstrackr eliminated 20%-88% of titles and abstracts (time saving of 7-86 hours) and 59% of the full-texts (62 h) from human review across four different cancer-related SRs. In comparison, RobotAnalyst (1% of titles and abstracts, 1 h), EPPI Review (38% of titles and abstracts, 58 h; 59% of full-texts, 62 h), DistillerSR (42% of titles and abstracts, 22 h) also provided similar or lower work savings for single cancer-related SRs. AI-based automation tools exhibited promising but varying levels of accuracy and efficiency during the screening process of medical literature for conducting SRs in the cancer field. Until further progress is made and thorough evaluations are conducted, AI tools should be utilized as supplementary aids rather than complete substitutes for human reviewers.


Subject(s)
Artificial Intelligence , Neoplasms , Humans , Systematic Reviews as Topic , Automation , Neoplasms/diagnosis
19.
Res Sq ; 2023 Oct 30.
Article in English | MEDLINE | ID: mdl-37961674

ABSTRACT

Refractoriness to initial chemotherapy and relapse after remission are the main obstacles to cure in T-cell Acute Lymphoblastic Leukemia (T-ALL). Biomarker guided risk stratification and targeted therapy have the potential to improve outcomes in high-risk T-ALL; however, cellular and genetic factors contributing to treatment resistance remain unknown. Previous bulk genomic studies in T-ALL have implicated tumor heterogeneity as an unexplored mechanism for treatment failure. To link tumor subpopulations with clinical outcome, we created an atlas of healthy pediatric hematopoiesis and applied single-cell multiomic (CITE-seq/snATAC-seq) analysis to a cohort of 40 cases of T-ALL treated on the Children's Oncology Group AALL0434 clinical trial. The cohort was carefully selected to capture the immunophenotypic diversity of T-ALL, with early T-cell precursor (ETP) and Near/Non-ETP subtypes represented, as well as enriched with both relapsed and treatment refractory cases. Integrated analyses of T-ALL blasts and normal T-cell precursors identified a bone-marrow progenitor-like (BMP-like) leukemia sub-population associated with treatment failure and poor overall survival. The single-cell-derived molecular signature of BMP-like blasts predicted poor outcome across multiple subtypes of T-ALL within two independent patient cohorts using bulk RNA-sequencing data from over 1300 patients. We defined the mutational landscape of BMP-like T-ALL, finding that NOTCH1 mutations additively drive T-ALL blasts away from the BMP-like state. We transcriptionally matched BMP-like blasts to early thymic seeding progenitors that have low NR3C1 expression and high stem cell gene expression, corresponding to a corticosteroid and conventional cytotoxic resistant phenotype we observed in ex vivo drug screening. To identify novel targets for BMP-like blasts, we performed in silico and in vitro drug screening against the BMP-like signature and prioritized BMP-like overexpressed cell-surface (CD44, ITGA4, LGALS1) and intracellular proteins (BCL-2, MCL-1, BTK, NF-κB) as candidates for precision targeted therapy. We established patient derived xenograft models of BMP-high and BMP-low leukemias, which revealed vulnerability of BMP-like blasts to apoptosis-inducing agents, TEC-kinase inhibitors, and proteasome inhibitors. Our study establishes the first multi-omic signatures for rapid risk-stratification and targeted treatment of high-risk T-ALL.

20.
Qual Health Res ; : 10497323231215950, 2023 Nov 30.
Article in English | MEDLINE | ID: mdl-38035631

ABSTRACT

A cancer diagnosis in patients who are parents of minor children is uniquely stressful for both parents and children. Children need developmentally appropriate information and support to help reduce their fears and worries. Child life specialists (CLSs) are health professionals who work in pediatric environments to support children and families with the stress and uncertainty of illnesses. Increasingly, CLSs have been called upon to support children of patients in adult clinical environments. Our objective was to elucidate CLS caregiving narratives related to working with children of adult cancer patients. We used narrative inquiry to interview four CLSs working in adult oncology. Canadian CLSs who have experience providing care for children and families affected by parental cancer were recruited via convenience sampling. We used narrative analysis methods that included multiple close reads of the data, generating narrative themes, and noting conflicts or tensions in the data. CLSs' caregiving stories often highlighted the complexities of working in an adult oncology environment. Their narratives included challenges in providing optimal care to the children, including family-level barriers (such as parental wishes to withhold information from their children) and systemic barriers (such as late referrals and limited options for bereavement support). CLS participants identified several challenges of working with families in adult oncology. The CLSs highlighted a desire for additional institutional support for children of adult oncology patients and for themselves working in these environments in order to achieve what they believed to be optimal care.

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