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Precision gene editing in primary hematopoietic stem and progenitor cells (HSPCs) would facilitate both curative treatments for monogenic disorders as well as disease modelling. Precise efficiencies even with the CRISPR/Cas system, however, remain limited. Through an optimization of guide RNA delivery, donor design, and additives, we have now obtained mean precise editing efficiencies >90% on primary cord blood HSCPs with minimal toxicity. Critically, editing is even across the progenitor hierarchy, and does not substantially distort the hierarchy or affect lineage outputs in colony-forming cell assays. As modelling of many diseases requires heterozygosity, we also demonstrated that the overall editing and zygosity can be tuned by adding in defined mixtures of mutant and wild-type donor. With these optimizations, editing at near-perfect efficiency can now be accomplished directly in human HSPCs. This will open new avenues in both therapeutic strategies and disease modelling.

Extended methods, supplementary figures and supplementary tables.

Processed data for S222A+ and S222A- cells by RNA and ATAC sequencing

RUNX1 mutations identified in the Leucegene cohort. Position of mutations are indicated using NM_001754 and NM_001001890, coding for RUNX1 proteins of 480 and 453 AA respectively. VAF: variant allele frequency.

Purpose: RUNX1-mutated (RUNX1mut) acute myeloid leukemia (AML) is associated with adverse outcome, highlighting the urgent need for a better genetic characterization of this AML subgroup and for the design of efficient therapeutic strategies for this disease. Toward this goal, we further dissected the mutational spectrum and gene expression profile of RUNX1mut AML and correlated these results to drug sensitivity to identify novel compounds targeting this AML subgroup.Experimental Design: RNA-sequencing of 47 RUNX1mut primary AML specimens was performed and sequencing results were compared to those of RUNX1 wild-type samples. Chemical screens were also conducted using RUNX1mut specimens to identify compounds selectively affecting the viability of RUNX1mut AML.Results: We show that samples with no remaining RUNX1 wild-type allele are clinically and genetically distinct and display a more homogeneous gene expression profile. Chemical screening revealed that most RUNX1mut specimens are sensitive to glucocorticoids (GCs) and we confirmed that GCs inhibit AML cell proliferation through their interaction with the glucocorticoid receptor (GR). We observed that specimens harboring RUNX1 mutations expected to result in low residual RUNX1 activity are most sensitive to GCs, and that coassociating mutations as well as GR levels contribute to GC sensitivity. Accordingly, acquired glucocorticoid sensitivity was achieved by negatively regulating RUNX1 expression in human AML cells.Conclusions: Our findings show the profound impact of RUNX1 allele dosage on gene expression profile and glucocorticoid sensitivity in AML, thereby opening opportunities for preclinical testing which may lead to drug repurposing and improved disease characterization. Clin Cancer Res; 23(22); 6969–81. ©2017 AACR.

Supplementary Figure 1. Additional examples of genes most correlated (> 0.50 or

Key Points Inhibition of RAB protein function mediates the anti–acute myeloid leukemia activity of statins.Statin sensitivity is associated with enhanced vesicle-mediated traffic., Visual Abstract, Cholesterol homeostasis has been proposed as one mechanism contributing to chemoresistance in AML and hence, inclusion of statins in therapeutic regimens as part of clinical trials in AML has shown encouraging results. Chemical screening of primary human AML specimens by our group led to the identification of lipophilic statins as potent inhibitors of AMLs from a wide range of cytogenetic groups. Genetic screening to identify modulators of the statin response uncovered the role of protein geranylgeranylation and of RAB proteins, coordinating various aspect of vesicular trafficking, in mediating the effects of statins on AML cell viability. We further show that statins can inhibit vesicle-mediated transport in primary human specimens, and that statins sensitive samples show expression signatures reminiscent of enhanced vesicular trafficking. Overall, this study sheds light into the mechanism of action of statins in AML and identifies a novel vulnerability for cytogenetically diverse AML.

Hematopoietic stem cells (HSCs) sustain blood cell homeostasis throughout life and can regenerate all blood lineages after transplantation. Despite this clear functional definition, highly enriched isolation of human HSCs can currently only be achieved through combinatorial assessment of multiple surface antigens. Although several transgenic HSC reporter mouse strains have been described, no analogous approach to prospectively isolate human HSCs has been reported. To identify genes with the most selective expression in human HSCs, we profiled population and single-cell transcriptomes of unexpanded and ex vivo cultured cord blood–derived hematopoietic stem and progenitor cells as well as peripheral blood, adult bone marrow, and fetal liver. On the basis of these analyses, we propose the master transcription factor HLF (hepatic leukemia factor) as one of the most specific HSC marker genes. To directly track its expression in human hematopoietic cells, we developed a genomic HLF reporter strategy, capable of selectively labeling the most immature blood cells on the basis of a single engineered parameter. Most importantly, HLF-expressing cells comprise all stem cell activity in culture and in vivo during serial transplantation. Taken together, these results experimentally establish HLF as a defining gene of the human HSC state and outline a new approach to continuously mark these cells with high fidelity.

Gene marker extraction to evaluate risk in cancer can refine the diagnosis process and lead to adapted therapies and better survival. These survival analyses can be done through computer systems and Machine Learning (ML) algorithms such as the Cox-Proportional-Hazard model from gene expression (GE) RNA-Seq data. However, optimal tuning of CPH from genome-wide GE data is challenging and poorly assessed so far. In this work we propose to interrogate an Acute Myeloid Leukemia (AML) dataset (Leucegene) to derive key components of the CPH driving down its performance and discovering its sensitivity to various factors in hoping to ameliorate the system. In this study, we compare the projection and selection data reduction techniques, mainly the PCA and LSC17 gene signature in combination with the CPH in a ML framework. Results reveals that CPH performs better with a combination of clinical and genetic expression features. We determine that projections performs better than selections without clinical information. We ascertain that CPH is affected by overfitting and that this overfitting is linked to the number and the content of input covariables. We show that PCA links clinical features via ability to learn from the input data directly and generalizes better than LSC17 on Leucegene. We postulate that projection are preferred than selection on harder task such as assessing risk in the intermediate subset of Leucegene. We extrapolate that these findings apply in the more general context of risk detection via machine learning in cancer. We see that higher capacity models such as CPH-DNNs systems can be improved via survival-derived projections and combat overfitting through heavy regularization.Author summaryThis study aims to investigate the feasibility of using gene expression to evaluate risk in cancer, and to compare the projection and selection data reduction techniques. The study used the Leucegene dataset to compare the PCA method and a previously published 17 genes signature in combination with the Cox-Proportional-Hazard model in a machine learning framework. Results showed that CPH was affected by overfitting and that this overfitting was linked to the number and the content of input covariables. The study found that PCA links clinical features via ability to learn from the input data directly and generalizes better than LSC17 on Leucegene. The study concluded that projections are preferred than selection on harder task such as assessing risk in the intermediate subset of Leucegene and can be tuned to improve their performance.Data availability statementSource code for pipelines and algorithms, as well as gene expression matrices, are available here:https://github.com/lemieux-lab/dimensions_coxph. Access to the Leucegene cohort’s survival times can be granted upon request and following ethical review.

Allogeneic hematopoietic cell transplantation (HCT) has curative potential in myeloma but remains hampered by high rates of relapse and chronic graft-versus-host disease (GVHD). We hypothesized that bortezomib (BTZ) as maintenance therapy after allo HCT could not only decrease the incidence of relapse but also the incidence and severity of chronic GVHD. The primary endpoint of this study was to determine whether BTZ maintenance decreases the incidence and severity of chronic GVHD using National Institutes of Health (NIH) criteria. The secondary endpoints were to determine the immunosuppression burden, organ involvement and survival (overall survival, progression-free survival) in patients either receiving or not receiving BTZ. In this retrospective study, we compared the outcome of 46 myeloma patients who received BTZ after upfront tandem auto-allo HCT between 2008 and 2020 to 61 patients without maintenance. We explored the impact of BTZ maintenance on incidence and severity of chronic GVHD using the 2014 NIH criteria. At 2 years, incidences of overall (61.2% versus 83.6%; P = .001), and moderate/severe chronic GVHD (44.5% versus 77.0%; P = .001) were significantly lower in BTZ recipients who had less mouth (43% versus 67%; P = .018) and eyes (9% versus 41%; P = .001) involvement at initial diagnosis. We report a lower use of systemic steroids (45.1% versus 76.4%; P.001), mycophenolate mofetil (15.5% versus 28.2%; P = .031) and tacrolimus (34.5% versus 70.6%; P.001) in BTZ recipients. Probability of being alive and off systemic immunosuppressants at 3 years was 77% in BTZ recipients and 56% in controls (P = .046). To date, there is no difference in survival between both groups. In summary, BTZ maintenance improved incidence and severity of chronic GVHD and should be considered as a valid option in myeloma patients receiving upfront tandem auto-allo HCT.

Haplo-identical donors have been increasingly used as an alternative source of stem cells in patients with severe aplastic anemia in need of an allogeneic transplantation but lack a matched donor. Single cord blood (CB) transplant also offers a curative option for this disease, but few adult patients have been reported due to low number of progenitor cells leading to prolonged cytopenias and a high risk of infections. CB stem cell expansion may theoretically solve these pitfalls but has not been used previously in non-malignant diseases, likely due to fear of graft rejection and lack of availability of expanded CBs outside clinical trials. We report the first case of an adult patient with severe aplastic anemia who was successfully transplanted with a UM171-expanded CB graft. After a conditioning of rabbit antithymocyte globulin, fludarabine, cyclophosphamide, and total body irradiation, a UM171 expanded graft of 3.29 × 106 CD34 + cells/kg (a 51-fold increase) was infused. Full donor chimerism was observed on day + 14, with neutrophil and platelet engraftment on days + 23 and + 27. There was no severe infection or graft-vs-host disease. UM171-expanded grafts offer a valuable option for patients with aplastic anemia in need of transplantation but have no suitable donor.

RUNX1 is mutated in ∼10% of adult acute myeloid leukemia (AML). Although most RUNX1 mutations in this disease are believed to be acquired, they can also be germline. Indeed, germline RUNX1 mutations result in the well-described autosomal-dominant familial platelet disorder with predisposition to hematologic malignancies (RUNX1-FPD, FPD/AML, FPDMM); ∼44% of affected individuals progress to AML or myelodysplastic syndromes. Using the Leucegene RUNX1 AML patient group, we sought to investigate the proportion of germline vs acquired RUNX1 mutations in this cohort. Our results showed that 30% of RUNX1 mutations in our AML cohort are germline. Molecular profiling revealed higher frequencies of NRAS mutations and other mutations known to activate various signaling pathways in these patients with RUNX1 germline–mutated AML. Moreover, 2 patients (mother and son) had co-occurrence of RUNX1 and CEBPA germline mutations, with variable AML disease onset at 59 and 27 years, respectively. Together, these data suggest a higher than anticipated frequency of germline RUNX1 mutations in the Leucegene cohort and further highlight the importance of testing for RUNX1 mutations in instances in which allogeneic stem cell transplantation using a related donor is envisioned.

Summary Background Benefits of cord blood transplantation include low rates of relapse and chronic graft-versus-host disease (GVHD). However, the use of cord blood is rapidly declining because of the high incidence of infections, severe acute GVHD, and transplant-related mortality. UM171, a haematopoietic stem cell self-renewal agonist, has been shown to expand cord blood stem cells and enhance multilineage blood cell reconstitution in mice. We aimed to investigate the safety and feasibility of single UM171-expanded cord blood transplantation in patients with haematological malignancies who do not have a suitable HLA-matched donor. Methods This single-arm, open-label, phase 1–2 safety and feasibility study was done at two hospitals in Canada. The study had two parts. In part 1, patients received two cord blood units (one expanded with UM171 and one unmanipulated cord blood) until UM171-expanded cord blood demonstrated engraftment. Once engraftment was documented we initiated part 2, reported here, in which patients received a single UM171-expanded cord blood unit with a dose de-escalation design to determine the minimal cord blood unit cell dose that achieved prompt engraftment. Eligible patients were aged 3–64 years, weighed 12 kg or more, had a haematological malignancy with an indication for allogeneic hematopoietic stem cell transplant and did not have a suitable HLA-matched donor, and a had a Karnofsky performance status score of 70% or more. Five clinical sites were planned to participate in the study; however, only two study sites opened, both of which only treated adult patients, thus no paediatric patients (aged ClinicalTrials.gov , NCT02668315 . Findings Between Feb 17, 2016, and Nov 11, 2018, we enrolled 27 patients, four of whom received two cord blood units for safety purposes in part 1 of the study. 23 patients were subsequently enrolled in part 2 to receive a single UM171-expanded cord blood transplant and 22 patients received a single UM171-expanded cord blood transplantation. At data cutoff (Dec 31, 2018), median follow-up was 18 months (IQR 12–22). The minimal cord blood unit cell dose at thaw that achieved prompt engraftment as a single cord transplant after UM171 expansion was 0·52 × 105 CD34-positive cells. We successfully expanded 26 (96%) of 27 cord blood units with UM171. Among the 22 patients who received single UM171-expanded cord blood transplantation, median time to engraftment of 100 neutrophils per μL was 9·5 days (IQR 8–12), median time to engraftment of 500 neutrophils per μL was 18 days (12·5–20·0), and no graft failure occurred. Median time to platelet recovery was 42 days (IQR 35–47). The most common non-haematological adverse events were grade 3 febrile neutropenia (16 [73%] of 22 patients) and bacteraemia (nine [41%]). No unexpected adverse events were observed. One (5%) of 22 patients died due to treatment-related diffuse alveolar haemorrhage. Interpretation Our preliminary findings suggest that UM171 cord blood stem cell expansion is feasible, safe, and allows for the use of small single cords without compromising engraftment. UM171-expanded cord blood might have the potential to overcome the disadvantages of other cord blood transplants while maintaining the benefits of low risk of chronic GVHD and relapse, and warrants further investigation in randomised trials. Funding Canadian Institutes of Health Research, Canadian Cancer Society and Stem Cell Network.

Despite high cure rates with frontline therapy for Hodgkin lymphoma (HL), approximately 30% of patients will relapse or develop primary refractory disease (R/r). Autologous hematopoietic stem cell transplantation (autoHSCT) is the standard of care for R/r disease, and allogeneic HSCT (alloHSCT) is a curative option for patients in second relapse. Novel agents are being incorporated for the treatment of R/r HL, such that the optimal timing of transplantation is currently being challenged. In this rapidly evolving field, we sought to offer a Canadian perspective on the optreatment of R/r HL and demonstrate the role and effectiveness of both autoHSCT and alloHSCT for the treatment of R/r HL. This single-center retrospective study examined outcomes in 89 consecutive patients with R/r HL treated with autoHSCT between January 2007 and December 2019. A total of 17 patients underwent alloHSCT either as a tandem auto-allo approach or as salvage therapy. With a median follow-up of 5.0 years, the estimated 5-year PFS and OS for patients undergoing autoHSCT were 57.5% (95% confidence interval [CI], 45.2% to 68.0%) and 81.3% (95% CI, 70.0% to 88.8%), respectively. Corresponding values for patients who underwent alloHSCT were 76.5% (95% CI, 48.8% to 90.4%) and 82.4% (95% CI, 54.7% to 93.9%). Nonrelapse mortality at 0% at 100 days and 9.4% at 5 years post-autoHSCT and 0% and 5.9%, respectively, post-alloHSCT. The cumulative incidence of acute graft-versus-host disease (GVHD) at day +100 was 35.3% (95% CI, 17.7% to 62.3%), and that of chronic GVHD at 1 year was 23.5% (95% CI, 6.9% to 45.8%). Both autoHSCT and alloHSCT provide robust and prolonged disease control New agents should be used as a bridge to improve the curative potential of these definitive cellular therapies.

Key Points CEACAM1 is a novel cell surface marker of ex vivo expanded LT-HSCs. Sorting umbilical cord blood cells based on CEACAM1 and known HSC marker expression allows purification of LT-HSCs with improved purity.

Cord blood (CB) stem cell transplantation offers a greater tolerance to HLA mismatches compared to adult-derived stem cell transplants (i.e., bone marrow or peripheral blood stem cells). Indeed, 4/6 or 5/8 HLA-matched CB transplantations are regularly performed for patients lacking a matched unrelated donor. Unfortunately, most banked CB units contain a stem cell dose that is too small to treat adult patients, resulting in only 4% to 5% of available CB units offering an adequate cell dose for prompt engraftment for adult patients. Ex vivo stem cell expansion appears to be an attractive strategy to circumvent this cell dose issue, while also enabling the selection of better HLA-matched CB units. In this study, we retrospectively performed HLA matching simulations to assess how the minimal cell content requirements associated with UM171 CB expansion may improve usability of existing CB unit inventories and donor availability for patients of different races and ethnicities. We analyzed a dataset of 58,971 adults for whom a donor search was initiated through the National Marrow Donor Program Be The Match registry against 142,942 CB units from major U.S. public CB banks listed on the Be The Match registry. Our results show that by enabling selection of smaller CB units, UM171-expanded CB transplantation increases donor availability from 72% to 84% for all patients compared to single unmanipulated CB transplantation. Furthermore, the low cell dose criteria for UM171-expanded CB also increases donor availability compared to double CB transplantation, while enabling better HLA matching between donor and recipient. UM171 expanded CB appears particularly beneficial for racial and ethnic minority patients as CB availability increases from 53% to 78% for African Americans, from 66% to 85% for Hispanics, and from 68% to 84% for Asians and Pacific Islanders, compared to single unmanipulated CB transplantation. In addition, UM171 expansion dramatically improves usability of CB units currently in inventories, as only 4.3% and 0.6% of banked CBs have sufficient cell doses for a 70 kg and 100 kg patient, respectively. UM171 raises this proportion to 53.8% and 20.2%, respectively, making CB banks potentially more cost effective. In conclusion, UM171 expansion allows the use of smaller CB units while also improving access to transplantation for racial and ethnic minorities.

Background This study aims to identify a novel potential use for web portals in health care and health research: their adoption for the purposes of rapidly sharing health research findings with clinicians, scientists, and patients. In the era of precision medicine and learning health systems, the translation of research findings into targeted therapies depends on the availability of big data and emerging research results. Web portals may work to promote the availability of novel research, working in tandem with traditional scientific publications and conference proceedings. Objective This study aims to assess the potential use of web portals, which facilitate the sharing of health research findings among researchers, clinicians, patients, and the public. It also summarizes the potential legal, ethical, and policy implications associated with such tools for public use and in the management of patient care for complex diseases. Methods This study broadly adopts the methods for scoping literature reviews outlined by Arskey and O’Malley in 2005. Raised by the integration of web portals into patient care for complex diseases, we systematically searched 3 databases, PubMed, Scopus, and WestLaw Next, for sources describing web portals for sharing health research findings among clinicians, researchers, and patients and their associated legal, ethical, and policy challenges. Of the 719 candidate source citations, 22 were retained for the review. Results We found varied and inconsistent treatment of web portals for sharing health research findings among clinicians, researchers, and patients. Although the literature supports the view that portals of this kind are potentially highly promising, they remain novel and are not yet widely adopted. We also found a wide range of discussions on the legal, ethical, and policy issues related to the use of web portals to share research data. Conclusions We identified 5 important legal and ethical challenges: privacy and confidentiality, patient health literacy, equity, training, and decision-making. We contend that each of these has meaningful implications for the increased integration of web portals into clinical care.

With the advent of new cellular and targeted therapies, treatment options for relapsed and refractory (r/R) lymphomas have multiplied, and the optimal approach offering the best outcomes remains a matter of passionate debate. High-dose chemotherapy followed by autologous stem cell transplantation (ASCT) is still considered a treatment option for patients with chemosensitive lymphoma when cure is the expected goal. The myeloablative conditioning regimen preceding the stem cell infusion is considered the effective component of this approach. Carmustine (BCNU)-based preparative regimens, such as BEAM and BEAC, are considered the standard of care and have shown efficacy and low nonrelapse mortality (NRM). Comparative studies between conditioning regimens have failed to identify a better option. After a BCNU drug shortage in Canada followed by a steep increase in price, we elected to substitute BCNU for bendamustine (benda) in the preparative regimen. The purpose of this substitution was to improve response while preserving safety and controlling costs. From May 2015 to May 2018, a total of 131 consecutive lymphoma patients received benda-EAM conditioning. These patients were compared with 96 consecutive patients who received BCNU-based conditioning from January 2012 to May 2015. Apart from conditioning, supportive care measures were the same in the 2 groups. Patients receiving benda were older (55.7 years versus 51.1 years; P = .002). The development of grade ≥3 mucositis was more frequent with benda conditioning (39.5% versus 7.8%; P.001) leading to a greater requirement for parenteral nutrition (48.9% versus 21.9%; P.001). A transient creatinine increase1.5 times the upper limit of normal (15.3% versus 4.2%; P.008) and intensive care unit admission (6.9% versus 1.1%; P.029) were more frequent with benda; however, there were no between-group differences in cardiac, pulmonary, or liver toxicity and NRM. With a median follow-up of 48 months for the benda group and 60 months for the BCNU group, benda was associated with significantly better progression-free survival (71% versus 61%; P = .040; hazard ratio [HR], 1.6; 95% confidence interval [CI], 1.0 to 2.7) and overall survival (86% vs 71%; P = .0066; HR, 2.6; 95% CI, 1.3 to 5.4) compared with BCNU-based conditioning regimens. While novel therapies emerge, our study demonstrates that benda-EAM is safe and effective and should be considered a valid alternative to BCNU conditioning to improve outcomes of patients with chemosensitive r/R lymphomas undergoing ASCT.