Hypoxia-inducible factors (HIFs) are master transcriptional regulators, central to cellular survival in hypoxia and frequently activated within malignancy. Whilst malignant context directs the role of HIFs within oncogenesis, these mechanisms are not well characterised. Applying the JAK2V617F myeloproliferative neoplasms (MPNs) oncogene-driver model, in which HIF-1α is stabilised in normoxia (20% O2), we sought to determine whether the modality of HIF-1 activation directs its function. Through direct analysis of hypoxia-activated vs. JAK2V617F-activated HIF-1 at the chromatin, we define a JAK2V617F-HIF-1 regulon that diverges from canonical HIF/hypoxia targets. In a cohort of 172 JAK2V617F-MPN patients, we observe significant association of the JAK2V617F-HIF-1 regulon, but not canonical HIF-1 gene signatures, with disease severity, progression, and patient survival. We further define a subset gene signature (HIF1-MPN-BP) significantly associated with spontaneous transformation to blast phase MPNs. Finally, we identify that JAK2V617F-induced HIF-1α stabilisation is mediated via PIM1 kinase. Our findings demonstrate that HIF-1 activation by the JAK2V617F-PIM1 axis significantly alters HIF-1 transcription function, desensitising HIF-1 activity to cellular oxygen levels, and restricting the HIF-1 regulon to a set of disease-associated target genes within JAK2V617F-MPNs. These findings restore the potential for specific therapeutic targeting of HIF-1 by delineating malignant activation from the physiological hypoxic response.

A major challenge in cancer therapeutics has been the identification of targets that are selectively toxic to cancer cells while displaying limited effects on healthy counterparts. Toxicities related to blood production from hematopoietic stem and progenitor cells (HSPCs) can be particularly problematic and can result in patient morbidity and mortality. MLLT1 has been identified as a key potential target in acute myeloid leukemia. Here, we evaluated the sensitivity of the MLLT1 inhibitor SGC-iMLLT using a panel of leukemia cell lines and healthy HSPCs. We found that SGC-iMLLT downregulated MLLT1 target genes and strongly inhibited KMT2A::AFF1-driven leukemia growth in vitro and in vivo. By contrast, SGC-iMLLT did not alter in vitro colony forming potential of human HSPCs or affect long-term in vivo function of mouse HSPCs. These results suggest that SGC-iMLLT may have a promising therapeutic window in the treatment of KMT2A::AFF1-driven leukemias and that further clinical development is warranted.

The biological mechanisms that sustain the vast blood production required for healthy life remain incompletely understood. To search for cell intrinsic regulators of hematopoiesis, we perform a genome-wide in vivo hematopoietic stem and progenitor cell (HSPC)-based CRISPR knockout screen. We discover SAGA complex members, including Tada2b and Taf5l, as key regulators of hematopoiesis. Loss of Tada2b or Taf5l strongly inhibits hematopoiesis in vivo, causing a buildup of immature hematopoietic cells in the bone marrow. The SAGA complex deposits histone H3 lysine 9 acetylation (H3K9ac) and removes histone H2B ubiquitination (H2Bub). Loss of Tada2b leads to a reduction in H3K9ac levels and altered H2Bub enrichment in HSPCs, implicating disruption of SAGA complex activity. This is associated with upregulation of interferon pathway genes, reduced mitochondrial activity, and increased megakaryocyte progenitor cell commitment. Loss of these factors also enhances the cell outgrowth and the interferon pathway in an in vivo human myelodysplastic syndrome cell line model. In summary, this study identifies the SAGA complex as an important regulator of hematopoiesis.

Haematopoietic stem cells (HSCs) are important for human health and clinical therapy. A heterogenous pool of HSCs sustain blood production through life by balancing self-renewal and multilineage differentiation. Aging is associated with a decline in the function of the HSC pool and haematopoietic perturbations. Additionally, aging correlates with clonal haematopoiesis, driven by the accumulation of genetic mutations in this long-lived cell population that can lead to altered cell function and ultimately to leukemic transformation. Alongside their natural role in sustaining haematopoiesis, healthy HSCs are also used clinically for their regenerative capacity in stem cell transplantation, where they reconstitute the entire adult blood system and can cure a range of blood disorders. Within these contexts, the term fitness is regularly used but often poorly defined. In this perspective, we summarise two distinct types of HSC fitness, clonal fitness and stem cell fitness. We go on to introduce mechanisms known to shape each and discuss the therapeutic implications for modulating HSC fitness mechanisms. Teaser Abstract This Perspective discusses two types of hematopoietic stem cell fitness, clonal fitness and stem cell fitness, and summarise mechanisms known to shape each and their therapeutic implications.

Infant ALL (iALL) is initiated in utero, most often by rearrangement of the KMT2A gene (KMT2Ar). It carries a very poor prognosis despite a lack of additional oncogenic driver mutations common in childhood ALL. Here, we aimed to identify specific properties of human fetal hematopoietic stem/progenitor cells (HSPC) that promote leukemic transformation in KMT2Ar iALL using molecular, functional and in vivo assays. Through comparison of human fetal HSPC with adult HSPC transcriptomes we derived a fetal-specific gene signature and identified the fetal oncogene LIN28B and its downstream effectors among the top hits. These genes were also expressed in iALL. Functional assays revealed that LIN28B was essential in human fetal liver (FL) CD34+ cells to maintain proliferation and stem-like properties, and support B- and NK-lymphopoiesis. To interrogate the role of LIN28B in iALL, we utilized a human FL-derived CRISPR-Cas9 KMT2A::AFF1 model. In this CRISPRKMT2A::AFF1 model, human FL CD34+ cells fail to transform upon induction of KMT2A::AFF1 translocation in the absence of LIN28B. Furthermore, LIN28B-expressing CRISPRKMT2A::AFF1 leukemias were more proliferative in vitro and in vivo, with this advantage being lost upon LIN28B knockdown. Mechanistic studies showed that LIN28B acts by stabilizing key early B-lymphoid genes, epigenetic regulators, and cell cycle and anti-apoptotic genes. Thus, LIN28B has an essential role in normal human fetal B-lymphopoiesis, and is necessary for the initiation of KMT2A::AFF1 iALL in human fetal cells in the absence of co-operating mutations. LIN28B activity may help explain why KMT2A::AFF1 leukemias are so aggressive, making it a potential target in LIN28B-expressing leukemias.

Here, we present a protocol for isolating and characterizing hematopoietic stem cells (HSCs) from mouse alveolar bone marrow. We describe steps for combining anatomical dissection of the mandibular alveolar region with flow cytometry analysis for identifying HSCs. The protocol enables the isolation of HSCs from a specific bone marrow niche harboring an enriched HSC population. For complete details on the use and execution of this protocol, please refer to Niizuma et al.1.

A major challenge in cancer therapeutics has been the identification of targets that are selectively toxic to cancer cells while displaying limited effects on healthy counterparts. Toxicities related to blood production from haematopoietic stem and progenitor cells (HSPCs) can be particularly problematic and result in patient morbidity and mortality. Within haematological malignancies, therapy response rates and patient survival vary widely between cancer subtypes, with leukaemias driven by the MLL-AF4 fusion protein associated with poor prognosis. MLLT1 has been recently identified as a key potential target in acute myeloid leukaemia. Here we evaluated a panel of leukaemia cell lines and healthy HSPCs for their sensitivity to the MLLT1 inhibitor SGC-iMLLT. We found that SGC-iMLLT strongly inhibited MLL-AF4-driven leukaemia growth in vitro and in vivo. By contrast, SGC-iMLLT did not alter in vitro colony forming potential of human HSPCs or affect long-term in vivo function of mouse HSPCs. These results suggest that SGC-iMLLT may have a promising therapeutic window in the treatment of MLL-AF4-driven leukaemias, and that further clinical development is warranted. ### Competing Interest Statement TAM, NTC, PEB, OF, CA and GF are paid consultants for and shareholders in Dark Blue Therapeutics Ltd., a company dedicated to creating novel compounds directed at MLLT1 and other factors. ACW is a consultant for ImmuneBRIDGE. Kay Kendall Leukaemia Fund, KKL1443 MRC, MC\_UU\_00016/6, MC\_UU\_00029/6 NIHR Wellcome Trust, https://ror.org/029chgv08 Krishnan-Ang Foundation

A long-sought goal of cancer immunotherapy is to mass-produce T cells that specifically target tumor neoantigens. One decisive challenge is the identification of neoantigens derived from cancer driver genes. Here, we identify T cells that recognize the NSCLC-associated EGFR C797S mutation, which confers resistance to current inhibitors and is linked to poor prognosis. To overcome limitations in T cell availability, we reprogrammed EGFR C797S-specific T cells into induced pluripotent stem cells (iPSCs) and re-differentiated them into CD8+ T cells. These iPSC-derived T cells specifically recognized the EGFR C797S mutation and effectively killed cancer cells expressing this mutation. Our findings underscore the potential of targeting driver mutation-derived neoantigens for immunotherapy and demonstrate that iPSC-derived T cells can mediate antitumor effects. Collectively, this approach combining neoantigen identification with T cell reprogramming may offer a promising strategy for targeting drug-resistant tumors.

In vivo gene therapy targeting hematopoietic stem cells (HSCs) holds significant therapeutic potential for treating hematological diseases. This study uses adeno-associated virus serotype 6 (AAV6) vectors and Cre recombination to systematically optimize the parameters for effective in vivo HSC transduction. We evaluated various genetic architectures and delivery methods of AAV6, establishing an optimized protocol that achieved functional recombination in more than two-thirds of immunophenotypic HSCs. Our findings highlight that second-strand synthesis is a critical limiting factor for transgene expression in HSCs, leading to significant under-detection of HSC transduction with single-stranded AAV6 vectors. We also demonstrate that HSCs in the bone marrow (BM) are readily accessible to transduction, with neither localized injection nor mobilization of HSCs into the bloodstream, enhancing transduction efficacy. Additionally, we observed a surprising preference for HSC transduction over other BM cells, regardless of the AAV6 delivery route. Together, these findings not only underscore the potential of AAV vectors for in vivo HSC gene therapy but also lay a foundation that can inform the development of both in vivo AAV-based HSC gene therapies and potentially in vivo HSC gene therapies that employ alternative delivery modalities.

JAK2 V617F is a common haematological driver mutation and underlies most cases of myeloproliferative neoplasms (MPNs). Reducing variant allele frequency (VAF) is an important treatment goal, but no current treatment modalities fully and specifically inhibit mutant signalling. Thus, the consequences of V617F inactivation are unclear, including whether selective inhibition of V617F signalling will eradicate mutant cells due to oncogene addiction. Here, we describe an allele-selective CRISPR-Cas genome editing strategy that achieves selective and efficient JAK2 V617F inactivation in patient stem and progenitor cells. We show that JAK2 V617F heterozygous cells are not oncogene addicted and maintain viability and differentiation potential upon loss of their mutant allele. In contrast, homozygous mutant cells are eradicated upon deletion of both mutant alleles. Across in vitro, organoid, xenotransplantation and single-cell assays, selective deletion of V617F alleles reverts MPN hallmarks including erythroid clonogenicity, inflammatory gene expression signatures, as well as myelofibrosis and splenomegaly phenotypes in an in vivo xenograft model. Collectively, our results show that is it possible to revert heterozygous JAK2 V617F mutant cells to a normal phenotype and suggest that ex vivo genome editing of stem and progenitor cells may be a viable treatment option to achieve rapid and deep reductions in VAF. ### Competing Interest Statement J.O.J.D. is a co-founder of Nucleome Therapeutics Ltd. and he holds personal shares and provides consultancy to the company. J.O.J.D. has received licencing revenue from BEAM therapeutics and holds personal shares in the company. A patent relating to the TARGET-seq technique is licensed to Alethiomics Ltd, a spin out company from the University of Oxford with equity owned by B.P. and A.J.M. A.C.W. is a scientific advisor for ImmuneBridge. Y.S. provides consultancy for Alethiomics Ltd. The other authors declare no competing interests. Medical Research Council, MC\_UU\_00029/04 Wellcome Trust, 225220/Z/22/Z National Institute for Health Research, https://ror.org/0187kwz08 Cancer Research UK, C42639/A26988, DRCNPG-Nov24/100003

The global rise in ageing populations is driving an increase in age-associated diseases, including haematological malignancies such as myelodysplastic syndromes and acute myeloid leukaemia. A major challenge in addressing this burden is the lack of experimental systems that enable mechanistic studies and therapeutic screening in ageing haematopoiesis. Here, we evaluate a polymer-based ex vivo culture platform for studying human haematopoietic stem and progenitor cells (HSPCs) in the context of ageing. Using CD34 + cells from cord blood, bone marrow and peripheral blood from different age groups, we show that this culture system enables robust expansion of HSPCs while preserving age-associated transcriptional programs. Single-cell RNA sequencing revealed enrichment of key progenitor populations with consistent transcriptional identities across donors. Importantly, expanded HSPCs from older individuals retained ageing-associated signatures, such as upregulation of inflammatory pathways. These findings demonstrate that our polymer-based expansion system enables robust modelling of ageing haematopoiesis and provide a single cell transcriptional landscape of this ageing model. We envision that this system could provide a versatile platform for mechanistic studies and pharmacological testing, addressing a critical gap in experimental frameworks for age-related haematological disease research.

ABSTRACT:Self-renewing multipotent hematopoietic stem cells (HSCs) are a rare but important cell population that can reconstitute the entire blood and immune system after transplantation. Due to their rarity, it has been difficult to comprehensively study the mechanisms regulating HSC activity. However, recent improvements in hematopoietic stem and progenitor cell (HSPC) culture methods using polyvinyl alcohol-based media now facilitate large-scale ex vivo HSC expansion. Here, we performed a genome-wide CRISPR knockout (KO) screen in primary mouse HSPCs to discover novel regulators of ex vivo expansion. The screen identified Runx2 as a strong negative regulator of HSC expansion, which we validated using ex vivo and in vivo assays. Loss of Runx2 increased the frequency of immunophenotypic HSCs in HSPC cultures by approximately threefold. After expansion, these Runx2-KO HSCs engrafted at approximately fivefold higher levels in transplantation assays. Noncultured Runx2-KO HSCs also displayed enhanced reconstitution potential, but loss of Runx2 did not alter blood parameters. Notably, however, T-cell reconstitution was diminished from Runx2-KO HSCs, and we further validated an additional role for Runx2 in T-cell commitment using ex vivo and in vivo assays. In summary, we have identified a multifaceted role for Runx2 in HSCs, as a negative regulator of HSC self-renewal and as a facilitator of T-cell commitment. These results contribute to our understanding of the transcriptional regulation of hematopoiesis and HSC therapies.

Hematopoietic stem cells (HSCs) are crucial for maintaining hematopoietic homeostasis and are localized within distinct bone marrow (BM) niches. While BM niches are often considered similar across different skeletal sites, we discovered that the alveolar BM (al-BM) in the mandible harbors the highest frequency of immunophenotypic HSCs in nine different skeletal sites. Transplantation assays revealed significantly increased engraftment from al-BM compared to femur, tibia, or pelvis BM, likely due to a higher proportion of alveolar HSCs. Moreover, hematopoietic progenitor cells (c-Kit+ Sca-1+ Lin-) in al-BM exhibited increased quiescence and reduced apoptosis, indicating superior maintenance and survival characteristics. We also observed an enrichment of mesenchymal stromal cells and skeletal stem cells in al-BM, suggesting a more supportive microenvironment. These findings indicate that al-BM provides a unique microenvironment conducive to higher frequency of HSCs, offering new insights into site-specific hematopoiesis.

In this issue of Blood , Chagraoui et al 1 uncover new insights into the mechanism of action of the small molecule agonist of ex vivo human hematopoietic stem cell (HSC) expansion, UM171.

Delineating cell-intrinsic and -extrinsic drivers of hematopoietic stem cell (HSC) self-renewal is critical to improve efforts in ex vivo HSC expansion and to better understand leukemia cell biology. To characterize molecular changes at the proteome level, we applied miniaturized, multiplexed sample preparation protocols in combination with mass spectrometry (MS)-based quantitative proteomics to compare normal and Tet2-deficient HSCs, and data-independent acquisition (DIA)-MS to characterize the extracellular environment of HSCs in vivo and during ex vivo expansion. We show that both the cellular and secreted proteome accurately stratify HSCs based on functional potency and mutational status and identify novel molecular components not captured in transcriptomic analyses. On the pre-leukemia side, we reveal that Tet2-deficient HSCs have altered expression of extracellular matrix (ECM) proteins and that interaction with these proteins in artificial niches affects cellular function. Extracellular proteomic analysis further reveals that Tet2-deficient cells create a microenvironment is pro-inflammatory and pro-thrombotic even in young, asymptomatic animals. In HSC expansion assays, proteomics identifies the requirement for intact DNA repair pathways, specifically mismatch repair proteins, as key components of HSC clones capable of extensive self-renewal compared to unsuccessful expansion cultures. Analysis of the secretome of unsuccessful cultures further identifies mast cell proteins as predictive of failure to expand engraftable HSCs. Collectively these data highlight novel proteins to which transcriptomic studies are blind, and open new opportunities for HSC expansion and preleukemic biology, paving the way for future ex vivo and in vivo modulation of HSC function via manipulation of the cells and their extracellular environment.

Abstract Background The composition of the gut microbiome is a key determinant in inflammatory bowel disease. Consequently, modifying the composition of the gut microbiota has the potential to transform the treatment of ulcerative colitis (UC). The clinical use of faecal microbiota transplantation (FMT) has become widespread, especially for the treatment of C. difficile associated diseases, as a method of changing the composition of the gut microbiome from a diseased to a healthy state. FMT is, by its nature, an undefined and variable therapy due to differences between donors. Microbiotica has taken a "patient-first" discovery approach to identify a defined consortium, which is being developed as a live bacterial therapeutic for treatment of mild-to-moderate UC patients in a Phase 1b clinical trial, the COMPOSER-1 study, in 2024. Methods A clinical trial in UC patients (Costello et al., 2019), in which patients were treated with FMT from healthy donors, showed a 32% clinical remission rate in the active treatment group, as compared to 9% in the placebo arm. Donor, pre-treatment recipient, and post-FMT recipient samples were analysed using shotgun metagenomic sequencing. All samples were analysed using Microbiotica’s precision microbiome analysis platform to identify bacteria associated with patient response. These bacteria were assessed in cellular assays using relevant human cell/cell lines including: Caco2, dendritic cells, M1 macrophages, and CD4+ T-cells. Results We defined a signature of therapeutic response based on bacteria that engrafted from the donor into UC patients and were associated with clinical benefit. A sub-species level analysis identified 8 bacteria, which have been developed into a defined live bacterial therapeutic, MB310. The consortium bacteria enhanced the barrier integrity of an epithelial cell monolayer, and protected the barrier from inflammatory challenge by LPS. In vitro, the bacteria also have an anti-inflammatory effect when incubated with different primary innate immune cells, dendritic cells and M1 macrophages. Specific MB310 bacteria, either directly or via metabolites, are able to regulate T-cell responses. Conclusion In summary, we have identified a consortium of bacteria using patient-first discovery in a successful FMT study that is being developed as a treatment for UC. The consortium of 8 bacteria is able to impact multiple disease-relevant mechanisms including epithelial barrier integrity and immunomodulation. MB310 is being advanced to a first-in-human study in 2024 to explore safety and initial signs of efficacy. Costello, et al. (2019) Jama 321.2: 156-164.

Hematopoietic stem cells (HSCs) are a rare but potent cell type that support life-long hematopoiesis and stably regenerate the entire blood and immune system following transplantation. HSC transplantation represents a mainstay treatment for various diseases of the blood and immune systems. The ex vivo expansion and manipulation of HSCs therefore represents an important approach to ask biological questions in experimental hematology and to help improve clinical HSC transplantation therapies. However, it has remained challenging to expand transplantable HSCs ex vivo. This review summarizes recent progress in ex vivo HSC expansion technologies and their applications to biological and clinical problems and discusses current questions in the field. (c) 2023 ISEH - Society for Hematology and Stem Cells. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/)

A differentiation method informed by developmental biology converts human pluripotent stem cells to engraftable hematopoietic stem and progenitor cells without the use of transgenes.

Hypoxia-inducible factors (HIFs) are master transcriptional regulators, central to physiological oxygen homeostasis and cellular survival under limited oxygen conditions (hypoxia) and are frequently activated within malignancy. The context within which HIFs are activated significantly impacts their role within oncogenesis; this is particularly evident within acute myeloid leukaemia (AML), where HIF-1 has been characterised as both oncogenic and tumour suppressive. The mechanisms that regulate these disparities are not well understood. We therefore sought to determine whether the modality of HIF-1 activation determines its function, applying the JAK2V617F (JVF) model of myeloproliferative neoplasms (MPNs) in which HIF-1 is stabilised under normal oxygen (normoxic) conditions and is oncogenic. First, we identify that HIF-1 is stabilised in JVF cells downstream of disproportionate STAT1/5 signalling and increased expression of PIM1. Inhibition of PIM1 kinase activity eradicates HIF-1 from normoxic JVF cells. We identify a novel phosphorylation couplet (T498/S500) within the oxygen dependent degradation (ODD) domain of HIF-1 phosphorylated in JVF cells that inhibits normoxic proteasomal degradation. Applying a single-input dual-omics output chromatin interactome methodology (MinatuRIME) in matched isogenic cell lines, we identify distinct transcriptional cofactors for HIF-1 in JVF cells and redistribution of HIF-1 across the genome, indicative of JVF HIF-1 performing pre- mRNA imprinting and aberrant transcriptional control. JVF-HIF-1 produces a non-canonical target gene signature that is differentially expressed in primary mouse and human JVF haematopoietic stem and progenitor cells (HPSCs). Analysing a cohort of 298 JVF-positive MPN patients, we observe significant association of the JVF-HIF signature- but strikingly not the hypoxia-induced HIF-1 signature- with disease severity, progression, and survival of these patients. Finally, we identify a core set of 13 genes within the JVF-HIF-1 signature whose differential expression is significantly associated with spontaneous transformation of MPNs to acute myeloid leukaemia (AML). These findings demonstrate that the context and modality of HIF-1 activation can substantially alter its transcriptional function and restore the potential for targeted HIF therapies that can delineate its activity co-opted by malignancy from its essential roles within physiological oxygen homeostasis. ### Competing Interest Statement The authors have declared no competing interest.