Pigs as Clinically Relevant Models for Synergizing Interventional Oncology and Immunotherapy

Traditionally, rodent cancer models have driven preclinical oncology research. However, they do not fully recapitulate characteristics of human cancers, and their size poses challenges when evaluating tools in the interventional oncologists' armamentarium. Pig models, however, have been the gold standard for validating surgical procedures. Their size enables the study of image-guided interventions using human ultrasound (US), computed tomography (CT), and magnetic resonance (MR) imaging platforms. Furthermore, pigs have immunologic features that are similar to those of humans, which can potentially be leveraged for studying immunotherapy. Novel pig models of cancer are being developed, but additional research is required to better understand both the pig immune system and malignancy to enhance the potential for pig models in interventional oncology research. This review aims to address the main advantages and disadvantages of using a pig model for interventional oncology and outline the specific characteristics of pig models that make them more suitable for investigation of locoregional therapies.

Targeting deoxycytidine kinase improves symptoms in mouse models of multiple sclerosis

Multiple sclerosis (MS) is an autoimmune disease driven by lymphocyte activation against myelin autoantigens in the central nervous system leading to demyelination and neurodegeneration. The deoxyribonucleoside salvage pathway with the rate-limiting enzyme deoxycytidine kinase (dCK) captures extracellular deoxyribonucleosides for use in intracellular deoxyribonucleotide metabolism. Previous studies have shown that deoxyribonucleoside salvage activity is enriched in lymphocytes and required for early lymphocyte development. However, specific roles for the deoxyribonucleoside salvage pathway and dCK in autoimmune diseases such as MS are unknown. Here we demonstrate that dCK activity is necessary for the development of clinical symptoms in the MOG35-55 and MOG1-125 experimental autoimmune encephalomyelitis (EAE) mouse models of MS. During EAE disease, deoxyribonucleoside salvage activity is elevated in the spleen and lymph nodes. Targeting dCK with the small molecule dCK inhibitor TRE-515 limits disease severity when treatments are started at disease induction or when symptoms first appear. EAE mice treated with TRE-515 have significantly fewer infiltrating leukocytes in the spinal cord, and TRE-515 blocks activation-induced B and T cell proliferation and MOG35-55 -specific T cell expansion without affecting innate immune cells or naïve T and B cell populations. Our results demonstrate that targeting dCK limits symptoms in EAE mice and suggest that dCK activity is required for MOG35-55 -specific lymphocyte activation-induced proliferation.

Abstract 1551: Phenotypic characteristics of T cells co-expressing SOX2, OCT3/4, and NANOG

Introduction: A small subset of T cells from patients treated with MART-1 engineered adoptive T cell transfer (ACT) were found to co-express Yamanaka transcription factors SOX2, OCT3/4, and NANOG (TSON). Identifying these T cells may have potential use in future T cell based immunotherapy.

Methods: Flow (FC) and mass cytometry (MC) were used to evaluate T cells with induced pluripotent stem cell (iPS)-like markers. Peripheral mononuclear cells (PBMC) were collected from 3 melanoma patients (MP) treated with ACT and 1 healthy donor (HD0). Bone marrow (BM) samples were collected from patients with Non-Hodgkin's lymphoma (NHL) and multiple myeloma (MM). T cell populations were then screened for stem cell markers: SOX2 OCT3/4 NANOG TRA-1-81 SSEA4 TRA-1-60 CD3+ CD34-. Naïve T cells (CD45RO- CD62L+) from HD0 were exposed to IL-7/IL-15/IL-21 with or without pan-AKT inhibitor (AKTi). These cells were analyzed after 7 days for TSON expression and the following surface markers: CD27 CD28 CD45RO CD45RA CD57 CD62L CD95 CD122 CD127 CCR4 CCR6 CCR7. PBMC collections from 5 healthy donors (HD) were expanded with or without IL-7/IL-15/IL-21 exposure in G-Rex bioreactors for 7 days. TSON expression was analyzed using MC and characterized for the already mentioned markers as well as CXCR3 and Ki67. Lastly, expanded CD95+ cells were single-cell sorted for TSON and their RNA was extracted using the FRISCR method for single-cell RNA sequencing (scRNA-seq). The iPS cell line H1 was included as a positive control.

Results: T cells across all 3 MP had a small percentage of TSON expression (0.0002%, 0.0001%, 0.0001%, respectively). This small cohort of T cells co-expressed TRA-1-81, SSEA4, and TRA-1-60 (0.05%, 0.05%, 0.8%, respectively). TSON expression for HD0 was 0.0000013%, while co-expression of TRA-1-81, SSEA4, and TRA-1-60 was undetectable. BM samples NHL and MM also showed TSON expression (0.18% vs 0.06%). Naïve T cells treated with IL-7/IL-15/IL-21 had a significantly higher percentage of TSON after 7 days of exposure compared to T cells treated with IL-7/IL-15/IL-21/AKTi (0.008% vs 0.001%, respectively). Furthermore TSON cell subsets in both treatment populations displayed a phenotype similar to T memory stem cells (TMSC) and central memory T cells (TCM) (CD45RA+ CD27+ CD28+ CD62L+ CCR7+ CD95+ CD57- CD45RO+). Concerning PBMCs from the 5 HD, the proliferation marker Ki67 was displayed on 3 non-stimulated HD and all stimulated HD with a range of median intensities [10, 67]. The presence of CD62L CD27 CD95 CCR7 CD28 CD45RO in both non-stimulated and stimulated cell populations was similar to TCM phenotype. Validation of scRNA-seq is still in process. Early results show that OCT3, NANOG, and cMYC are detected in both TSON and H1 while SOX2 could only be detected in H1.

Conclusion: Our data show evidence of T cells with natural TSON expression. However, additional studies are needed to further understand the role of TSON in immunotherapy.

Citation Format: Michael Cerniglia, Helena Escuin-Ordinas, Caroline Porter, Maria Alexandrovna Aleshin, Gardenia Cheung-Lau, Zoran Galic, Inbal Abraham-Davidi, Daniel Sanghoon Shin, Orit Rosenblatt-Rosen, Antoni Ribas, Begoña Comin-Anduix. Phenotypic characteristics of T cells co-expressing SOX2, OCT3/4, and NANOG [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1551.

Development of Hematopoietic Stem Cell-Engineered Invariant Natural Killer T Cell Therapy for Cancer

Invariant natural killer T (iNKT) cells are potent immune cells for targeting cancer; however, their clinical application has been hindered by their low numbers in cancer patients. Here, we developed a proof-of-concept for hematopoietic stem cell-engineered iNKT (HSC-iNKT) cell therapy with the potential to provide therapeutic levels of iNKT cells for a patient's lifetime. Using a human HSC engrafted mouse model and a human iNKT TCR gene engineering approach, we demonstrated the efficient and long-term generation of HSC-iNKT cells in vivo. These HSC-iNKT cells closely resembled endogenous human iNKT cells, could deploy multiple mechanisms to attack tumor cells, and effectively suppressed tumor growth in vivo in multiple human tumor xenograft mouse models. Preclinical safety studies showed no toxicity or tumorigenicity of the HSC-iNKT cell therapy. Collectively, these results demonstrated the feasibility, safety, and cancer therapy potential of the proposed HSC-iNKT cell therapy and laid a foundation for future clinical development.

Germline competency of human embryonic stem cells depends on eomesodermin

In humans, germline competency and the specification of primordial germ cells (PGCs) are thought to occur in a restricted developmental window during early embryogenesis. Despite the importance of specifying the appropriate number of PGCs for human reproduction, the molecular mechanisms governing PGC formation remain largely unexplored. Here, we compared PGC-like cell (PGCLC) differentiation from 18 independently derived human embryonic stem cell (hESC) lines, and discovered that the expression of primitive streak genes were positively associated with hESC germline competency. Furthermore, we show that chemical inhibition of TGFβ and WNT signaling, which are required for primitive streak formation and CRISPR/Cas9 deletion of Eomesodermin (EOMES), significantly impacts PGCLC differentiation from hESCs. Taken together, our results suggest that human PGC formation involves signaling and transcriptional programs associated with somatic germ layer induction and expression of EOMES.

Medial HOXA genes demarcate haematopoietic stem cell fate during human development

Pluripotent stem cells (PSC) may provide a potential source of haematopoietic stem/progenitor cells (HSPCs) for transplantation; however, unknown molecular barriers prevent the self-renewal of PSC-HSPCs. Using two-step differentiation, human embryonic stem cells (hESCs) differentiated in vitro into multipotent haematopoietic cells that had CD34⁺CD38^−/loCD90⁺CD45⁺GPI-80⁺ foetal liver (FL) HSC immunophenotype, but displayed poor expansion potential and engraftment ability. Transcriptome analysis of immunophenotypic hESC-HSPCs revealed that, despite their molecular resemblance to FL-HSPCs, medial HOXA genes remained suppressed. Knockdown of HOXA7 disrupted FL-HSPC function and caused transcriptome dysregulation that resembled hESC-derived progenitors. Overexpression of medial HOXA genes prolonged FL-HSPC maintenance but was insufficient to confer self-renewal to hESC-HSPCs. Stimulation of retinoic acid signalling during endothelial-to-haematopoietic transition induced the HOXA cluster and other HSC/definitive haemogenic endothelium genes, and prolonged HSPC maintenance in culture. Thus, retinoic acid signalling-induced medial HOXA gene expression marks the establishment of the definitive HSC fate and controls HSC identity and function.

Lymphoid regeneration from gene-corrected SCID-X1 subject-derived iPSCs

X-linked Severe Combined Immunodeficiency (SCID-X1) is a genetic disease that leaves newborns at high risk of serious infection and a predicted life span of less than 1 year in the absence of a matched bone marrow donor. The disease pathogenesis is due to mutations in the gene encoding the Interleukin-2 receptor gamma chain (IL-2Rγ), leading to a lack of functional lymphocytes. With the leukemogenic concerns of viral gene therapy there is a need to explore alternative therapeutic options. We have utilized induced pluripotent stem cell (iPSC) technology and genome editing mediated by TALENs to generate isogenic subject-specific mutant and gene-corrected iPSC lines. While the subject-derived mutant iPSCs have the capacity to generate hematopoietic precursors and myeloid cells, only wild-type and gene-corrected iPSCs can additionally generate mature NK cells and T cell precursors expressing the correctly spliced IL-2Rγ. This study highlights the potential for the development of autologous cell therapy for SCID-X1 subjects.

Human developmental chondrogenesis as a basis for engineering chondrocytes from pluripotent stem cells

Joint injury and osteoarthritis affect millions of people worldwide, but attempts to generate articular cartilage using adult stem/progenitor cells have been unsuccessful. We hypothesized that recapitulation of the human developmental chondrogenic program using pluripotent stem cells (PSCs) may represent a superior approach for cartilage restoration. Using laser-capture microdissection followed by microarray analysis, we first defined a surface phenotype (CD166^low/negCD146^low/negCD73⁺CD44^lowBMPR1B⁺) distinguishing the earliest cartilage committed cells (prechondrocytes) at 5–6 weeks of development. Functional studies confirmed these cells are chondrocyte progenitors. From 12 weeks, only the superficial layers of articular cartilage were enriched in cells with this progenitor phenotype. Isolation of cells with a similar immunophenotype from differentiating human PSCs revealed a population of CD166^low/negBMPR1B⁺ putative cartilage-committed progenitors. Taken as a whole, these data define a developmental approach for the generation of highly purified functional human chondrocytes from PSCs that could enable substantial progress in cartilage tissue engineering.

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BMPR1B and LIFR mark immature primary chondrocytes throughout ontogeny

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LIF is highly expressed by synovial cells

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LIF inhibits chondrocyte maturation and hypertrophy

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Human development dictates how to generate chondrocyte-enriched progenitors from PSCs

A spatially and chemically defined platform for the uniform growth of human pluripotent stem cells

We report the design of a chemically defined platform engineered for the culture of human pluripotent stem cells (hPSCs) that supports the long-term maintenance of self-renewing hPSC populations in a more uniform manner than standard culture systems. Microcontact printing (μCP) of alkanethiol self-assembled monolayers (SAMs) was used to spatially direct hPSC adherence. This technique not only establishes control over hPSC colony size and shape but also preserves genetic stability and provides unprecedented uniformity in the pluripotency of hPSC populations that is quantitatively assessed in the present study.

GIS-based probability assessment of natural hazards in forested landscapes of Central and South-Eastern Europe

We assessed the probability of three major natural hazards--windthrow, drought, and forest fire--for Central and South-Eastern European forests which are major threats for the provision of forest goods and ecosystem services. In addition, we analyzed spatial distribution and implications for a future oriented management of forested landscapes. For estimating the probability of windthrow, we used rooting depth and average wind speed. Probabilities of drought and fire were calculated from climatic and total water balance during growing season. As an approximation to climate change scenarios, we used a simplified approach with a general increase of pET by 20%. Monitoring data from the pan-European forests crown condition program and observed burnt areas and hot spots from the European Forest Fire Information System were used to test the plausibility of probability maps. Regions with high probabilities of natural hazard are identified and management strategies to minimize probability of natural hazards are discussed. We suggest future research should focus on (i) estimating probabilities using process based models (including sensitivity analysis), (ii) defining probability in terms of economic loss, (iii) including biotic hazards, (iv) using more detailed data sets on natural hazards, forest inventories and climate change scenarios, and (v) developing a framework of adaptive risk management.

A highly efficient short hairpin RNA potently down-regulates CCR5 expression in systemic lymphoid organs in the hu-BLT mouse model

Inhibiting the expression of the HIV-1 coreceptor CCR5 holds great promise for controlling HIV-1 infection in patients. Here we report stable knockdown of human CCR5 by a short hairpin RNA (shRNA) in a humanized bone marrow/liver/thymus (BLT) mouse model. We delivered a potent shRNA against CCR5 into human fetal liver-derived CD34(+) hematopoietic progenitor/stem cells (HPSCs) by lentiviral vector transduction. We transplanted vector-transduced HPSCs solidified with Matrigel and a thymus segment under the mouse kidney capsule. Vector-transduced autologous CD34(+) cells were subsequently injected in the irradiated mouse, intended to create systemic reconstitution. CCR5 expression was down-regulated in human T cells and monocytes/macrophages in systemic lymphoid tissues, including gut-associated lymphoid tissue, the major site of HIV-1 replication. The shRNA-mediated CCR5 knockdown had no apparent adverse effects on T-cell development as assessed by polyclonal T-cell receptor Vbeta family development and naive/memory T-cell differentiation. CCR5 knockdown in the secondary transplanted mice suggested the potential of long-term hematopoietic reconstitution by the shRNA-transduced HPSCs. CCR5 tropic HIV-1 infection was effectively inhibited in mouse-derived human splenocytes ex vivo. These results demonstrate that lentiviral vector delivery of shRNA into human HPSCs could stably down-regulate CCR5 in systemic lymphoid organs in vivo.

A self-renewal program controls the expansion of genetically unstable cancer stem cells in pluripotent stem cell-derived tumors

Human germ cell tumors are often metastatic, presumably due to distal site tumor growth by cancer stem cells. To determine whether cancer stem cells can be identified in a transplantation model of testicular germ cell tumor, we transplanted murine embryonic germ cells (EGCs) into the testis of adult severe combined immunodeficient mice. Transplantation resulted in a locally invasive solid tumor, with a cellular component that generated secondary tumors upon serial transplantation. The secondary tumors were invariably metastatic, a feature not observed in the primary tumors derived from EGCs. To characterize the differences between EGCs and the tumor-derived stem cells, we performed karyotype and microarray analysis. Our results show that generation of cancer stem cells is associated with the acquisition of nonclonal genomic rearrangements not found in the originating population. Furthermore, pretreatment of EGCs with a potent inhibitor of self-renewal, retinoic acid, prevented tumor formation and the emergence of these genetically unstable cancer stem cells. Microarray analysis revealed that EGCs and first- and second-generation cancer stem cells were highly similar; however, approximately 1,000 differentially expressed transcripts could be identified corresponding to alterations in oncogenes and genes associated with motility and development. Combined, the data suggest that the activation of oncogenic pathways in a cellular background of genetic instability, coupled with an inherent ability to self-renew, is involved in the acquisition of metastatic behavior in the cancer stem cell population of tumors derived from pluripotent cells.

Derivation of primordial germ cells from human embryonic and induced pluripotent stem cells is significantly improved by coculture with human fetal gonadal cells

The derivation of germ cells from human embryonic stem cells (hESCs) or human induced pluripotent stem (hIPS) cells represents a desirable experimental model and potential strategy for treating infertility. In the current study, we developed a triple biomarker assay for identifying and isolating human primordial germ cells (PGCs) by first evaluating human PGC formation during the first trimester in vivo. Next, we applied this technology to characterizing in vitro derived PGCs (iPGCs) from pluripotent cells. Our results show that codifferentiation of hESCs on human fetal gonadal stromal cells significantly improves the efficiency of generating iPGCs. Furthermore, the efficiency was comparable between various pluripotent cell lines regardless of origin from the inner cell mass of human blastocysts (hESCs), or reprogramming of human skin fibroblasts (hIPS). To better characterize the iPGCs, we performed Real-time polymerase chain reaction, microarray, and bisulfite sequencing. Our results show that iPGCs at day 7 of differentiation are transcriptionally distinct from the somatic cells, expressing genes associated with pluripotency and germ cell development while repressing genes associated with somatic differentiation (specifically multiple HOX genes). Using bisulfite sequencing, we show that iPGCs initiate imprint erasure from differentially methylated imprinted regions by day 7 of differentiation. However, iPGCs derived from hIPS cells do not initiate imprint erasure as efficiently. In conclusion, our results indicate that triple positive iPGCs derived from pluripotent cells differentiated on hFGS cells correspond to committed first trimester germ cells (before 9 weeks) that have initiated the process of imprint erasure.

Macrophage differentiation from embryoid bodies derived from human embryonic stem cells

Human embryonic stem cells can differentiate into CD34+ hematopoietic progenitors by co-culture on murine feeders such as OP9 and S17. These CD34+ progenitors can be further differentiated into several cells of the hematopoietic lineage including macrophages. However, co-culture on murine feeders is time consuming and involves extensive manipulations. Furthermore, CD45 expression is low on hematopoietic cultures derived from stromal co-cultures. In this study we describe a novel and highly efficient system of generating differentiated macrophages from hematopoietic progenitors generated from embryoid body cultures of human embryonic stem cells. The hematopoietic progenitors generated from these embryoid bodies express higher numbers of CD45+ cells and are able to differentiate to macrophages when cultured in presence of cytokines. Using this system we were able to generate higher yields of CD14+ macrophages compared to traditional stromal cell culture methods. The embryoid body derived macrophages are phagocytic, respond to Toll-like receptor stimulation and express phenotypic markers of mature macrophages. Importantly, the embryoid body system generates hematopoietic progenitors suitable for clinical use by eliminating the need for murine feeder cells. Furthermore, this system is amenable to genetic manipulation and may thus be used to study important mechanisms of macrophage differentiation and function.

beta-Adrenoreceptors reactivate Kaposi's sarcoma-associated herpesvirus lytic replication via PKA-dependent control of viral RTA

Reactivation of Kaposi's sarcoma-associated herpesvirus (KSHV) lytic replication is mediated by the viral RTA transcription factor, but little is known about the physiological processes controlling its expression or activity. Links between autonomic nervous system activity and AIDS-associated Kaposi's sarcoma led us to examine the potential influence of catecholamine neurotransmitters. Physiological concentrations of epinephrine and norepinephrine efficiently reactivated lytic replication of KSHV in latently infected primary effusion lymphoma cells via beta-adrenergic activation of the cellular cyclic AMP/protein kinase A (PKA) signaling pathway. Effects were blocked by PKA antagonists and mimicked by pharmacological and physiological PKA activators (prostaglandin E2 and histamine) or overexpression of the PKA catalytic subunit. PKA up-regulated RTA gene expression, enhanced activity of the RTA promoter, and posttranslationally enhanced RTA's trans-activating capacity for its own promoter and heterologous lytic promoters (e.g., the viral PAN gene). Mutation of predicted phosphorylation targets at RTA serines 525 and 526 inhibited PKA-mediated enhancement of RTA trans-activating capacity. Given the high catecholamine levels at sites of KSHV latency such as the vasculature and lymphoid organs, these data suggest that beta-adrenergic control of RTA might constitute a significant physiological regulator of KSHV lytic replication. These findings also suggest novel therapeutic strategies for controlling the activity of this oncogenic gammaherpesvirus in vivo.

Expression-based monitoring of transcription factor activity: the TELiS database

MOTIVATION

In microarray studies it is often of interest to identify upstream transcription control pathways mediating observed changes in gene expression. The Transcription Element Listening System (TELiS) combines sequence-based analysis of gene regulatory regions with statistical prevalence analyses to identify transcription-factor binding motifs (TFBMs) that are over-represented among the promoters of up- or down-regulated genes. Efficiency is maximized by decomposing the problem into two steps: (1) a priori compilation of prevalence matrices specifying the number of putative binding sites for a variety of transcription factors in promoters from all genes assayed by a given microarray, and (2) real-time statistical analysis of pre-compiled prevalence matrices to identify TFBMs that are over- or under-represented in promoters of differentially expressed genes. The interlocking JAVA applications namely, PromoterScan and PromoterStats carry out these tasks, and together constitute the TELiS database for reverse inference of transcription factor activity.

RESULTS

In two validation studies, TELiS accurately detected in vivo activation of NF-kappaB and the Type I interferon system by HIV-1 infection and pharmacologic activation of the glucocorticoid receptor in peripheral blood mononuclear cells. The population-based statistical inference underlying TELiS out-performed conventional statistical tests in analytic sensitivity, with parametric studies demonstrating accurate identification of transcription factor activity from as few as 20 differentially expressed genes. TELiS thus provides a simple, rapid and sensitive tool for identifying transcription control pathways mediating observed gene expression dynamics.

The CD4 molecule on CD8+ T lymphocytes directly enhances the immune response to viral and cellular antigens

CD8+ T lymphocytes play a major role in cellular-mediated immune responses to foreign antigen. We have previously demonstrated that costimulation of purified human CD8+ T cells induces de novo expression of the CD4 molecule and that ligation of CD4 on this cell type modulates CD8+ T cell activity in vitro. Herein, we investigate how the CD4 molecule expressed on murine CD8+ T cells contributes to CD8+ cell responses in vivo by employing adoptive transfer of CD8 cells from CD4 knockout mice into severe combined immunodeficient (SCID) recipients. Transfer of these cells into syngeneic SCID mice resulted in a decreased immune response to infection by lymphocytic choriomeningitis virus. These decreased responses occurred even in the presence of CD4+ T cells, indicating that this was truly a CD8-cell defect. Similarly, transfer of CD8+ T cells incapable of expressing CD4 into allogeneic SCID mice resulted in a decreased response to alloantigens compared with that of normal CD8+ T cells. Therefore, CD4 expression on CD8 T lymphocytes modulates cytotoxic T lymphocyte function and is critical in vivo for optimal cell-mediated immunity to viral and alloantigens.

CD4 on CD8(+) T cells directly enhances effector function and is a target for HIV infection

Costimulation of purified CD8(+) T lymphocytes induces de novo expression of CD4, suggesting a previously unrecognized function for this molecule in the immune response. Here, we report that the CD4 molecule plays a direct role in CD8(+) T cell function by modulating expression of IFN-gamma and Fas ligand, two important CD8(+) T cell effector molecules. CD4 expression also allows infection of CD8 cells by HIV, which results in down-regulation of the CD4 molecule and impairs the induction of IFN-gamma, Fas ligand, and the cytotoxic responses of activated CD8(+) T cells. Thus, the CD4 molecule plays a direct role in CD8 T cell function, and infection of these cells by HIV provides an additional reservoir for the virus and also may contribute to the immunodeficiency seen in HIV disease.

Controlling false-negative errors in microarray differential expression analysis: a PRIM approach

MOTIVATION

Theoretical considerations suggest that current microarray screening algorithms may fail to detect many true differences in gene expression (Type II analytic errors). We assessed 'false negative' error rates in differential expression analyses by conventional linear statistical models (e.g. t-test), microarray-adapted variants (e.g. SAM, Cyber-T), and a novel strategy based on hold-out cross-validation. The latter approach employs the machine-learning algorithm Patient Rule Induction Method (PRIM) to infer minimum thresholds for reliable change in gene expression from Boolean conjunctions of fold-induction and raw fluorescence measurements.

RESULTS

Monte Carlo analyses based on four empirical data sets show that conventional statistical models and their microarray-adapted variants overlook more than 50% of genes showing significant up-regulation. Conjoint PRIM prediction rules recover approximately twice as many differentially expressed transcripts while maintaining strong control over false-positive (Type I) errors. As a result, experimental replication rates increase and total analytic error rates decline. RT-PCR studies confirm that gene inductions detected by PRIM but overlooked by other methods represent true changes in mRNA levels. PRIM-based conjoint inference rules thus represent an improved strategy for high-sensitivity screening of DNA microarrays.

AVAILABILITY

Freestanding JAVA application at http://microarray.crump.ucla.edu/focus

Combinatorial regulation of the murine RAG-2 promoter by Sp1 and distinct lymphocyte-specific transcription factors

The recombination activation genes, RAG-1 and RAG-2, encode the critical components of the recombinase complex responsible for the generation of functional antigen receptor genes. In order to gain an insight into the transcription factors and cis-acting elements that regulate the lymphocyte-specific expression of RAG-2, the promoter-region of this gene was isolated and characterized. This analysis demonstrated that a relatively small promoter fragment could confer lymphocyte-restricted expression to a reporter construct. Our work and that of others subsequently revealed that RAG-2 promoter expression is positively regulated by BSAP (PAX-5) and c-Myb transcription factors in B- and T-lineage cells, respectively. Although BSAP and c-Myb were deemed necessary for lymphocyte-specific expression, our analysis also uncovered a G-rich region at the 5'-end of the core promoter that was essential for full activity in lymphocyte cell lines. Site-directed mutagenesis revealed that a GA-box within the G-rich region was required for full promoter activity and subsequent DNA binding assays demonstrated that this element was specifically recognized by Sp1. Apart from showing that Sp1 interacts within the RAG-2 promoter, we also demonstrate that the Sp1-binding site is necessary for the high-level activation of this promoter.

Characterization of a novel DNA binding domain within the amino-terminal region of the RAG-1 protein

Rag-1 and Rag-2 are the critical components of the V-(D)-J recombinase required for site-specific recombination of the antigen receptor genes. In this study, we have examined the ability of recombinant (r) Rag-1 and Rag-2 to bind the recombination signal sequences (RSS) and have determined that rRag-1, but not rRag-2, is able to directly bind DNA. rRAG-1 DNA binding activity was found to reside within a novel amino-terminal arginine-rich (RR) domain with partial homology to a variety of nucleic acid binding domains. Although the RR-domain did not demonstrate RSS-specificity, this DNA binding domain may stabilize the interaction of RAG-1 with, or increase the affinity for, the V-(D)-J recombination signals.

Regulation of the RAG-1 promoter by the NF-Y transcription factor

We have cloned the RAG-1 promoter region and have determined that almost all detectable promoter activity resides within a 208-bp fragment. Sequence analysis of this promoter region has identified potential recognition motifs for a number of lymphocyte-restricted and ubiquitous transcription factors. Subsequent assays have revealed that the NF-Y transcription factor interacts with a CCAAT site within the RAG-1 promoter and appears to play an important role in the positive transcriptional regulation of this gene.

Regulation of the RAG-1 promoter by the NF-Y transcription factor

We have cloned the RAG-1 promoter region and have determined that almost all detectable promoter activity resides within a 208-bp fragment. Sequence analysis of this promoter region has identified potential recognition motifs for a number of lymphocyte-restricted and ubiquitous transcription factors. Subsequent assays have revealed that the NF-Y transcription factor interacts with a CCAAT site within the RAG-1 promoter and appears to play an important role in the positive transcriptional regulation of this gene.