Brd2/4 and Myc regulate alternative cell lineage programmes during early osteoclast differentiation in vitro

Osteoclast (OC) development in response to nuclear factor kappa-Β ligand (RANKL) is critical for bone homeostasis in health and in disease. The early and direct chromatin regulatory changes imparted by the BET chromatin readers Brd2-4 and OC-affiliated transcription factors (TFs) during osteoclastogenesis are not known. Here, we demonstrate that in response to RANKL, early OC development entails regulation of two alternative cell fate transcriptional programmes, OC vs macrophage, with repression of the latter following activation of the former. Both programmes are regulated in a non-redundant manner by increased chromatin binding of Brd2 at promoters and of Brd4 at enhancers/super-enhancers. Myc, the top RANKL-induced TF, regulates OC development in co-operation with Brd2/4 and Max and by establishing negative and positive regulatory loops with other lineage-affiliated TFs. These insights into the transcriptional regulation of osteoclastogenesis suggest the clinical potential of selective targeting of Brd2/4 to abrogate pathological OC activation

MAF functions as a pioneer transcription factor that initiates and sustains myelomagenesis

Deregulated expression of lineage-affiliated transcription factors (TFs) is a major mechanism of oncogenesis. However, how the deregulation of nonlineage affiliated TF affects chromatin to initiate oncogenic transcriptional programs is not well-known. To address this, we studied the chromatin effects imposed by oncogenic MAF as the cancer-initiating driver in the plasma cell cancer multiple myeloma. We found that the ectopically expressed MAF endows myeloma plasma cells with migratory and proliferative transcriptional potential. This potential is regulated by the activation of enhancers and superenhancers, previously inactive in healthy B cells and plasma cells, and the cooperation of MAF with the plasma cell-defining TF IRF4. Forced ectopic MAF expression confirms the de novo ability of oncogenic MAF to convert transcriptionally inert chromatin to active chromatin with the features of superenhancers, leading to the activation of the MAF-specific oncogenic transcriptome and the acquisition of cancer-related cellular phenotypes such as CCR1-dependent cell migration. These findings establish oncogenic MAF as a pioneer transcription factor that can initiate as well as sustain oncogenic transcriptomes and cancer phenotypes. However, despite its pioneer function, myeloma cells remain MAF-dependent, thus validating oncogenic MAF as a therapeutic target that would be able to circumvent the challenges of subsequent genetic diversification driving disease relapse and drug resistance

Chromatin-based, in cis and in trans regulatory rewiring underpins distinct oncogenic transcriptomes in multiple myeloma

Multiple myeloma is a genetically heterogeneous cancer of the bone marrow plasma cells (PC). Distinct myeloma transcriptome profiles are primarily driven by myeloma initiating events (MIE) and converge into a mutually exclusive overexpression of the CCND1 and CCND2 oncogenes. Here, with reference to their normal counterparts, we find that myeloma PC enhanced chromatin accessibility combined with paired transcriptome profiling can classify MIE-defined genetic subgroups. Across and within different MM genetic subgroups, we ascribe regulation of genes and pathways critical for myeloma biology to unique or shared, developmentally activated or de novo formed candidate enhancers. Such enhancers co-opt recruitment of existing transcription factors, which although not transcriptionally deregulated per se, organise aberrant gene regulatory networks that help identify myeloma cell dependencies with prognostic impact. Finally, we identify and validate the critical super-enhancer that regulates ectopic expression of CCND2 in a subset of patients with MM and in chronic lymphocytic leukemia

The innate sensor ZBP1-IRF3 axis regulates cell proliferation in multiple myeloma

Multiple myeloma is a malignancy of plasma cells (PC) initiated and driven by primary and secondary genetic events. Nevertheless, myeloma PC survival and proliferation might be sustained by non-genetic drivers. Z-DNA-binding protein 1 (ZBP1; also known as DAI) is an interferon-inducible, Z-nucleic acid sensor that triggers RIPK3-MLKL-mediated necroptosis in mice. ZBP1 also interacts with TBK1 and the transcription factor IRF3 but the function of this interaction is unclear, and the role of ZBP1-IRF3 axis in cancer is not known. Here we show that ZBP1 is selectively expressed in late B cell development in both human and mouse cells and it is required for optimal T-cell-dependent humoral immune responses. In myeloma PC, interaction of constitutively expressed ZBP1 with TBK1 and IRF3 results in IRF3 phosphorylation. IRF3 directly binds and activates cell cycle genes, in part through co-operation with the PC lineage-defining transcription factor IRF4, and thereby promoting myeloma cell proliferation. This generates a novel, potentially therapeutically targetable and relatively selective myeloma cell addiction to the ZBP1-IRF3 axis. Our data also show a non-canonical function of constitutive ZBP1 in human cells and expand our knowledge of the role of cellular immune sensors in cancer biology

Systems medicine dissection of chr1q-amp reveals a novel PBX1-FOXM1 axis for targeted therapy in multiple myeloma

Understanding the biological and clinical impact ofcopy number aberrations (CNA)for the development of precision therapies in cancer remains anunmet challenge. Genetic amplification of chromosome 1q (chr1q-amp) is a major CNAconferring adverse prognosis in several types of cancer, including in the blood cancer multiple myeloma (MM). Although severalgenes across chr1q portend high-risk MM disease, the underpinning molecular aetiology remains elusive. Here, with reference to the 3D chromatin structure, we integrate MMpatient multi-omics datasets with genetic variables to obtain an associated clinical risk map across chr1q and to identify 103 adverse prognosis genes in chr1q-amp MM. Prominent amongst these genes, the transcription factor PBX1 is ectopically expressed by genetic amplification and epigenetic activation of its own preserved 3D regulatory domain. By binding to reprogrammed super-enhancers, PBX1 directly regulates critical oncogenic pathways and a FOXM1-dependent transcriptional programme. Together, PBX1 and FOXM1 activate a proliferative gene signature which predicts adverse prognosis across multiple types of cancer. Notably, pharmacological disruption of the PBX1-FOXM1 axis with existing agents (thiostrepton) and a novel PBX1 small-molecule inhibitor (T417) is selectively toxic against chr1q-amplified myeloma and solid tumour cells. Overall, our systems medicine approach successfully identifies CNA-driven oncogenic circuitries, links them to clinical phenotypes and proposes novel CNA-targeted therapystrategies in multiple myeloma and other types of cancer

Poly(ADP-ribose) polymerase family member 14 (PARP14) is a novel effector of the JNK2-dependent pro-survival signal in multiple myeloma

Copyright @ 2013 Macmillan Publishers Limited. This is the author's accepted manuscript. The final published article is available from the link below.Regulation of cell survival is a key part of the pathogenesis of multiple myeloma (MM). Jun N-terminal kinase (JNK) signaling has been implicated in MM pathogenesis, but its function is unclear. To elucidate the role of JNK in MM, we evaluated the specific functions of the two major JNK proteins, JNK1 and JNK2. We show here that JNK2 is constitutively activated in a panel of MM cell lines and primary tumors. Using loss-of-function studies, we demonstrate that JNK2 is required for the survival of myeloma cells and constitutively suppresses JNK1-mediated apoptosis by affecting expression of poly(ADP-ribose) polymerase (PARP)14, a key regulator of B-cell survival. Strikingly, we found that PARP14 is highly expressed in myeloma plasma cells and associated with disease progression and poor survival. Overexpression of PARP14 completely rescued myeloma cells from apoptosis induced by JNK2 knockdown, indicating that PARP14 is critically involved in JNK2-dependent survival. Mechanistically, PARP14 was found to promote the survival of myeloma cells by binding and inhibiting JNK1. Moreover, inhibition of PARP14 enhances the sensitization of MM cells to anti-myeloma agents. Our findings reveal a novel regulatory pathway in myeloma cells through which JNK2 signals cell survival via PARP14, and identify PARP14 as a potential therapeutic target in myeloma.Kay Kendall Leukemia Fund, NIH, Cancer Research UK, Italian Association for Cancer Research and the Foundation for Liver Research

MAF functions as a pioneer transcription factor that initiates and sustains myelomagenesis

Deregulated expression of lineage-affiliated transcription factors (TFs) is a major mechanism of oncogenesis. However, how the deregulation of nonlineage affiliated TF affects chromatin to initiate oncogenic transcriptional programs is not well-known. To address this, we studied the chromatin effects imposed by oncogenic MAF as the cancer-initiating driver in the plasma cell cancer multiple myeloma. We found that the ectopically expressed MAF endows myeloma plasma cells with migratory and proliferative transcriptional potential. This potential is regulated by the activation of enhancers and superenhancers, previously inactive in healthy B cells and plasma cells, and the cooperation of MAF with the plasma cell-defining TF IRF4. Forced ectopic MAF expression confirms the de novo ability of oncogenic MAF to convert transcriptionally inert chromatin to active chromatin with the features of superenhancers, leading to the activation of the MAF-specific oncogenic transcriptome and the acquisition of cancer-related cellular phenotypes such as CCR1-dependent cell migration. These findings establish oncogenic MAF as a pioneer transcription factor that can initiate as well as sustain oncogenic transcriptomes and cancer phenotypes. However, despite its pioneer function, myeloma cells remain MAF-dependent, thus validating oncogenic MAF as a therapeutic target that would be able to circumvent the challenges of subsequent genetic diversification driving disease relapse and drug resistance

Reusable Non-Interactive Secure Computation

We consider the problem of Non-Interactive Secure Computation (NISC), a 2-message ``Sender-Receiver\u27\u27 secure computation protocol that retains its security even when both parties can be malicious. While such protocols are easy to construct using garbled circuits and general non-interactive zero-knowledge proofs, this approach inherently makes a non-black-box use of the underlying cryptographic primitives and is infeasible in practice. Ishai et al. (Eurocrypt 2011) showed how to construct NISC protocols that only use parallel calls to an ideal oblivious transfer (OT) oracle, and additionally make only a black-box use of any pseudorandom generator. Combined with the efficient 2-message OT protocol of Peikert et al. (Crypto 2008), this leads to a practical approach to NISC that has been implemented in subsequent works. However, a major limitation of all known OT-based NISC protocols is that they are subject to selective failure attacks that allows a malicious sender to entirely compromise the security of the protocol when the receiver\u27s first message is reused. Motivated by the failure of the OT-based approach, we consider the problem of basing \emph{reusable} NISC on parallel invocations of a standard arithmetic generalization of OT known as oblivious linear-function evaluation (OLE). We obtain the following results: - We construct an information-theoretically secure reusable NISC protocol for arithmetic branching programs and general zero-knowledge functionalities in the OLE-hybrid model. Our zero-knowledge protocol only makes an absolute constant number of OLE calls per gate in an arithmetic circuit whose satisfiability is being proved. As a corollary, we get reusable NISC/OLE for general Boolean circuits using any one-way function. - We complement this by a negative result, showing that reusable NISC/OT is impossible to achieve, and a more restricted negative result for the case of the zero-knowledge functionality. This provides a formal justification for the need to replace OT by OLE. - We build a universally composable 2-message OLE protocol in the CRS model that can be based on the security of Paillier encryption and requires only a constant number of modular exponentiations. This provides the first arithmetic analogue of the 2-message OT protocols of Peikert et al. (Crypto 2008). - By combining our NISC/OLE protocol and the 2-message OLE protocol, we get protocols with new attractive asymptotic and concrete efficiency features. In particular, we get the first (designated-verifier) NIZK protocols where following a statement-independent preprocessing, both proving and verifying are entirely ``non-cryptographic\u27\u27 and involve only a constant computational overhead

Chromatin-based, in cis and in trans regulatory rewiring underpins distinct oncogenic transcriptomes in multiple myeloma

Multiple myeloma is a genetically heterogeneous cancer of the bone marrow plasma cells (PC). Distinct myeloma transcriptome profiles are primarily driven by myeloma initiating events (MIE) and converge into a mutually exclusive overexpression of the CCND1 and CCND2 oncogenes. Here, with reference to their normal counterparts, we find that myeloma PC enhanced chromatin accessibility combined with paired transcriptome profiling can classify MIE-defined genetic subgroups. Across and within different MM genetic subgroups, we ascribe regulation of genes and pathways critical for myeloma biology to unique or shared, developmentally activated or de novo formed candidate enhancers. Such enhancers co-opt recruitment of existing transcription factors, which although not transcriptionally deregulated per se, organise aberrant gene regulatory networks that help identify myeloma cell dependencies with prognostic impact. Finally, we identify and validate the critical super-enhancer that regulates ectopic expression of CCND2 in a subset of patients with MM and in chronic lymphocytic leukemia

Exploring Constructions of Compact NIZKs from Various Assumptions

A non-interactive zero-knowledge (NIZK) protocol allows a prover to non-interactively convince a verifier of the truth of the statement without leaking any other information. In this study, we explore shorter NIZK proofs for all NP languages. Our primary interest is NIZK proofs from falsifiable pairing/pairing-free group-based assumptions. Thus far, NIZKs in the common reference string model (CRS-NIZKs) for NP based on falsifiable pairing-based assumptions all require a proof size at least as large as $O(|C| k)$, where $C$ is a circuit computing the NP relation and $k$ is the security parameter. This holds true even for the weaker designated-verifier NIZKs (DV-NIZKs). Notably, constructing a (CRS, DV)-NIZK with proof size achieving an additive-overhead $O(|C|) + poly(k)$, rather than a multiplicative-overhead $|C| \cdot poly(k)$, based on any falsifiable pairing-based assumptions is an open problem. In this work, we present various techniques for constructing NIZKs with compact proofs, i.e., proofs smaller than $O(|C|) + poly(k)$, and make progress regarding the above situation. Our result is summarized below. - We construct CRS-NIZK for all NP with proof size $|C| + poly(k)$ from a (non-static) falsifiable Diffie-Hellman (DH) type assumption over pairing groups. This is the first CRS-NIZK to achieve a compact proof without relying on either lattice-based assumptions or non-falsifiable assumptions. Moreover, a variant of our CRS-NIZK satisfies universal composability (UC) in the erasure-free adaptive setting. Although it is limited to NP relations in NC1, the proof size is $|w| \cdot poly(k)$ where $w$ is the witness, and in particular, it matches the state-of-the-art UC-NIZK proposed by Cohen, shelat, and Wichs (EPRINT\u2718) based on lattices. - We construct (multi-theorem) DV-NIZKs for NP with proof size $|C|+poly(k)$ from the computational DH assumption over pairing-free groups. This is the first DV-NIZK that achieves a compact proof from a standard DH type assumption. Moreover, if we further assume the NP relation to be computable in NC1 and assume hardness of a (non-static) falsifiable DH type assumption over pairing-free groups, the proof size can be made as small as $|w| + poly(k)$. Another related but independent issue is that all (CRS, DV)-NIZKs require the running time of the prover to be at least $|C|\cdot poly(k)$. Considering that there exists NIZKs with efficient verifiers whose running time is strictly smaller than $|C|$, it is an interesting problem whether we can construct prover-efficient NIZKs. To this end, we construct prover-efficient CRS-NIZKs for NP with compact proof through a generic construction using laconic functional evaluation schemes (Quach, Wee, and Wichs (FOCS\u2718)). This is the first NIZK in any model where the running time of the prover is strictly smaller than the time it takes to compute the circuit $C$ computing the NP relation. Finally, perhaps of an independent interest, we formalize the notion of homomorphic equivocal commitments, which we use as building blocks to obtain the first result, and show how to construct them from pairing-based assumptions