Multifaceted roles for STAT3 in gammaherpesvirus latency revealed through in vivo B cell knockout models

Cancers associated with the oncogenic gammaherpesviruses, Epstein-Barr virus and Kaposi sarcoma herpesvirus, are notable for their constitutive activation of the transcription factor signal transducer and activator of transcription 3 (STAT3). To better understand the role of STAT3 during gammaherpesvirus latency and the B cell response to infection, we used the model pathogen murine gammaherpesvirus 68 (MHV68). Genetic deletion of STAT3 in B cells of CD19cre/+Stat3f/f mice reduced peak MHV68 latency approximately sevenfold. However, infected CD19cre/+Stat3f/f mice exhibited disordered germinal centers and heightened virus-specific CD8 T cell responses compared to wild-type (WT) littermates. To circumvent the systemic immune alterations observed in the B cell-STAT3 knockout mice and more directly evaluate intrinsic roles for STAT3, we generated mixed bone marrow chimeric mice consisting of WT and STAT3 knockout B cells. We discovered a dramatic reduction in latency in STAT3 knockout B cells compared to their WT B cell counterparts in the same lymphoid organ. RNA sequencing of sorted germinal center B cells revealed that MHV68 infection shifts the gene signature toward proliferation and away from type I and type II IFN responses. Loss of STAT3 largely reversed the virus-driven transcriptional shift without impacting the viral gene expression program. STAT3 promoted B cell processes of the germinal center, including IL-21-stimulated downregulation of surface CD23 on B cells infected with MHV68 or EBV. Together, our data provide mechanistic insights into the role of STAT3 as a latency determinant in B cells for oncogenic gammaherpesviruses.IMPORTANCEThere are no directed therapies to the latency program of the human gammaherpesviruses, Epstein-Barr virus and Kaposi sarcoma herpesvirus. Activated host factor signal transducer and activator of transcription 3 (STAT3) is a hallmark of cancers caused by these viruses. We applied the murine gammaherpesvirus pathogen system to explore STAT3 function upon primary B cell infection in the host. Since STAT3 deletion in all CD19+ B cells of infected mice led to altered B and T cell responses, we generated chimeric mice with both normal and STAT3-deleted B cells. B cells lacking STAT3 failed to support virus latency compared to normal B cells from the same infected animal. Loss of STAT3 impaired B cell proliferation and differentiation and led to a striking upregulation of interferon-stimulated genes. These findings expand our understanding of STAT3-dependent processes that are key to its function as a pro-viral latency determinant for oncogenic gammaherpesviruses in B cells and may provide novel therapeutic targets.

Intrinsic p53 Activation Restricts Gammaherpesvirus-Driven Germinal Center B Cell Expansion during Latency Establishment

Gammaherpesviruses (GHV) are DNA tumor viruses that establish lifelong latent infections in lymphocytes. For viruses such as Epstein-Barr virus (EBV) and murine gammaherpesvirus 68 (MHV68), this is accomplished through a viral gene-expression program that promotes cellular proliferation and differentiation, especially of germinal center (GC) B cells. Intrinsic host mechanisms that control virus-driven cellular expansion are incompletely defined. Using a small-animal model of GHV pathogenesis, we demonstrate in vivo that tumor suppressor p53 is activated specifically in B cells that are latently infected by MHV68. In the absence of p53, the early expansion of MHV68 latency was greatly increased, especially in GC B cells, a cell-type whose proliferation was conversely restricted by p53. We identify the B cell-specific latency gene M2, a viral promoter of GC B cell differentiation, as a viral protein sufficient to elicit a p53-dependent anti-proliferative response caused by Src-family kinase activation. We further demonstrate that EBV-encoded latent membrane protein 1 (LMP1) similarly triggers a p53 response in primary B cells. Our data highlight a model in which GHV latency gene-expression programs that promote B cell proliferation and differentiation to facilitate viral colonization of the host trigger aberrant cellular proliferation that is controlled by p53.

IMPORTANCE

Gammaherpesviruses cause lifelong infections of their hosts, commonly referred to as latency, that can lead to cancer. Latency establishment benefits from the functions of viral proteins that augment and amplify B cell activation, proliferation, and differentiation signals. In uninfected cells, off-schedule cellular differentiation would typically trigger anti-proliferative responses by effector proteins known as tumor suppressors. However, tumor suppressor responses to gammaherpesvirus manipulation of cellular processes remain understudied, especially those that occur during latency establishment in a living organism. Here we identify p53, a tumor suppressor commonly mutated in cancer, as a host factor that limits virus-driven B cell proliferation and differentiation, and thus, viral colonization of a host. We demonstrate that p53 activation occurs in response to viral latency proteins that induce B cell activation. This work informs a gap in our understanding of intrinsic cellular defense mechanisms that restrict lifelong GHV infection.

Uracil-DNA glycosylase of murine gammaherpesvirus 68 binds cognate viral replication factors independently of its catalytic residues

Herpesviruses are large double-stranded DNA viruses that encode core replication proteins and accessory factors involved in nucleotide metabolism and DNA repair. Mammalian uracil-DNA glycosylases (UNG) excise deleterious uracil residues from their genomic DNA. Each herpesvirus UNG studied to date has demonstrated conservation of the enzymatic function to excise uracil residues from DNA. We previously reported that a murine gammaherpesvirus (MHV68) with a stop codon in ORF46 (ORF46.stop) that encodes for vUNG was defective in lytic replication and latency in vivo. However, a mutant virus that expressed a catalytically inactive vUNG (ORF46.CM) had no replication defect unless coupled with additional mutations in the catalytic motif of the viral dUTPase (ORF54.CM). The disparate phenotypes observed in the vUNG mutants led us to explore the non-enzymatic properties of vUNG. Immunoprecipitation of vUNG followed by mass spectrometry in MHV68-infected fibroblasts identified a complex comprising the cognate viral DNA polymerase, vPOL, encoded by ORF9, and the viral DNA polymerase processivity factor, vPPF, encoded by ORF59. MHV68 vUNG co-localized with vPOL and vPPF in subnuclear structures consistent with viral replication compartments. In reciprocal co-immunoprecipitations, the vUNG formed a complex with the vPOL and vPPF upon transfection with either factor alone or in combination. Lastly, we determined that key catalytic residues of vUNG are not required for interactions with vPOL and vPPF upon transfection or in the context of infection. We conclude that the vUNG of MHV68 associates with vPOL and vPPF independently of its catalytic activity. IMPORTANCE Gammaherpesviruses encode a uracil-DNA glycosylase (vUNG) that is presumed to excise uracil residues from viral genomes. We previously identified the vUNG enzymatic activity, but not the protein itself, as dispensable for gammaherpesvirus replication in vivo. In this study, we report a non-enzymatic role for the viral UNG of a murine gammaherpesvirus in forming a complex with two key components of the viral DNA replication machinery. Understanding the role of the vUNG in this viral DNA replication complex may inform the development of antiviral drugs that combat gammaherpesvirus-associated cancers.

Replication-dead gammaherpesvirus vaccine protects against acute replication, reactivation from latency, and lethal challenge in mice

Gammaherpesviruses (GHVs) are oncogenic viruses that establish lifelong infections and are significant causes of human morbidity and mortality. While several vaccine strategies to limit GHV infection and disease are in development, there are no FDA-approved vaccines for human GHVs. As a new approach to gammaherpesvirus vaccination, we developed and tested a replication-dead virus (RDV) platform, using murine gammaherpesvirus 68 (MHV68), a well-established mouse model for gammaherpesvirus pathogenesis studies and preclinical therapeutic evaluations. We employed codon-shuffling-based complementation to generate revertant-free RDV lacking expression of the essential replication and transactivator protein (RTA) encoded by ORF50 to arrest viral gene expression early after de novo infection. Inoculation with RDV-50.stop exposes the host to intact virion particles and leads to limited lytic gene expression in infected cells. Prime-boost vaccination of mice with RDV-50.stop elicited virus-specific neutralizing antibody and effector T cell responses in the lung and spleen. Vaccination with RDV-50.stop resulted in a near complete abolishment of virus replication in the lung 7 days post-challenge and virus reactivation from spleen 16 days post-challenge with WT MHV68. Ifnar1-/- mice, which lack the type I interferon receptor, exhibit severe disease upon infection with WT MHV68. RDV-50.stop vaccination of Ifnar1-/- mice prevented wasting and mortality upon challenge with WT MHV68. These results demonstrate that prime-boost vaccination with a GHV that is unable to undergo lytic replication offers protection against acute replication, reactivation, and severe disease upon WT virus challenge.

A longitudinal study of SARS-CoV-2 antibody seroprevalence and mitigation behaviors among college students at an Arkansas University

Objective: Assess university students' SARS-CoV-2 antibody seroprevalence and mitigation behaviors over time. Participants: Randomly selected college students (N = 344) in a predominantly rural Southern state. Methods: Participants provided blood samples and completed self-administered questionnaires at three timepoints over the academic year. Adjusted odds ratios and 95% confidence intervals were estimated from logistic regression analyses. Results: SARS-CoV-2 antibody seroprevalence was 18.2% in September 2020, 13.1% in December, and 45.5% in March 2021 (21% for those with no vaccination history). SARS-CoV-2 antibody seroprevalence was associated with large social gatherings, staying local during the summer break, symptoms of fatigue or rhinitis, Greek affiliation, attending Greek events, employment, and using social media as the primary COVID-19 information source. In March 2021, seroprevalence was associated with receiving at least one dose of a COVID-19 vaccination. Conclusion: SARS-CoV-2 seroprevalence was higher in this population of college students than previous studies. Results can assist leaders in making informed decisions as new variants threaten college campuses.

Uracil-DNA Glycosylase of Murine Gammaherpesvirus 68 Binds Cognate Viral Replication Factors Independently of its Catalytic Residues

Herpesviruses are large double-stranded DNA viruses that encode core replication proteins and accessory factors involved in nucleotide metabolism and DNA repair. Mammalian Uracil-DNA glycosylases (UNG) excise deleterious uracil residues from their genomic DNA. Each herpesvirus UNG studied to date has demonstrated conservation of the enzymatic function to excise uracil residues from DNA. We previously reported that a murine gammaherpesvirus (MHV68) with a stop codon in ORF46 (ORF46.stop) that encodes for vUNG was defective in lytic replication and latency in vivo. However, a mutant virus that expressed a catalytically inactive vUNG (ORF46.CM) had no replication defect, unless coupled with additional mutations in the catalytic motif of the viral dUTPase (ORF54.CM). The disparate phenotypes observed in the vUNG mutants led us to explore the non-enzymatic properties of vUNG. Immunoprecipitation of vUNG followed by mass spectrometry in MHV68-infected fibroblasts identified a complex comprised of the cognate viral DNA polymerase, vPOL encoded by ORF9 , and the viral DNA polymerase processivity factor, vPPF encoded by ORF59 . MHV68 vUNG colocalized with vPOL and vPPF in subnuclear structures consistent with viral replication compartments. In reciprocal co-immunoprecipitations, the vUNG formed a complex with the vPOL and vPPF upon transfection with either factor alone, or in combination. Last, we determined that key catalytic residues of vUNG are not required for interactions with vPOL and vPPF upon transfection or in the context of infection. We conclude that the vUNG of MHV68 associates with vPOL and vPPF independently of its catalytic activity.

IMPORTANCE

Gammaherpesviruses encode a uracil-DNA glycosylase (vUNG) that is presumed to excise uracil residues from viral genomes. We previously identified the vUNG enzymatic activity, but not the protein itself, as dispensable for gammaherpesvirus replication in vivo . In this study, we report a non-enzymatic role for the viral UNG of a murine gammaherpesvirus to form a complex with two key components of the viral DNA replication machinery. Understanding the role of the vUNG in this viral DNA replication complex may inform the development of antiviral drugs that combat gammaherpesvirus associated cancers.

B cell-intrinsic STAT3-mediated support of latency and interferon suppression during murine gammaherpesvirus 68 infection revealed through an in vivo competition model

Cancers associated with the oncogenic gammaherpesviruses, Epstein-Barr virus and Kaposi sarcoma herpesvirus, are notable for their constitutive activation of the transcription factor STAT3. To better understand the role of STAT3 during gammaherpesvirus latency and immune control, we utilized murine gammaherpesvirus 68 (MHV68) infection. Genetic deletion of STAT3 in B cells of CD19cre/+Stat3f/f mice reduced peak latency approximately 7-fold. However, infected CD19cre/+Stat3f/f mice exhibited disordered germinal centers and heightened virus-specific CD8 T cell responses compared to WT littermates. To circumvent the systemic immune alterations observed in the B cell-STAT3 knockout mice and more directly evaluate intrinsic roles for STAT3, we generated mixed bone marrow chimeras consisting of WT and STAT3-knockout B cells. Using a competitive model of infection, we discovered a dramatic reduction in latency in STAT3-knockout B cells compared to their WT B cell counterparts in the same lymphoid organ. RNA sequencing of sorted germinal center B cells revealed that STAT3 promotes proliferation and B cell processes of the germinal center but does not directly regulate viral gene expression. Last, this analysis uncovered a STAT3-dependent role for dampening type I IFN responses in newly infected B cells. Together, our data provide mechanistic insight into the role of STAT3 as a latency determinant in B cells for oncogenic gammaherpesviruses.

Pediatric SARS-CoV-2 Seroprevalence in Arkansas Over the First Year of the COVID-19 Pandemic

BACKGROUND

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) seroprevalence studies largely focus on adults, but little is known about spread in children. We determined SARS-CoV-2 seroprevalence in children and adolescents from Arkansas over the first year of the coronavirus disease of 2019 (COVID-19) pandemic.

METHODS

We tested remnant serum samples from children ages 1-18 years who visited Arkansas hospitals or clinics for non-COVID-19-related reasons from April 2020 through April 2021 for SARS-CoV-2 antibodies. We used univariable and multivariable regression models to determine the association between seropositivity and participant characteristics.

RESULTS

Among 2357 participants, seroprevalence rose from 7.9% in April/May 2020 (95% CI, 4.9-10.9) to 25.0% in April 2021 (95% CI, 21.5-28.5). Hispanic and black children had a higher association with antibody positivity than non-Hispanic and white children, respectively, in multiple sampling periods.

CONCLUSIONS

By spring 2021, most children in Arkansas were not infected with SARS-CoV-2. With the emergence of SARS-CoV-2 variants, recognition of long-term effects of COVID-19, and the lack of an authorized pediatric SARS-CoV-2 vaccine at the time, these results highlight the importance of including children in SARS-CoV-2 public health, clinical care, and research strategies.

State-wide random seroprevalence survey of SARS-CoV-2 past infection in a southern US State, 2020

The purpose of this cross-sectional study was to estimate the proportion of Arkansas residents who were infected with the SARS-CoV-2 virus between May and December 2020 and to assess the determinants of infection. To estimate seroprevalence, a state-wide population-based random-digit dial sample of non-institutionalized adults in Arkansas was surveyed. Exposures were age, sex, race/ethnicity, education, occupation, contact with infected persons, comorbidities, height, and weight. The outcome was past COVID-19 infection measured by serum antibody test. We found a prevalence of 15.1% (95% CI: 11.1%, 20.2%) by December 2020. Seropositivity was significantly elevated among participants who were non-Hispanic Black, Hispanic (prevalence ratio [PRs]:1.4 [95% CI: 0.8, 2.4] and 2.3 [95% CI: 1.3, 4.0], respectively), worked in high-demand essential services (PR: 2.5 [95% CI: 1.5, 4.1]), did not have a college degree (PR: 1.6 [95% CI: 1.0, 2.4]), had an infected household or extra-household contact (PRs: 4.7 [95% CI: 2.1, 10.1] and 2.6 [95% CI: 1.2, 5.7], respectively), and were contacted in November or December (PR: 3.6 [95% CI: 1.9, 6.9]). Our results indicate that by December 2020, one out six persons in Arkansas had a past SARS-CoV-2 infection.

Oral Shedding of an Oncogenic Virus Alters the Oral Microbiome in HIV+ Patients

Kaposi's Sarcoma (KS) caused by Kaposi's sarcoma-associated herpesvirus (KSHV) continues to be the most common AIDS-associated tumor. Involvement of the oral cavity represents one of the most common clinical manifestations of this tumor. Numerous types of cancer are associated with the alterations of in components of the microbiome. However, little is known about how KSHV coinfection affects the oral microbiome in HIV+ patients, especially in a "pre-cancer" niche. Using 16S rRNA pyrosequencing, we found that oral shedding of KSHV correlated with altered oral microbiome signatures in HIV+ patients, including a reduction in the microbiota diversity, changing the relative composition of specific phyla and species, and regulating microbial functions. Furthermore, we found that Streptococcus sp., one of the most increased species in the oral cavity of HIV+/KSHV+ patients, induced KSHV lytic reactivation in primary oral cells. Together, these data indicate that oral shedding of KSHV may manipulate the oral microbiome to promote viral pathogenesis and tumorigenesis especially in immunocompromised patients.

Temporal Variations in Seroprevalence of SARS-CoV-2 Infections by Race and Ethnicity in Arkansas

Background

The aim of this study was to estimate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection rates in the small rural state of Arkansas, using SARS-CoV-2 antibody prevalence as an indicator of infection.

Methods

We collected residual serum samples from adult outpatients seen at hospitals or clinics in Arkansas for non–coronavirus disease 2019 (COVID-19)–related reasons. A total of 5804 samples were identified over 3 time periods: 15 August–5 September 2020 (time period 1), 12 September–24 October 2020 (time period 2), and 7 November–19 December 2020 (time period 3).

Results

The age-, sex-, race-, and ethnicity-standardized SARS-CoV-2 seroprevalence during each period, from 2.6% in time period 1 to 4.1% in time period 2 and 7.4% in time period 3. No statistically significant difference in seroprevalence was found based on age, sex, or residence (urban vs rural). However, we found higher seroprevalence rates in each time period for Hispanics (17.6%, 20.6%, and 23.4%, respectively) and non-Hispanic Blacks (4.8%, 5.4%, and 8.9%, respectively) relative to non-Hispanic Whites (1.1%, 2.6%, and 5.5%, respectively).

Conclusions

Our data imply that the number of Arkansas residents infected with SARS-CoV-2 rose steadily from 2.6% in August to 7.4% in December 2020. There was no statistical difference in seroprevalence between rural and urban locales. Hispanics and Blacks had higher rates of SARS-CoV-2 antibodies than Whites, indicating that SARS-CoV-2 spread disproportionately in racial and ethnic minorities during the first year of the COVID-19 pandemic.

The Serological Sciences Network (SeroNet) for COVID-19: Depth and Breadth of Serology Assays and Plans for Assay Harmonization

Background

In October 2020, the National Cancer Institute (NCI) Serological Sciences Network (SeroNet) was established to study the immune response to COVID-19, and "to develop, validate, improve, and implement serological testing and associated technologies." SeroNet is comprised of 25 participating research institutions partnering with the Frederick National Laboratory for Cancer Research (FNLCR) and the SeroNet Coordinating Center. Since its inception, SeroNet has supported collaborative development and sharing of COVID-19 serological assay procedures and has set forth plans for assay harmonization.

Methods

To facilitate collaboration and procedure sharing, a detailed survey was sent to collate comprehensive assay details and performance metrics on COVID-19 serological assays within SeroNet. In addition, FNLCR established a protocol to calibrate SeroNet serological assays to reference standards, such as the U.S. SARS-CoV-2 serology standard reference material and First WHO International Standard (IS) for anti-SARS-CoV-2 immunoglobulin (20/136), to facilitate harmonization of assay reporting units and cross-comparison of study data.

Results

SeroNet institutions reported development of a total of 27 ELISA methods, 13 multiplex assays, 9 neutralization assays, and use of 12 different commercial serological methods. FNLCR developed a standardized protocol for SeroNet institutions to calibrate these diverse serological assays to reference standards.

Conclusions

SeroNet institutions have established a diverse array of COVID-19 serological assays to study the immune response to SARS-CoV-2 virus and vaccines. Calibration of SeroNet serological assays to harmonize results reporting will facilitate future pooled data analyses and study cross-comparisons.

Development of ACE2 autoantibodies after SARS-CoV-2 infection

Background

Activation of the immune system is implicated in the Post-Acute Sequelae after SARS-CoV-2 infection (PASC) but the mechanisms remain unknown. Angiotensin-converting enzyme 2 (ACE2) cleaves angiotensin II (Ang II) resulting in decreased activation of the AT1 receptor and decreased immune system activation. We hypothesized that autoantibodies against ACE2 may develop after SARS-CoV-2 infection, as anti-idiotypic antibodies to anti-spike protein antibodies.

Methods and findings

We tested plasma or serum for ACE2 antibodies in 67 patients with known SARS-CoV-2 infection and 13 with no history of infection. None of the 13 patients without history of SARS-CoV-2 infection and 1 of the 20 outpatients that had a positive PCR test for SARS-CoV-2 had levels of ACE2 antibodies above the cutoff threshold. In contrast, 26/32 (81%) in the convalescent group and 14/15 (93%) of patients acutely hospitalized had detectable ACE2 antibodies. Plasma from patients with antibodies against ACE2 had less soluble ACE2 activity in plasma but similar amounts of ACE2 protein compared to patients without ACE2 antibodies. We measured the capacity of the samples to inhibit ACE2 enzyme activity. Addition of plasma from patients with ACE2 antibodies led to decreased activity of an exogenous preparation of ACE2 compared to patients that did not have antibodies.

Conclusions

Many patients with a history of SARS-CoV-2 infection have antibodies specific for ACE2. Patients with ACE2 antibodies have lower activity of soluble ACE2 in plasma. Plasma from these patients also inhibits exogenous ACE2 activity. These findings are consistent with the hypothesis that ACE2 antibodies develop after SARS-CoV-2 infection and decrease ACE2 activity. This could lead to an increase in the abundance of Ang II, which causes a proinflammatory state that triggers symptoms of PASC.

The potential impacts of early secreted antigenic target of 6 kDa of Mycobacterium tuberculosis on KSHV-infected cells

Kaposi's sarcoma-associated herpesvirus (KSHV) causes several human cancers, including Kaposi's sarcoma (KS) and primary effusion lymphoma, which are mostly seen in immunocompromised patients, such as human immunodefeciency virus (HIV)+ individuals. Tuberculosis (TB), caused by the bacterial pathogen Mycobacterium tuberculosis (Mtb), remains one of the deadliest infectious diseases in the world. The risk of developing TB is dramatically higher in people living with HIV than among those without HIV infection. Case reports link cutaneous or pulmonary KS in HIV+ patients with mycobacterial co-infections, however, impacts of Mtb infection or its products on KSHV-infected cells are not known. We report here that ESAT-6, a secreted Mtb virulence factor, induces viral reactivation from KSHV-infected cells. KSHV-infected pulmonary endothelial cells were resistant to ESAT-6 induced inhibition of cell growth. Our data demonstrate that Mtb virulence factors influence the biology of KSHV-infected cells, highlighting the need to study the interactions between these two pathogens commonly found in people living with HIV.

Identification of new antiviral agents against Kaposi's sarcoma-associated herpesvirus (KSHV) by high-throughput drug screening reveals the role of histamine-related signaling in promoting viral lytic reactivation

Kaposi's sarcoma-associated herpesvirus (KSHV) causes several human cancers, such as Kaposi's sarcoma (KS) and primary effusion lymphoma (PEL). Current treatment options for KSHV infection and virus associated diseases are sometimes ineffective, therefore, more effectively antiviral agents are urgently needed. As a herpesvirus, lytic replication is critical for KSHV pathogenesis and oncogenesis. In this study, we have established a high-throughput screening assay by using an inducible KSHV+ cell-line, iSLK.219. After screening a compound library that consisted of 1280 Food and Drug Administration (FDA)-approved drugs, 15 hit compounds that effectively inhibited KSHV virion production were identified, most of which have never been reported with anti-KSHV activities. Interestingly, 3 of these drugs target histamine receptors or signaling. Our data further confirmed that antagonists targeting different histamine receptors (HxRs) displayed excellent inhibitory effects on KSHV lytic replication from induced iSLK.219 or BCBL-1 cells. In contrast, histamine and specific agonists of HxRs promoted viral lytic replication from induced iSLK.219 or KSHV-infected primary cells. Mechanistic studies indicated that downstream MAPK and PI3K/Akt signaling pathways were required for histamine/receptors mediated promotion of KSHV lytic replication. Direct knockdown of HxRs in iSLK.219 cells effectively blocked viral lytic gene expression during induction. Using samples from a cohort of HIV+ patients, we found that the KSHV+ group has much higher levels of histamine in their plasma and saliva than the KSHV- group. Taken together, our data have identified new anti-KSHV agents and provided novel insights into the molecular bases of host factors that contribute to lytic replication and reactivation of this oncogenic herpesvirus.

Expression of PD-1 and PD-Ls in Kaposi's sarcoma and regulation by oncogenic herpesvirus lytic reactivation

Kaposi's sarcoma-associated herpesvirus (KSHV) causes several cancers such as Kaposi's sarcoma (KS) and primary effusion lymphoma (PEL). PD-1/PD-Ls immune checkpoint molecules play important roles in cancer cell immune escape. The expression of PD-1/PD-Ls and their regulation by oncogenic viruses, in particular KSHV, remain largely undefined. Here we demonstrate strong PD-1/PD-L1/PD-L2 expression in KS tissues from a cohort of HIV + patients. We found that induction of KSHV lytic reactivation significantly upregulates PD-L1 expression on infected tumor cells, potentially through several major cellular signaling pathways and IL-1β, which may represent a novel mechanism for virus-associated tumor cell immune escape.

IRF4 promotes Epstein-Barr virus activation in Burkitt's lymphoma cells

Epstein-Barr virus (EBV) establishes a life-long latency in memory B cells, whereas plasma cell differentiation is linked to EBV lytic reactivation from latently infected B cells. EBV lytic replication is mediated by the two immediate-early switch proteins Zta and RTA. Both plasma cell transcription factors XBP-1 and Blimp-1 have been shown to enable the triggering of EBV lytic reactivation by activating the transcription of Zta or RTA. Here we show that interferon regulatory factor 4 (IRF4), another plasma cell transcription factor that is either not expressed or expressed at a low level in EBV-positive Burkitt's lymphoma (BL) cells, can activate the promoters of EBV Zta and RTA, but is not sufficient to elicit EBV lytic reactivation in latently infected BL cells. However, ectopic IRF4 expression can augment EBV lytic gene expression induced by anti-immunoglobulin (anti-Ig) or sodium butyrate treatment in all tested lymphoma cells, whereas IRF4 knockout in Raji cells, the only BL cell line with detectable endogenous IRF4 expression, abolishes EBV lytic gene expression induced by anti-Ig, and this is accompanied by the reduction of Blimp-1 expression, whose overexpression, in turn, can rescue EBV lytic gene expression in IRF4 knockout Raji cells. Furthermore, IRF4 knockout impairs B cell receptor (BCR) signalling activation, which is required for BCR-mediated EBV reactivation. Altogether, these results demonstrate that IRF4 facilitates EBV lytic reactivation in BL cells, which involves the regulation of Blimp-1 expression and BCR signalling pathways.

Conditional mutagenesis in vivo reveals cell type- and infection stage-specific requirements for LANA in chronic MHV68 infection

Gammaherpesvirus (GHV) pathogenesis is a complex process that involves productive viral replication, dissemination to tissues that harbor lifelong latent infection, and reactivation from latency back into a productive replication cycle. Traditional loss-of-function mutagenesis approaches in mice using murine gammaherpesvirus 68 (MHV68), a model that allows for examination of GHV pathogenesis in vivo, have been invaluable for defining requirements for specific viral gene products in GHV infection. But these approaches are insufficient to fully reveal how viral gene products contribute when the encoded protein facilitates multiple processes in the infectious cycle and when these functions vary over time and from one host tissue to another. To address this complexity, we developed an MHV68 genetic platform that enables cell-type-specific and inducible viral gene deletion in vivo. We employed this system to re-evaluate functions of the MHV68 latency-associated nuclear antigen (mLANA), a protein with roles in both viral replication and latency. Cre-mediated deletion in mice of loxP-flanked ORF73 demonstrated the necessity of mLANA in B cells for MHV68 latency establishment. Impaired latency during the transition from draining lymph nodes to blood following mLANA deletion also was observed, supporting the hypothesis that B cells are a major conduit for viral dissemination. Ablation of mLANA in infected germinal center (GC) B cells severely impaired viral latency, indicating the importance of viral passage through the GC for latency establishment. Finally, induced ablation of mLANA during latency resulted in complete loss of affected viral genomes, indicating that mLANA is critically important for maintenance of viral genomes during stable latency. Collectively, these experiments provide new insights into LANA homolog functions in GHV colonization of the host and highlight the potential of a new MHV68 genetic platform to foster a more complete understanding of viral gene functions at discrete stages of GHV pathogenesis.

Gammaherpesviruses (GHVs), including the human pathogens Epstein-Barr virus and Kaposi sarcoma-associated herpesvirus, establish lifelong infections that can lead to cancer. Defining the functions of viral gene products in acute replication and chronic infection is important for understanding how these viruses cause disease. Infection of mice with the related GHV, murine gammaherpesvirus 68 (MHV68), provides a tractable small animal model for defining how viral gene products function in chronic infection and understanding how host factors limit disease. Here we describe the development of a new viral genetic platform that enables the targeted deletion of specific genes from the viral genome in discrete host cells or at distinct times during infection. We utilize this system to better define requirements for the conserved latency-associated nuclear antigen in MHV68 lytic replication and latency in mice. This work highlights the utility of this MHV68 genetic platform for defining mechanisms of GHV infection and disease.

A screen of the NIH Clinical Collection small molecule library identifies potential anti-coronavirus drugs

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High-throughput screening identified 84 of the 727 drugs in the NCC library to have anti-coronavirus effect.

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Results revealed that 51 candidate drugs blocked virus entry while 19 others inhibited viral replication.

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Homoharringtonine was found to be the most potent inhibitor against animal and human coronaviruses.

With the recent emergence of Middle East Respiratory Syndrome coronavirus in humans and the outbreak of devastating porcine epidemic diarrhea coronavirus in swine, therapeutic intervention is urgently needed. However, anti-coronavirus drugs currently are not available. In an effort to assist rapid development of anti-coronavirus drugs, here we screened the NIH Clinical Collection in cell culture using a luciferase reporter-expressing recombinant murine coronavirus. Of the 727 compounds screened, 84 were found to have a significant anti-coronavirus effect. Further experiments revealed that 51 compounds blocked virus entry while 19 others inhibited viral replication. Additional validation studies with the top 3 inhibitors (hexachlorophene, nitazoxanide and homoharringtonine) demonstrated robust anti-coronavirus activities (a reduction of 6 to 8 log₁₀ in virus titer) with an IC₅₀ ranging from 11 nM to 1.2 μM. Furthermore, homoharringtonine and hexachlorophene exhibited broad antiviral activity against diverse species of human and animal coronaviruses. Since the NIH Clinical Collection consists of compounds that have already been through clinical trials, these small molecule inhibitors have a great potential for rapid development as anti-coronavirus drugs.

Phosphoproteomic analyses reveal signaling pathways that facilitate lytic gammaherpesvirus replication

Lytic gammaherpesvirus (GHV) replication facilitates the establishment of lifelong latent infection, which places the infected host at risk for numerous cancers. As obligate intracellular parasites, GHVs must control and usurp cellular signaling pathways in order to successfully replicate, disseminate to stable latency reservoirs in the host, and prevent immune-mediated clearance. To facilitate a systems-level understanding of phosphorylation-dependent signaling events directed by GHVs during lytic replication, we utilized label-free quantitative mass spectrometry to interrogate the lytic replication cycle of murine gammaherpesvirus-68 (MHV68). Compared to controls, MHV68 infection regulated by 2-fold or greater ca. 86% of identified phosphopeptides - a regulatory scale not previously observed in phosphoproteomic evaluations of discrete signal-inducing stimuli. Network analyses demonstrated that the infection-associated induction or repression of specific cellular proteins globally altered the flow of information through the host phosphoprotein network, yielding major changes to functional protein clusters and ontologically associated proteins. A series of orthogonal bioinformatics analyses revealed that MAPK and CDK-related signaling events were overrepresented in the infection-associated phosphoproteome and identified 155 host proteins, such as the transcription factor c-Jun, as putative downstream targets. Importantly, functional tests of bioinformatics-based predictions confirmed ERK1/2 and CDK1/2 as kinases that facilitate MHV68 replication and also demonstrated the importance of c-Jun. Finally, a transposon-mutant virus screen identified the MHV68 cyclin D ortholog as a viral protein that contributes to the prominent MAPK/CDK signature of the infection-associated phosphoproteome. Together, these analyses enhance an understanding of how GHVs reorganize and usurp intracellular signaling networks to facilitate infection and replication.

Development of technology for the early post mortem prediction of water holding capacity and drip loss in fresh pork

Two different technologies were tested on the slaughterline for their ability to predict drip loss at 24 h, namely near infrared reflectance (NIR) and impedance measurements using a tetra polar measuring geometry at a frequency of 1000 Hz. The results demonstrate that NIR measurements (900-1800 nm) acquired during a 6 min period starting only 30 min post exsanguination through a fibre optic probe in combination with multivariate data analysis can be used for predicting drip loss 24 h after slaughter. A correlation higher than 0.8 was observed for a trial on 99 carcasses measured at a commercial slaughterhouse. The tetrapolar impedance measurements did not perform as well as NIR yielding a correlation of 0.5 with 24 h drip loss.

Unbiased mutagenesis of MHV68 LANA reveals a DNA-binding domain required for LANA function in vitro and in vivo

The Latency-Associated Nuclear Antigen (LANA), encoded by ORF73, is a conserved gene among the γ2-herpesviruses (rhadinoviruses). The Kaposi's Sarcoma-Associated Herpesvirus (KSHV) LANA is consistently expressed in KSHV-associated malignancies. In the case of the rodent γ2-herpesvirus, murine gammaherpesvirus 68 (MHV68), the LANA homolog (mLANA) is required for efficient virus replication, reactivation from latency and immortalization of murine fetal liver-derived B cells. To gain insights into mLANA function(s), knowing that KSHV LANA binds DNA and can modulate transcription of a variety of promoters, we sought out and identified a mLANA-responsive promoter which maps to the terminal repeat (TR) of MHV68. Notably, mLANA strongly repressed activity from this promoter. We extended these analyses to demonstrate direct, sequence-specific binding of recombinant mLANA to TR DNA by DNase I footprinting. To assess whether the DNA-binding and/or transcription modulating function is important in the known mLANA phenotypes, we generated an unbiased library of mLANA point mutants using error-prone PCR, and screened a large panel of mutants for repression of the mLANA-responsive promoter to identify loss of function mutants. Notably, among the mutant mLANA proteins recovered, many of the mutations are in a predicted EBNA-1-like DNA-binding domain. Consistent with this prediction, those tested displayed loss of DNA binding activity. We engineered six of these mLANA mutants into the MHV68 genome and tested the resulting mutant viruses for: (i) replication fitness; (ii) efficiency of latency establishment; and (iii) reactivation from latency. Interestingly, each of these mLANA-mutant viruses exhibited phenotypes similar to the mLANA-null mutant virus, indicating that DNA-binding is critical for mLANA function.

The human gammaherpesviruses Epstein-Barr virus (EBV) and Kaposi's sarcoma-associated herpesvirus (KSHV) are tightly associated with a number of different cancers. Unfortunately, due to their very narrow host tropism, characterizing the pathogenesis of these viruses has been difficult. Infection of laboratory mice with the rodent gammaherpesvirus, murine gammaherpesvirus 68 (MHV68), has proven to be an excellent approach for understanding how these viruses cause disease. One of the MHV68 encoded proteins, which is also found in KSHV, is called LANA and in the case of KSHV-associated diseases LANA expression is consistently detected in infected cells. Here we show that the MHV68 LANA shares a key function with the KSHV homolog—namely, modulating gene expression. Using a random mutagenesis protocol, we identified mLANA mutants that had lost transcriptional regulatory activity. We engineered these mutations back into the virus, used the viruses to infect mice, and find that this function is critical to LANA function in vivo and in vitro. This method, combined with the knowledge gained here, sets the stage for future studies to identify mutant forms of LANA that could be used to block wild type LANA function or, alternatively, to design drugs that target LANA function.

The de novo methyltransferases DNMT3a and DNMT3b target the murine gammaherpesvirus immediate-early gene 50 promoter during establishment of latency

The role of epigenetic modifications in the regulation of gammaherpesvirus latency has been a subject of active study for more than 20 years. DNA methylation, associated with transcriptional silencing in mammalian genomes, has been shown to be an important mechanism in the transcriptional control of several key gammaherpesvirus genes. In particular, DNA methylation of the functionally conserved immediate-early replication and transcription activator (RTA) has been shown to regulate Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus Rta expression. Here we demonstrate that the murine gammaherpesvirus (MHV68) homolog, encoded by gene 50, is also subject to direct repression by DNA methylation, both in vitro and in vivo. We observed that the treatment of latently MHV68-infected B-cell lines with a methyltransferase inhibitor induced virus reactivation. In addition, we show that the methylation of the recently characterized distal gene 50 promoter represses activity in a murine macrophage cell line. To evaluate the role of de novo methyltransferases (DNMTs) in the establishment of these methylation marks, we infected mice in which conditional DNMT3a and DNMT3b alleles were selectively deleted in B lymphocytes. DNMT3a/DNMT3b-deficient B cells were phenotypically normal, displaying no obvious compromise in cell surface marker expression or antibody production either in naïve mice or in the context of nonviral and viral immunogens. However, mice lacking functional DNMT3a and DNMT3b in B cells exhibited hallmarks of deregulated MHV68 lytic replication, including increased splenomegaly and the presence of infectious virus in the spleen at day 18 following infection. In addition, total gene 50 transcript levels were elevated in the spleens of these mice at day 18, which correlated with the hypomethylation of the distal gene 50 promoter. However, by day 42 postinfection, aberrant virus replication was resolved, and we observed wild-type frequencies of viral genome-positive splenocytes in mice lacking functional DNMT3a and DNMT3b in B lymphocytes. The latter correlated with increased CpG methylation in the distal gene 50 promoter, which was restored to levels similar to those of littermate controls harboring functional DNMT3a and DNMT3b alleles in B lymphocytes, suggesting the existence of an alternative mechanism for the de novo methylation of the MHV68 genome. Importantly, this DNMT3a/DNMT3b-independent methylation appeared to be targeted specifically to the gene 50 promoter, as we observed that the promoters for MHV68 gene 72 (v-cyclin) and M11 (v-bcl2) remained hypomethylated at day 42 postinfection. Taken together, these data provide the first evidence of the importance of DNA methylation in regulating gammaherpesvirus RTA/gene 50 transcription during virus infection in vivo and provide insight into the hierarchy of host machinery required to establish this modification.

Evaluation of the prediction of alternative measures of pork carcass composition by three optical probes

The accuracy of 3 optical probes (HGP4 Hennessey Grading Probe, Destron-Feering PG-100 probe, and Giraldo OPTO-Electronic PG-200 probe) to predict the carcass percentage of 5 alternative measures of carcass composition (fat-tissue-free lean, lipid-free soft tissue, lipid-free lean, total fat tissue, and soft tissue lipid) was evaluated on 203 barrows and gilts of 7 genetic populations. The optical probe backfat depths were more closely correlated (P < 0.001, 0.963 to 0.983) than the LM depths (r = 0.695 to 0.734). The optical probe backfat depths were related to lean percentage (r = -0.82 to -0.88), total fat tissue percentage (r = 0.84 to 0.88), and soft tissue lipid percentage (r = 0.86 to 0.87). Optical probe LM depths were weakly related (P < 0.05; r = 0.23 to 0.34) to measures of carcass lean percentage and total fat tissue percentage (r = -0.16 to -0.26). Fat-free lean percentage was predicted with residual SD (RSD) of 3.7% for equations including last-rib midline backfat thickness, 2.4 to 2.7% for equations including optical probe backfat and LM depth, and 2.3% for ribbed carcass measurements. The RSD for the optical probe equations ranged from 2.1 to 2.4% for lipid-free soft tissue percentage and from 2.0 to 2.3% for lipid-free lean percentage. The RSD for the optical probe equations ranged from 2.9 to 3.3% for total fat tissue percentage and 2.5 to 2.8% for soft tissue lipid percentage. Quadratic and cross-product variables of optical probe fat depth, LM depth, and carcass weight were significant (P < 0.05) and reduced the RSD of the equations. Optical probe backfat and LM measurements can be used to predict alternative measures of carcass composition. The predicted relationships in fat-free lean percentage to backfat depth were nearly identical for each optical probe.

ORF73-null murine gammaherpesvirus 68 reveals roles for mLANA and p53 in virus replication

Gammaherpesviruses establish lifelong, latent infections in host lymphocytes, during which a limited subset of viral gene products facilitates maintenance of the viral episome. Among the gamma-2-herpesvirus (rhadinovirus) subfamily, this includes expression of the conserved ORF73-encoded LANA proteins. We previously demonstrated by loss-of-function mutagenesis that the murine gammaherpesvirus 68 (MHV68) ORF73 gene product, mLANA, is required for the establishment of latency following intranasal inoculation of mice (N. J. Moorman, D. O. Willer, and S. H. Speck, J. Virol. 77:10295-10303, 2003). mLANA-deficient viruses also exhibited a defect in acute virus replication in the lungs of infected mice. The latter observation led us to examine the role of mLANA in productive viral replication. We assessed the capacity of mLANA-deficient virus (73.Stop) to replicate in cell culture at low multiplicities of infection (MOIs) and found that 73.Stop growth was impaired in murine fibroblasts but not in Vero cells. A recombinant virus expressing an mLANA-green fluorescent protein (GFP) fusion revealed that mLANA is expressed throughout the virus replication cycle. In addition, 73.Stop infection of murine fibroblasts at high MOIs was substantially more cytotoxic than infection with a genetically repaired marker rescue virus (73.MR), a phenotype that correlated with enhanced kinetics of viral gene expression and increased activation of p53. Notably, augmented cell death, viral gene expression, and p53 induction were independent of viral DNA replication. Expression of a mLANA-GFP fusion protein in fibroblasts correlated with both reduced p53 stabilization and reduced cell death following treatment with p53-inducing agonists. In agreement, accentuated cell death associated with 73.Stop infection was reduced in p53-deficient murine embryonic fibroblasts. Additionally, replication of 73.Stop in p53-deficient cells was restored to levels comparable to those of 73.MR. More remarkably, the absence of p53 led to an overall delay in replication for both 73.Stop and 73.MR viruses, which correlated with delayed viral gene expression, indicating a role for p53 in MHV68 replication. Consistent with these findings, the expression of replication-promoting viral genes was positively influenced by p53 overexpression or treatment with the p53 agonist etoposide. Overall, these data demonstrate the importance of mLANA in MHV68 replication and suggest that LANA proteins limit the induction of cellular stress responses to regulate the viral gene expression cascade and limit host cell injury.

Beta1 integrin mediates internalization of mammalian reovirus

Reovirus infection is initiated by interactions between the attachment protein sigma1 and cell surface carbohydrate and junctional adhesion molecule A (JAM-A). Expression of a JAM-A mutant lacking a cytoplasmic tail in nonpermissive cells conferred full susceptibility to reovirus infection, suggesting that cell surface molecules other than JAM-A mediate viral internalization following attachment. The presence of integrin-binding sequences in reovirus outer capsid protein lambda2, which serves as the structural base for sigma1, suggests that integrins mediate reovirus endocytosis. A beta1 integrin-specific antibody, but not antibodies specific for other integrin subunits, inhibited reovirus infection of HeLa cells. Expression of a beta1 integrin cDNA, along with a cDNA encoding JAM-A, in nonpermissive chicken embryo fibroblasts conferred susceptibility to reovirus infection. Infectivity of reovirus was significantly reduced in beta1-deficient mouse embryonic stem cells in comparison to isogenic cells expressing beta1. However, reovirus bound equivalently to cells that differed in levels of beta1 expression, suggesting that beta1 integrins are involved in a postattachment entry step. Concordantly, uptake of reovirus virions into beta1-deficient cells was substantially diminished in comparison to viral uptake into beta1-expressing cells. These data provide evidence that beta1 integrin facilitates reovirus internalization and suggest that viral entry occurs by interactions of reovirus virions with independent attachment and entry receptors on the cell surface.

JAM-A-independent, antibody-mediated uptake of reovirus into cells leads to apoptosis

Apoptosis plays a major role in the cytopathic effect induced by reovirus following infection of cultured cells and newborn mice. Strain-specific differences in the capacity of reovirus to induce apoptosis segregate with the S1 and M2 gene segments, which encode attachment protein sigma1 and membrane penetration protein mu1, respectively. Virus strains that bind to both junctional adhesion molecule-A (JAM-A) and sialic acid are the most potent inducers of apoptosis. In addition to receptor binding, events in reovirus replication that occur during or after viral disassembly but prior to initiation of viral RNA synthesis also are required for reovirus-induced apoptosis. To determine whether reovirus infection initiated in the absence of JAM-A and sialic acid results in apoptosis, Chinese hamster ovary (CHO) cells engineered to express Fc receptors were infected with reovirus using antibodies directed against viral outer-capsid proteins. Fc-mediated infection of CHO cells induced apoptosis in a sigma1-independent manner. Apoptosis following this uptake mechanism requires acid-dependent proteolytic disassembly, since treatment of cells with the weak base ammonium chloride diminished the apoptotic response. Analysis of T1L x T3D reassortant viruses revealed that the mu1-encoding M2 gene segment is the only viral determinant of the apoptosis-inducing capacity of reovirus when infection is initiated via Fc receptors. Additionally, a temperature-sensitive, membrane penetration-defective M2 mutant, tsA279.64, is an inefficient inducer of apoptosis. These data suggest that signaling pathways activated by binding of sigma1 to JAM-A and sialic acid are dispensable for reovirus-mediated apoptosis and that the mu1 protein plays an essential role in stimulating proapoptotic signaling.

Junctional adhesion molecule a serves as a receptor for prototype and field-isolate strains of mammalian reovirus

Reovirus infections are initiated by the binding of viral attachment protein sigma1 to receptors on the surface of host cells. The sigma1 protein is an elongated fiber comprised of an N-terminal tail that inserts into the virion and a C-terminal head that extends from the virion surface. The prototype reovirus strains type 1 Lang/53 (T1L/53) and type 3 Dearing/55 (T3D/55) use junctional adhesion molecule A (JAM-A) as a receptor. The C-terminal half of the T3D/55 sigma1 protein interacts directly with JAM-A, but the determinants of receptor-binding specificity have not been identified. In this study, we investigated whether JAM-A also mediates the attachment of the prototype reovirus strain type 2 Jones/55 (T2J/55) and a panel of field-isolate strains representing each of the three serotypes. Antibodies specific for JAM-A were capable of inhibiting infections of HeLa cells by T1L/53, T2J/55, and T3D/55, demonstrating that strains of all three serotypes use JAM-A as a receptor. To corroborate these findings, we introduced JAM-A or the structurally related JAM family members JAM-B and JAM-C into Chinese hamster ovary cells, which are poorly permissive for reovirus infection. Both prototype and field-isolate reovirus strains were capable of infecting cells transfected with JAM-A but not those transfected with JAM-B or JAM-C. A sequence analysis of the sigma1-encoding S1 gene segment of the strains chosen for study revealed little conservation in the deduced sigma1 amino acid sequences among the three serotypes. This contrasts markedly with the observed sequence variability within each serotype, which is confined to a small number of amino acids. Mapping of these residues onto the crystal structure of sigma1 identified regions of conservation and variability, suggesting a likely mode of JAM-A binding via a conserved surface at the base of the sigma1 head domain.

Organ-specific roles for transcription factor NF-kappaB in reovirus-induced apoptosis and disease

Reovirus induces apoptosis in cultured cells and in vivo. In cell culture models, apoptosis is contingent upon a mechanism involving reovirus-induced activation of transcription factor NF-kappaB complexes containing p50 and p65/RelA subunits. To explore the in vivo role of NF-kappaB in this process, we tested the capacity of reovirus to induce apoptosis in mice lacking a functional nfkb1/p50 gene. The genetic defect had no apparent effect on reovirus replication in the intestine or dissemination to secondary sites of infection. In comparison to what was observed in wild-type controls, apoptosis was significantly diminished in the CNS of p50-null mice following reovirus infection. In sharp contrast, the loss of p50 was associated with massive reovirus-induced apoptosis and uncontrolled reovirus replication in the heart. Levels of IFN-beta mRNA were markedly increased in the hearts of wild-type animals but not p50-null animals infected with reovirus. Treatment of p50-null mice with IFN-beta substantially diminished reovirus replication and apoptosis, which suggests that IFN-beta induction by NF-kappaB protects against reovirus-induced myocarditis. These findings reveal an organ-specific role for NF-kappaB in the regulation of reovirus-induced apoptosis, which modulates encephalitis and myocarditis associated with reovirus infection.

Structure-function analysis of reovirus binding to junctional adhesion molecule 1. Implications for the mechanism of reovirus attachment

Mammalian reoviruses are nonenveloped viruses with a long, filamentous attachment protein that dictates disease phenotypes following infection of newborn mice and is a structural homologue of the adenovirus attachment protein. Reoviruses use junctional adhesion molecule 1 (JAM1) as a serotype-independent cellular receptor. JAM1 is a broadly expressed immunoglobulin superfamily protein that forms stable homodimers and regulates tight-junction permeability and lymphocyte trafficking. We employed a series of structure-guided binding and infection experiments to define residues in human JAM1 (hJAM1) important for reovirus-receptor interactions and to gain insight into mechanisms of reovirus attachment. Binding and infection experiments using chimeric and domain deletion mutant receptor molecules indicate that the amino-terminal D1 domain of hJAM1 is required for reovirus attachment, infection, and replication. Reovirus binding to hJAM1 occurs more rapidly than homotypic hJAM1 association and is competed by excess hJAM1 in vitro and on cells. Cross-linking hJAM1 diminishes the capacity of reovirus to bind hJAM1 in vitro and on cells and negates the competitive effects of soluble hJAM1 on reovirus attachment. Finally, mutagenesis studies demonstrate that residues intimately associated with the hJAM1 dimer interface are critical for reovirus interactions with hJAM1. These results suggest that reovirus attachment disrupts hJAM1 dimers and highlight similarities between the attachment strategies of reovirus and adenovirus.

Utilization of sialic acid as a coreceptor is required for reovirus-induced biliary disease

Infection of neonatal mice with some reovirus strains produces a disease similar to infantile biliary atresia, but previous attempts to correlate reovirus infection with this disease have yielded conflicting results. We used isogenic reovirus strains T3SA- and T3SA+, which differ solely in the capacity to bind sialic acid as a coreceptor, to define the role of sialic acid in reovirus encephalitis and biliary tract infection in mice. Growth in the intestine was equivalent for both strains following peroral inoculation. However, T3SA+ spread more rapidly from the intestine to distant sites and replicated to higher titers in spleen, liver, and brain. Strikingly, mice infected with T3SA+ but not T3SA- developed steatorrhea and bilirubinemia. Liver tissue from mice infected with T3SA+ demonstrated intense inflammation focused at intrahepatic bile ducts, pathology analogous to that found in biliary atresia in humans, and high levels of T3SA+ antigen in bile duct epithelial cells. T3SA+ bound 100-fold more efficiently than T3SA- to human cholangiocarcinoma cells. These observations suggest that the carbohydrate-binding specificity of a virus can dramatically alter disease in the host and highlight the need for epidemiologic studies focusing on infection by sialic acid-binding reovirus strains as a possible contributor to the pathogenesis of neonatal biliary atresia.

Crystal structure of human junctional adhesion molecule 1: implications for reovirus binding

Reovirus attachment to cells is mediated by the binding of viral attachment protein sigma 1 to junctional adhesion molecule 1 (JAM1). The crystal structure of the extracellular region of human JAM1 (hJAM1) reveals two concatenated Ig-type domains with a pronounced bend at the domain interface. Two hJAM1 molecules form a dimer that is stabilized by extensive ionic and hydrophobic contacts between the N-terminal domains. This dimeric arrangement is similar to that observed previously in the murine homolog of JAM1, indicating physiologic relevance. However, differences in the dimeric structures of hJAM1 and murine JAM1 suggest that the interface is dynamic, perhaps as a result of its ionic nature. We demonstrate that hJAM1, but not the related proteins hJAM2 and hJAM3, serves as a reovirus receptor, which provides insight into sites in hJAM1 that likely interact with sigma 1. In addition, we present evidence that the previously reported structural homology between sigma 1 and the adenovirus attachment protein, fiber, also extends to their respective receptors, which form similar dimeric structures. Because both receptors are located at regions of cell-cell contact, this similarity suggests that reovirus and adenovirus use conserved mechanisms of entry and pathways of infection.

Ractopamine treatment biases in the prediction of pork carcass composition

Carcass and live measurements of 45 barrows were used to evaluate the magnitude of ractopamine (RAC) treatment prediction biases for measures of carcass composition. Barrows (body weight = 69.6 kg) were allotted by weight to three dietary treatments and fed to an average body weight of 114 kg. Treatments were: 1) 16% crude protein, 0.82% lysine control diet (CON); 2) control diet + 20 ppm RAC (RAC16); 3) a phase feeding sequence with 20 ppm RAC (RAC-P) consisting of 18% crude protein (1.08% lysine) during wk 1 and 4, 20% crude protein (1.22% lysine) during wk 2 and 3, 16% crude protein (0.94% lysine) during wk 6, and 16% crude protein (0.82% lysine) during wk 6. The four lean cuts from the right side of the carcasses (n = 15/treatment) were dissected into lean and fat tissue. The other cut soft tissue was collected from the jowl, ribs, and belly. Proximate analyses were completed on these three tissue pools and a sample of fat tissue from the other cut soft tissue. Prediction equations were developed for each of five measures of carcass composition: fat-free lean, lipid-free soft tissue, dissected lean in the four lean cuts, total carcass fat tissue, and soft-tissue lipid mass. Ractopamine treatment biases were found for equations in which midline backfat, ribbed carcass, and live ultrasonic measures were used as single technology sets of measurements. Prediction equations from live or carcass measurements underpredicted the lean mass of the RAC-P pigs and underpredicted the lean mass of the CON pigs. Only 20 to 50% of the true difference in fat-free lean mass or lipid-free soft-tissue mass between the control pigs and pigs fed RAC was predicted from equations including standard carcass measurements. The soft-tissue lipid and total carcass fat mass of RAC-P pigs was overpredicted from the carcass and live ultrasound measurements. Prediction equations including standard carcass measurements with dissected ham lean alone or with dissected loin lean reduced the residual standard deviation and magnitude of biases for the three measures of carcass leanmass. Prediction equations including the percentage of lipid of the other cut soft tissue improved residual standard deviation and reduced the magnitude of biases for total carcass fat mass and soft-tissue lipid. Prediction equations for easily obtained carcass or live ultrasound measures will only partially predict the true effect of RAC to increase carcass leanness. Accurate prediction of the carcass composition of RAC-fed pigs requires some partial dissection, chemical analysis, or alternative technologies.

Junction adhesion molecule is a receptor for reovirus

Virus attachment to cells plays an essential role in viral tropism and disease. Reovirus serotypes 1 and 3 differ in the capacity to target distinct cell types in the murine nervous system and in the efficiency to induce apoptosis. The binding of viral attachment protein sigma1 to unidentified receptors controls these phenotypes. We used expression cloning to identify junction adhesion molecule (JAM), an integral tight junction protein, as a reovirus receptor. JAM binds directly to sigma1 and permits reovirus infection of nonpermissive cells. Ligation of JAM is required for reovirus-induced activation of NF-kappaB and apoptosis. Thus, reovirus interaction with cell-surface receptors is a critical determinant of both cell-type specific tropism and virus-induced intracellular signaling events that culminate in cell death.

Utilization of sialic acid as a coreceptor enhances reovirus attachment by multistep adhesion strengthening

Many serotype 3 reoviruses bind to two different host cell molecules, sialic acid and an unidentified protein, using discrete receptor-binding domains in viral attachment protein, final sigma1. To determine mechanisms by which these receptor-binding events cooperate to mediate cell attachment, we generated isogenic reovirus strains that differ in the capacity to bind sialic acid. Strain SA+, but not SA-, bound specifically to sialic acid on a biosensor chip with nanomolar avidity. SA+ displayed 5-fold higher avidity for HeLa cells when compared with SA-, although both strains recognized the same proteinaceous receptor. Increased avidity of SA+ binding was mediated by increased k(on). Neuraminidase treatment to remove cell-surface sialic acid decreased the k(on) of SA+ to that of SA-. Increased k(on) of SA+ enhanced an infectious attachment process, since SA+ was 50-100-fold more efficient than SA- at infecting HeLa cells in a kinetic fluorescent focus assay. Sialic acid binding was operant early during SA+ attachment, since the capacity of soluble sialyllactose to inhibit infection decreased rapidly during the first 20 min of adsorption. These results indicate that reovirus binding to sialic acid enhances virus infection through adhesion of virus to the cell surface where access to a proteinaceous receptor is thermodynamically favored.

Evaluation of alternative measures of pork carcass composition

Carcass and live measurements of 203 pigs representing seven genetic populations and four target live weights (100, 114, 128, and 152 kg) were used to evaluate alternative measures of carcass composition. Measures of carcass lean (fat tissue-free lean, FFLM; lipid-free soft tissue, LFSTIS; and dissected lean in the four lean cuts, DL), fat (total carcass fat tissue, TOFAT), and lipid mass (soft tissue lipid, STLIP) were evaluated. Overall, LFSTIS was 22.8% greater than FFLM (47.8 vs 38.9 kg) and TOFAT was 30% greater than STLIP (38.5 vs 29.6 kg). The allometric growth coefficients relative to carcass weight were different for the measures: b = 0.776, 0.828, 0.794, 1.37, and 1.49 for FFLM, LFSTIS, DL, TOFAT, and STLIP, respectively. At 90 kg carcass weight, the predicted growth of FFLM, LFSTIS, TOFAT, and STLIP was 0.314, 0.420, 0.553, and 0.446 kg/kg increase in carcass weight. The difference between FFLM and LFSTIS, representing nonlipid components of the carcass fat tissue, was greater for barrows than for gilts (9.2 vs 8.6 kg). Lipid-free soft tissue mass was predicted more accurately from carcass or live animal measurements than FFLM with smaller relative RSD (4.6 vs 6.5% of their mean values). The alternative measures of carcass composition were evaluated as predictors of empty body protein (MTPRO) and lipid (MTLIP) mass. Empty body protein was predicted with similar accuracy (R2 = 0.74 to 0.81) from either DL, FFLM, LFSTIS, or ribbed carcass measurements. Empty body lipid was predicted more accurately from TOFAT (R2 = 0.92) or STLIP (R2 = 0.93) than ribbed carcass measurements (R2 = 0.88). Although the alternative measures of lean mass (LFSTIS vs FFLM) and lipid mass (TOFAT vs STLIP) were highly related to each other (r = 0.93 to 0.98), they had different relative growth rates (allometric coefficients) and thus cannot be predicted as linear functions of the similar alternative variable without significant weight group biases. From the 100- to 152-kg target weight groups, gilts gained 12.9% greater FFLM and 12.1% greater MTPRO but only 4.4% greater LFSTIS than barrows. Fat-free lean mass is more precise as a measure of muscle growth and as a predictor of lysine requirements. Lipid-free soft tissue can be obtained more quickly and predicted more accurately from carcass or live animal measurements.

Assessment of fresh pork color with color machine vision

Currently, fresh pork color is visually evaluated using either the Japanese Pork Color Standards (JPCS) or the National Pork Producers Council Pork Quality Standards (NPPC) as a reference. Although useful, visual evaluation of meat color can vary with evaluator and may be quite expensive. In this study, three separate studies were used to compare the ability of color machine vision (CMV) and untrained panelists to evaluate pork color. Panels visually evaluated over 200 pork loin chops using either the JPCS or NPPC reference standards. Results from each panel were used to evaluate the ability of the CMV to sort pork loin chops based on the same criteria. Representative samples, typical of each color class, were used to train neural-network-based image processing software. After training, the CMV system was used to evaluate quality classes of pork samples based on color distribution. Classification by CMV was compared with the average panel score, rounded to the nearest integer. Training the CMV system using images of actual meat samples resulted in a stronger correlation to panel scores than training with either set of artificial color standards. Agreement between the CMV system and the panels was as high as 90%. Agreement between individual panelists and the integer panel average (52 to 85%) was less than that observed for CMV classification. Finally, the on-line performance of CMV using a laboratory conveyor system was simulated by repeatedly classifying 37 samples at a speed of 1 sample per second. Collectively, these results demonstrate that CMV is a rapid and repeatable means of evaluating pork color.

Using current on-line carcass evaluation parameters to estimate boneless and bone-in pork carcass yield as influenced by trim level

The objective of this study was to develop prediction equations for estimating proportional carcass yield to a variety of external trim levels and bone-in and boneless pork primal cuts. Two hundred pork carcasses were selected from six U.S. pork processing plants and represented USDA carcass grades (25% USDA #1, 36% USDA #2, 25% USDA #3, and 14% USDA #4). Carcasses were measured (prerigor and after a 24 h chill) for fat and muscle depth at the last rib (LR) and between the third and fourth from last rib (TH) with a Hennessy optical grading probe (OGP). Carcasses were shipped to Texas A&M University, where one was randomly assigned for fabrication. Selected sides were fabricated to four lean cuts (ham, loin, Boston butt, and picnic shoulder) then fabricated progressively into bone-in (BI) and boneless (BL) four lean cuts (FLC) trimmed to .64, .32, and 0 cm of s.c. fat, and BL 0 cm trim, seam fat removed, four lean cuts (BLS-OFLC). Total dissected carcass lean was used to calculate the percentage of total carcass lean (PLEAN). Lean tissue subsamples were collected for chemical fat-free analysis and percentage carcass fat-free lean (FFLEAN) was determined. Longissimus muscle area and fat depth also were collected at the 10th and 11th rib interface during fabrication. Regression equations were developed from linear carcass and OGP measurements predicting FLC of each fabrication point. Loin muscle and fat depths from the OPG obtained on warm, prerigor carcasses at the TH interface were more accurate predictors of fabrication end points than warm carcass probe depth obtained at the last rib or either of the chilled carcass probe sites (probed at TH or LR). Fat and loin muscle depth obtained via OGP explained 46.7, 52.6, and 57.1% (residual mean square error [RMSE] = 3.30, 3.19, and 3.04%) of the variation in the percentage of BI-FLC trimmed to .64, .32, and 0 cm of s.c. fat, respectively, and 49.0, 53.9, and 60.7% (RMSE = 2.91, 2.81, and 2.69%) of the variation in the percentage of BL-FLC trimmed to .64, .32, and 0 cm of s.c. fat, respectively. Fat and loin muscle depth from warm carcass OGP probes at the TH interface accounted for 62.4 and 63.5% (RMSE = 3.38 and 3.27%) of the variation in PLEAN and FFLEAN, respectively. These equations provide an opportunity to estimate pork carcass yield for a variety of procurement end point equations using existing on-line techniques.

Analysis of body composition changes of swine during growth and development

This study was conducted to model the growth of carcass, viscera, and empty body components and component composition of pigs. Quantitative tissue and chemical composition of 319 swine, representative of barrows and gilts from five commercial genetic populations, was determined at eight stages of growth between 25 and 152 kg. After whole body grinding and carcass dissection, proximate analyses were performed to calculate concentrations of protein, lipid, moisture, and ash of carcass, viscera, empty body, carcass lean, and carcass fat. Linear and nonlinear equations were developed to investigate the growth patterns of each component. Nonlinear growth functions accounted for the greatest amount of variation in empty body protein, lipid, moisture, and ash mass. Differences (P < .05) existed between barrows and gilts for nearly all components investigated. Carcass lean and fat tissues significantly increased in lipid percentage and decreased in moisture percentage as live weight increased. There were significant changes in the ratio and composition of the tissues of barrows and gilts during growth. Nonlinear models fitted the data better than allometric equations for nearly all of the components investigated.

Biases associated with genotype and sex in prediction of fat-free lean mass and carcass value in hogs

Carcass and live measurements of 165 market hogs that represented seven genotypes were used to investigate genotype and sex biases associated with the prediction of fat-free lean mass (FFLM) and carcass value. Carcass value was determined as the sum of the product of weight of individual cuts and their average unit prices adjusted for slaughter and processing costs. Independent variables used in the prediction equations included carcass measurements, such as optical probe, midline ruler, ribbed carcass measurements, and electromagnetic scanning (EMSCAN), and live animal ultrasonic scanning. The effect of including subpopulation mean values of independent variables in the prediction equations for FFLM and carcass value was also investigated. Genotype and sex biases were found in equations in which midline backfat, ribbed carcass, EMSCAN, and live ultrasonic scanning were used as single technology sets of measurements. The prediction equations generally undervalued genotypes with above-average carcass value. Biases were reduced when measurements of combined technologies and mean adjusted variables were used. The FFLM and carcass value of gilts were underestimated, and they were overestimated of barrows. Equations that combined OP and EMSCAN technologies were the most accurate and least biased for both FFLM and carcass value. Equations that included carcass weight and midline last-rib backfat thickness measurements were the least accurate and most biased. Genotype and sex biases must be considered when predicting FFLM and carcass value.

Pork carcass composition derived from a neural network model of electromagnetic scans

We used an advanced computer logic system (NETS 3.0) to decipher electromagnetic (EM) scans in lieu of traditional linear regression for estimation of pork carcass composition. Fifty EM scans of pork carcasses were obtained on-line (prerigor) at a swine slaughter facility. Right sides were cut into wholesale parts and dissected into fat, lean, and bone to obtain total dissected carcass and primal cut lean. In this study, the input layer consisted of 81 nodes (80-point EM scan curve and warm carcass weight), one hidden layer of 42 nodes, and an output layer consisting of one node, which were run separately for outputs of ham, loin, or shoulder lean. The hidden layer connected to the output of total lean contained 50 nodes. Thirty-five scans were used for training of the network. The new network was then tested with 15 previously unseen input/output pairs. Separate neural networks were developed for the estimation of dissected total carcass, ham, loin, and shoulder lean. The NETS configuration improved on linear regression equations for estimation of total carcass lean by .31 kg, ham lean by .284 kg, and shoulder lean by .148 kg. Our results show that advanced computer logic systems have the capacity to improve upon traditional linear regression equations for prediction of pork carcass composition.

Evaluation of electronic technology to assess lamb carcass composition

Accurate price signals are essential for producers of American lamb to ensure production of uniformly lean animals. Development of carcass merit-pricing systems will require the use of objective technology for assessing carcass composition or lean distribution. The objective of this study was to evaluate electronic technologies for accurate determination of lamb carcass composition. Lambs (n = 106) were selected as a representation of U.S. market lambs that transcended geographic location, sex, breed, carcass weight, yield grade, and production system. The independent variables used to predict lamb composition varied with the technology. The electronic technologies tested included realtime ultrasound, optical reflectance probe, bioelectrical impedance analysis, and electromagnetic scanning (TOBEC). All technologies, except realtime ultrasound, were tested on warm (prerigor) carcasses and repeated after a 24-h chill. Longitudinal ultrasonic scans of fat and muscle tissue depth and grading probe fat depths were marginal predictors of proportional carcass yield. The TOBEC measurements often accounted for more variability associated with kilograms of dissected lean and percentage of carcass lean than did carcass weight. Equations from TOBEC measurements were the most accurate predictors of weight and percentage of dissected and fat-free lean. Bioelectrical impedance measurements of resistance and reactance combined with carcass weight were also good predictors of carcass composition. Prediction of carcass lean distribution by measures of TOBEC were the most accurate for prediction of leg lean. The implications of usefulness of these technologies will depend on the commitment of the U. S. sheep industry in development of a lamb price discovery system based on carcass composition.

Assessment of lamb carcass composition from live animal measurement of bioelectrical impedance or ultrasonic tissue depths

Market weight lambs, average weight 52.5 kg (+/-6.1), were used to evaluate nontraditional live animal measurements as predictors of carcass composition. The sample population (n = 106) represented U.S. market lambs and transcended geographic location, breed, carcass weight, yield grade, and production system. Realtime ultrasonic (RU) measurements and bioelectrical impedance analysis (BIA) were used for development and evaluation of prediction equations for % boneless, closely trimmed primal cuts (BCTPC), weight or % of dissected lean tissue (TDL), and chemically derived weight or % fat-free lean (FFL). Longitudinal ultrasonic images were obtained parallel to the longissimus thoracis et lumborum (LTL), positioning the last costae in the center of the transducer head. Images were saved and fat and LTL depths were derived from printed images of the ultrasonic scans. Bioelectrical impedance analysis was administered via a four-terminal impedance plethysmograph operating at 800 microA at 50 kHz. Impedance measurements of whole-body resistance and reactance were recorded. Prediction equations including common linear measurements of live weight, heart girth, hindsaddle length, and shoulder height were also evaluated. All measurements were taken just before slaughter. Bioelectrical impedance measurements (as compared to RU and linear measurements) provided equations for %BCTPC, TDL, %TDL, FFL and %FFL with the highest R2 and lowest root mean square error. Even though BIA provided the best equations of the three methodologies tested, prediction of proportional yield (%BCTPC, %TDL, and %FFL) was marginal (R2 = .296, .551, and .551, respectively). Equations combining BIA, RU, and linear measurements greatly improved equations for prediction of proportional lean yield.

Electrical measurement for detecting early postmortem changes in porcine muscle

Use of electrical measurements to detect quality defects in porcine muscle in the early postmortem period was evaluated. Justification for use of a tetrapolar, constant current electrode configuration instead of bipolar electrodes was provided for measurements at low frequencies. Interrelationships among electrical properties, pH values, ATP decline, temperature, time postmortem, and final water-holding capacity (WHC) of porcine muscle were quantified using 25 hogs. Immediately after exsanguination, a section of the left longissimus muscle (LM) was excised to obtain rigor shortening patterns and complex impedance measurements over a 10-h period at 37 degrees C. Complex impedance measurements were taken using a tetrapolar electrode configuration at 1 kHz and .156 mA. At 15, 45, and 90 min postmortem, pH, ATP/IMP absorbance (R), and conductivity measured by the Tecpro Pork Quality Meter (PQM) were measured on the right side LM. At 24 h postmortem, WHC, pH, R, PQM, Hunter Color Lab values, and subjective quality scores were evaluated on the left LM. The WHC measurements were used to group carcasses into normal (n = 17) and abnormal (n = 8) categories. Mean pH and R at 45 and 90 min were different (P < .05) but pH at 24 h was not different between the normal and abnormal groups. Onset and completion of rigor were more rapid in carcasses with low WHC (P < .05). The PQM values were greater (P < .05) in the abnormal group at 90 min and 24 h postmortem. Excised muscle measurements of relative impedance (Z*) and phase (theta*) showed Z* and theta* increased more rapidly within the first 15 min postmortem (P < .1) for samples with abnormal WHC. However, one PSE carcass showed an immediate rapid decrease in Z* and theta*. Results suggest measurement of rate of change of impedance and phase angle before 90 min postmortem would be a better prediction of ultimate quality than absolute magnitude of impedance.

Alternative pork carcass evaluation techniques: I. Differences in predictions of value

Dissected and predicted wholesale and lean boneless values for 154 pork carcasses representing seven genotypes with substantial variation in carcass composition and percentage of lean were determined. Dissected carcass value was determined using a component pricing model, and four alternative models were specified to predict that value. The models included measurements from a ruler (RULER) and two carcass evaluation technologies, Hennessy probe (PROBE) and electromagnetic scanner (EMS1). A combination of the PROBE and EMS1 models (EMS2) was also used. For wholesale value, R2 were .40, .70, .59, and .74, and the RSD were 8.18, 5.77, 6.76, and 5.38 ($/100 kg of carcass value) for RULER, PROBE, EMS1, and EMS2, respectively. For lean boneless value, the R2 were .41, .73, .59, and .74, and the RSD were 8.34, 5.67, 6.99, and 5.51 ($/100 kg of carcass value) for RULER, PROBE, EMS1, and EMS2, respectively. The results indicate that a combination of probe and electromagnetic scanner measurements provided the best fit to dissected value.

Alternative pork carcass evaluation techniques: II. Statistical analysis of error attributable to sex, genotype, and weight

Carcasses of 154 hogs representing seven genotypes with substantial variation in carcass composition and percentage of lean were completely dissected and analyzed. Measurements from a ruler, Hennessy probe, and electromagnetic scanner were each used to predict wholesale and lean boneless carcass value. Error, defined as dissected value minus predicted value, due to the omission of sex, genotype, weight, and their interactions was estimated for each model. The errors were significantly different from zero for the models using ruler and electromagnetic scanning measurements separately (P < .01). Errors due to sex, genotype, weight, and their interactions were greatest for the less lean barrows. A combination of probe and electromagnetic scanner measurements resulted in the least error. The value of barrows with low percentage of lean was consistently overpredicted, whereas the value of leaner gilts was underpredicted for the models using ruler and electromagnetic scanning separately (P < .001).

Electromagnetic scanning of beef quarters to predict carcass and primal lean content

To study the use of electromagnetic scanning in prediction of lean content in beef carcasses and cuts, 100 beef cattle (60 steers and 40 heifers), representing a broad range in external fat thickness (.1 to 2.9 cm) and live weight (414 to 742 kg), were selected. Chilled right sides were divided into streamlined (foreshank, brisket, and ventral plate removed) forequarters (FQ) and full hindquarters (HQ) and scanned. Primal rounds, loins, ribs, and chucks were fabricated from the right side, scanned, and physically separated into lean, fat, and bone. Prediction equations for dissected lean content and percentage of lean included the peak of the electromagnetic scan response curve (obtained from scanning the HQ or FQ), length, temperature and weight of the scanned cut, and fat thickness at the 12th rib. Using the coefficient of determination, root mean square error, and Mallows' Cp statistic, the best model for each dependent variable (weight and percentage of lean) that included up to five independent variables was selected. Prediction equations for the HQ or FQ of steers accounted for 84 to 93% of the variation in lean weight of beef sides and quarters and 71 to 93% of primals. Sixty-one to 75% of the variation in percentage of lean in sides and quarters and 48 to 65% of primals was also explained. Similar results were obtained for heifer carcasses. Predicting percentage of lean in any scanned cut, rather than weight of lean, accounted for less of the variation. Weight and fat thickness contributed significantly when predicting percentage of lean.(ABSTRACT TRUNCATED AT 250 WORDS)