Rht12b, a widely used ancient allele of TaGA2oxA13, reduces plant height and enhances yield potential in wheat.

KEY MESSAGE: We identified a new wheat dwarfing allele Rht12b conferring reduced height and higher grain yield, pinpointed its causal variations, developed a breeding-applicable marker, and traced its origin and worldwide distribution. Plant height control is essential to optimize lodging resistance and yield gain in crops. RHT12 is a reduced height (Rht) locus that is identified in a mutationally induced dwarfing mutant and encodes a gibberellin 2-oxidase TaGA2oxA13. However, the artificial dwarfing allele is not used in wheat breeding due to excessive height reduction. Here, we confirmed a stable Rht locus, overlapping with RHT12, in a panel of wheat cultivars and its dwarfing allele reduced plant height by 5.4-8.2 cm, equivalent to Rht12b, a new allele of RHT12. We validated the effect of Rht12b on plant height in a bi-parent mapping population. Importantly, wheat cultivars carrying Rht12b had higher grain yield than those with the contrasting Rht12a allele. Rht12b conferred higher expression level of TaGA2oxA13. Transient activation assays defined SNP-390(C/A) in the promoter of TaGA2oxA13 as the causal variation. An efficient kompetitive allele-specific PCR marker was developed to diagnose Rht12b. Conjoint analysis showed that Rht12b plus the widely used Rht-D1b, Rht8 and Rht24b was the predominant Rht combination and conferred a moderate plant height in tested wheat cultivars. Evolutionary tracking uncovered that RHT12 locus arose from a tandem duplication event with Rht12b firstly appearing in wild emmer. The frequency of Rht12b was approximately 70% (700/1005) in a worldwide wheat panel and comparable to or higher than those of other widely used Rht genes, suggesting it had been subjected to positive selection. These findings not only identify a valuable Rht gene for wheat improvement but also develop a functionally diagnostic tool for marker-assisted breeding.

Fine mapping and characterization of a major QTL for plant height on chromosome 5A in wheat.

KEY MESSAGE: We precisely mapped QPH.caas-5AL for plant height in wheat, predicted candidate genes and confirmed genetic effects in a panel of wheat cultivars. Plant height is an important agronomic trait, and appropriately reduced height can improve yield potential and stability in wheat, usually combined with sufficient water and fertilizer. We previously detected a stable major-effect quantitative trait locus QPH.caas-5AL for plant height on chromosome 5A in a recombinant inbred line population of the cross 'Doumai × Shi 4185' using the wheat 90 K SNP assay. Here , QPH.caas-5AL was confirmed using new phenotypic data in additional environment and new-developed markers. We identified nine heterozygous recombinant plants for fine mapping of QPH.caas-5AL and developed 14 breeder-friendly kompetitive allele-specific PCR markers in the region of QPH.caas-5AL based on the genome re-sequencing data of parents. Phenotyping and genotyping analyses of secondary populations derived from the self-pollinated heterozygous recombinant plants delimited QPH.caas-5AL into an approximate 3.0 Mb physical region (521.0-524.0 Mb) according to the Chinese Spring reference genome. This region contains 45 annotated genes, and six of them were predicted as the candidates of QPH.caas-5AL based on genome and transcriptome sequencing analyses. We further validated that QPH.caas-5AL has significant effects on plant height but not yield component traits in a diverse panel of wheat cultivars; its dwarfing allele is frequently used in modern wheat cultivars. These findings lay a solid foundation for the map-based cloning of QPH.caas-5AL and also provide a breeding-applicable tool for its marker-assisted selection. Keymessage We precisely mapped QPH.caas-5AL for plant height in wheat, predicted candidate genes and confirmed genetic effects in a panel of wheat cultivars.

Genetic dissection of grain morphology and yield components in a wheat line with defective grain filling.

KEY MESSAGE: We identified stable QTL for grain morphology and yield component traits in a wheat defective grain filling line and validated genetic effects in a panel of cultivars using breeding-relevant markers. Grain filling capacity is essential for grain yield and appearance quality in cereal crops. Identification of genetic loci for grain filling is important for wheat improvement. However, there are few genetic studies on grain filling in wheat. Here, a defective grain filling (DGF) line wdgf1 characterized by shrunken grains was identified in a population derived from multi-round crosses involving nine parents and a recombinant inbreed line (RIL) population was generated from the cross between wdgf1 and a sister line with normal grains. We constructed a genetic map of the RIL population using the wheat 15K single nucleotide polymorphism chip and detected 25 stable quantitative trait loci (QTL) for grain morphology and yield components, including three for DGF, eleven for grain size, six for thousand grain weight, three for grain number per spike and two for spike number per m2. Among them, QDGF.caas-7A is co-located with QTGW.caas-7A and can explain 39.4-64.6% of the phenotypic variances, indicating that this QTL is a major locus controlling DGF. Sequencing and linkage mapping showed that TaSus2-2B and Rht-B1 were candidate genes for QTGW.caas-2B and the QTL cluster (QTGW.caas-4B, QGNS.caas-4B, and QSN.caas-4B), respectively. We developed kompetitive allele-specific PCR markers tightly linked to the stable QTL without corresponding to known yield-related genes, and validated their genetic effects in a diverse panel of wheat cultivars. These findings not only lay a solid foundation for genetic dissection underlying grain filling and yield formation, but also provide useful tools for marker-assisted breeding.

Efficient proteome-wide identification of transcription factors targeting Glu-1: A case study for functional validation of TaB3-2A1 in wheat.

High-molecular-weight glutenin subunits (HMW-GS), a major component of seed storage proteins (SSP) in wheat, largely determine processing quality. HMW-GS encoded by GLU-1 loci are mainly controlled at the transcriptional level by interactions between cis-elements and transcription factors (TFs). We previously identified a conserved cis-regulatory module CCRM1-1 as the most essential cis-element for Glu-1 endosperm-specific high expression. However, the TFs targeting CCRM1-1 remained unknown. Here, we built the first DNA pull-down plus liquid chromatography-mass spectrometry platform in wheat and identified 31 TFs interacting with CCRM1-1. TaB3-2A1 as proof of concept was confirmed to bind to CCRM1-1 by yeast one hybrid and electrophoretic mobility shift assays. Transactivation experiments demonstrated that TaB3-2A1 repressed CCRM1-1-driven transcription activity. TaB3-2A1 overexpression significantly reduced HMW-GS and other SSP, but enhanced starch content. Transcriptome analyses confirmed that enhanced expression of TaB3-2A1 down-regulated SSP genes and up-regulated starch synthesis-related genes, such as TaAGPL3, TaAGPS2, TaGBSSI, TaSUS1 and TaSUS5, suggesting that it is an integrator modulating the balance of carbon and nitrogen metabolism. TaB3-2A1 also had significant effects on agronomic traits, including heading date, plant height and grain weight. We identified two major haplotypes of TaB3-2A1 and found that TaB3-2A1-Hap1 conferred lower seed protein content, but higher starch content, plant height and grain weight than TaB3-2A1-Hap2 and was subjected to positive selection in a panel of elite wheat cultivars. These findings provide a high-efficiency tool to detect TFs binding to targeted promoters, considerable gene resources for dissecting regulatory mechanisms underlying Glu-1 expression, and a useful gene for wheat improvement.

Dissecting pleiotropic functions of the wheat Green Revolution gene Rht-B1b in plant morphogenesis and yield formation.

The utilization of reduced plant height genes Rht-B1b and Rht-D1b, encoding homeologous DELLA proteins, led to the wheat Green Revolution (GR). However, the specific functions of GR genes in yield determination and the underlying regulatory mechanisms remained unknown. Here, we validated that Rht-B1b, as a representative of GR genes, affects plant architecture and yield component traits. Upregulation of Rht-B1b reduced plant height, leaf size and grain weight, but increased tiller number, tiller angle, spike number per unit area, and grain number per spike. Dynamic investigations showed that Rht-B1b increased spike number by improving tillering initiation rather than outgrowth, and enhanced grain number by promoting floret fertility. Rht-B1b reduced plant height by reducing cell size in the internodes, and reduced grain size or weight by decreasing cell number in the pericarp. Transcriptome analyses uncovered that Rht-B1b regulates many homologs of previously reported key genes for given traits and several putative integrators for different traits. These findings specify the pleiotropic functions of Rht-B1b in improving yield and provide new insights into the regulatory mechanisms underlying plant morphogenesis and yield formation.

Fine mapping and characterization of a major QTL for grain weight on wheat chromosome arm 5DL.

KEY MESSAGE: We fine mapped QTL QTKW.caas-5DL for thousand kernel weight in wheat, predicted candidate genes and developed a breeding-applicable marker. Thousand kernel weight (TKW) is an important yield component trait in wheat, and identification of the underlying genetic loci is helpful for yield improvement. We previously identified a stable quantitative trait locus (QTL) QTKW.caas-5DL for TKW in a Doumai/Shi4185 recombinant inbred line (RIL) population. Here we performed fine mapping of QTKW.caas-5DL using secondary populations derived from 15 heterozygous recombinants and delimited the QTL to an approximate 3.9 Mb physical interval from 409.9 to 413.8 Mb according to the Chinese Spring (CS) reference genome. Analysis of genomic synteny showed that annotated genes in the physical interval had high collinearity among CS and eight other wheat genomes. Seven genes with sequence variation and/or differential expression between parents were predicted as candidates for QTKW.caas-5DL based on whole-genome resequencing and transcriptome assays. A kompetitive allele-specific PCR (KASP) marker for QTKW.caas-5DL was developed, and genotyping confirmed a significant association with TKW but not with other yield component traits in a panel of elite wheat cultivars. The superior allele of QTKW.caas-5DL was frequent in a panel of cultivars, suggesting that it had undergone positive selection. These findings not only lay a foundation for map-based cloning of QTKW.caas-5DL but also provide an efficient tool for marker-assisted selection.

CD8+ T cells and fatty acids orchestrate tumor ferroptosis and immunity via ACSL4.

Tumor cell intrinsic ferroptosis-initiating mechanisms are unknown. Here, we discover that T cell-derived interferon (IFN)γ in combination with arachidonic acid (AA) induces immunogenic tumor ferroptosis, serving as a mode of action for CD8+ T cell (CTL)-mediated tumor killing. Mechanistically, IFNγ stimulates ACSL4 and alters tumor cell lipid pattern, thereby increasing incorporations of AA into C16 and C18 acyl chain-containing phospholipids. Palmitoleic acid and oleic acid, two common C16 and C18 fatty acids in blood, promote ACSL4-dependent tumor ferroptosis induced by IFNγ plus AA. Moreover, tumor ACSL4 deficiency accelerates tumor progression. Low-dose AA enhances tumor ferroptosis and elevates spontaneous and immune checkpoint blockade (ICB)-induced anti-tumor immunity. Clinically, tumor ACSL4 correlates with T cell signatures and improved survival in ICB-treated cancer patients. Thus, IFNγ signaling paired with selective fatty acids is a natural tumor ferroptosis-promoting mechanism and a mode of action of CTLs. Targeting the ACSL4 pathway is a potential anti-cancer approach.

Molecular mapping and characterization of QBp.caas-3BL for black point resistance in wheat (Triticum aestivum L.).

KEY MESSAGE: We fine-mapped QBp.caas-3BL for black point resistance in an interval of 1.7 Mb containing five high-confidence annotated genes and developed a KASP marker suitable for selection of QBp.caas-3BL. Wheat black point, which occurs in most wheat-growing regions of the world, is detrimental to grain appearance, processing and nutrient quality. Mining and characterization of genetic loci for black point resistance are helpful for breeding resistant wheat cultivars. We previously identified a major QTL QBp.caas-3BL in a recombinant inbred line (RIL) population of Linmai 2/Zhong 892 across five environments. Here we confirmed the QTL in two additional environments. The genetic region of QBp.caas-3BL was enriched with newly developed markers. Using four sets of near isogenic lines, QBp.caas-3BL was narrowed down to a physical interval of approximately 1.7 Mb, including five annotated genes according to IWGSC reference genome. TraesCS3B02G404300, TraesCS3B02G404600 and TraesCS3B02G404700 were predicted as candidate genes based on the analyses of sequence polymorphisms and differential expression. We also converted a SNP of TraesCS3B02G404700 into a breeding-applicable KASP marker and verified its efficacy for marker-assisted breeding in a panel of germplasm. The findings not only lay a foundation for map-based cloning of QBp.caas-3BL but also provide a useful marker for selection of resistant cultivars genotypes in wheat breeding.

Non-functional GoFLA19s are responsible for the male sterility caused by hybrid breakdown in cotton (Gossypium spp.).

Hybrid breakdown (HB) functions as a common reproductive barrier and reduces hybrid fitness in many species, including cotton. However, the related genes and the underlying genetic mechanisms of HB in cotton remain unknown. Here, we found that the photosensitive genetic male sterile line CCRI9106 was a hybrid progeny of Gossypium hirsutum and Gossypium barbadense and probably a product of HB. Fine mapping with F2 s (CCRI9106 × G. hirsutum/G. barbadense lines) identified a pair of male sterility genes GoFLA19s (encoding fasciclin-like arabinogalactan family protein) located on chromosomes A12 and D12. Crucial variations occurring in the fasciclin-like domain and the arabinogalactan protein domain were predicted to cause the non-functionalization of GbFLA19-D and GhFLA19-A. CRISPR/Cas9-mediated knockout assay confirmed the effects of GhFLA19s on male sterility. Sequence alignment analyses showed that variations in GbFLA19-D and GhFLA19-A likely occurred after the formation of allotetraploid cotton species. GoFLA19s are specifically expressed in anthers and contribute to tapetal development, exine assembly, intine formation, and pollen grain maturation. RNA-sequencing and quantitative reverse transcriptase-polymerase chain reaction analyses illustrated that genes related to these biological processes were significantly downregulated in the mutant. Our research on male sterility genes, GoFLA19s, improves the understanding of the molecular characteristics and evolutionary significance of HB in interspecific hybrid breeding.

Stanniocalcin 1 is a phagocytosis checkpoint driving tumor immune resistance.

Immunotherapy induces durable clinical responses in a fraction of patients with cancer. However, therapeutic resistance poses a major challenge to current immunotherapies. Here, we identify that expression of tumor stanniocalcin 1 (STC1) correlates with immunotherapy efficacy and is negatively associated with patient survival across diverse cancer types. Gain- and loss-of-function experiments demonstrate that tumor STC1 supports tumor progression and enables tumor resistance to checkpoint blockade in murine tumor models. Mechanistically, tumor STC1 interacts with calreticulin (CRT), an "eat-me" signal, and minimizes CRT membrane exposure, thereby abrogating membrane CRT-directed phagocytosis by antigen-presenting cells (APCs), including macrophages and dendritic cells. Consequently, this impairs APC capacity of antigen presentation and T cell activation. Thus, tumor STC1 inhibits APC phagocytosis and contributes to tumor immune evasion and immunotherapy resistance. We suggest that STC1 is a previously unappreciated phagocytosis checkpoint and targeting STC1 and its interaction with CRT may sensitize to cancer immunotherapy.

Liver metastasis restrains immunotherapy efficacy via macrophage-mediated T cell elimination.

Metastasis is the primary cause of cancer mortality, and cancer frequently metastasizes to the liver. It is not clear whether liver immune tolerance mechanisms contribute to cancer outcomes. We report that liver metastases diminish immunotherapy efficacy systemically in patients and preclinical models. Patients with liver metastases derive limited benefit from immunotherapy independent of other established biomarkers of response. In multiple mouse models, we show that liver metastases siphon activated CD8+ T cells from systemic circulation. Within the liver, activated antigen-specific Fas+CD8+ T cells undergo apoptosis following their interaction with FasL+CD11b+F4/80+ monocyte-derived macrophages. Consequently, liver metastases create a systemic immune desert in preclinical models. Similarly, patients with liver metastases have reduced peripheral T cell numbers and diminished tumoral T cell diversity and function. In preclinical models, liver-directed radiotherapy eliminates immunosuppressive hepatic macrophages, increases hepatic T cell survival and reduces hepatic siphoning of T cells. Thus, liver metastases co-opt host peripheral tolerance mechanisms to cause acquired immunotherapy resistance through CD8+ T cell deletion, and the combination of liver-directed radiotherapy and immunotherapy could promote systemic antitumor immunity.

Cancer SLC43A2 alters T cell methionine metabolism and histone methylation.

Abnormal epigenetic patterns correlate with effector T cell malfunction in tumours1-4, but the cause of this link is unknown. Here we show that tumour cells disrupt methionine metabolism in CD8+ T cells, thereby lowering intracellular levels of methionine and the methyl donor S-adenosylmethionine (SAM) and resulting in loss of dimethylation at lysine 79 of histone H3 (H3K79me2). Loss of H3K79me2 led to low expression of STAT5 and impaired T cell immunity. Mechanistically, tumour cells avidly consumed methionine and outcompeted T cells for methionine by expressing high levels of the methionine transporter SLC43A2. Genetic and biochemical inhibition of tumour SLC43A2 restored H3K79me2 in T cells, thereby boosting spontaneous and checkpoint-induced tumour immunity. Moreover, methionine supplementation improved the expression of H3K79me2 and STAT5 in T cells, and this was accompanied by increased T cell immunity in tumour-bearing mice and patients with colon cancer. Clinically, tumour SLC43A2 correlated negatively with T cell histone methylation and functional gene signatures. Our results identify a mechanistic connection between methionine metabolism, histone patterns, and T cell immunity in the tumour microenvironment. Thus, cancer methionine consumption is an immune evasion mechanism, and targeting cancer methionine signalling may provide an immunotherapeutic approach.

Autophagic adaptation to oxidative stress alters peritoneal residential macrophage survival and ovarian cancer metastasis.

Tumor-associated macrophages (TAMs) affect cancer progression and therapy. Ovarian carcinoma often metastasizes to the peritoneal cavity. Here, we found 2 peritoneal macrophage subsets in mice bearing ID8 ovarian cancer based on T cell immunoglobulin and mucin domain containing 4 (Tim-4) expression. Tim-4+ TAMs were embryonically originated and locally sustained while Tim-4- TAMs were replenished from circulating monocytes. Tim-4+ TAMs, but not Tim-4- TAMs, promoted tumor growth in vivo. Relative to Tim-4- TAMs, Tim-4+ TAMs manifested high oxidative phosphorylation and adapted mitophagy to alleviate oxidative stress. High levels of arginase-1 in Tim-4+ TAMs contributed to potent mitophagy activities via weakened mTORC1 activation due to low arginine resultant from arginase-1-mediated metabolism. Furthermore, genetic deficiency of autophagy element FAK family-interacting protein of 200 kDa resulted in Tim-4+ TAM loss via ROS-mediated apoptosis and elevated T cell immunity and ID8 tumor inhibition in vivo. Moreover, human ovarian cancer-associated macrophages positive for complement receptor of the immunoglobulin superfamily (CRIg) were transcriptionally, metabolically, and functionally similar to murine Tim-4+ TAMs. Thus, targeting CRIg+ (Tim-4+) TAMs may potentially treat patients with ovarian cancer with peritoneal metastasis.

Author Correction: A next-generation tumor-targeting IL-2 preferentially promotes tumor-infiltrating CD8+ T-cell response and effective tumor control.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Dual-targeting nanoparticle vaccine elicits a therapeutic antibody response against chronic hepatitis B.

Chronic hepatitis B is caused by prolonged infection with the hepatitis B virus (HBV), which can substantially increase the risk of developing liver disease. Despite the development of preventive vaccines against HBV, a therapeutic vaccine inducing an effective antibody response still remains elusive. The preS1 domain of the large HBV surface protein is the major viral attachment site on hepatocytes and thus offers a therapeutic target; however, its poor immunogenicity limits clinical translation. Here, we design a ferritin nanoparticle vaccine that can deliver preS1 to specific myeloid cells, including SIGNR1+ dendritic cells (which activate T follicular helper cells) and lymphatic sinus-associated SIGNR1+ macrophages (which can activate B cells). This nanoparticle vaccine induces a high-level and persistent anti-preS1 response that results in efficient viral clearance and partial serological conversion in a chronic HBV mouse model, offering a promising translatable vaccination strategy for the functional cure of chronic hepatitis B.

A next-generation tumor-targeting IL-2 preferentially promotes tumor-infiltrating CD8+ T-cell response and effective tumor control.

While IL-2 can potently activate both NK and T cells, its short in vivo half-life, severe toxicity, and propensity to amplify Treg cells are major barriers that prevent IL-2 from being widely used for cancer therapy. In this study, we construct a recombinant IL-2 immunocytokine comprising a tumor-targeting antibody (Ab) and a super mutant IL-2 (sumIL-2) with decreased CD25 binding and increased CD122 binding. The Ab-sumIL2 significantly enhances antitumor activity through tumor targeting and specific binding to cytotoxic T lymphocytes (CTLs). We also observe that pre-existing CTLs within the tumor are sufficient and essential for sumIL-2 therapy. This next-generation IL-2 can also overcome targeted therapy-associated resistance. In addition, preoperative sumIL-2 treatment extends survival much longer than standard adjuvant therapy. Finally, Ab-sumIL2 overcomes resistance to immune checkpoint blockade through concurrent immunotherapies. Therefore, this next-generation IL-2 reduces toxicity while increasing TILs that potentiate combined cancer therapies.

Targeting IFNα to tumor by anti-PD-L1 creates feedforward antitumor responses to overcome checkpoint blockade resistance.

Many patients remain unresponsive to intensive PD-1/PD-L1 blockade therapy despite the presence of tumor-infiltrating lymphocytes. We propose that impaired innate sensing might limit the complete activation of tumor-specific T cells after PD-1/PD-L1 blockade. Local delivery of type I interferons (IFNs) restores antigen presentation, but upregulates PD-L1, dampening subsequent T-cell activation. Therefore, we armed anti-PD-L1 antibody with IFNα (IFNα-anti-PD-L1) to create feedforward responses. Here, we find that a synergistic effect is achieved to overcome both type I IFN and checkpoint blockade therapy resistance with the least side effects in advanced tumors. Intriguingly, PD-L1 expressed in either tumor cells or tumor-associated host cells is sufficient for fusion protein targeting. IFNα-anti-PD-L1 activates IFNAR signaling in host cells, but not in tumor cells to initiate T-cell reactivation. Our data suggest that a next-generation PD-L1 antibody armed with IFNα improves tumor targeting and antigen presentation, while countering innate or T-cell-driven PD-L1 upregulation within tumor.

Vaccines targeting preS1 domain overcome immune tolerance in hepatitis B virus carrier mice.

Strong tolerance to hepatitis B virus (HBV) surface antigens limits the therapeutic effect of the conventional hepatitis B surface antigen (HBsAg) vaccination in both preclinical animal models and patients with chronic hepatitis B (CHB) infection. In contrast, we observed that clinical CHB patients presented less immune tolerance to the preS1 domain of HBV large surface antigen. To study whether targeting the weak tolerance of the preS1 region could improve therapy gain, we explored vaccination with the long peptide of preS1 domain for HBV virions clearance. Our study showed that this preS1-polypeptide rather than HBsAg vaccination induced robust immune responses in HBV carrier mice. The anti-preS1 rapidly cleared HBV virions in vivo and blocked HBV infection to hepatocytes in vitro. Intriguingly, vaccination of preS1-polypeptide even reduced the tolerized status of HBsAg, opening a therapeutic window for the host to respond to the HBsAg vaccine. A sequential administration of antigenically distinct preS1-polypeptide and HBsAg vaccines in HBV carrier mice could finally induce HBsAg/hepatitis B surface antibody serological conversion and clear chronic HBV infection in carrier mice. CONCLUSION: These results suggest that preS1 can function as a therapeutic vaccine for the control of CHB. (Hepatology 2017;66:1067-1082).

Clearing Persistent Extracellular Antigen of Hepatitis B Virus: An Immunomodulatory Strategy To Reverse Tolerance for an Effective Therapeutic Vaccination.

Development of therapeutic vaccines/strategies to control chronic hepatitis B virus (HBV) infection has been challenging because of HBV-induced tolerance. In this study, we explored strategies for breaking tolerance and restoring the immune response to the HBV surface Ag in tolerant mice. We demonstrated that immune tolerance status is attributed to the level and duration of circulating HBsAg in HBV carrier models. Removal of circulating HBsAg by a monoclonal anti-HBsAg Ab in tolerant mice could gradually reduce tolerance and reestablish B cell and CD4(+) T cell responses to subsequent Engerix-B vaccination, producing protective IgG. Furthermore, HBsAg-specific CD8(+) T cells induced by the addition of a TLR agonist resulted in clearance of HBV in both serum and liver. Thus, generation of protective immunity can be achieved by clearing extracellular viral Ag with neutralizing Abs followed by vaccination.