Potential gene editing targets for developing haploid inducer stocks in rice and wheat with high haploid induction frequency

Doubled haploid (DH) breeding is a powerful technique to ensure global food security via accelerated crop improvement. DH can be produced in planta by employing haploid inducer stock (HIS). Widely used HIS in maize is known to be governed by ZmPLA, ZmDMP, ZmPLD3, and ZmPOD65 genes. To develop such HIS in rice and wheat, we have identified putative orthologs of these genes using in silico approaches. The OsPLD1; TaPLD1, and OsPOD6; TaPOD8 were identified as putative orthologs of ZmPLD3 and ZmPOD65 in rice and wheat, respectively. Despite being closely related to ZmPLD3, OsPLD1 and TaPLD1 have shown higher anther-specific expression. Similarly, OsPOD6 and TaPOD8 were found closely related to the ZmPOD65 based on both phylogenetic and expression analysis. However, unlike ZmPLD3 and ZmPOD65, two ZmDMP orthologs have been found for each crop. OsDMP1 and OsDMP2 in rice and TaDMP3 and TaDMP13 in wheat have shown similarity to ZmDMP in terms of both sequence and expression pattern. Furthermore, analogs to maize DMP proteins, these genes possess four transmembrane helices making them best suited to be regarded as ZmDMP orthologs. Modifying these predicted orthologous genes by CRISPR/Cas9-based genome editing can produce a highly efficient HIS in both rice and wheat. Besides revealing the genetic mechanism of haploid induction, the development of HIS would advance the genetic improvement of these crops.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03857-9.

PHEOCHROMOCYTOMA, THE GREAT MASQUERADER, PRESENTING AS REVERSIBLE CARDIOMYOPATHY: PRIMUM NON NOCERE

Background

Pheochromocytoma, the great masquerader, can have a varied spectrum of clinical manifestations. It can often cause a diagnostic challenge despite the availability of modern investigation modalities.

Case

We present the case of a 38-year-old male who presented with uncontrolled hypertension for the past 10 years and heart failure for one year. The diagnosis of pheochromocytoma was missed in the initial setting, leading to a biopsy of the retroperitoneal mass. Fortunately, the patient survived the procedure. Subsequently, with the involvement of a multi-disciplinary team, he was optimized for surgery under strict cardiac monitoring. After the complete excision of the tumour, he showed significant improvement not only in his clinical symptoms but also in his cardiac status.

Conclusions

This case emphasizes the age-old medical phrase of 'Primum non nocere or first, do no harm'. Any invasive procedure in a pheochromocytoma can lead to a massive release of catecholamines causing a hypertensive crisis, pulmonary oedema, and even cardiac arrest. Any young patient presenting with hypertension or heart failure should be investigated for secondary causes. Cardiomyopathy due to pheochromocytoma is because of catecholamine overload and usually reverses or improves after curative surgery.

Unlocking the hidden variation from wild repository for accelerating genetic gain in legumes

The fluctuating climates, rising human population, and deteriorating arable lands necessitate sustainable crops to fulfil global food requirements. In the countryside, legumes with intriguing but enigmatic nitrogen-fixing abilities and thriving in harsh climatic conditions promise future food security. However, breaking the yield plateau and achieving higher genetic gain are the unsolved problems of legume improvement. Present study gives emphasis on 15 important legume crops, i.e., chickpea, pigeonpea, soybean, groundnut, lentil, common bean, faba bean, cowpea, lupin, pea, green gram, back gram, horse gram, moth bean, rice bean, and some forage legumes. We have given an overview of the world and India's area, production, and productivity trends for all legume crops from 1961 to 2020. Our review article investigates the importance of gene pools and wild relatives in broadening the genetic base of legumes through pre-breeding and alien gene introgression. We have also discussed the importance of integrating genomics, phenomics, speed breeding, genetic engineering and genome editing tools in legume improvement programmes. Overall, legume breeding may undergo a paradigm shift once genomics and conventional breeding are integrated in the near future.

How I treat biliary tract cancer

Management of biliary tract cancers (BTCs) is rapidly evolving. Curative management relies on surgical resection followed by adjuvant capecitabine for cholangiocarcinoma and gallbladder cancers. Unfortunately relapse rate remains high, and better adjuvant strategies are urgently required. A majority of patients are diagnosed with advanced disease, when chemotherapy with cisplatin and gemcitabine followed by second-line 5-FU and oxaliplatin /irinotecan is the cornerstone of treatment for most patients in the absence of targetable alterations. Targeted therapies, including therapies for tumours with fibroblast growth factor receptor-2 (FGFR-2) fusions, isocitrate dehydrogenase-1 (IDH-1) mutations, B-Raf proto-oncogene serine/threonine kinase (BRAF) V600E mutations, neurotrophic tyrosine receptor kinase (NTRK) fusions, Human epidermal growth factor-2 (HER-2) amplifications, and/or microsatellite instability are rapidly changing the treatment paradigm for many patients with advanced BTC, especially for patients with intrahepatic cholangiocarcinoma. Because of this, molecular profiling should be considered early on patients pathway to allow adequate planning of therapy. Ongoing research is likely to clarify the role of immunotherapy, liver-directed therapy, and liver transplant for BTCs in the future.

Phase I, first-in-human study of futibatinib, a highly selective, irreversible FGFR1-4 inhibitor in patients with advanced solid tumors

BACKGROUND

Futibatinib is an oral, irreversible, highly selective fibroblast growth factor receptor (FGFR)1-4 inhibitor with potent preclinical activity against tumors harboring FGFR aberrations. This first-in-human, phase I dose-escalation trial (NCT02052778) evaluates the safety and pharmacokinetics/pharmacodynamics of futibatinib in advanced solid tumors.

PATIENTS AND METHODS

Following a standard 3+3 dose-escalation design, eligible patients with advanced solid tumors refractory to standard therapies received 8-200 mg futibatinib three times a week (t.i.w.) or 4-24 mg once daily (q.d.).

RESULTS

A total of 86 patients were enrolled in the nine t.i.w. (n = 42) and five q.d. cohorts (n = 44); 71 patients (83%) had tumors harboring FGF/FGFR aberrations. Three of nine patients in the 24-mg q.d. cohort experienced dose-limiting toxicities, including grade 3 increases in alanine transaminase, aspartate transaminase, and blood bilirubin (n = 1 each). The maximum tolerated dose (MTD) was determined to be 20 mg q.d.; no MTD was defined for the t.i.w. schedule. Across cohorts (n = 86), the most common treatment-emergent adverse events (TEAEs) were hyperphosphatemia (59%), diarrhea (37%), and constipation (34%); 48% experienced grade 3 TEAEs. TEAEs led to dose interruptions, dose reductions, and treatment discontinuations in 55%, 14%, and 3% of patients, respectively. Pharmacokinetics were dose proportional across all q.d. doses but not all t.i.w. doses evaluated, with saturation observed between 80 and 200 mg t.i.w. Serum phosphorus increased dose dependently with futibatinib on both schedules, but a stronger exposure-response relationship was observed with q.d. dosing, supporting 20 mg q.d. as the recommended phase II dose (RP2D). Overall, partial responses were observed in five patients [FGFR2 fusion-positive intrahepatic cholangiocarcinoma (n = 3) and FGFR1-mutant primary brain tumor (n = 2)], and stable disease in 41 (48%).

CONCLUSIONS

Futibatinib treatment resulted in manageable safety, pharmacodynamic activity, and preliminary responses in patients with advanced solid tumors. The results of this phase I dose-escalation trial support 20 mg q.d. futibatinib as the RP2D.

CLINICAL TRIAL REGISTRATION

FOENIX-101 (ClinicalTrials.gov, NCT02052778).

Phase II study of gemcitabine, oxaliplatin in combination with panitumumab in KRAS wild-type unresectable or metastatic biliary tract and gallbladder cancer

BACKGROUND

Current data suggest that platinum-based combination therapy is the standard first-line treatment for biliary tract cancer. EGFR inhibition has proven beneficial across a number of gastrointestinal malignancies; and has shown specific advantages among KRAS wild-type genetic subtypes of colon cancer. We report the combination of panitumumab with gemcitabine (GEM) and oxaliplatin (OX) as first-line therapy for KRAS wild-type biliary tract cancer.

METHODS

Patients with histologically confirmed, previously untreated, unresectable or metastatic KRAS wild-type biliary tract or gallbladder adenocarcinoma with ECOG performance status 0-2 were treated with panitumumab 6 mg kg(-1), GEM 1000 mg m(-2) (10 mg m(-2) min(-1)) and OX 85 mg m(-2) on days 1 and 15 of each 28-day cycle. The primary objective was to determine the objective response rate by RECIST criteria v.1.1. Secondary objectives were to evaluate toxicity, progression-free survival (PFS), and overall survival.

RESULTS

Thirty-one patients received at least one cycle of treatment across three institutions, 28 had measurable disease. Response rate was 45% and disease control rate was 90%. Median PFS was 10.6 months (95% CI 5-24 months) and median overall survival 20.3 months (95% CI 9-25 months). The most common grade 3/4 adverse events were anaemia 26%, leukopenia 23%, fatigue 23%, neuropathy 16% and rash 10%.

CONCLUSIONS

The combination of gemcitabine, oxaliplatin and panitumumab in KRAS wild type metastatic biliary tract cancer showed encouraging efficacy, additional efforts of genetic stratification and targeted therapy is warranted in biliary tract cancer.

Comparison of 1- and 2-dimensional measurements with volumetric measurements for evaluation of change in tumor size

3563

Background: Change in tumor size is commonly used as a surrogate endpoint for clinical outcome. Measurement of tumor volume, the gold standard for determining tumor size, is not clinically practical. The 2 most commonly used measurements of tumor size ie, longest diameter in axial plane (LD, used in RECIST) and cross product (CP) of LD and the longest perpendicular dimension in axial plane (used in WHO), are surrogates for tumor volume and assume simple tumor geometry. Since most tumors grow and regress irregularly, we determined which of these measurements most accurately reflects change in tumor volume by comparing change in tumor volume calculated using LD or CP with change in measured tumor volume. Methods: Computed tomography (CT) scans of the chest, abdomen, and pelvis were acquired at baseline and 8-week intervals during treatment in 22 patients (pts) enrolled in 2 first-in-human (FIH) clinical trials. CT scans were analyzed by a central reader to obtain LD, CP, and tumor volume. LD (assuming spherical tumor geometry) or CP (assuming spherical or elliptical tumor geometry) was used to calculate volume. The mean bias (μ: mean difference between measured and calculated percent change in tumor volume from baseline [%ΔVol]) and limits of agreement (μ ± 2s [s = standard deviation of difference]) from Bland-Altman analyses (used for assessing agreement between 2 measurement methods) were used for comparisons between measured and calculated %ΔVol. A nested effects model (tumor lesions considered as nested within pts) was used to test significance of differences between measured and calculated %ΔVol. Results: Bland-Altman analyses showed that μ ± 2s was -5% ± 70% for LD, 5% ± 38% for CP (spherical), and 7% ± 33% for CP (elliptical). Nested analyses indicated consistent results with an observed significant difference (p-value = 0.02) between measured and calculated %ΔVol using LD and non-significant differences (p-values = 0.28 and 0.05) using CP (assuming elliptical and spherical geometry respectively). Conclusions: In this diverse FIH population, 2-dimensional tumor measurements (using CP) are better than 1-dimensional tumor measurements (using LD) in representing changes in tumor volume and should decrease noise in the measurement of treatment response.

No significant financial relationships to disclose.

First-in-human study of AMG 655, a pro-apoptotic TRAIL receptor-2 agonist, in adult patients with advanced solid tumors

3534

Introduction: AMG 655 is a fully human monoclonal agonist antibody that binds human TRAIL receptor 2 (TR-2/DR5), activates caspases, and induces apoptosis in sensitive tumor cells. The primary objectives of this ongoing first-in-human study were to assess the safety, tolerability, and pharmacokinetics (PK) of AMG 655 in patients (pts) with advanced solid tumors. Methods: Three to 9 pts were enrolled into 1 of 5 sequential dose cohorts (0.3, 1, 3, 10, or 20 mg/kg) of AMG 655 administered intravenously Q2W. No AMG 655 was administered on day 43 to allow assessment of terminal PK parameters. RECIST and FDG-PET were analyzed by central radiology. Pts remained on study until tumor progression or unacceptable toxicities occurred. Results: As of October 19, 2006, 16 pts (4 in the 10 mg/kg cohort; 3 in each of the other cohorts) had received = 1 dose of AMG 655; 12 pts were men, mean (SD) age was 53 (±8.9) years. No DLTs or AMG 655-related serious AEs were reported. The MTD was not reached. Nine pts reported AMG 655-related AEs. Treatment-related AEs in 3 or more pts were: pyrexia (4 pts), fatigue (3 pts), and hypomagnesaemia (3 pts). Fatigue and elevated serum lipase were the only grade 3 or higher AMG 655-related AEs and both occurred in the same pt (0.3-mg/kg cohort). No anti-AMG 655 antibodies were detected. PK data were available from dose cohorts 1 to 3 (0.3, 1, and 3 mg/kg); AMG 655 demonstrated dose-linear kinetics with a half-life of ∼10 days. Tumor- response data were available for 13 pts. Partial response was observed in 1 pt with non-small cell lung cancer (NSCLC) who experienced a 46% reduction in tumor volume by RECIST and remains on study after 48 weeks. Stable disease was reported in 4 pts (range 6 to 35 weeks), and progressive disease in 8 pts. One pt with colorectal cancer and stable disease demonstrated a metabolic partial response with a 34% reduction in maximum standardized uptake value (SUVmax). Conclusions: AMG 655 administered up to 20 mg/kg Q2W appeared to be well tolerated in these pts. The anti-tumor activity of AMG 655 was confirmed with observation of a partial response in NSCLC and a metabolic partial response in colorectal cancer. Further studies evaluating AMG 655 in combination with chemotherapy and targeted agents are warranted.

No significant financial relationships to disclose.

Status of geriatric oncology in India: A national multicentric survey of oncology professionals

16035

Background: Elderly cancer patients are underrepresented in cancer services utilization and clinical research in India. National data on providers’ knowledge, attitude and practices with regard to elderly cancer patients is sparse and is urgently required to address needs of this vulnerable and growing population. Methods: A self administered questionnaire was mailed to nationally representative sample of practicing oncologists all over India. 112 Oncologists (Medical Oncologists-51%; Radiation Oncologists-25%; Surgical Oncologists-20%; allied fields-4%) responded out of 250 mailed Questionnaires. Results: A designated Geriatric Oncology unit is in existence in very few (<5%) centers. Majority (51%) considered patients with chronological age of >60 years as elderly for India. Although 75% of elderly patients receive some therapy, only 50% of potentially curable patients and a similar percentage of potentially incurable patients receive standard of care. Also, 50% patients require modification in their treatment and only two-third of treated patients complete therapy. The existent barriers to treatment included poor performance status (53%), advanced stage (16%), and co-morbidities (15%). Only 51% Oncologists always discussed and 28% always enrolled elderly patients in clinical trials. Standard of care and evidence based recommendations for elderly patients were felt to be lacking by 49% and 92% of respondents respectively. The need of separate trials for elderly and a separate discipline of Geriatric Oncology was voiced by 93% and 89% of respondents respectively. Major differences in treatment practice between medical oncologists and non medical oncologists are shown in table . Conclusions: Treatment practices and accrual of elderly cancer patients in clinical trials in India is far from optimal. Formation of a National Geriatric Oncology society and creation of designated Geriatric oncology services at key centers may enhance the understanding and clinical care of this population.

[Table: see text]

No significant financial relationships to disclose.

Results of chemotherapy (CT) based protocol for treatment of retinoblastoma (RB)

9068

Background: One the main reasons for delayed presentation of children with RB in India is non acceptance of enucleation. CT is being increasingly utilized as primary treatment of RB to reduce the tumor volume and thus avoid enucleation and/or external beam radiation (EBRT) in early stage disease and reduce the risk of relapse in advanced stage disease. Methods: This retrospective (from 1996 to 2001) study involved 62 Patients (pts) (30 were bilateral) who received CT consisting of monthly cycles of carboplatin, etoposide, vincristine and cyclophosphomide. Pts with stage I disease, were started on CT alone, whereas most of the other pts were also started on concurrent EBRT (50Gy). Where indicated, pts also received local therapy, usually cryotherapy & EBRT. Eyes which did not show response or had stable disease, were advised enucleation. Results: Majority of pts had Reese-Ellsworth groups IV-V (74.1%). 17 pts had Stg I, 22 Stg II, 17 Stg III & 6 Stg IV disease (St Jude’s). All pts received CT (median 12 cycles). Out of 92 eyes only 79 were evaluable (13 were already enucleated).The response rate was 73.2% (51.8% CR or near CR); 12.9% had progressive disease. 47 Pts (74%) received RT. Only 23 pts received focal treatment (Cryotherapy 15, laser 3, combination 5). Vision was present in 38 eyes (48.1%) at presentation. 26 eyes (68.4%) were finally saved with useful vision. 20 pts had recurrence. 18 have died (17 died of disease, 1 treatment related sepsis). In those following up in the clinic, survival is 77% for stage I; 78.5% for stage II; 41.6% for stage III. All stage IV pts have died except 1 with nodal disease. Conclusions: CT has a role in the management of RB, however unless it is coupled with good focal therapy the results are poor as shown here. Also longer follow-ups are required because of late recurrences. This data highlights that in developing countries the social reasons complicate patient treatment & compliance. Further efforts are needed to spread awareness of this disease so that patients are diagnosed and treated in earlier stages so as to improve the outcomes.

No significant financial relationships to disclose.

Automatic Segmentation of Intra-treatment CT Images for Adaptive Radiation Therapy of the Prostate

We have been developing an approach for automatically quantifying organ motion for adaptive radiation therapy of the prostate. Our approach is based on deformable image registration, which makes it possible to establish a correspondence between points in images taken on different days. This correspondence can be used to study organ motion and to accumulate inter-fraction dose. In prostate images, however, the presence of bowel gas can cause significant correspondence errors. To account for this problem, we have developed a novel method that combines large deformation image registration with a bowel gas segmentation and deflation algorithm. In this paper, we describe our approach and present a study of its accuracy for adaptive radiation therapy of the prostate. All experiments are carried out on 3-dimensional CT images.

Discrete analysis of plasma oxalate with alkylamine glass bound sorghum oxalate oxidase and horseradish peroxidase

We have reported a simple method of determination of plasma oxalate using a Cl(-) and NO(3)(-) insensitive oxalate oxidase purified from grain sorghum leaf and commercially available peroxidase from horseradish [Pundir et al., Ind. J. Biochem. Biophys., 35 (1998) 120-122]. The present report describes the immobilization of both the enzymes onto alkylamine glass, their kinetic properties and application for discrete analysis of plasma oxalate. In the analytic method, H(2)O(2) generated from plasma oxalate by immobilized oxalate oxidase is measured colorimetrically at 520 nm by oxidative coupling with 4-aminophenazone, and phenol catalyzed by immobilized peroxidase. The minimum detection limit of the method is 2.5 micromol/l. Analytic recovery of added oxalate in plasma was 89. 5+/-4.1% (mean+/-S.D.). The within and between day CV for plasma oxalate measurement were <9.37 and <11.0%, respectively. The normal range of plasma oxalate as measured by the present method was 3.6 to 5.7 micromol/l. The method is not only free from interference by plasma Cl(-) and NO(3)(-) but also provides the reuse of glass beads and thus reduces the cost of analysis for routine.

Immobilization of sorghum leaf oxalate oxidase onto alkylamine and arylamine glass

An oxalate oxidase (EC 1.2.3.4) purified from grain sorghum leaves was immobilized onto alkylamine and arylamine glass beads through glutaraldehyde coupling and diazotization with a conjugation yield of 10.8 mg/g support and 9.2 mg/g support, respectively. The enzyme retained 67.5% and 34.1% of its initial specific activity after immobilization onto alkylamine and arylamine glass, respectively. The enzyme exhibited an increase in optimum pH, temperature for maximum activity, energy of activation (Ea) and time for linearity but decrease in thermal stability at 60 degrees C after immobilization on both types of beads. The K(m) value for oxalate was increased by 9- to 10-fold but Vmax remained unaltered after immobilization. Both alkyl and arylamine glass bound enzyme was unaffected by physiological concentrations of Cl- and NO3-. The analytic importance of this work is demonstrated.