BDL-SP: A Bio-inspired DL model for the identification of altered Signaling Pathways in Multiple Myeloma using WES data

Identification of the genomic features responsible for the progression of Multiple Myeloma (MM) cancer from its precancerous stage MGUS can improve the understanding of the disease pathogenesis and, in devising suitable preventive and treatment measures. We have designed an innovative AI-based model, namely, the Bio-inspired Deep Learning architecture for the identification of altered Signaling Pathways (BDL-SP) to discover pivotal genomic biomarkers that can potentially distinguish MM from MGUS. The proposed BDL-SP model comprehends gene-gene interactions using the PPI network and analyzes genomic features using a deep learning (DL) architecture to identify significantly altered genes and signaling pathways in MM and MGUS. For this, whole exome sequencing data of 1174 MM and 61 MGUS patients were analyzed. In the quantitative benchmarking with the other popular machine learning models, BDL-SP performed almost similar to the two other best performing predictive ML models of Random Forest and CatBoost. However, an extensive post-hoc explainability analysis, capturing the application specific nuances, clearly established the significance of the BDL-SP model. This analysis revealed that BDL-SP identified a maximum number of previously reported oncogenes, tumor-suppressor genes, and actionable genes of high relevance in MM as the top significantly altered genes. Further, the post-hoc analysis revealed a significant contribution of the total number of single nucleotide variants (SNVs) and genomic features associated with synonymous SNVs in disease stage classification. Finally, the pathway enrichment analysis of the top significantly altered genes showed that many cancer pathways are selectively and significantly dysregulated in MM compared to its precursor stage of MGUS, while a few that lost their significance with disease progression from MGUS to MM were actually related to the other disease types. These observations may pave the way for appropriate therapeutic interventions to halt the progression to overt MM in the future.

A Unified Computational Framework for a Robust, Reliable, and Reproducible Identification of Novel miRNAs From the RNA Sequencing Data

In eukaryotic cells, miRNAs regulate a plethora of cellular functionalities ranging from cellular metabolisms, and development to the regulation of biological networks and pathways, both under homeostatic and pathological states like cancer.Despite their immense importance as key regulators of cellular processes, accurate and reliable estimation of miRNAs using Next Generation Sequencing is challenging, largely due to the limited availability of robust computational tools/methods/pipelines. Here, we introduce miRPipe, an end-to-end computational framework for the identification, characterization, and expression estimation of small RNAs, including the known and novel miRNAs and previously annotated pi-RNAs from small-RNA sequencing profiles. Our workflow detects unique novel miRNAs by incorporating the sequence information of seed and non-seed regions, concomitant with clustering analysis. This approach allows reliable and reproducible detection of unique novel miRNAs and functionally same miRNAs (paralogues). We validated the performance of miRPipe with the available state-of-the-art pipelines using both synthetic datasets generated using the newly developed miRSim tool and three cancer datasets (Chronic Lymphocytic Leukemia, Lung cancer, and breast cancer). In the experiment over the synthetic dataset, miRPipe is observed to outperform the existing state-of-the-art pipelines (accuracy: 95.23% and F1-score: 94.17%). Analysis on all the three cancer datasets shows that miRPipe is able to extract more number of known dysregulated miRNAs or piRNAs from the datasets as compared to the existing pipelines.

Desidustat in Anemia due to Dialysis-Dependent Chronic Kidney Disease: A Phase 3 Study (DREAM-D)

Background

A phase 3 study to assess the efficacy and safety of the desidustat, an oral hypoxia-inducible factor prolyl hydroxylase inhibitor, against the epoetin alfa for the treatment of anemia in patients with chronic kidney disease (CKD) with dialysis dependency.

Methods

DREAM-D was a phase 3, multicenter, open-label, randomized, active-controlled clinical study conducted across 38 centers in India. A total of 392 patients with clinical diagnosis of anemia due to CKD with dialysis need (Erythrocyte Stimulating Agent [ESA] naïve or prior ESA users) and with baseline hemoglobin levels of 8.0–11.0 g/dL (inclusive) were randomized in a 1:1 ratio to receive either desidustat oral tablets (thrice a week) or epoetin alfa subcutaneous injection for 24 weeks to maintain a hemoglobin level of 10–12 g/dL. The primary endpoint was to assess the change in the hemoglobin level between the desidustat and the epoetin alfa groups from the baseline to evaluation period week 16–24. The key secondary efficacy endpoint was the number of patients with hemoglobin response.

Results

The least square mean (standard error) change in hemoglobin from the baseline to week 16–24 was 0.95 (0.09) g/dL in the desidustat group and 0.80 (0.09) g/dL in the epoetin alfa group (difference: 0.14 [0.14] g/dL; 95% confidence interval: −0.1304, 0.4202), which met the prespecified noninferiority margin. The number of hemoglobin responders was significantly higher in the desidustat group (106 [59.22%]) when compared to the epoetin alfa group (89 [48.37%]) (p = 0.0382). The safety profile of the desidustat oral tablet was comparable with the epoetin alfa injection. There were no new risks or no increased risks seen with the use of desidustat compared to epoetin alfa.

Conclusion

In this study, desidustat was found to be noninferior to epoetin in the treatment of anemia in CKD patients on dialysis and it was well-tolerated.

Clinical Trial Registry Identifier

CTRI/2019/12/022312 (India).

Desidustat in Anemia due to Non-Dialysis-Dependent Chronic Kidney Disease: A Phase 3 Study (DREAM-ND)

BACKGROUND

Desidustat, an oral hypoxia-inducible factor prolyl hydroxylase inhibitor, is being developed to treat anemia in patients with chronic kidney disease (CKD) without dialysis dependency.

METHODS

In total, 588 patients with a clinical diagnosis of anemia due to CKD without dialysis need and with baseline hemoglobin of 7.0-10.0 g/dL (inclusive) were randomized in a 1:1 ratio to receive either desidustat 100 mg oral tablets thrice a week for 24 weeks or biosimilar darbepoetin subcutaneous injection 0.75 μg/kg once in 2 weeks for 24 weeks. The primary outcome was the change from baseline in hemoglobin to evaluation period of Weeks 16-24. Key secondary outcomes included the number of patients with hemoglobin response, changes in the hepcidin levels, changes in the vascular endothelial growth factor (VEGF) levels, and changes in the lipid and lipoprotein profiles.

RESULTS

Hemoglobin change from baseline to Weeks 16-24 was 1.95 g/dL in the desidustat group and 1.83 g/dL in the darbepoetin group (difference: 0.11 g/dL; 95% CI: -0.12, 0.34), which met prespecified non-inferiority margin (-0.75 g/dL). The hemoglobin responders were significantly higher (p = 0.0181) in the desidustat group (196 [77.78%]) compared to the darbepoetin group (176 [68.48%]). The difference of change in hepcidin from baseline to Week 12 and Week 24 (p = 0.0032 at Week 12, p = 0.0016 at Week 24) and the difference of change in low-density lipoprotein from baseline to Week 24 (p value = 0.0269) between the two groups was statistically significant. The difference of change from baseline in VEGF to Weeks 12 and 24 between the two groups was not statistically significant.

CONCLUSION

Desidustat is non-inferior to darbepoetin in the treatment of anemia due to non-dialysis dependent CKD and it is well-tolerated.

Characterizing the mutational landscape of MM and its precursor MGUS

Mutational Signatures and Tumor mutational burden (TMB) have emerged as prognostic biomarkers in cancer genomics. However, the association of TMB with overall survival (OS) is still unknown in newly diagnosed multiple myeloma (NDMM) patients. Further, the change in the mutational spectrum involving both synonymous and non-synonymous mutations as MGUS progresses to MM is unexplored. This study addresses both these aspects via extensive evaluation of the mutations in MGUS and NDMM. WES data of 1018 NDMM patients and 61 MGUS patients collected from three different global regions were analyzed in this study. Single base substitutions, mutational signatures and TMB were inferred from the variants identified in MGUS and MM patients. The cutoff value for TMB was estimated to divide patients into low TMB and high TMB (hypermutators) groups. This study finds a change in the mutational spectrum with a statistically significant increase from MGUS to MM. There was a statistically significant increase in the frequency of all the three categories of variants, non-synonymous (NS), synonymous (SYN), and others (OTH), from MGUS to MM (P<0.05). However, there was a statistically significant rise in the TMB values for TMB_NS and TMB_SYN only. We also observed that 3' and 5'UTR mutations were more frequent in MM and might be responsible for driving MGUS to MM via regulatory binding sites. NDMM patients were also examined separately along with their survival outcomes. The frequency of hypermutators was low in MM with poor OS and PFS outcome. We observed a statistically significant rise in the frequency of C>A and C>T substitutions and a statistically significant decline in T>G substitutions in the MM patients with poor outcomes. Additionally, there was a statistically significant increase in the TMB of the patients with poor outcome compared to patients with a superior outcome. A statistically significant association between the APOBEC activity and poor overall survival in MM was discovered. These findings have potential clinical relevance and can assist in designing risk-adapted therapies to inhibit the progression of MGUS to MM and prolong the overall survival in high-risk MM patients.

Role of Endovascular Treatment in Dysfunctional Hemodialysis Fistulae: A Single Center Experience

Introduction

Arteriovenous fistulas (AVFs) are the preferred route of hemodialysis in end-stage renal disease. However, recurrent patency loss is an obstacle in long-term maintenance. Endovascular treatments may provide a durable option for prolongation of patency in AVFs.

Methods

Retrospective observational study was done on 46 patients with AVF for hemodialysis in the Department of Diagnostic and Interventional Radiology for a period of 1 year from September 2020 to August 2021. The characters of dysfunctional fistulas and results of various interventional procedures were assessed for technical and clinical success rates. Short-term follow-up records of patients were assessed for post-intervention primary patency (PIPP) and post-intervention assisted primary patency (PIAPP) of various procedures.

Results

The most successful outcomes post intervention were seen in radio-cephalic fistulas formed more than 1 year ago with juxta-anastomotic narrowing. The overall technical success rate was 89.13% with a PIPP of 78.26% and a PIAPP of 82.60% at 3 months. PTA had better technical success rates (88.23%) as compared to dysfunctional segments with thrombosis that underwent angioplasty and thromboaspiration (84.2%). Central venous stenosis undergoing PTA and stenting had a 100% success rate. At 3 months follow-up, PIPP was better among the angioplasty plus thromboaspiration group (73.7%), while PIAPP rate was better in the angioplasty subgroup at 82.35%.

Conclusion

Endovascular intervention is the first-line treatment in dysfunctional AVFs attributable to the multitude of options available, all of which have comparable outcomes, high success rates, and notable short-term patency.

Predictors of Renal Recovery among Patients of Obstructive Urolithiasis with Renal FailureA Prospective Observational Study

Introduction: Timely intervention in patients of obstructive uropathy secondary to renal and /or ureteric stones can reduce the morbidity and mortality in such patients. Aim: To determine the factors predicting recovery in patients of urinary stones and obstructive uropathy. Materials and Methods: This prospective observational study was conducted at Shri Mahant Inderesh Hospital, Dehradun, Uttrakhand, India, between December 2018 and June 2020. All patients with renal failure (serum creatinine >1.5 mg/dL) secondary to urinary stones presenting to the Emergency Department were included in the study. Baseline demographic data, clinical, haematological, biochemical and microbiological parameters were recorded at presentation and after Double J Stent (DJS) insertion at postintervention day 1, 3 and 7. Total 40 patients were divided into two groups i.e, recovered (n=25) and non recovered (n=15) groups. Receiver Operating Characteristic (ROC) curves was used to obtain optimal threshold duration of illness, the values of serum creatinine, serum urea, haemoglobin and serum potassium, and time to nadir creatinine for predicting renal recovery. The graphs were made using both Microsoft excel and SPSS software. Results: Out of total 40 pateints, 29 were males and 11 were females. The mean duration of symptoms in the recovered and non recovered groups was 4.64 and 15.53 days, respectively (p-value=0.001). Thirteen out of 15 patients (86.6%) in the non recovered group and 10 out of 25 (40%) in the recovered group had pre-existing co-morbidities (p-value=0.004). Postobstructive diuresis was present in 84% patients in the recovered and 46.6% in the non recovered group (p-value=0.016). The nadir serum creatinine level was 1.26 mg/dL in recovered as compared to 6.08 mg/dL in the non recovered patients (p-value=0.001). The ROC curves were plotted for various parameters in order to find the prognostic accuracy in predicting recovery. The best criteria were symptom duration ≤6 days, serum creatinine at presentation ≤6.2 mg/dL, serum potassium ≤5.5 mg/dL, and haemoglobin level >9.4 gm/dL. Conclusion: Short duration of symptoms (≤6 days), lower serum creatinine levels (≤6.2 mg/dL), lower serum potassium levels (≤5.5 mg/dL), and higher haemoglobin level (>9.4 gm/dL) were found to predict a greater chance of recovery. These factors can help in formulating treatment protocols for early intervention leading to a better prognosis in this subgroup of patients.

RNA-Seq profiling of deregulated miRs in CLL and their impact on clinical outcome

Abnormal expression patterns of regulatory small non-coding RNA (sncRNA) molecules such as microRNAs (miRs), piwi-interacting RNAs (piRNAs), and small nucleolar RNAs (snoRNAs) play an important role in the development and progression of cancer. Identification of clinically relevant sncRNA signatures could, therefore, be of tremendous translational value. In the present study, genome-wide small RNA sequencing identified a unique pattern of differential regulation of eight miRs in Chronic Lymphocytic Leukemia (CLL). Among these, three were up-regulated (miR-1295a, miR-155, miR-4524a) and five were down-regulated (miR-30a, miR-423, miR-486*, let-7e, and miR-744) in CLL. Altered expression of all these eight differentially expressed miRs (DEMs) was validated by RQ-PCR. Besides, seven novel sequences identified to have elevated expression levels in CLL turned out to be transfer RNA (tRNA)/piRNAs (piRNA-30799, piRNA-36225)/snoRNA (SNORD43) related. Multivariate analysis showed that miR-4524a (HR: 1.916, 95% CI: 1.080–3.4, p value: 0.026) and miR-744 (HR: 0.415, 95% CI: 0.224–0.769, p value: 0.005) were significantly associated with risk and time to first treatment. Further investigations could help establish the scope of integration of these DEM markers into risk stratification designs and prognostication approaches for CLL.

Seronegative invasive gastro-intestinal cytomegalovirus disease in renal allograft recipients a diagnostic dilemma! - Tissue PCR the saviour?

Seronegative Invasive Gastro-intestinal cytomegalovirus disease in renal allograft recipients Background -CMV as oppurtunistic infection affecting the gastrointerstinal tract is the most common cause for tissue invasive CMV disease occuring in 10-30% of organ transplant recepients. Gastrointerstinal CMV disease can be diagnosed in presence of clinical suspecion along with histopathological findings (CMV inclusions) and presence of mucosal lesion(s) on endoscopic examination with collaborative evidences via molecular technique. Aims-Few cases of CMV infection affecting the gastrointerstinal tract show no evidences of dissemintion despite use of highly sensitive molecular techniques. We encountered 6 cases where in despite strong clinical suspecion of Gastrointerstinal CMV disease there were seronegative and endoscopic negative evidences for CMV, blind tissue biopsy yeilded positive results for CMV disease with excellent improvement with antiviral therapy. Conclusions-Blind biopsy specimen for tissue PCR could serve as saviour in an immunocompromised individiual who has a strong clinical symptomatology for GI-CMV disease in absence of viremia, normal endoscopy and histopathology, so that the early therapeutic interventions could help in excellent patient and graft survival.

Cryptosporidium infection after renal transplantation in an endemic area

BACKGROUND

Cryptosporidium is one of the common causes of infective diarrhea in post-transplant patients in endemic areas. However, data are limited on Cryptosporidium infection in recipients of solid organ transplantation. The aim of this study was to determine the incidence, disease manifestation, management, and outcome of Cryptosporidium infection in living-donor renal transplant recipients (RTR).

METHODS

We performed a detailed retrospective review of the data on all RTR who had diarrheal illness requiring evaluation and hospitalization, and Cryptosporidium infection.

RESULTS

During the study period, 119/1235 (8.98%) RTR developed diarrhea, and Cryptosporidium was found in 34/119 (28.5%). Nine of 680 (1.3%) patients were on a cyclosporine (CSA)-based regimen, and 25/643 (3.8%) patients were on a tacrolimus (Tac)-based regimen. The relative risk of developing Cryptosporidium infection was lower on the CSA-based regimen, compared with the Tac-based regimen (odds ratio [OR]: 0.35, 95% confidence interval [CI]: 0.17-0.72, P = 0.003). Twelve of the 34 patients had acute graft dysfunction, mainly caused by combined Tac toxicity and dehydration. Mean serum creatinine and trough Tac level were 2.04 ± 0.65 mg/dL and 8.24 ± 1.19 ng/dL, respectively. Nitazoxanide alone was used in 13 patients, and nitazoxanide in combination with fluoroquinolone in 21 patients, with duration of treatment ranging from 16 to 60 days. Tac was changed to CSA in 8/11 patients. The clearance of cysts and response to nitazoxanide alone were significantly lower, compared with combination therapy (61.53% vs. 95.23%, P = 0.01, 38.46 vs. 85.71%, P = 0.004, respectively). The OR for cyst clearance and response was also significantly lower with nitazoxanide alone, in comparison with combination therapy (OR: 0.65, 95% CI: 0.34-0.92, P = 0.01, OR: 0.45, 95% CI: 0.21-0.81, respectively). Four (16%) of 24 patients with response had relapse.

CONCLUSION

Patients with Tac and mycophenolate mofetil combination therapy had a significantly high risk of Cryptosporidium infection. Cryptosporidial infection may require prolonged nitazoxanide therapy, either alone or in combination, with or without reduction in immunosuppression.

Rapidly progressive renal failure-a rare presentation of granulomatous interstitial nephritis due to tuberculosis-case report and review of literature

Granulomatous interstitial nephritis (GIN) is a rare manifestation of renal tuberculosis (TB). We report a case of rapidly progressive renal failure (RPRF), granulomatous inflammation of cervical lymph node and GIN as presenting manifestations of TB. Aspiration cytology of cervical lymph node showed granulomatous necrotizing inflammation with acid-fast bacilli (AFB). The renal biopsy and urine specimen did not show AFB. Urine polymerase chain reaction (PCR) for Mycobacterium tuberculosis was positive. We observe that GIN due to TB can present as RPRF and emphasize the value of PCR-based techniques in making a correct diagnosis.