Systemic Amyloidosis and Kidney Transplantation: An Update

Amyloidosis is a heterogeneous disorder characterized by abnormal protein aggregate deposition that often leads to kidney involvement and end-stage kidney disease. With advancements in diagnostic techniques and treatment options, the prevalence of patients with amyloidosis requiring chronic dialysis has increased. Kidney transplantation is a promising avenue for extending survival and enhancing quality of life in these patients. However, the complex and heterogeneous nature of amyloidosis presents challenges in determining optimal referral timing for transplantation and managing post-transplantation course. This review focuses on recent developments and outcomes of kidney transplantation for amyloidosis-related end-stage kidney disease. This review also aims to guide clinical decision-making and improve management of patients with amyloidosis-associated kidney disease, offering insights into optimizing patient selection and post-transplant care for favorable outcomes.

Abstract 3132: CLUMPS-PTM: Spatial clustering of post-translational modifications across cancer types

Post-translational modifications (PTMs) play key roles in regulating cell signaling in health and disease processes. Recent advances in mass spectrometry enable comprehensive investigation of PTMs. However, identifying functionally relevant PTMs and protein domains implicated in disease remains a key challenge. We present CLUMPS-PTM, an algorithm for spatial clustering of PTMs to propose functional domains. We apply CLUMPS-PTM to the Clinical Proteomic Tumor Analysis Consortium (CPTAC) dataset (one of the largest proteogenomic pan-cancer PTM datasets) comprising 1110 samples spanning 11 tumor types.

First, we map over 14K phospho-sites and 13K acetyl-sites detected in the CPTAC dataset to protein data bank (PDB) files. We expand this to the predicted AlphaFold proteome and recover additional 12K phospho-sites and 10K acetyl-sites exceeding model confidence (pLDDT) of 70%. Consistent with previous research, phospho-sites are found on residues with lower AlphaFold prediction confidence than acetyl-sites due to their abundance in unstructured domains (p-value < 1e-4).

To identify functionally relevant protein domains in the pan-cancer context, we characterize the 1110 samples by applying SignatureAnalyzer, a Bayesian non-negative matrix factorization method, to discover multi-omic patterns. This analysis identifies strong signatures associated with DNA damage response (DDR) and stratifies the CPTAC cohort into DDR-high (n=442) and DDR-low (n=668) groups. Next, we applied CLUMPS-PTM to differentially modified phospho/acetyl-sites between these groups. We identified 22 proteins (including GMPS, NCBP1, and ANPEP (CD13)) with significant clusters of differentially phosphorylated sites (q-value < 0.1) in DDR-high samples. ANPEP is a zinc-dependent aminopeptidase with a significant cluster (q-value = 0.0129) of differentially phosphorylated sites in the ERAP1-C domain that faces peptidase active sites known to have proliferative activity via the MAPK pathway. CLUMPS-PTM also identified a significant cluster of acetyl-sites on ARID1A (a SWI/SNF chromatin remodeler known to be mutated in cancer) in DDR-high samples (q-value = 0.085). The ARID1A cluster is on the C-terminal tail of the protein within the glucocorticoid receptor (GR) domain, an upstream regulator of proteins that increase catabolism, reduce inflammation, and increase cell survival. Increased acetylation may block a ubiquitination site at the C-terminus of the protein, resulting in increased protein levels, likely due to reduced ARID1A degradation, and increased GR signaling.

Overall, CLUMPS-PTM is an open-source tool that allows near proteome-wide spatial analysis with the growing availability of PTM data. We anticipate that it will be useful to the broader proteomic community for the discovery of novel targets and generation of insights into functional mechanisms.

Citation Format: Shankara K. Anand, Yifat Geffen, Yo Akiyama, Francois Aguet, Gad Getz. CLUMPS-PTM: Spatial clustering of post-translational modifications across cancer types [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3132.

Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication

Multiple coronaviruses have emerged independently in the past 20 years that cause lethal human diseases. Although vaccine development targeting these viruses has been accelerated substantially, there remain patients requiring treatment who cannot be vaccinated or who experience breakthrough infections. Understanding the common host factors necessary for the life cycles of coronaviruses may reveal conserved therapeutic targets. Here, we used the known substrate specificities of mammalian protein kinases to deconvolute the sequence of phosphorylation events mediated by three host protein kinase families (SRPK, GSK-3, and CK1) that coordinately phosphorylate a cluster of serine and threonine residues in the viral N protein, which is required for viral replication. We also showed that loss or inhibition of SRPK1/2, which we propose initiates the N protein phosphorylation cascade, compromised the viral replication cycle. Because these phosphorylation sites are highly conserved across coronaviruses, inhibitors of these protein kinases not only may have therapeutic potential against COVID-19 but also may be broadly useful against coronavirus-mediated diseases.

The FDA-approved drug Alectinib compromises SARS-CoV-2 nucleocapsid phosphorylation and inhibits viral infection in vitro

While vaccines are vital for preventing COVID-19 infections, it is critical to develop new therapies to treat patients who become infected. Pharmacological targeting of a host factor required for viral replication can suppress viral spread with a low probability of viral mutation leading to resistance. In particular, host kinases are highly druggable targets and a number of conserved coronavirus proteins, notably the nucleoprotein (N), require phosphorylation for full functionality. In order to understand how targeting kinases could be used to compromise viral replication, we used a combination of phosphoproteomics and bioinformatics as well as genetic and pharmacological kinase inhibition to define the enzymes important for SARS-CoV-2 N protein phosphorylation and viral replication. From these data, we propose a model whereby SRPK1/2 initiates phosphorylation of the N protein, which primes for further phosphorylation by GSK-3a/b and CK1 to achieve extensive phosphorylation of the N protein SR-rich domain. Importantly, we were able to leverage our data to identify an FDA-approved kinase inhibitor, Alectinib, that suppresses N phosphorylation by SRPK1/2 and limits SARS-CoV-2 replication. Together, these data suggest that repurposing or developing novel host-kinase directed therapies may be an efficacious strategy to prevent or treat COVID-19 and other coronavirus-mediated diseases.

Quorum sensing and expression of virulence in Escherichia coli O157:H7

Enterohaemorrhagic Escherichia coli O157:H7 causes a characteristic histopathology in intestinal cells known as attaching and effacing lesion. The genes for the lesion are encoded by the Locus of Enterocyte Effacement (LEE) pathogenicity island, that encodes a type III secretion system, the intimin intestinal colonization factor, and the translocated intimin receptor protein that is translocated from the bacterium to the host epithelial cells. Expression of the operons encoded within LEE is complex, but recent studies have demonstrated that quorum sensing influences transcription from four of the LEE operon promoters. A transcriptional regulator (LuxR homologue), signal synthase (LuxI homologue), and autoinducer (acylhomoserine lactone) are indispensable for this system in most gram-negative bacteria. Vibrio harveyi, a gram-negative bioluminescent marine bacterium, regulates light production in response to two autoinducers (AI-1 and AI-2). AI-1 is a homoserine lactone produced by most gram-negative bacteria. The structure of AI-2 is not known, but many species of gram positive and gram-negative bacteria, including E. coli and more specifically O157:H7, have been shown to produce AI-2 depending on the function encoded by the luxS gene. The LuxS acts as an AI-2 synthase and the AI-2 is produced from S-adenosylmethionine in three enzymatic steps. The substrate for LuxS is S-ribosylhomocysteine, which is cleaved to form two products, one of which is homocysteine, and the other is AI-2. The biosynthetic pathways and the biochemical intermediates in AI-2 biosynthesis have been observed to be identical in several gram-negative bacteria, such as E. coli, Salmonella typhimurium, V. harveyi, Vibrio cholerae, and Enterococcus faecalis. Thus, unlike quorum sensing via the family of related homoserine autoinducers, AI-2 is a universal signal, which may be used by a variety of bacteria for communication among and between species and may be responsible for regulation of virulence genes in E. coli O157:H7.

Repair and recovery of thermally injured cells of Yersinia enterocolitica in milk

One standard strain of the organism MTCC-861 and the two culture isolates VRW-22 and CRW-15 were exposed to batch pasteurization (62.8 degrees C for 30 min) in brain heart infusion broth, skim milk, and whole milk. The trials were repeated three times. None of the isolates survived pasteurization treatment. However, the studies were further directed toward the repair and recovery of thermally injured cells, if any, in peptone sorbitol bile broth, skim milk, and whole milk. The results revealed that only a low number of test cultures were recovered in peptone sorbitol bile broth after 8 days of incubation at 10 degrees C. On the other hand, the recovery was still slower in skim and whole milk, with a detection of the test isolates only on 10 days of incubation under similar conditions.

Significance of microbial biofilms in food industry: a review

Biofilms have been of considerable interest in the context of food hygiene. Of special significance is the ability of microorganisms to attach and grow on food and food-contact surfaces under favourable conditions. Biofilm formation is a dynamic process and different mechanisms are involved in their attachment and growth. Extracellular polymeric substances play an important role in the attachment and colonization of microorganisms to food-contact surfaces. Various techniques have been adopted for the proper study and understanding of biofilm attachment and control. If the microorganisms from food-contact surfaces are not completely removed, they may lead to biofilm formation and also increase the biotransfer potential. Therefore, various preventive and control strategies like hygienic plant lay-out and design of equipment, choice of materials, correct use and selection of detergents and disinfectants coupled with physical methods can be suitably applied for controlling biofilm formation on food-contact surfaces. In addition, bacteriocins and enzymes are gaining importance and have an unique potential in the food industry for the effective biocontrol and removal of biofilms. These newer biocontrol strategies are considered important for the maintenance of biofilm-free systems, for quality and safety of foods.

Airway simulation to guide stent placement for tracheobronchial obstruction in lung cancer

BACKGROUND

To effectively palliate large airway obstruction in advanced unresectable lung cancer (stage IIIB or IV), we developed an airway imaging technique to guide selective endobronchial metallic stent placement.

METHODS

Fourteen consecutive patients with severe dyspnea (American Thoracic Society grade 4) had a combination of fiberoptic bronchoscopy, chest roentgenography, computed tomographic scanning, helical computed tomography with three-dimensional reconstruction, and intraluminal bronchography with selective bronchial guidewire placement under fluoroscopy to visually reconstruct and simulate the abnormal airway before and during stent placement. Wallstent or Gianturco intraluminal stents were used alone or in combination (up to five stents) to establish patency of the distal trachea and the major bronchi.

RESULTS

All 14 patients had successful deployment with initial relief of airway stenosis (>75% predicted diameter). No procedural complications were noted. However, technical problems included stent foreshortening and imprecision of placement, misinterpretation of bronchography (mucous versus tumor), and airway maintenance during manipulation. Length of stay attributable to the procedure averaged 4 days. Stent placement initially improved the dyspnea score in 7 of 14 patients. Five of 14 died in less than 1 month, with the remainder alive at up to 8 months' follow-up. Of those surviving more than 1 month, the Karnofsky score improved in 4 and was unchanged in 5, with 2 dependent (Karnofsky score <50), 3 functional (Karnofsky score, 50 to 70), and 4 active (Karnofsky score >70).

CONCLUSIONS

A protocol combining helical computed tomography with three-dimensional reconstruction, bronchography, and bronchoscopy allows accurate assessment of malignant airway obstruction to facilitate intralumenal stent placement for relief of stenosis. Patient selection to favor effective palliation and cost effectiveness has yet to be defined.

The effect of chronic furosemide administration on urinary calcium excretion and calcium balance in growing rats

The study was designed to determine the calciuretic effect of furosemide and its impact upon calcium balance during chronic (25 days) furosemide administration to growing rats. Experiments were performed on 18 six-wk-old rats. Nine animals received furosemide, and 9 served as controls. The administration of furosemide in a dose of 40 mg resulted in a significant increase in calcium excretion in the treated group; urinary calcium excretion almost doubled that of the controls during the first 24-hr collection (3.74 +/- 0.44 mg in the treated animals compared with 1.90 +/- 0.15 mg in the controls; P less than 0.05). The average daily urinary calcium excretion during each of four subsequent 6-day periods remained approximately three-fold higher in animals which received furosemide compared with controls (P less than 0.001 for each 6-day period). The furosemide-induced increase in urinary calcium excretion did not diminish with time. Sodium excretion did not significantly increase either acutely or chronically in response to furosemide. Daily urinary volume increased approximately 40 to 60% in the furosemide-treated group compared with that of the controls (P less than 0.001). The cumulative calcium balance in the control group exceeded by 7% that of the furosemide-treated animals [2696.3 +/- 20.8 mg versus 2518.6 +/- 20.1 mg (P less than .001]. The findings indicate that distal nephron compensatory mechanisms effecting sodium conservation following furosemide do not result in similar conservation of calcium. Calcium balance may be deleteriously affected.

Congenital nephrogenic diabetes insipidus in a baby girl

A 6-week-old girl with fever, hypernatraemia, dehydration, and polyuria failed to concentrate urine in response to exogenous vasopressin administration. There was no family history of nephrogenic diabetes insipidus. When she was 15 months old, the infusion of vasopressin did not produce an increase in urinary cyclic-AMP.

A profile of health sciences libraries in Southeast Asia

This paper reports the results of a survey undertaken by the World Health Organization of health sciences libraries in Southeast Asia. It includes information on clientele, budget, personnel, collections, lending policy, dissemination of information, and reference services. The survey indicates that the collections in most of the health sciences libraries in Southeast Asia are deficient and that services provided to readers are inadequate. Recommendations for improvement are outlined.

Acute renal failure in newborn infants

The clinical course and follow-up of 14 neonates who developed acute renal failure are reported. Renal failure in these patients was secondary to major perinatal disorders, e.g., hyaline membrane disease, pneumonia, hemorrhage, or sepsis. Thirteen patients had hypoxia and nine were in shock when renal failure developed. Five patients died during the acute stage of renal failure. Of nine survivors, five patients sustained residual renal damage.

Neonatal renal papillary and cortical necrosis

Renal papillary and cortical necrosis (RPCN) in newborn infants has been generally fatal. This report describes three survivors of neonatal RPCN who have been followed up from 23 to 57 months. The cause of RPCN was hemorrhage and asphyxia neonatorum in two patients and hemorrhage and shock in one. The diagnosis was confirmed in one patient by an excretory urogram at 3 weeks of age and in another by renal biopsy at 5 weeks of age. In the third, diagnosis was made retrospectively. Findings from subsequent examination showed that creatinine clearance was normal in one patient, slightly reduced in another, and moderately reduced in the third. Maximum ability to concentrate urine was decreased in all. Follow-up excretory urograms in all three patients showed dilated bizarre-appearing calices and renal cortical atrophy. These radiologic findings are similar to those found in segmental hypoplasia or chronic (atrophic) pyelonephritis.

Unusual manifestations of Henoch-Schönlein syndrome

Henoch-Schönlein syndrome represents a diagnostic challenge when the abdominal and/or joint manifestations precede the cutaneous lesions. Laparotomy is often performed unnecessarily. We describe a patient whose abdominal symptoms antedated the appearance of cutaneous lesions by three months. Gastrointestinal blood loss, thrombocytosis, hypoproteinemia, and the roentgenographic appearance of the small intestine suggested the correct diagnosis. His course was further complicated by hypertension associated with elevated plasma renin levels without evidence of nephritis. Joint manifestations were mild and transient as were testicular pain and swelling.

Pseudohypoaldosteronism due to sweat gland dysfunction

Pseudohypoaldosteronism is an uncommon disorder characterized by urinary sodium wasting and is attributed to a defect in distal renal tubular sodium handling with failure to respond to endogenous aldosterone. Sweat electrolyte values in other reported patients, when measured, have been normal. A 3.5-year-old girl developed repeated episodes of dehydration, hyponatremia, and hyperkalemia during the first 19 months of life. Serum sodium was as low as 113 mEq/liter and potassium as high as 11.1 mEq/liter. Her plasma and urinary aldosterone levels were persistently elevated (Figs. 1-4). Unlike patients with classic pseudohypoaldosteronism she demonstrated no urinary sodium wasting (Figs. 2 and 3). During episodes of hyponatremia and reduced sodium intake her urinary sodium was less than 5 mEq/liter. In addition, her sweat sodium concentration was consistently above 125 mEq/liter and salivary sodium concentration above 58 mEq/liter. Her chest x-ray, 72-hr fecal fat excretion, serum and urinary pancreatic amylase (amy-2) were normal, providing no evidence for cystic fibrosis. It is proposed that this patient represents a new variant of pseudohypoaldosteronism with excessive loss of sodium from the sweat and salivary glands instead of the kidneys.

Extracapillary proliferative glomerulonephritis in children

The clinical course and renal pathology of 17 children with acute extracapillary proliferative glomerulonephritis is reported. Patients with systemic diseases associated with renal involvement were excluded. The onset followed streptococcal infection in ten; of these, four have died, one has been transplanted, and the remaining five have completely healed. The mean follow-up of the latter five patients was 32 months (range, 18 to 57 months). Of the other seven patients without evidence of precedeing streptococcal infection, two have died, two have been transplanted, and the remaining three all have hypertension, proteinuria, and reduced creatinine clearance. The mean follow-up of the latter three patients was 29 months (range, 14 to 38 months). The initial renal histopathologic changes and their progress in later renal biopsies is described. The role of various therapeutic agents is discussed. The prognosis in acute extracapillary proliferative glomerulonephritis following streptococcal infection appears to be better than in ones without preceding streptococcal infection.

Polycystic disease and hepatic fibrosis in children. Renal function studies

Renal function studies were done in five children with infantile polycystic disease (IPCD)of kidneys and liver and in four with congenital hepatic fibrosis (CHF). Glomerular filtration rate was reduced in all IPCD patients and in two of four CHF patients. Urinary concentrating ability following water deprivation and vasopressin administration was impaired in all IPCD patients and in three of four CHF patients. During control period, all patients had asymptomatic metabolic acidosis with total carbon dioxide content less than or equal to 20.5 millimols/liter, and net acid excretion (NAE) was reduced in all but one. Ammonium chloride was administered to seven patients; NAE increased in all, but the increments were subnormal in four. The inability to excrete maximally concentrated urine and an adequate amount of net acid may best be explained by abnormal tubular structure or alterations in medullary architecture secondary to progressive scarring, or both.